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Sample records for subgroup 16sri-a phytoplasma

  1. A novel subgroup 16SrVII-D phytoplasma identified in association with Erigeron witches' broom.

    Science.gov (United States)

    Flôres, Daniela; Amaral Mello, Ana Paula de Oliveira; Pereira, Thays Benites Camargo; Rezende, Jorge Alberto Marques; Bedendo, Ivan Paulo

    2015-08-01

    Erigeron sp. plants showing symptoms of witches' broom and stunting were found near orchards of passion fruit in São Paulo state, Brazil. These symptoms were indicative of infection by phytoplasmas. Thus, the aim of this study was to detect and identify possible phytoplasmas associated with diseased plants. Total DNA was extracted from symptomatic and asymptomatic plants and used in nested PCR conducted with the primer pairs P1/Tint and R16F2n/16R2. Amplification of genomic fragments of 1.2 kb from the 16S rRNA gene confirmed the presence of phytoplasma in all symptomatic samples. The sequence identity scores between the 16S rRNA gene of the phytoplasma strain identified in the current study and those of previously reported 'Candidatus Phytoplasma fraxini'-related strains ranged from 98% to 99% indicating the phytoplasma to be a strain affiliated with 'Candidatus Phytoplasma fraxini'. The results from a phylogenetic analysis and virtual RFLP analysis of the 16S rRNA gene sequence with 17 restriction enzymes revealed that the phytoplasma strain belongs to the ash yellows phytoplasma group (16SrVII); the similarity coefficient of RFLP patterns further suggested that the phytoplasma represents a novel subgroup, designated 16SrVII-D. The representative of this new subgroup was named EboWB phytoplasma (Erigeron bonariensis Witches' Broom).

  2. Use of a fragment of the tuf gene for phytoplasma 16Sr group/subgroup differentiation

    DEFF Research Database (Denmark)

    Contaldo, Nicoletta; Canel, Alessandro; Makarova, Olga

    2011-01-01

    The usefulness of RFLP analyses on a 435 bp fragment of the tuf gene for preliminary identification of phytoplasmas from a number of phytoplasma ribosomal groups and/or 'Candidatus. Phytoplasma' was verified. The strains employed belong to thirteen 16Sr DNA groups and 22 different subgroups and w...

  3. Genetic diversity among phytoplasmas infecting Opuntia species: virtual RFLP analysis identifies new subgroups in the peanut witches'-broom phytoplasma group.

    Science.gov (United States)

    Cai, Hong; Wei, Wei; Davis, Robert E; Chen, Hairu; Zhao, Yan

    2008-06-01

    Phytoplasmas were detected in cactus (Opuntia species) plants exhibiting witches'-broom disease symptoms in Yunnan Province, south-western China. Comparative and phylogenetic analyses of 16S rRNA gene sequences indicated that an overwhelming majority of the cactus-infecting phytoplasmas under study belonged to the peanut witches'-broom phytoplasma group (16SrII). Genotyping through use of computer-simulated restriction fragment length polymorphism (RFLP) analysis of 16S rRNA genes revealed a remarkable genetic diversity among these cactus-infecting phytoplasma strains. Based on calculated coefficients of RFLP pattern similarities, seven new 16SrII subgroups were recognized, bringing the total of described group 16SrII subgroups to 12 worldwide. Geographical areas differed from one another in the extent of genetic diversity among cactus-infecting phytoplasma strains. The findings have implications for relationships between ecosystem distribution and the emergence of group 16SrII subgroup diversity.

  4. Criteria for phytoplasma 16Sr group/subgroup delineation and the need of a platform for proper registration of new groups and subgroups

    Science.gov (United States)

    As more phytoplasmas are discovered in emerging and re-emerging plant diseases worldwide, the scheme for classification of phytoplasmas into 16S rRNA gene RFLP (16Sr) groups and subgroups is experiencing an ongoing rapid expansion. Improper delineation or designation of new groups and subgroups can...

  5. Phytoplasmas

    DEFF Research Database (Denmark)

    Vladimirovna Makarova, Olga

    Phytoplasmas are plant pathogenic bacteria that are transmitted by leafhopper vectors. These phytopathogens cause disease in over 100 economically important plants, including apple, grapevine, rice, coconut, pear, apricot, cotton and potato. When infected, susceptible plants usually fail...... to germinate or die. Currently, disease management is limited to control of insect vectors and elimination of infected plants, where correct identification plays a crucial role. As phytoplasmas cannot be cultured in vitro and do not possess a distinct morphology, traditional microbiological identification...... difficulties with disease management and pathogen identification) and an interesting lifestyle that involves colonisation and manipulation of two highly dissimilar hosts. The present Ph.D. project addresses two main research questions: (i) whether it is possible to develop a universal sequence...

  6. Draft Genome Sequence of a 16SrII-A Subgroup Phytoplasma Associated with Purple Coneflower (Echinacea purpurea) Witches' Broom Disease in Taiwan.

    Science.gov (United States)

    Chang, Shu-Heng; Cho, Shu-Ting; Chen, Chung-Li; Yang, Jun-Yi; Kuo, Chih-Horng

    2015-11-25

    The bacterial genus "Candidatus Phytoplasma" contains a group of insect-transmitted plant pathogens in the class Mollicutes. Here, we report a draft genome assembly and annotation of strain NCHU2014, which belongs to the 16SrII-A subgroup within this genus and is associated with purple coneflower witches' broom disease in Taiwan. Copyright © 2015 Chang et al.

  7. Molecular detection of 16SrI-B and 16SrII-D subgroups of phytoplasma associated with flat stem and witches' broom disease of Celosia argentea L.

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    Madhupriya; Yadav, Amit; Thorat, Vipool; Rao, G P

    2017-10-01

    Symptoms of stunting (shortening of internodes), twisting and flat stem (the fasciation of a stem), discoloration of petals, deformed flowers, and witches' broom were recorded on an ornamental plant, plumed cockscomb (Celosia argentea L., fam: Amaranthaceae). The survey conducted at Indian Agricultural Research Institute (IARI) campus, New Delhi and Karnal region, Haryana, India, during September 2014 to March 2015 revealed disease incidence of 40 and 10%, respectively. The 16S rRNA gene sequence comparison and phylogenetic relationships of Celosia phytoplasma strains under study confirmed that they were associated with two different phytoplasma groups ('Candidatus Phytoplasma australasia' and 'Ca. P. asteris'). Virtual RFLP analysis of 16S rRNA gene sequences allowed further classification of the Celosia phytoplasma strains into the 16SrI-B and 16SrII-D subgroups. Notably, the detection of 'Ca. P. asteris' phytoplasma was reported in seeds of C. argentea by nested PCR assays; however, no evidence of phytoplasma presence was detected in seedlings raised from these seeds. This observation is the first record of the association of 16SrI-B and 16SrII-D subgroups of phytoplasmas with flat stem and witches' broom disease of C. argentea anywhere from the world.

  8. Molecular characterization of an aster yellows phytoplasma ...

    African Journals Online (AJOL)

    STORAGESEVER

    2010-04-12

    Apr 12, 2010 ... restriction endonulease enzymes revealed identical patterns to phytoplasmas members of Aster yellows phytoplasma subgroup B. A phylogenetic tree based on 16S rDNA sequences, secA gene sequences and virtual RFLP revealed that the periwinkle proliferation phytoplasma is closely related to.

  9. Molecular characterization of an aster yellows phytoplasma ...

    African Journals Online (AJOL)

    African Journal of Biotechnology ... The virtual restriction fragment length polymorphism (RFLP) analysis with 10 restriction endonulease enzymes revealed identical patterns to phytoplasmas members of Aster yellows phytoplasma subgroup B. A phylogenetic tree based on 16S rDNA sequences, secA gene sequences and ...

  10. First report of 'Candidatus Phytoplasma trifolii'-related strain of 16SrVI-A phytoplasma subgroup, associated with elm yellows disease in American elm (Ulmus americana L.) in Ohio, USA

    Science.gov (United States)

    Charles Elliot Flower; Nancy L Hayes-Plazolles; Cristina Rosa; James M Slavicek

    2017-01-01

    During the investigation of the sudden and early onset of yellowing and mortality of American elm (Ulmus americana L.) trees at the USDA Forest Service Northern Research Station in Delaware, OH, a phytoplasma of the clover proliferation group (16SrVI) was detected as the putative causal agent of the disease outbreak.

  11. 'Candidatus Phytoplasma hispanicum', a novel taxon associated with Mexican periwinkle virescence disease of Catharanthus roseus.

    Science.gov (United States)

    Davis, Robert E; Harrison, Nigel A; Zhao, Yan; Wei, Wei; Dally, Ellen L

    2016-09-01

    Mexican periwinkle virescence (MPV) phytoplasma was originally discovered in diseased plants of Madagascar periwinkle (Catharanthus roseus) in Yucatán, Mexico. On the basis of results from RFLP analysis of PCR-amplified 16S rRNA gene sequences, strain MPV was previously classified as the first known member of phytoplasma group 16SrXIII, and a new subgroup (16SrXIII-A) was established to accommodate MPV phytoplasma. Phylogenetic analysis of 16S rRNA gene sequences indicated that strain MPV represents a lineage distinct from previously described 'CandidatusPhytoplasma' species. Nucleotide sequence alignments revealed that strain MPV shared less than 97.5 % 16S rRNA gene sequence similarity with all previously described 'Ca.Phytoplasma' species. Based on unique properties of the DNA, we propose recognition of Mexican periwinkle virescence phytoplasma strain MPV as representative of a novel taxon, 'CandidatusPhytoplasma hispanicum'.

  12. Draft Genome Sequence of a 16SrII-A Subgroup Phytoplasma Associated with Purple Coneflower (Echinacea purpurea) Witches’ Broom Disease in Taiwan

    Science.gov (United States)

    Chang, Shu-Heng; Cho, Shu-Ting; Chen, Chung-Li

    2015-01-01

    The bacterial genus “Candidatus Phytoplasma” contains a group of insect-transmitted plant pathogens in the class Mollicutes. Here, we report a draft genome assembly and annotation of strain NCHU2014, which belongs to the 16SrII-A subgroup within this genus and is associated with purple coneflower witches’ broom disease in Taiwan. PMID:26607900

  13. Genetic diversity and vector transmission of phytoplasmas associated with sesame phyllody in Iran.

    Science.gov (United States)

    Salehi, M; Esmailzadeh Hosseini, S A; Salehi, E; Bertaccini, A

    2017-03-01

    During 2010-14 surveys in the major sesame growing areas of Fars, Yazd and Isfahan provinces (Iran), genetic diversity and vector transmission of phytoplasmas associated with sesame phyllody were studied. Virtual RFLP, phylogenetic, and DNA homology analyses of partial 16S ribosomal sequences of phytoplasma strains associated with symptomatic plants revealed the presence of phytoplasmas referable to three ribosomal subgroups, 16SrII-D, 16SrVI-A, and 16SrIX-C. The same analyses using 16S rDNA sequences from sesame phyllody-associated phytoplasmas retrieved from GenBank database showed the presence of phytoplasmas clustering with strains in the same subgroups in other Iranian provinces including Bushehr and Khorasan Razavi. Circulifer haematoceps and Orosius albicinctus, known vectors of the disease in Iran, were tested for transmission of the strains identified in this study. C. haematoceps transmitted 16SrII-D, 16SrVI-A, and 16SrIX-C phytoplasmas, while O. albicinctus only transmitted 16SrII-D strains. Based on the results of the present study and considering the reported presence of phytoplasmas belonging to the same ribosomal subgroups in other crops, sesame fields probably play an important role in the epidemiology of other diseases associated with these phytoplasmas in Iran.

  14. Description of 'Candidatus Phytoplasma meliae', a phytoplasma associated with Chinaberry (Melia azedarach L.) yellowing in South America.

    Science.gov (United States)

    Fernández, Franco Daniel; Galdeano, Ernestina; Kornowski, Marcela Victoria; Arneodo, Joel Demián; Conci, Luis Rogelio

    2016-12-01

    China tree yellows (ChTY) phytoplasma is associated with the yellowing disease of the China tree (Melia azedarach) in Argentina. According to partial 16S rRNA gene analysis, ChTY phytoplasma belongs to the 16Sr XIII group, subgroup G. Strains of species of ChTY have 98-99 % 16S rDNA gene sequence similarity with 16SrXIII-group phytoplasmas, and less than 97.5 % when compared to all 'CandidatusPhytoplasma' described so far, except for the novel 'CandidatusPhytoplasma hispanicum'. However, strains of species of ChTY are differentiated from the latter due to having additional molecular and biological attributes. The presence of unique features in the 16S rDNA sequence distinguishes ChTY from all species of 'CandidatusPhytoplasma' currently described. The in silico RFLP profile of 16S rDNA (1.2 kb) and rpLV-rpsC (1.3 kb) genes distinguished ChTY, as in the 16SrXIII-G subgroup within the 16SrXIIII group. The phylogenetic analyses, based on 16S rDNA, rpLV-rpsC and secA gene sequences, in addition to the restricted host range, characteristic symptoms and geographical distribution, confirm that the collective strains of the species ChTY represent a distinct lineage within the phytoplasma clade and support the description of a novel species of 'CandidatusPhytoplasma meliae' with the reference strain being ChTY-Mo3 (Montecarlo, Argentina).

  15. Molecular Diagnosis of Phytoplasmas

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    C. Marzachì

    2004-08-01

    Full Text Available Phytoplasmas are wall-less prokaryotes associated with diseases in numerous plant species worldwide. In nature they are transmitted by phloem-sucking insects. Yellowing, decline, witches’ broom, leaf curl, floral virescence and phyllody are the most conspicuous symptoms associated with phytoplasmas, although infections are sometimes asymptomatic. Since phytoplasmas cannot be cultured in vitro, molecular techniques are needed for their diagnosis and characterization. The titer of phytoplasma cells in the phloem of infected plants may vary according to the season and the plant species, and it is often very low in woody hosts. Different DNA extraction procedures have therefore been tried out to obtain phytoplasma DNA at a concentration and purity high enough for effective diagnosis. DNA/DNA hybridization methods were reported in the nineties to be appropriate for the detection of phytoplasmas, but at present PCR is considered the most suitable. Universal and group-specific primers have been designed on the rRNA operon of the phytoplasma genome and on plasmid sequences. RFLP analysis of the obtained amplicons has classified these pathogens into major 16Sr RNA groups. Group-specific primers have also been designed on other genomic sequences. PCR is a very sensitive technique, but due to the low titre of phytoplasmas a further increase in sensitivity may be required for accurate diagnosis. This is routinely obtained with a second round of PCR (nested PCR. The drawback of nested PCR is that there is a greater chance of obtaining false positives due to contamination. Many authors have therefore developed protocols based on hybridization (PCR/dot blot or serological approaches (PCR/ELISA to increase the sensitivity and specificity of the direct PCR, reducing the risks due to nested PCR. Real time PCR protocols may also improve the sensitivity and specificity of the direct PCR assay.

  16. Molecular identification of a new phytoplasma associated with alfalfa witches'-broom in oman.

    Science.gov (United States)

    Khan, A J; Botti, S; Al-Subhi, A M; Gundersen-Rindal, D E; Bertaccini, A F

    2002-10-01

    ABSTRACT Alfalfa (Medicago sativa) plants showing witches'-broom symptoms typical of phytoplasmas were observed from Al-Batinah, Al-Sharqiya, Al-Bureimi, and interior regions of the Sultanate of Oman. Phytoplasmas were detected from all symptomatic samples by the specific amplification of their 16S-23S rRNA gene. Polymerase chain reaction (PCR), utilizing phytoplasma-specific universal primer pairs, consistently amplified a product of expected lengths when DNA extract from symptomatic samples was used as template. Asymptomatic plant samples and the negative control yielded no amplification. Restriction fragment length polymorphism profiles of PCR-amplified 16S-23S rDNA of alfalfa using the P1/P7 primer pair identified phytoplasmas belonging to peanut witches'-broom group (16SrII or faba bean phyllody). Restriction enzyme profiles showed that the phytoplasmas detected in all 300 samples belonged to the same ribosomal group. Extensive comparative analyses on P1/P7 amplimers of 20 phytoplasmas with Tru9I, Tsp509I, HpaII, TaqI, and RsaI clearly indicated that this phytoplasma is different from all the other phytoplasmas employed belonging to subgroup 16SrII, except tomato big bud phytoplasma from Australia, and could be therefore classified in subgroup 16SrII-D. The alfalfa witches'-broom (AlfWB) phytoplasma P1/P7 PCR product was sequenced directly after cloning and yielded a 1,690-bp product. The homology search showed 99% similarity (1,667 of 1,690 base identity) with papaya yellow crinkle (PapayaYC) phytoplasma from New Zealand. A phylogenetic tree based on 16S plus spacer regions sequences of 35 phytoplasmas, mainly from the Southern Hemisphere, showed that AlfWB is a new phytoplasma species, with closest relationships to PapayaYC phytoplasmas from New Zealand and Chinese pigeon pea witches'-broom phytoplasmas from Taiwan but distinguishable from them considering the different associated plant hosts and the extreme geographical isolation.

  17. Multigene characterization of a new 'Candidatus Phytoplasma rubi'-related strain associated with blackberry witches' broom in Portugal.

    Science.gov (United States)

    Fránová, Jana; de Sousa, Esmeraldina; Koloniuk, Igor; Mimoso, Céu; Matos, José; Cardoso, Fernando; Contaldo, Nicoletta; Paltrinieri, Samanta; Bertaccini, Assunta

    2016-01-13

    A new phytoplasma was identified in naturally infected blackberry plants exhibiting witches' broom symptoms in Portugal. The 16S rRNA gene sequence revealed that it is related to 'Candidatus Phytoplasma rubi' (16SrV-E ribosomal subgroup) and RFLP analysis showed a unique profile following MseI endonuclease digestion of R16F2n/R2 amplicons that distinguished it from the strains belonging to previously established 16SrV phytoplasma subgroups. The in silico restriction analyses confirmed that the phytoplasma strain from blackberry is different from all the other strains reported in group 16SrV. Phylogeny of the 16S rRNA gene sequences, sequence analyses of 16S-23S, tuf, rplV-rpsC, rplF-rplR, rplO-SecY-map and uvrB-degV genetic loci, as well as the variability of unique oligonucleotide sequences defined for 'Candidatus Phytoplasma rubi' confirmed the uniqueness of this phytoplasma strain from Portugal for which a novel ribosomal subgroup, 16SrV-I, is proposed. The representative of this new subgroup was named blackPort phytoplasma (Portuguese blackberry phytoplasma).

  18. Stolbur Phytoplasma Transmission to Maize by Reptalus panzeri and the Disease Cycle of Maize Redness in Serbia

    Science.gov (United States)

    Maize redness (MR), induced by stolbur phytoplasma (Candidatus Phytoplasma solani, subgroup 16SrXII-A), is characterized by midrib, leaf and stalk reddening and abnormal ear development. MR has been reported from Serbia, Romania and Bulgaria for 50 years, and recent epiphytotics reduced yields by 4...

  19. Leafhoppers and Cixiids in Phytoplasma-infected Carrot Fields: Species Composition and Potential Phytoplasma Vectors

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    Tanja Drobnjaković

    2010-01-01

    Full Text Available The first molecular analysis of samples collected in southern Bačka (Serbia confirmed the presence of aster yellows (16SrI and stolbur phytoplasmas (16SrXII in insects belonging to the family Cicadellidae, as well as in carrot plants where the insects were collected. A correct identification of the phytoplasmas and their vectors is essential to arrange effective control strategies to prevent diseases associated with phytoplasmas from spreading to carrots and other vegetable crops. In order to enhance knowledgeabout insect vectors of aster yellows and stolbur phytoplasmas in Serbia, Cicadellidae and Cixiidae (Homoptera Auchenorrhyncha, the most common vectors of these phytoplasmas,were monitored in southern Bačka during 2008. Adults leaf- and planthoppers were collected and identified at species level using standard entomological methods,and tested for phytoplasma presence by means of PCR/RFLP. A total of 13 insect species of Cicadellidae were identified, as follows: a three species of the subfamily Agallinae: Anaceratagallia ribauti (Ossiannilsson, Anaceratagallia venosa (Fourcroy,and Anaceratagallia laevis (Ribaut; b seven species of the subfamily Deltocephalinae: Psammotettix confinis (Dahlbom, Psammotettix striatus (Linnaues Psammottettix alienus (Dahlbom, Macrosteles sexnotatus (Fallén, Ophiola decumana (Kontkanen,Errastunus ocellaris Fallén, and Scaphoideus titanus Ball; c three species of the subfamily Typhlocibinae: Eupteryx atropunctata (Goeze, Eupteryx mellissae Curtis, Zyginidia pullula (Boheman. Female specimens of the genus Euscelis (Deltocephalinae were also collected, as well as one species of Reptalus quinquecostatus (Dufour of the family Cixiidae. Stolbur phytoplasmas were detected in A. laevis, A. ribauti, A. venosa, P. striatus, P. confinis and P. alienus. The species: A. laevis, O. decumana, and P. confinis were AY-infected (subgroup 16SrI-A, while subgroup 16SrI-C was found only in one specimen of P. confinis. Since some

  20. Molecular Diversity of Phytoplasmas Associated with Grapevine Yellows Disease in North-Eastern Italy.

    Science.gov (United States)

    Zambon, Yuri; Canel, Alessandro; Bertaccini, Assunta; Contaldo, Nicoletta

    2017-12-04

    A 3-year survey was conducted in Northern Italy to verify the presence and diversity of phytoplasmas in selected vineyards showing symptoms of severe yellows. Symptomatic and asymptomatic grapevines were sampled, and insects were collected using yellow sticky traps. The phytoplasmas detected in grapevine samples were different according to the years: "flavescence dorée" (16SrV-C/D) was detected together with other phytoplasmas such as 16SrXII-A ('Candidatus Phytoplasma solani'-related, bois noir), 16SrI-B ('Ca. P. asteris'-related, aster yellows), 16SrX-B ('Ca. P. prunorum'-related, European stone fruit yellows), and 16SrV-A ('Ca. P. ulmi'-related, elm yellows). Moreover, phytoplasmas belonging to 16SrVII-A ('Ca. P. fraxini'-related) and 16SrVI ('Ca. P. trifolii'-related) subgroups were also identified. Identification of phytoplasmas was also carried out from insects and showed the presence of some of these phytoplasmas in Scaphoideus titanus and Orientus ishidae: 16SrXII-A, 16SrVII, and 16SrVI phytoplasmas were detected in specimens of both species, while 16SrXII-A and 16SrI-B phytoplasma strains were identified in Orientus ishidae and Hyalesthes obsoletus, and 16SrX-B in S. titanus. Direct sequencing of selected amplicons obtained from 16S rRNA, rp, and tuf genes from grapevine and insect samples confirmed the phytoplasma identification. The 16SrVII-A and 16SrVI phytoplasmas were never detected before in grapevine, S. titanus and Orientus ishidae in Europe and their epidemiological importance is being monitored.

  1. 'Candidatus Phytoplasma luffae', a novel taxon associated with witches' broom disease of loofah, Luffa aegyptica Mill.

    Science.gov (United States)

    Davis, Robert E; Zhao, Yan; Wei, Wei; Dally, Ellen L; Lee, Ing-Ming

    2017-08-01

    The phytoplasma associated with witches' broom disease of loofah [Luffa aegyptica Mill., syn. Luffa cylindrica (L.) M.J. Roem.] in Taiwan was classified in group 16SrVIII, subgroup A (16SrVIII-A), based on results from actual and in silico RFLP analysis of 16S rRNA gene sequences. Nucleotide sequencing of PCR-amplified, cloned DNA segments revealed rrn interoperon sequence heterogeneity in the loofah witches' broom (LfWB) phytoplasma. Whereas the 16S-23S rRNA spacer region of rrnA contained a complete tRNA-Ile gene, the spacer of rrnB contained a nonfunctional remnant of a tRNA gene. Phylogenetic analysis of the rrnA and rrnB 16S rRNA genes revealed that the LfWB phytoplasma represented a distinct lineage within the phytoplasma clade, and the LfWB phytoplasma shared less than 97.5 % nucleotide sequence similarity of 16S rRNA genes with previously described 'CandidatusPhytoplasma' taxa. Based on unique properties of DNA, we propose recognition of loofah witches' broom phytoplasma strain LfWBR as representative of a novel taxon, 'CandidatusPhytoplasma luffae'.

  2. Q-bank phytoplasma database

    DEFF Research Database (Denmark)

    Contaldo, Nicoletta; Bertaccini, Assunta; Nicolaisen, Mogens

    2014-01-01

    The setting of the Q-Bank database free available on line for quarantine phytoplasma and also for general phytoplasma identification is described. The tool was developed in the frame of the EU-FP7 project Qbol and is linked with a new project Q-collect in order to made widely available the identi......The setting of the Q-Bank database free available on line for quarantine phytoplasma and also for general phytoplasma identification is described. The tool was developed in the frame of the EU-FP7 project Qbol and is linked with a new project Q-collect in order to made widely available...

  3. Phytoplasma and phytoplasma diseases: a review of recent research

    Directory of Open Access Journals (Sweden)

    A. Bertaccini

    2010-01-01

    Full Text Available Numerous yellows-type diseases of plants have been associated with wall-less prokaryote pathogens – phytoplasma over the last 40 years. These pathogens cannot be grown in axenic culture so that advances in their study are mainly achieved by molecular techniques. Severe disease epidemics associated with a phytoplasma presence have been described worldwide. These include coconut lethal yellowing in Africa and the Caribbean, grapevine yellows in major viticultural areas and various diseases affecting stone and pome fruit plants. Phytoplasma-infected plants exhibit symptoms suggesting a profound disturbance in the normal balance of growth regulators and also yellows symptoms, but very often the symptomatology is not diagnostic. Detection and characterization of phytoplasmas infecting different plant species are now possible with molecular methods, based on the study of 16S rDNA polymorphisms. Molecular diversity of phytoplasmas is also demonstrated by studying genes coding the ribosomal proteins S3, tuf, SecY, amp, imp and other genes. Four phytoplasma genomes have been fully sequenced, including those of two ‘Candidatus Phytoplasma asteris’ strains, and those of strains of ‘Ca. P. mali’ and ‘Ca. P. australiense’. Three of these genomes contain large amounts of repeated DNA sequence, and the fourth carries multiple copies of almost 100 genes. Considering that phytoplasmas have unusually small genomes, these repeats might be related to their transkingdom habitat and to their pathogenic activity. An outlook of recent findings in the field is also reported.

  4. [Cloning and analysis of tuf and rp gene of the phytoplasma associated with jujube witches' -broom].

    Science.gov (United States)

    Lin, Wenli; Mou, Haiqing; Zhao, Wenjun; Xu, Qicong; Tian, Guozhong; Liao, Xiaolan; Zhu, Shuifang

    2010-10-01

    Jujube witches' -broom (JWB) is an important plant disease caused by phytoplasma. The major objective of our research was to classify JWB in Beijing and Hebei districts and to provide reference for classification in subgroup level. By use of PCR, the elongation factor Tu (tuf gene) and ribosomal protein (rp) gene of phytoplasma associated with JWB in Beijing and Hebei districts were amplified separately with universal primer pairs fTufu/rTufu and rp(v)F1A/rp(v) R1A. Partial tuf gene and rp gene were sequenced and similarity analysed with other phytoplasmas. We obtained partial tuf gene sequence (824bp) and complete rp gene (1196bp) from the diseased sample. In tuf gene, JWB in Beijing shared most similarity (92.84%) with Flavescence dorée (FD) phytoplasma (Candidatus Phytoplasma vitis), however, shared a low similarity (57.29%) with JWB in Shaanxi district which had been already reported. The similarity analysis for sequences of rp gene showed a high identity (> 96%) with members of the 16SrV group phytoplasmas. It shared most identity (99.83%) with JWB strain Taishan and Hemp fiber witches' -broom phytoplasma (HFWB) of the 16SrV group. The JWB strains in Beijing and Hebei are members of 16Sr V; JWB in Beijing and Hebei share high similarity, and show a diversity with JWB in Shaanxi.

  5. DNA barcoding for identification of 'Candidatus Phytoplasmas' using a fragment of the elongation factor Tu gene.

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    Olga Makarova

    Full Text Available BACKGROUND: Phytoplasmas are bacterial phytopathogens responsible for significant losses in agricultural production worldwide. Several molecular markers are available for identification of groups or strains of phytoplasmas. However, they often cannot be used for identification of phytoplasmas from different groups simultaneously or are too long for routine diagnostics. DNA barcoding recently emerged as a convenient tool for species identification. Here, the development of a universal DNA barcode based on the elongation factor Tu (tuf gene for phytoplasma identification is reported. METHODOLOGY/PRINCIPAL FINDINGS: We designed a new set of primers and amplified a 420-444 bp fragment of tuf from all 91 phytoplasmas strains tested (16S rRNA groups -I through -VII, -IX through -XII, -XV, and -XX. Comparison of NJ trees constructed from the tuf barcode and a 1.2 kbp fragment of the 16S ribosomal gene revealed that the tuf tree is highly congruent with the 16S rRNA tree and had higher inter- and intra- group sequence divergence. Mean K2P inter-/intra- group divergences of the tuf barcode did not overlap and had approximately one order of magnitude difference for most groups, suggesting the presence of a DNA barcoding gap. The use of the tuf barcode allowed separation of main ribosomal groups and most of their subgroups. Phytoplasma tuf barcodes were deposited in the NCBI GenBank and Q-bank databases. CONCLUSIONS/SIGNIFICANCE: This study demonstrates that DNA barcoding principles can be applied for identification of phytoplasmas. Our findings suggest that the tuf barcode performs as well or better than a 1.2 kbp fragment of the 16S rRNA gene and thus provides an easy procedure for phytoplasma identification. The obtained sequences were used to create a publicly available reference database that can be used by plant health services and researchers for online phytoplasma identification.

  6. Phytoplasma associated with witches'-broom disease of Ulmus minor MILL . in the Czech Republic: Electron microscopy and molecular characterization.

    Science.gov (United States)

    Navrátil, M; Safárová, D; Válová, P; Fránová, J; Simková, M

    2009-01-01

    Visual inspections of elm trees in south Moravia in 1997-2007 revealed a rare occurrence of plants with smaller and cowl-forming leaves on some twigs, i.e. a feature resembling witches'-broom disease observed on the end of twigs. The presence of phytoplasma-like bodies was observed by transmission electron microscopy of phloem tissue. On the other hand, no phytoplasmas were found in asymptomatic trees. Nucleic acids extracted from these plants were used in nested-PCR assays with primers amplifying 16S rRNA sequences specific for phytoplasmas. Sequence analyses of the 16S-23S ribosomal operon (1852 bp) allowed for the classification of the detected phytoplasmas in the elm yellows group, but its position remained on the boundary of the 16SrV-A and 16SrV-C ribosomal subgroups. Sequence analyses of the ribosomal protein of the rpl22-rps3 and secY genes lead to further classification and revealed the phytoplasmas' affiliations to the 'Candidates Phytoplasma ulmi'. Some exceptions in unique oligonucleotide sequences defined for 'Ca. Phytoplasma ulmi' were found in the Czech isolate. This is the northernmost confirmed occurrence of phytoplasma on elm trees within Europe.

  7. Current View on Phytoplasma Genomes and Encoded Metabolism

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    Michael Kube

    2012-01-01

    Full Text Available Phytoplasmas are specialised bacteria that are obligate parasites of plant phloem tissue and insects. These bacteria have resisted all attempts of cell-free cultivation. Genome research is of particular importance to analyse the genetic endowment of such bacteria. Here we review the gene content of the four completely sequenced ‘Candidatus Phytoplasma’ genomes that include those of ‘Ca. P. asteris’ strains OY-M and AY-WB, ‘Ca. P. australiense,’ and ‘Ca. P. mali’. These genomes are characterized by chromosome condensation resulting in sizes below 900 kb and a G + C content of less than 28%. Evolutionary adaption of the phytoplasmas to nutrient-rich environments resulted in losses of genetic modules and increased host dependency highlighted by the transport systems and limited metabolic repertoire. On the other hand, duplication and integration events enlarged the chromosomes and contribute to genome instability. Present differences in the content of membrane and secreted proteins reflect the host adaptation in the phytoplasma strains. General differences are obvious between different phylogenetic subgroups. ‘Ca. P. mali’ is separated from the other strains by its deviating chromosome organization, the genetic repertoire for recombination and excision repair of nucleotides or the loss of the complete energy-yielding part of the glycolysis. Apart from these differences, comparative analysis exemplified that all four phytoplasmas are likely to encode an alternative pathway to generate pyruvate and ATP.

  8. [Cloning and sequencing of 16S rRNA gene of Phytoplasma CWB1 strain associated with cactus witches' broom].

    Science.gov (United States)

    Cai, H; Li, F; Kong, B; Chen, H

    2001-12-01

    A 1.5 kb DNA fragment was amplified in DNA samples extracted from Opuntia salmiana porm showed witches'-broom symptom. The result indicates the existence of phytoplasma associated with this disease and this phytoplasma was designated as CWB1. The amplified fragment was ligated to pGEM-T easy vector and then transformed into JM109 strain of E. coli. Cloned DNA fragments were verified by PCR, restriction endonuclease (EcoRI) digestion and sequence analysis. The result revealed that the 16S rRNA gene of CWB1 consists of 1489 bp and shared 99.7% homology with Faba bean phyllody which belongs to phytoplasma 16S rII-C subgroup. So we can classify this strain into phytoplasma 16S rII-C subgroup.

  9. DNA Bar-Coding for Phytoplasma Identification

    DEFF Research Database (Denmark)

    Makarova, Olga; Contaldo, Nicoletta; Paltrinieri, Samanta

    2013-01-01

    Phytoplasma identi fi cation has proved dif fi cult due to their inability to be maintained in vitro. DNA barcoding is an identi fi cation method based on comparison of a short DNA sequence with known sequences from a database. A DNA barcoding tool has been developed for phytoplasma identi fi...... cation. While other sequencebased methods may be well adapted to identification of particular strains of phytoplasmas, often they cannot be used for the simultaneous identification of phytoplasmas from different groups. The phytoplasma DNA barcoding protocol in this chapter, based on the tuf and 16Sr...

  10. Molecular detection of ‘Candidatus Phytoplasma australasia’ and ‘Ca. P. cynodontis’ in Iraq

    Directory of Open Access Journals (Sweden)

    Alkuwaiti Nawres Abdulelah Sadeq

    2017-10-01

    Full Text Available The association of phytoplasma was investigated in symptomatic tomato (Solanum lycopersicum L., eggplant (Solanum melongen L., mallow (Malva spp. and Bermuda grass (Cynodon dactylon L. plants exhibiting witches’ broom and white leaf diseases, respectively. Total DNA was extracted from tomato (n=3, eggplant (n=2, mallow (n=2 and Bermuda grass (n=8 samples. Direct polymerase chain reaction (PCR was performed using P1/P7 primer set, then PCR products were sequenced. Sequences obtained from tomato, eggplant and mallow shared 99% maximum nucleotide identity with phytoplasma belonging to subgroup 16SrII-D, and resulted therefore ‘Candidatus Phytoplasma australasia’-related. Sequences obtained from Bermuda grass showed 100% maximum nucleotide identity to 16SrXIV-A subgroup and were ‘Ca. P. cynodontis’-related. The study presents the first molecular confirmation and sequence data of presence of ‘Ca. P. australasia’ and ‘Ca. P. cynodontis’ in Iraq.

  11. Use of heteroduplex mobility assay for identification and differentiation of phytoplasmas in the aster yellows group and the clover proliferation group.

    Science.gov (United States)

    Wang, K; Hiruki, C

    2001-06-01

    ABSTRACT This paper describes the identification and differentiation of phytoplasmas by a highly sensitive diagnostic technique, DNA heteroduplex mobility assay (HMA). Closely related phytoplasma isolates of clover proliferation (CP), potato witches'-broom (PWB), and alfalfa witches'-broom (AWB) were collected from the field from 1990 to 1999. The entire 16S rRNA gene and 16/23S spacer region were amplified by polymerase chain reaction (PCR) from the field samples and standard CP, PWB, and AWB phytoplasmas and were subjected to restriction fragment length polymorphism (RFLP) analysis and HMA. Two subgroups (I and II) of phytoplasmas in the CP group were identified by HMA but not by RFLP analysis. The results were confirmed by 16/23S spacer region sequence data analysis. After HMA analyses of the PCR-amplified 16/23S spacer region, 14 phytoplasma isolates from field samples were classified into two aster yellows subgroups: subgroup I, phytoplasma isolates from China aster (Callistephus chinensis) yellows, French marigold (Tagetes patula) yellows, cosmos (Cosmos bipinnatus cv. Dazzler) yellows, clarkia (Clarkia unguiculata) yellows, California poppy (Eschscholzia californica cv. Tai Silk) yellows, monarda (Monarda fistulosa) yellows, and strawflower (Helichrysum bracteatum) yellows; and subgroup II, phytoplasma isolates from zinnia (Zinnia elegans cv. Dahlia Flower) yellows, Queen-Annes-Lace (Daucus carota) yellows, scabiosa (Scabiosa atropurpurea cv. Giant Imperial) yellows, Swan River daisy (Brachycombe multifida cv. Misty Pink) yellows, pot marigold (Calendula officinalis) yellows, purple coneflower (Echinacea purpurea) yellows, and feverfew (Chrysanthemum parthenium) yellows. The results indicate that HMA is a simple, rapid, highly sensitive and accurate method not only for identifying and classifying phytoplasmas but also for studying the molecular epidemiology of phytoplasmas.

  12. Q-Bank Phytoplasma: A DNA Barcoding Tool for Phytoplasma Identification

    DEFF Research Database (Denmark)

    Contaldo, Nicoletta; Paltrinieri, Samanta; Makarova, Olga

    2015-01-01

    DNA barcoding is an identification method based on comparison of a short DNA sequence with known sequences from a database. A DNA barcoding tool has been developed for phytoplasma identification. This phytoplasma DNA barcoding protocol based on the tuf gene has been shown to identify phytoplasmas...

  13. Preparation of phytoplasma membrane recombinant proteins.

    Science.gov (United States)

    Galetto, Luciana; Siampour, Majid; Marzachì, Cristina

    2013-01-01

    The study of phytoplasma membrane protein interactions with host cell proteins is crucial to understand the life cycle of these unculturable microorganisms within their hosts. A step-by-step protocol for the heterologous expression of phytoplasma membrane proteins in Escherichia coli is described, together with a procedure to purify a suitable quantity of fusion antigen for application in the study of phytoplasma-host interactions.

  14. Molecular survey of the Texas Phoenix decline phytoplasma ...

    African Journals Online (AJOL)

    user

    and the gcp gene using a three restriction enzymes showed that the population of the phytoplasmas infecting S. palmetto in West Central Florida is probably homogenous. The S. palmetto phytoplasma also appeared similar to all the 16SrIV-D phytoplasmas infecting other palm species and different from all phytoplasmas ...

  15. 'Candidatus Phytoplasma spartii', 'Candidatus Phytoplasma rhamni' and 'Candidatus Phytoplasma allocasuarinae', respectively associated with spartium witches'-broom, buckthorn witches'-broom and allocasuarina yellows diseases.

    Science.gov (United States)

    Marcone, C; Gibb, K S; Streten, C; Schneider, B

    2004-07-01

    Spartium witches'-broom (SpaWB), buckthorn witches'-broom (BWB) and allocasuarina yellows (AlloY) are witches'-broom and yellows diseases of Spartium junceum (Spanish broom), Rhamnus catharticus (buckthorn) and Allocasuarina muelleriana (Slaty she-oak), respectively. These diseases are associated with distinct phytoplasmas. The SpaWB, BWB and AlloY phytoplasmas share <97.5 % 16S rDNA sequence similarity with each other and with other known phytoplasmas, including the closely related phytoplasmas of the apple proliferation group. Also, the SpaWB, BWB and AlloY phytoplasmas each have a different natural plant host. Based on their unique properties, it is proposed to designate the mentioned phytoplasmas as novel 'Candidatus' species under the names 'Candidatus Phytoplasma spartii', 'Candidatus Phytoplasma rhamni' and 'Candidatus Phytoplasma allocasuarinae', respectively.

  16. Molecular characterization of Yucatan tomato phytoplasma (Group ...

    African Journals Online (AJOL)

    Tomato (Lycopersicon esculentum) is an important vegetable crop in Mexico. Recently, a phytoplasma associated with leaf yellowing and curling, severe stunting and little leaf in tomato plant was identified as Yucatan tomato phytoplasma (16SrIII group). DNAs extracted from tomato leaves with symptoms were examined for ...

  17. Molecular characterization of Yucatan tomato phytoplasma (Group ...

    African Journals Online (AJOL)

    Yomi

    2012-01-31

    Jan 31, 2012 ... Tomato (Lycopersicon esculentum) is an important vegetable crop in Mexico. Recently, a phytoplasma associated with leaf yellowing and curling, severe stunting and little leaf in tomato plant was identified as Yucatan tomato phytoplasma (16SrIII group). DNAs extracted from tomato leaves with symptoms.

  18. ‘Candidatus Phytoplasma luffae’, a novel taxon associated with a witches’-broom disease of loofah, Luffa aegyptica Mill

    Science.gov (United States)

    The phytoplasma associated with witches’ broom disease of loofah (Luffa aegyptica Mill., syn. L.uffa cylindrica (L.) M.J. Roem.) in Taiwan was classified in group 16SrVIII, subgroup A (16SrVIII-A), based on results from actual and in silico RFLP analysis of 16S rRNA gene sequences. Nucleotide sequ...

  19. 'Candidatus Phytoplasma brasiliense', a new phytoplasma taxon associated with hibiscus witches' broom disease.

    Science.gov (United States)

    Montano, H G; Davis, R E; Dally, E L; Hogenhout, S; Pimentel, J P; Brioso, P S

    2001-05-01

    Hibiscus rosa-sinensis is a valuable ornamental species widely planted in Brazil. Many plants are affected by witches' broom disease, which is characterized by excessive axillary branching, abnormally small leaves, and deformed flowers, symptoms that are characteristic of diseases attributed to phytoplasmas. A phytoplasma was detected in diseased Hibiscus by amplification of rRNA operon sequences by PCRs, and was characterized by RFLP and nucleotide sequence analyses of 16S rDNA. The collective RFLP patterns of amplified 16S rDNA differed from the patterns described previously for other phytoplasmas. On the basis of the RFLP patterns, the hibiscus witches' broom phytoplasma was classified in a new 16S rRNA RFLP group, designated group 16SrXV. A phylogenetic analysis of 16S rDNA sequences from this and other phytoplasmas identified the hibiscus witches' broom phytoplasma as a member of a distinct subclade (designated subclade xiv) of the class Mollicutes. A phylogenetic tree constructed on the basis of 16S rRNA gene sequences was consistent with the hypothesis that there was divergent evolution of hibiscus witches' broom phytoplasma and its closest relatives (members of 16S rRNA RFLP group 16SrII) from a common ancestor. On the basis of unique properties of the DNA from hibiscus witches' broom phytoplasma, it is proposed that it represents a new taxon, namely 'Candidatus Phytoplasma brasiliense'.

  20. [Molecular detection and variability of jujube witches'-broom phytoplasmas from different cultivars in various regions of China].

    Science.gov (United States)

    Xu, Qicong; Tian, Guozhong; Wang, Zhengliang; Kong, Fanhua; Li, Yong; Wang, He

    2009-11-01

    Jujube witches'-broom is an important disease in jujube cultivation areas, which causes serious losses in jujube fruit production. To understand the genetic variability and diversity of jujube witches'-broom phytoplasma population from the different cultivars and various regions of China. We collected 32 samples from 14 cultivars or wild sour jujubes in 7 regions of China and detected them with PCR with the primers R16mF2/R16mR1 for phytoplasma 16S rDNA, SR1/SR for 16S-23SrRNA space region (SR) and FD9f/r for secretion proteins (secY). The direct sequencing of PCR products and sequencing by cloned PCR products were used for sequence polymorphism and phylogenetic analyses by comparison to the databases of known conserved gene sequences. We detected phytoplasmas by PCR amplification of 16SrDNA from all the diseased jujube samples. All the phytoplasma isolates infected various jujube cultivars belonged to subgroup 16SrV-B of elm yellows group and had closer homology with Bischofia polycarpa witches'-broom and cherry lethal yellows phytoplasmas occurred in China than other 16SrV phytoplasmas in other countries. The sequence polymorphism at different extent in 16SrDNA, SR and secY gene and genetic diversity were revealed in phytoplasma strain population related to different habitats, among which the dominant strains were always detected by the direct sequencing of PCR products in all the diseased areas of China. The degree of variability on secY gene of collected phytoplasma strains was greater than that of 16SrDNA and SR sequences, and some base substitutions could not alter encoded amino acid, however certain single base deletions detected in a Shandong and a Beijing strains may have impact on the gene structure or function. Phytoplasma strains from different cultivars and regions show dramatic genetic diversity. Compared with direct sequencing of PCR products, the sequencing by cloning PCR products was more useful for the displaying of variants and phylogeny in

  1. Molecular characterization of Yucatan tomato phytoplasma (Group ...

    African Journals Online (AJOL)

    Yomi

    2012-01-31

    Medina JA, Méndez-Lozano J, Leyva-. López NE (2008). Detection and molecular characterization of two little leaf phytoplasma strains associated with pepper and tomato diseases in Guanajuato and Sinaloa, Mexico. Plant Dis.

  2. Grapevine phytoplasma disease in Georgia

    Directory of Open Access Journals (Sweden)

    N.M. Chkhaidze

    2016-09-01

    Full Text Available Results of grapevine yellows disease (GY studies in 2005–2015 are reported. Based on symptoms and Dienes' staining method the disease was detected in Kartli, Kakheti and Guria regions on Vitis vinifera (L. Rkatsiteli, Saperavi, Shavkapito, Tavkveri, Aladasturi, Kachichi, Ganjuri, Chardonnay, Vitis labrusca (L. cultivar Isabella, species hybrid cultivar Noah. The phytoplasmas were also visualized by using electron microscopy. The disease seriously modifies the structure of leaf the grapevine phloem, the chlorophyll content and the functioning of sink–source system. According to anatomical characters the studied cultivars showed a decreasing resistance from Noah, to Aladasturi, Rkatsiteli, Kachichi and Saperavi. In the areas of disease epidemic 12 leafhopper species were identified: Agalmatium grylloides (Fabricius, 1794, Cicadella viridis (Linnaeus, 1758, Dictyophara europaea (Linnaeus, 1767, Empoasca vitis (Gothe, 1875, Erythroneura imeretina Dekanoidze, 1962, Hyalesthes mlokosieviczi Signoret, 1879, Hyalesthes obsoletus Signoret, 1865, Lepironia coleoptrata (Linnaeus, 1758, Pentastiridius leporinus (Linnaeus, 1761, Philaenus spumarius (Linnaeus, 1758, Metcalfa pruinosa (Say, 1830, Ricania japonica (Melichar, 1898, which may be possible vectors of grapevine phytoplasmas in Georgia.

  3. 'Candidatus Phytoplasma lycopersici', a phytoplasma associated with 'hoja de perejil' disease in Bolivia.

    Science.gov (United States)

    Arocha, Yaima; Antesana, Olivia; Montellano, Ernesto; Franco, Pablo; Plata, G; Jones, Phil

    2007-08-01

    New diseases known locally as 'hoja de perejil' of tomato (Lycopersicon esculentum Mill) and 'brotes grandes' of potato (Solanum tuberosum L.) were first recognized in surveys of production fields in Bolivia during 2000-2003. Alfalfa (Medicago sativa) witches' broom and little leaf diseases of native weeds Morrenia variegata and mora-mora (Serjania perulacea) were also identified near to production fields. Phytoplasma aetiology was attributed to each of these diseases following detection and initial identification of aster yellows group (16SrI) phytoplasmas in all five diseased plant species. While potato, alfalfa and mora-mora plants contained indistinguishable 16SrI-B strains, 'hoja de perejil' (THP) and morrenia little leaf (MVLL)-associated phytoplasma strains shared 97.5 % 16S rRNA gene sequence similarity with 'Candidatus Phytoplasma asteris' and related strains and <95 % similarity with all other 'Candidatus Phytoplasma' species. Phylogenetic analysis of 16S rRNA gene sequences indicated that the THP and MVLL phytoplasmas represent a novel lineage within the aster yellows (16SrI) group and, on the basis of unique 16S rRNA gene sequences, we propose that THP and MVLL phytoplasmas represent 'Candidatus Phytoplasma lycopersici', with THP as the reference strain.

  4. Multilocus sequences confirm the close genetic relationship of four phytoplasmas of peanut witches'-broom group 16SrII-A.

    Science.gov (United States)

    Li, Yong; Piao, Chun-gen; Tian, Guo-zhong; Liu, Zhi-xin; Guo, Min-wei; Lin, Cai-li; Wang, Xi-zhuo

    2014-08-01

    Four witches'-broom diseases associated with Arachis hypogaea (peanut), Crotalaria pallida, Tephrosia purpurea, and Cleome viscosa were observed in Hainan Province, China during field surveys in 2004, 2005, and 2007. In previously reported studies, we identified these four phytoplasmas as members of subgroup 16SrII-A, and discovered that their 16S rRNA gene sequences were 99.9-100% identical to one another. In this study, we performed extensive phylogenetic analyses to elucidate relationships among them. We analyzed sequences of the 16S rRNA gene and rplV-rpsC, rpoB, gyrB, dnaK, dnaJ, recA, and secY combined sequence data from two strains each of the four phytoplasmas from Hainan province, as well as strains of peanut witches'-broom from Taiwan (PnWB-TW), "Candidatus Phytoplasma australiense", "Ca. Phytoplasma mali AT", aster yellows witches'-broom phytoplasma AYWB, and onion yellows phytoplasma OY-M. In the 16S rRNA phylogenetic tree, the eight Hainan strains form a clade with PnWB-TW. Analysis of the seven concatenated gene regions indicated that the four phytoplasmas collected from Hainan province cluster most closely with one another, but are closely related to PnWB-TW. The results of field survey and phylogenetic analysis indicated that Cr. pallida, T. purpurea, and Cl. viscosa may be natural plant hosts of peanut witches'-broom phytoplasma. © 2014 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  5. Phytoplasma associated with shoot proliferation in begonia

    Directory of Open Access Journals (Sweden)

    Ribeiro Luiz Fernando Caldeira

    2006-01-01

    Full Text Available Begonia is a very appreciated genus of ornamental plants, of economic relevancy, having species of flowers and foliage. In commercial croppings, plants exhibiting characteristic symptoms of phytoplasma infection have been observed, such as shoot proliferation, reduced plant, size small leaves and flowers, and phyllody. Leaves were sampled and total DNA was extracted to be used in nested Polymerase Chain Reaction (PCR, in order to detect and identify an expected phytoplasma. The results confirmed consistently the presence of a phytoplasma associated with symptomatic plants through the amplification of a typical genomic fragment of 1.2 kb by using the universal primers R16mF2/mR1 and R16F2n/R2. The use of specific primers R16(IIIF2/R1 allowed to identify the phytoplasma detected as a representative of the group 16SrIII. This information is very expressive, because different diseases caused by fungus, bacteria, virus and nematodes have been reported for begonia, however, reports have not been found for begonia diseases associated with phytoplasmas.

  6. Palm yellows phytoplasmas and their genetic classification

    African Journals Online (AJOL)

    ntushk

    Observaciones sobre la enfermedad de la 'hoja bronceado' del cocotero en Venequela. Rev. Fac. Agron. Medellin, 9: 17-26. Contaldo N, Bertaccini A, Paltrinieri S, Windsor HM, Windsor GD. (2012). Axenic culture of plant pathogenic phytoplasmas. Phytopathol. Mediterr. 51(3): 607−617. Dabek AJ, Johnson CG, Harries HC ...

  7. Cytopathological evidence for transport of phytoplasma in infected plants

    Directory of Open Access Journals (Sweden)

    Anna Rudzińska-Langwald

    2014-01-01

    Full Text Available Pleomorphic phytoplasmas were observed in sieve tubes, companion cells and in phloem parenchyma of Tagetes patula L., Helichrysum bracteatum Willd. and Gladiolus sp. L. plants with morphological changes typical for phytoplasma infection. In the pores of the sieve plate phytoplasma cells were seen which suggests that the vertical transport of this pathogen goes in the sieve tubes of infected plants throughout the sieve tube pores. The contact of the sieve tube with the neighbouring cells goes through the plasmodesmata, but no changes of the plasmodesmata were observed in the phloem of infected plants. The size and structure of unchanged plasmodesmata does not allow passing through such big structures like phytoplasma. Instead close contact between phytoplasma cells and vertical sieve tube walls takes place. Damages to the cell wall were observed forming cavities in which the phytoplasma cells were present. The damages of parenchyma and companion cells walls also were seen. In cells where the damages of the walls were observed phytoplasmas were present. The phytoplasma cells were sporadically seen also in the intercellular spaces of parenchyma. These data suggest that horizontal transport depends on damages to the infected plant cell walls caused by the phytoplasma itself.

  8. Microarrays for Universal Detection and Identification of Phytoplasmas

    DEFF Research Database (Denmark)

    Nicolaisen, Mogens; Nyskjold, Henriette; Bertaccini, Assunta

    2013-01-01

    Detection and identification of phytoplasmas is a laborious process often involving nested PCR followed by restriction enzyme analysis and fine-resolution gel electrophoresis. To improve throughput, other methods are needed. Microarray technology offers a generic assay that can potentially detect...... and differentiate all types of phytoplasmas in one assay. The present protocol describes a microarray-based method for identification of phytoplasmas to 16Sr group level.......Detection and identification of phytoplasmas is a laborious process often involving nested PCR followed by restriction enzyme analysis and fine-resolution gel electrophoresis. To improve throughput, other methods are needed. Microarray technology offers a generic assay that can potentially detect...

  9. Phytoplasmas and their insect vectors: Implications for date palm

    Science.gov (United States)

    Date palm is affected by a variety of plant diseases and those associated with phytoplasma presence are increasingly recognised as an emerging threat to the crop. Phytoplasmas are bacteria characterised by a small genome size and the lack of a cell wall. Unlike other bacteria, they are transmitted c...

  10. "Candidatus phytoplasma costaricanum" a new phytoplasma associated with a newly emerging disease in soybean in Costa Rica

    Science.gov (United States)

    A new phytoplasma associated with a newly emerging disease, soybean stunt (SoyST), in soybean (Glycine max) was found in 2002 in a soybean plantation in Alajuela Province, Costa Rica. The same or very closely related phytoplasma also infected sweet pepper (Capsicum annuum) with purple vein syndrome ...

  11. Phytoplasma-host interactions: tomato gibberellin homeostasis and its role in defense against potato purple top phytoplasma infection

    Science.gov (United States)

    Phytoplasmas are cell wall-less bacteria that parasitize plant phloem sieve cells and cause numerous diseases in diverse plant species. Plants infected by phytoplasmas often exhibit symptoms such as general stunting, excessive shoot proliferation, witches’-broom growth, rapid senescence, and a...

  12. 'Candidatus Phytoplasmas pruni', a novel taxon associated with X-disease of stone fruits, Prunus spp.: multilocus characterization based on 16S rRNA, secY, and ribosomal protein genes

    Science.gov (United States)

    X-disease is one of the most serious diseases known in peach (Prunus persica). Based on RFLP analysis of 16S rRNA gene sequences, peach X-disease phytoplasma strains from eastern and western United States and eastern Canada were classified in 16S rDNA RFLP group 16SrIII, subgroup A. Phylogenetic a...

  13. THE CICADA FAUNA AS PHYTOPLASMA VECTORS IN ISTRIAN VINEYARDS

    Directory of Open Access Journals (Sweden)

    Đanfranko Pribetić

    2009-12-01

    Full Text Available The cicada fauna represents a considerable group of insects in vine-growing. Phytoplasma vine vectors insects are significant. They are fed from the phloem tissues of plants like cicadas from the families Cicadelidae, Coccidae, Fulgoridae and Psyilloidaea. Their phytoplasma is transmitted in a persistent way. Researches on cicada fauna, on the floristic structure of weeds and host plants of vine phytoplasma were done in 2005 and 2006 in Istrian vineyards. The research was being done in 10 vineyards on 11 localities. Cicade collecting was done with an entomological net by means of yellow sticky plates using an exhauster and a method of clonting. The collected cicadas were identified by means of binoculars and keys to identify species while the presence of phytoplasmas BN and Fd was defined by means of molecular analysis (PCR, RFLP. Listing and identifying the floristic structure of weeds were being cloned in the explored vineyards by means of keys to identify species. Samples of plant materials were taken for the analysis using PCR method by checking visually the typical symptoms caused by phytoplasma. Cicadas identifying and molecular analyses were being done at the Viticulture Institute for Research in Conegliano – Italy. During the researches, 243 insect samples were collected. Of the above mentioned number cicadas of 40 genus were identified in 207 samples. On the list of the floristic structure of Weeds 105 species of 36 families were identified. Corylus avellana L and Clematis vitalba L species were included in this list. These species showed sigus of phytoplasma disease and they were found near the explored vineyards. These two species were analysed on the presence for FD and BN phytoplasmas. The PCR method used in the molecular research on the presence of Fd and BN phytoplasmas was done on 34 insect samples and 22 plant samples. None of the mentioned sample was positive for FD and BN. The phytoplasma BN was found in the vine leaves of

  14. Photosynthetic responses to phytoplasma infection in Chinese jujube.

    Science.gov (United States)

    Liu, Zhiguo; Zhao, Jin; Liu, Mengjun

    2016-08-01

    Phytoplasma is one of the most devastating plant pathogens. Jujube witches' broom (JWB) is a typical and highly fatal phytoplasma disease of Chinese jujube (Ziziphus jujuba Mill.), which is widely cultivated in Asia. To further elucidate the mechanism of plant-phytoplasma interaction, we first compared the effects of phytoplasma infection on photosynthetic pigments and activities between a JWB-resistant cultivar (Xingguang) and a susceptible cultivar (Pozao). Total chlorophyll and carotenoid levels were significantly decreased in the susceptible cultivar at later stages of infection, but were remarkably increased in the resistant cultivar at the earlier stages. Compared to uninfected plant, a significant decrease in the main photochemical parameters (Fv/Fm, ΦPSII and qP) was recorded at the initial stages of infection in the resistant cultivar, but occurred at later stages in the susceptible cultivar. Meanwhile, the qRT-PCR results of four key photosynthesis-related genes (ZjGluTR, ZjCBP, ZjRubisco and ZjRCA2) demonstrated that the expression patterns were similar in uninfected cultivars, but up-regulated in resistant cultivar and down-regulated in the susceptible one at 12 wks after grafting inoculation. Collectively, our data indicated that the resistant cultivar 'Xingguang' undergoes a decrease in initial stage (inhibiting phytoplasma multiplication) and then a rapid enhancement of photosynthetic activity (helping jujube recovery) in response to phytoplasma infection, while the susceptible cultivar 'Pozao' displays a later decrease in photosynthetic activity. The novel photosynthetic response pattern of the resistant cultivar may contribute to its stronger immunity to phytoplasma infection, which provides new insights into plant-phytoplasma interactions. Copyright © 2016 Elsevier Masson SAS. All rights reserved.

  15. 'Candidatus Phytoplasma balanitae' associated with witches' broom disease of Balanites triflora.

    Science.gov (United States)

    Win, Nang Kyu Kyu; Lee, Seung-Yeol; Bertaccini, Assunta; Namba, Shigetou; Jung, Hee-Young

    2013-02-01

    A phytoplasma was identified in naturally infected wild Balanites triflora plants exhibiting typical witches' broom symptoms (Balanites witches' broom: BltWB) in Myanmar. The 16S rRNA gene sequence revealed that BltWB phytoplasma had the highest similarity to that of 'Candidatus Phytoplasma ziziphi' and it was also closely related to that of 'Candidatus Phytoplasma ulmi'. Phylogenetic analysis of the 16S rRNA gene sequences indicated that the BltWB phytoplasma clustered as a discrete subclade with Elm yellows phytoplasmas. RFLP analysis of the 16S rRNA gene including the 16S-23S spacer region differentiated the BltWB phytoplasma from 'Ca. P. ziziphi', 'Ca. P. ulmi' and 'Candidatus Phytoplasma trifolii'. Analysis of additional ribosomal protein (rp) and translocase protein (secY) gene sequences and phylogenetic analysis of BltWB showed that this phytoplasma was clearly distinguished from those of other 'Candidatus Phytoplasma' taxa. Taking into consideration the unique plant host and the restricted geographical occurrence in addition to the 16S rRNA gene sequence similarity, the BltWB phytoplasma is proposed to represent a novel taxon, 'Candidatus Phytoplasma balanitae'.

  16. Potato purple top phytoplasma-induced disruption of gibberellin homeostasis in tomato plants

    Science.gov (United States)

    Phytoplasmas are phloem-inhabiting, cell wall-less bacteria that cause numerous plant diseases worldwide. Plants infected by phytoplasmas often exhibit various symptoms indicative of hormonal imbalance. In the present study, we investigated the effects of potato purple top (PPT) phytoplasma infect...

  17. Deep amplicon sequencing reveals mixed phytoplasma infection within single grapevine plants

    DEFF Research Database (Denmark)

    Nicolaisen, Mogens; Contaldo, Nicoletta; Makarova, Olga

    2011-01-01

    The diversity of phytoplasmas within single plants has not yet been fully investigated. In this project, deep amplicon sequencing was used to generate 50,926 phytoplasma sequences from 11 phytoplasma-infected grapevine samples from a PCR amplicon in the 5' end of the 16S region. After clustering ...

  18. 'Candidatus Phytoplasma tamaricis', a novel taxon discovered in witches'-broom-diseased salt cedar (Tamarix chinensis Lour.).

    Science.gov (United States)

    Zhao, Yan; Sun, Qingrong; Wei, Wei; Davis, Robert E; Wu, Wei; Liu, Qingzhong

    2009-10-01

    Salt cedar trees with pronounced witches'-broom symptoms were observed in their natural habitat in China. 16S rRNA gene sequences unique to phytoplasmas were detected in every DNA sample extracted from stem and leaf tissues of the symptomatic trees, revealing a direct association between phytoplasma infection and the salt cedar witches'-broom (SCWB) disease. Phylogenetic analysis of the SCWB phytoplasma 16S rRNA gene sequence indicated that the SCWB phytoplasma belonged to a subclade consisting of several mutually distinct 'Candidatus Phytoplasma' taxa including 'Ca. Phytoplasma prunorum', 'Ca. Phytoplasma mali', 'Ca. Phytoplasma pyri' and 'Ca. Phytoplasma spartii'. Pairwise sequence similarity scores calculated from an alignment of near full-length 16S rRNA genes revealed that SCWB phytoplasma shared 96.6 % or less sequence similarity with each previously described or proposed 'Ca. Phytoplasma' taxon, justifying the recognition of SCWB phytoplasma as a novel taxon, 'Candidatus Phytoplasma tamaricis'. The distinct virtual RFLP pattern derived from the SCWB phytoplasma 16S rRNA gene sequence, together with its lower-than-threshold similarity coefficient values with RFLP patterns of any of the 29 previously established groups, supported the recognition of a new 16Sr group, designated 16SrXXX, salt cedar witches'-broom phytoplasma group.

  19. Diverse targets of phytoplasma effectors: from plant development to defense against insects.

    Science.gov (United States)

    Sugio, Akiko; MacLean, Allyson M; Kingdom, Heather N; Grieve, Victoria M; Manimekalai, R; Hogenhout, Saskia A

    2011-01-01

    Phytoplasma research begins to bloom (75). Indeed, this review shows that substantial progress has been made with the identification of phytoplasma effectors that alter flower development, induce witches' broom, affect leaf shape, and modify plant-insect interactions. Phytoplasmas have a unique life cycle among pathogens, as they invade organisms of two distinct kingdoms, namely plants (Plantae) and insects (Animalia), and replicate intracellularly in both. Phytoplasmas release effectors into host cells of plants and insects to target host molecules, and in plants these effectors unload from the phloem to access distal tissues and alter basic developmental processes. The effectors provide phytoplasmas with a fitness advantage by modulating their plant and insect hosts. We expect that further research on the functional characterization of phytoplasma effectors will generate new knowledge that is relevant to fundamental aspects of plant sciences and entomology, and for agriculture by improving yields of crops affected by phytoplasma diseases. Copyright © 2011 by Annual Reviews. All rights reserved.

  20. 'Candidatus Phytoplasma pini', a novel taxon from Pinus silvestris and Pinus halepensis.

    Science.gov (United States)

    Schneider, Bernd; Torres, Ester; Martín, María P; Schröder, Manfred; Behnke, Heinz-Dietmar; Seemüller, Erich

    2005-01-01

    Pinus silvestris and Pinus halepensis trees grown in Germany and Spain, respectively, showing abnormal shoot branching, dwarfed needles and other symptoms were examined for the presence of plant-pathogenic mollicutes (phytoplasmas). While phytoplasmas could not be detected unambiguously with microscopical methods, PCR amplification using universal phytoplasma primers yielded positive results. Samples collected from symptomatic and non-symptomatic plant parts of both symptomatic Pinus silvestris and Pinus halepensis trees tested positive. Also, surrounding non-symptomatic trees proved to be phytoplasma-infected. Comparisons revealed that the 16S rRNA gene sequences of the phytoplasmas identified in Pinus silvestris and Pinus halepensis were nearly identical. However, the pine phytoplasma is only distantly related to other phytoplasmas. The closest relatives are members of the palm lethal yellowing and rice yellow dwarf groups and 'Candidatus Phytoplasma castaneae', which share between 94.5 and 96.6 % 16S rRNA gene sequence similarity. From these data it can be concluded that the phytoplasmas identified in the two Pinus species represent a coherent but discrete taxon; it is proposed that this taxon be distinguished at putative species level under the name 'Candidatus Phytoplasma pini'.

  1. Grapevine yellows diseases in Spain: eight year survey of disease spread and molecular characterization of phytoplasmas involved

    Directory of Open Access Journals (Sweden)

    Torres, Ester

    2005-12-01

    Full Text Available Among grapevine yellows phytoplasma diseases in Europe, flavescence dorée (FD is the most devastating and in the last decade has reached Spanish vineyards, mainly in Catalonia. An eight-year survey was carried out in the areas where the disease has spread (Alt Empordà, Catalonia, Northern Spain and in the remaining vine-growing areas of Catalonia. Sequence analyses of a portion of the 16S-23S ribosomal DNA cistron, from selected grapevine samples from Catalonia, showed that the phytoplasmas involved in grapevine yellows belong to 16S ribosomal subgroups V-D (flavescence dorée, FD and XII-A (bois noir, BN. A set of Spanish FD isolates collected during these years were further studied by RFLP analyses of the 16S-23S ribosomal DNA fragment, as well as the rpS3 and SecY genes. All the FD phytoplasma strains studied were related to phytoplasmas belonging to ribosomal protein subgroup rp-E.La flavescencia dorada (FD es la enfermedad más agresiva de entre todas las enfermedades de fitoplasmas que causan amarilleos de vid en Europa, y que en la última década ha alcanzado también a los viñedos de España, principalmente en Cataluña. Se ha realizado un seguimiento durante ocho años en las zonas donde la enfermedad se había difundido (Alt Empordà, Cataluña y en el resto de zonas con cultivo de vid de Cataluña. El análisis del fragmento del gen DNA ribosomal 16S-23S, de una selección de muestras de vides de Cataluña, indica que los fitoplasmas que están implicados en los amarilleos de vid pertenecen a los subgrupos ribosomales 16S V-D (flavescencia dorada, FD y XII-A (bois noir, BN. Una selección de aislados españoles de FD obtenidos durante estos años se ha examinado mediante análisis RFLP del fragmento del gen ribosomal 16S-23S, y de los genes rpS3 y SecY. Todos los aislamientos de fitoplasmas FD estudiados están relacionados con fitoplasmas pertenecientes al subgrupo de proteína ribosomal rp-E.

  2. Differences between the Texas phoenix palm phytoplasma and the ...

    African Journals Online (AJOL)

    ntushk

    Restriction fragment length polymorphisms analysis of the PCR-amplified nusA and the ... Four restriction enzymes were used for the nusA gene and 16 were used for the hflB genes. Key words: nusA, hflB, phytoplasma, Texas Phoenix decline. ..... Lee I-M, Gundersen-Rindall DE, Davis RE, Bottner KD, Marcone C,.

  3. Differences between the Texas phoenix palm phytoplasma and the ...

    African Journals Online (AJOL)

    From the sabal DNA sample and from one coconut DNA sample two copies of the hflB gene were amplified by nested PCR. Restriction fragment length polymorphisms analysis of the PCR-amplified nusA and the hflB gene copies showed that these genes vary in the phytoplasma strains examined. Four restriction enzymes ...

  4. Molecular survey of the Texas Phoenix decline phytoplasma ...

    African Journals Online (AJOL)

    RFLP) analysis of the PCR-amplified 16S-23S IGS region and the gcp gene using a three restriction enzymes showed that the population of the phytoplasmas infecting S. palmetto in West Central Florida is probably homogenous. The S.

  5. Real-Time PCR for Universal Phytoplasma Detection and Quantification

    DEFF Research Database (Denmark)

    Christensen, Nynne Meyn; Nyskjold, Henriette; Nicolaisen, Mogens

    2013-01-01

    Currently, the most efficient detection and precise quantification of phytoplasmas is by real-time PCR. Compared to nested PCR, this method is less sensitive to contamination and is less work intensive. Therefore, a universal real-time PCR method will be valuable in screening programs and in other...

  6. Sharing information and collections on phytoplasmas: from QBOL to QBANK

    DEFF Research Database (Denmark)

    Bertaccini, Assunta; Paltrinieri, Samanta; Makarova, Olga

    2011-01-01

    A total of 154 phytoplasma strains from 15 ribosomal groups were employed for barcode sequences production. Besides strains in periwinkle, 36 strains in natural infected plants such as napier grass, grapevine, plum, jujube, apple, pear, spartium, pine tree, hibiscus and erigeron were employed. Ba...

  7. Living with genome instability: the adaptation of phytoplasmas todiverse environments of their insect and plant hosts

    Energy Technology Data Exchange (ETDEWEB)

    Bai, Xiaodong; Zhang, Jianhua; Ewing, Adam; Miller, Sally A.; Radek, Agnes; Shevchenko, Dimitriy; Tsukerman, Kiryl; Walunas, Theresa; Lapidus, Alla; Campbell, John W.; Hogenhout Saskia A.

    2006-02-17

    Phytoplasmas (Candidatus Phytoplasma, Class Mollicutes) cause disease in hundreds of economically important plants, and are obligately transmitted by sap-feeding insects of the order Hemiptera, mainly leafhoppers and psyllids. The 706,569-bp chromosome and four plasmids of aster yellows phytoplasma strain witches broom (AY-WB) were sequenced and compared to the onion yellows phytoplasma strain M (OY-M) genome. The phytoplasmas have small repeat-rich genomes. The repeated DNAs are organized into large clusters, potential mobile units (PMUs), which contain tra5 insertion sequences (ISs), and specialized sigma factors and membrane proteins. So far, PMUs are unique to phytoplasmas. Compared to mycoplasmas, phytoplasmas lack several recombination and DNA modification functions, and therefore phytoplasmas probably use different mechanisms of recombination, likely involving PMUs, for the creation of variability, allowing phytoplasmas to adjust to the diverse environments of plants and insects. The irregular GC skews and presence of ISs and large repeated sequences in the AY-WB and OY-M genomes are indicative of high genomic plasticity. Nevertheless, segments of {approx}250 kb, located between genes lplA and glnQ are syntenic between the two phytoplasmas, contain the majority of the metabolic genes and no ISs. AY-WB is further along in the reductive evolution process than OY-M. The AY-WB genome is {approx}154 kb smaller than the OY-M genome, primarily as a result of fewer multicopy sequences, including PMUs. Further, AY-WB lacks genes that are truncated and are part of incomplete pathways in OY-M. This is the first comparative phytoplasma genome analysis and report of the existence of PMUs in phytoplasma genomes.

  8. First report of 16SrII subgroup D phytoplasma in alfalfa in Sudan

    Science.gov (United States)

    In 2016, alfalfa (Medicago sativa) plants from four commercial fields in Sudan, each about 60 ha, were observed with leaf yellowing symptoms and stunted growth. Total nucleic acid was extracted from leaves of 14 symptomatic samples by a CTAB protocol and used as the template in PCR assays with the u...

  9. Identification and characterization of conserved and variable regions of lime witches' broom phytoplasma genome.

    Science.gov (United States)

    Siampour, Majid; Izadpanah, Keramatollah; Marzachi, Cristina; Salehi Abarkoohi, Mohammad

    2015-09-01

    Several segments (∼20  kbp) of the lime witches' broom (LWB) phytoplasma genome (16SrII group) were sequenced and analysed. A 5.7  kbp segment (LWB-C) included conserved genes whose phylogenetic tree was consistent with that generated using 16S rRNA genes. Another 6.4  kbp LWB phytoplasma genome segment (LWB-NC) was structurally similar to the putative mobile unit or sequence variable mosaic genomic region of phytoplasmas, although it represented a new arrangement of genes or pseudogenes such as phage-related protein genes and tra5 insertion sequences. Sequence- and phylogenetic-based evidence suggested that LWB-NC is a genomic region which includes horizontally transferred genes and could be regarded as a hot region to incorporate more foreign genes into the genome of LWB phytoplasma. The presence of phylogenetically related fragments of retroelements was also verified in the LWB phytoplasma genome. Putative intragenomic retrotransposition or retrohoming of these elements might have been determinant in shaping and manipulating the LWB phytoplasma genome. Altogether, the results of this study suggested that the genome of LWB phytoplasma is colonized by a variety of genes that have been acquired through horizontal gene transfer events, which may have further affected the genome through intragenomic mobility and insertion at cognate or incognate sites. Some of these genes are expected to have been involved in the development of features specific to LWB phytoplasma.

  10. “Candidatus Phytoplasma pyri” affects behavior of Cacopsylla pyricola (Hemiptera: Psyllidae)

    Science.gov (United States)

    Pear psylla, Cacopsylla pyricola (Hemiptera: Psyllidae), is a key pest of pear and is a vector of "Candidatus Phytoplasma pyri", the pathogen associated with pear decline disease. Although commercial pear trees are grafted to Phytoplasma-resistant rootstock, a recent report indicated that many C. p...

  11. 'Candidatus Phytoplasma omanense', associated with witches'-broom of Cassia italica (Mill.) Spreng. in Oman.

    Science.gov (United States)

    Al-Saady, Nadiya Abubakar; Khan, Akhtar Jamal; Calari, Alberto; Al-Subhi, Ali Masoud; Bertaccini, Assunta

    2008-02-01

    Samples from plants of Cassia italica exhibiting typical witches'-broom symptoms (Cassia witches'-broom; CWB) were examined for the presence of plant pathogenic phytoplasmas by PCR amplification using universal phytoplasma primers. All affected plants yielded positive results. RFLP analyses of rRNA gene products indicated that the phytoplasmas detected were different from those described previously. Phylogenetic analysis of 16S rRNA gene sequences confirmed that CWB represents a distinct lineage and shares a common ancestor with 'Candidatus Phytoplasma phoenicium'. Molecular comparison revealed that the 16S rRNA gene sequences of the four CWB strains (IM-1, IM-2, IM-3 and IM-4) identified in symptomatic C. italica samples were nearly identical (99.6-100 % similarity). The closest relatives were members of the pigeon pea witches'-broom phytoplasma ribosomal group (16SrIX; 95-97 % sequence similarity). On the basis of unique 16S rRNA gene sequences and biological properties, the phytoplasma associated with witches'-broom of C. italica in Oman represents a coherent but discrete novel phytoplasma, 'Candidatus Phytoplasma omanense', with GenBank/DDBJ/EMBL accession number EF666051 representing the reference strain.

  12. Phytoplasma adapt to the diverse environments of their plant and insect hosts by altering gene expression

    DEFF Research Database (Denmark)

    Makarova, Olga; MacLean, Allyson M.; Nicolaisen, Mogens

    2015-01-01

    Phytoplasmas are intracellular insect-transmitted phytopathogenic bacteria with small genomes. To understand how Aster Yellows phytoplasma strain witches' broom (AY-WB) adapts to their hosts, we performed qRT-PCR analysis of 179 in silico functionally annotated AY-WB genes that are likely to have...

  13. Transcriptomic analysis of Paulownia infected by Paulownia witches'-broom Phytoplasma.

    Science.gov (United States)

    Mou, Hai-Qing; Lu, Jie; Zhu, Shui-Fang; Lin, Cai-Li; Tian, Guo-Zhong; Xu, Xia; Zhao, Wen-Jun

    2013-01-01

    Phytoplasmas are plant pathogenic bacteria that have no cell wall and are responsible for major crop losses throughout the world. Phytoplasma-infected plants show a variety of symptoms and the mechanisms they use to physiologically alter the host plants are of considerable interest, but poorly understood. In this study we undertook a detailed analysis of Paulownia infected by Paulownia witches'-broom (PaWB) Phytoplasma using high-throughput mRNA sequencing (RNA-Seq) and digital gene expression (DGE). RNA-Seq analysis identified 74,831 unigenes, which were subsequently used as reference sequences for DGE analysis of diseased and healthy Paulownia in field grown and tissue cultured plants. Our study revealed that dramatic changes occurred in the gene expression profile of Paulownia after PaWB Phytoplasma infection. Genes encoding key enzymes in cytokinin biosynthesis, such as isopentenyl diphosphate isomerase and isopentenyltransferase, were significantly induced in the infected Paulownia. Genes involved in cell wall biosynthesis and degradation were largely up-regulated and genes related to photosynthesis were down-regulated after PaWB Phytoplasma infection. Our systematic analysis provides comprehensive transcriptomic data about plants infected by Phytoplasma. This information will help further our understanding of the detailed interaction mechanisms between plants and Phytoplasma.

  14. Occurrence of Stolbur Phytoplasma Disease in Spreading Type Petunia hybrida Cultivars in Korea

    Directory of Open Access Journals (Sweden)

    Bong Nam Chung

    2013-12-01

    Full Text Available In January 2012, spreading type petunia cv. Wave Pink plants showing an abnormal growth habit of sprouting unusual multiple plantlets from the lateral buds were collected from a greenhouse in Gwacheon, Gyeonggi Province, Korea. The presence of phytoplasma was investigated using PCR with the primer pairs P1/P6, and R16F1/R1 for nested-PCR. In the nested PCR, 1,096 bp PCR products were obtained, and through sequencing 12 Pet-Stol isolates were identified. Comparison of the nucleotide sequences of 16S rRNA gene of the 12 Pet-Stol isolates with other phytoplasmas belonging to aster yellows or Stolbur showed that Pet-Stol isolates were members of Stolbur. The presence of phytoplasma in petunia was also confirmed by microscopic observation of the pathogens. In this study, Stolbur phytoplasma was identified from spreading type petunia cultivars by sequence analysis of 16S rRNA gene of phytoplasma and microscopic observation of phytoplasma bodies. This is the first report of Stolbur phytoplasma in commercial Petunia hybrida cultivars.

  15. Identification of putative effector genes and their transcripts in three strains related to 'Candidatus Phytoplasma aurantifolia'.

    Science.gov (United States)

    Anabestani, Ameneh; Izadpanah, Keramat; Abbà, Simona; Galetto, Luciana; Ghorbani, Abozar; Palmano, Sabrina; Siampour, Majid; Veratti, Flavio; Marzachì, Cristina

    2017-06-01

    Molecular mechanisms underlying phytoplasma interactions with host plants are largely unknown. In this study attempts were made to identify effectors of three phytoplasma strains related to 'Ca. P. aurantifolia', crotalaria phyllody (CrP), faba bean phyllody (FBP), and witches' broom disease of lime (WBDL), using information from draft genome of peanut witches' broom phytoplasma. Seven putative effectors were identified in WBDL genome (SAP11, SAP21, Eff64, Eff115, Eff197, Eff211 and EffSAP67), five (SAP11, SAP21, Eff64, Eff99 and Eff197) in CrP and two (SAP11, Eff64) in FBP. No homologs to Eff64, Eff197 and Eff211 in phytoplasmas of other phylogenetic groups were found. SAP11 and Eff64 homologs of 'Ca. P. aurantifolia' strains shared at least 95.9% identity and were detected in the three phytoplasmas, supporting their role within the group. Five of the putative effectors (SAP11, SAP21, Eff64, Eff115, and Eff99) were transcribed from total RNA extracts of periwinkle plants infected with these phytoplasmas. Transcription profiles of selected putative effectors of CrP, FBP and WBDL indicated that SAP11 transcripts were the most abundant in the three phytoplasmas. SAP21 transcript levels were comparable to those of SAP11 for CrP and not measurable for the other phytoplasmas. Eff64 had the lowest transcription level irrespective of sampling date and phytoplasma isolate. Eff115 transcript levels were the highest in WBDL infected plants. This work reports the first sequence information for 14 putative effectors in three strains related to 'Ca. P. aurantifolia', and offers novel insight into the transcription profile of five of them during infection of periwinkle. Copyright © 2017 Elsevier GmbH. All rights reserved.

  16. The stable subgroup graph

    Directory of Open Access Journals (Sweden)

    Behnaz Tolue

    2018-07-01

    Full Text Available In this paper we introduce stable subgroup graph associated to the group $G$. It is a graph with vertex set all subgroups of $G$ and two distinct subgroups $H_1$ and $H_2$ are adjacent if $St_{G}(H_1\\cap H_2\

  17. Diversity of bacterial endosymbionts associated with Macrosteles leafhoppers vectoring phytopathogenic phytoplasmas.

    Science.gov (United States)

    Ishii, Yoshiko; Matsuura, Yu; Kakizawa, Shigeyuki; Nikoh, Naruo; Fukatsu, Takema

    2013-08-01

    Here, we investigate the endosymbiotic microbiota of the Macrosteles leafhoppers M. striifrons and M. sexnotatus, known as vectors of phytopathogenic phytoplasmas. PCR, cloning, sequencing, and phylogenetic analyses of bacterial 16S rRNA genes identified two obligate endosymbionts, "Candidatus Sulcia muelleri" and "Candidatus Nasuia deltocephalinicola," and five facultative endosymbionts, Wolbachia, Rickettsia, Burkholderia, Diplorickettsia, and a novel bacterium belonging to the Rickettsiaceae, from the leafhoppers. "Ca. Sulcia muelleri" and "Ca. Nasuia deltocephalinicola" exhibited 100% infection frequencies in the host species and populations and were separately harbored within different bacteriocytes that constituted a pair of coherent bacteriomes in the abdomen of the host insects, as in other deltocephaline leafhoppers. Wolbachia, Rickettsia, Burkholderia, Diplorickettsia, and the novel Rickettsiaceae bacterium exhibited infection frequencies at 7%, 31%, 12%, 0%, and 24% in M. striifrons and at 20%, 0%, 0%, 20%, and 0% in M. sexnotatus, respectively. Although undetected in the above analyses, phytoplasma infections were detected in 16% of M. striifrons and 60% of M. sexnotatus insects by nested PCR of 16S rRNA genes. Two genetically distinct phytoplasmas, namely, "Candidatus Phytoplasma asteris," associated with aster yellows and related plant diseases, and "Candidatus Phytoplasma oryzae," associated with rice yellow dwarf disease, were identified from the leafhoppers. These results highlight strikingly complex endosymbiotic microbiota of the Macrosteles leafhoppers and suggest ecological interactions between the obligate endosymbionts, the facultative endosymbionts, and the phytopathogenic phytoplasmas within the same host insects, which may affect vector competence of the leafhoppers.

  18. An effector of apple proliferation phytoplasma targets TCP transcription factors-a generalized virulence strategy of phytoplasma?

    Science.gov (United States)

    Janik, Katrin; Mithöfer, Axel; Raffeiner, Margot; Stellmach, Hagen; Hause, Bettina; Schlink, Katja

    2017-04-01

    The plant pathogen Candidatus Phytoplasma mali (P. mali) is the causative agent of apple proliferation, a disease of increasing importance in apple-growing areas within Europe. Despite its economic importance, little is known about the molecular mechanisms of disease manifestation within apple trees. In this study, we identified two TCP (TEOSINTE BRANCHED/CYCLOIDEA/PROLIFERATING CELL FACTOR) transcription factors of Malus x domestica as binding partners of the P. mali SAP11-like effector ATP_00189. Phytohormone analyses revealed an effect of P. mali infection on jasmonates, salicylic acid and abscisic acid levels, showing that P. mali affects phytohormonal levels in apple trees, which is in line with the functions of the effector assumed from its binding to TCP transcription factors. To our knowledge, this is the first characterization of the molecular targets of a P. mali effector and thus provides the basis to better understand symptom development and disease progress during apple proliferation. As SAP11 homologues are found in several Phytoplasma species infecting a broad range of different plants, SAP11-like proteins seem to be key players in phytoplasmal infection. © 2016 BSPP AND JOHN WILEY & SONS LTD.

  19. First report of a new subgroup 16SrIX-E, 'Candidatus Phytoplasma phoenicium'-related, phytoplasma associated with juniper witches' broom disease in Oregon

    Science.gov (United States)

    Western juniper (Juniperus occidentalis) is a native tree indigenous to parts of Oregon, Washington, Idaho, Nevada and California. The tree has increased in density since settlement of these areas, raising concern over loss of understory plants, decreased wildlife habitat, and increased soil erosio...

  20. Recilia banda Kramer (Hemiptera: Cicadellidae), a vector of Napier stunt phytoplasma in Kenya

    Science.gov (United States)

    Obura, Evans; Midega, Charles A. O.; Masiga, Daniel; Pickett, John A.; Hassan, Mohamed; Koji, Shinsaku; Khan, Zeyaur R.

    2009-10-01

    Napier grass ( Pennisetum purpureum) is the most important fodder crop in smallholder dairy production systems in East Africa, characterized by small zero-grazing units. It is also an important trap crop used in the management of cereal stemborers in maize in the region. However, production of Napier grass in the region is severely constrained by Napier stunt disease. The etiology of the disease is known to be a phytoplasma, 16SrXI strain. However, the putative insect vector was yet unknown. We sampled and identified five leafhopper and three planthopper species associated with Napier grass and used them as candidates in pathogen transmission experiments. Polymerase chain reaction (PCR), based on the highly conserved 16S gene, primed by P1/P6-R16F2n/R16R2 nested primer sets was used to diagnose phytoplasma on test plants and insects, before and after transmission experiments. Healthy plants were exposed for 60 days to insects that had fed on diseased plants and acquired phytoplasma. The plants were then incubated for another 30 days. Nested PCR analyses showed that 58.3% of plants exposed to Recilia banda Kramer (Hemiptera: Cicadellidae) were positive for phytoplasma and developed characteristic stunt disease symptoms while 60% of R. banda insect samples were similarly phytoplasma positive. We compared the nucleotide sequences of the phytoplasma isolated from R. banda, Napier grass on which these insects were fed, and Napier grass infected by R. banda, and found them to be virtually identical. The results confirm that R. banda transmits Napier stunt phytoplasma in western Kenya, and may be the key vector of Napier stunt disease in this region.

  1. Digital PCR technology for detection of palm infecting phytoplasmas belonging to group 16SrIV that occur in Florida

    Science.gov (United States)

    Phytoplasmas are an economically important group of plant pathogens that negatively impact a wide variety of plants in agricultural and natural ecosystems. In Florida, palms are essential elements in the nursery and landscaping industries that suffer from diseases caused by phytoplasmas that are rel...

  2. Recent advances in phytoplasma research: from genetic diversity and genome evolution to pathogenic redirection of plant stem cell fate

    Science.gov (United States)

    Parasitizing phloem sieve cells and being transmitted by insects, phytoplasmas are a unique group of cell wall-less bacteria responsible for numerous plant diseases worldwide. Due to difficulties in establishing axenic culture of phytoplasmas, phenotypic characters suitable for conventional microbia...

  3. [Cloning, expression and characterization of tRNA-isopentenyltransferase genes (tRNA-ipt) from paulownia witches'-broom phytoplasma].

    Science.gov (United States)

    Hu, Jiaxu; Tian, Guozhong; Lin, Caili; Song, Chuansheng; Mu, Haiqing; Ren, Zhengguang; Guo, Song; Zhou, Tao; Fan, Zaifeng; Li, Huaifang

    2013-08-04

    To identify the tRNA-ipt gene of phytoplasmas and analyze the relationship between tRNA-ipt and synthesis of cytokinin as well as pathogenesis in phytoplasmas. The paulownia witches'-broom phytoplasma (PaWB) tRNA-ipt gene was expressed in E. coli and specific antibody was prepared. Then the growth curve and cytokinin contents of E. coli with PaWB tRNA-ipt were measured by photodensitometry and ELISA respectively. The length of tRNA-ipt genes from PaWB as well as mulberry dwarf, periwinkle virescence and Chinaberry witches'-broom phytoplasmas were 876 bp. All these genes encoded the proteins consisting of 291 amino acids. They contained and indentical motif (GPTASGKT) at N-terminal region related to the ATP or GTP binding sites. Four phytoplasma tRNA-IPTs shared the 99.1-99.5%, amino acid sequence indentity with each other, shared 95.4-99.3% sequence identity with the same group phytoplasmas, whereas the less than 70% identity with 16SrX apple proliferation and 16SrXII Australia grapevine yellows phytoplasmas. The expression of the tRNA-IPT protein and localization in the phloem in phytoplasma-infected paulownia were confirmed by Western blotting and immunofluorescence detection. The determination of growth curve suggested that the growth rate increase of E. coli was affected by the transformation of exogenous tRNA-ipt gene,which might be associated with the cytokinin accumulation. This protein was assumed to be involved in the cytokinin synthesis in phytoplasmas as well as other bacteria, which may play an important role in pathogenic processes of phytoplasmas and symptom development.

  4. Survey of leafhopper species in almond orchards infected with almond witches'-broom phytoplasma in Lebanon.

    Science.gov (United States)

    Dakhil, Hala A; Hammad, Efat Abou-Fakhr; El-Mohtar, Choaa; Abou-Jawdah, Yusuf

    2011-01-01

    Leafhoppers (Hemiptera: Auchenorrhyncha: Cicadellidae) account for more than 80% of all "Auchenorrhynchous" vectors that transmit phytoplasmas. The leafhopper populations in two almond witches'-broom phytoplasma (AlmWB) infected sites: Tanboureet (south of Lebanon) and Bourj El Yahoudieh (north of Lebanon) were surveyed using yellow sticky traps. The survey revealed that the most abundant species was Asymmetrasca decedens, which represented 82.4% of all the leafhoppers sampled. Potential phytoplasma vectors in members of the subfamilies Aphrodinae, Deltocephalinae, and Megophthalminae were present in very low numbers including: Aphrodes makarovi, Cicadulina bipunctella, Euscelidius mundus, Fieberiella macchiae, Allygus theryi, Circulifer haematoceps, Neoaliturus transversalis, and Megophthalmus scabripennis. Allygus theryi (Horváth) (Deltocephalinae) was reported for the first time in Lebanon. Nested PCR analysis and sequencing showed that Asymmetrasca decedens, Empoasca decipiens, Fieberiella macchiae, Euscelidius mundus, Thamnottetix seclusis, Balclutha sp., Lylatina inexpectata, Allygus sp., and Annoplotettix danutae were nine potential carriers of AlmWB phytoplasma. Although the detection of phytoplasmas in an insect does not prove a definite vector relationship, the technique is useful in narrowing the search for potential vectors. The importance of this information for management of AlmWB is discussed.

  5. Shotgun proteomic analysis of the Mexican lime tree infected with "CandidatusPhytoplasma aurantifolia".

    Science.gov (United States)

    Monavarfeshani, Aboozar; Mirzaei, Mehdi; Sarhadi, Elham; Amirkhani, Ardeshir; Khayam Nekouei, Mojtaba; Haynes, Paul A; Mardi, Mohsen; Salekdeh, Ghasem Hosseini

    2013-02-01

    Infection of Mexican lime trees (Citrus aurantifolia L.) with the specialized bacterium "CandidatusPhytoplasma aurantifolia" causes witches' broom disease. Witches' broom disease has the potential to cause significant economic losses throughout western Asia and North Africa. We used label-free quantitative shotgun proteomics to study changes in the proteome of Mexican lime trees in response to infection by "Ca. Phytoplasma aurantifolia". Of 990 proteins present in five replicates of healthy and infected plants, the abundances of 448 proteins changed significantly in response to phytoplasma infection. Of these, 274 proteins were less abundant in infected plants than in healthy plants, and 174 proteins were more abundant in infected plants than in healthy plants. These 448 proteins were involved in stress response, metabolism, growth and development, signal transduction, photosynthesis, cell cycle, and cell wall organization. Our results suggest that proteomic changes in response to infection by phytoplasmas might support phytoplasma nutrition by promoting alterations in the host's sugar metabolism, cell wall biosynthesis, and expression of defense-related proteins. Regulation of defense-related pathways suggests that defense compounds are induced in interactions with susceptible as well as resistant hosts, with the main differences between the two interactions being the speed and intensity of the response.

  6. Molecular Characterization of the 16S rRNA Gene of Phytoplasmas Detected in Two Leafhopper Species Associated with Alfalfa Plants Infected with Witches' Broom in Oman

    Directory of Open Access Journals (Sweden)

    A.J. Khan

    2003-12-01

    Full Text Available Two leafhopper species, Austroagallia avicula and Empoasca sp., were consistently found in alfalfa fields infected with witches’ broom phytoplasma (OmanAlfWB in the Al-Batinah, Dakhliya, North and South Sharqiya, Muscat, and Al-Bureimi regions of the Sultanate of Oman. Phytoplasmas from both leafhoppers were detected by specific polymerase chain reaction (PCR amplification of the 16S rRNA gene and the spacer region in direct PCR using P1/P7 primer pairs. Comparative RFLP profiles of the amplified rRNA gene and the spacer region from leafhopper phytoplasmas and from 20 phytoplasma controls yielded patterns referable to phytoplasmas belonging to the peanut witches’ broom group (16SrII group. In particular, extensive RFLP analyses with the endonucleases HpaII, Tru9I, Tsp509I, and RsaI indicated that the phytoplasmas in A. avicula and Empoasca sp. were identical but showed some differences from OmanAlfWB; however, RFLP patterns obtained with TaqI showed the OmanAlfWB and the phytoplasmas from the two leafhoppers to be identical. Direct PCR products amplified from phytoplasma leafhopper DNA using the P1/P7 primer pair were cloned and sequenced yielding 1758 bp and 1755 bp products from A. avicula and Empoasca sp. respectively; the homology of these sequences with OmanAlfWB and papaya yellow crinkle phytoplasmas was more than 98%. A phylogenetic tree based on the 16S rRNA gene and spacer region sequences from 44 phytoplasmas revealed that the phytoplasmas from the leafhoppers clustered with OmanAlfWB, papaya yellow crinkle, and gerbera phyllody phytoplasmas, all belonging to 16SrII group, but were distinct from lime witches’ broom phytoplasma, the most commonly found phytoplasma in the Sultanate of Oman.

  7. Molecular subgroups of medulloblastoma

    Science.gov (United States)

    Northcott, Paul A; Dubuc, Adrian M; Pfister, Stefan; Taylor, Michael D

    2014-01-01

    Recent efforts at stratifying medulloblastomas based on their molecular features have revolutionized our understanding of this morbidity. Collective efforts by multiple independent groups have subdivided medulloblastoma from a single disease into four distinct molecular subgroups characterized by disparate transcriptional signatures, mutational spectra, copy number profiles and, most importantly, clinical features. We present a summary of recent studies that have contributed to our understanding of the core medulloblastoma subgroups, focusing largely on clinically relevant discoveries that have already, and will continue to, shape research. PMID:22853794

  8. A phytoplasma closely related to the pigeon pea witches'-broom phytoplasma (16Sr IX) is associated with citrus huanglongbing symptoms in the state of São Paulo, Brazil.

    Science.gov (United States)

    Teixeira, D C; Wulff, N A; Martins, E C; Kitajima, E W; Bassanezi, R; Ayres, A J; Eveillard, S; Saillard, C; Bové, J M

    2008-09-01

    In February 2007, sweet orange trees with characteristic symptoms of huanglongbing (HLB) were encountered in a region of São Paulo state (SPs) hitherto free of HLB. These trees tested negative for the three liberibacter species associated with HLB. A polymerase chain reaction (PCR) product from symptomatic fruit columella DNA amplifications with universal primers fD1/rP1 was cloned and sequenced. The corresponding agent was found to have highest 16S rDNA sequence identity (99%) with the pigeon pea witches'-broom phytoplasma of group 16Sr IX. Sequences of PCR products obtained with phytoplasma 16S rDNA primer pairs fU5/rU3, fU5/P7 confirm these results. With two primers D7f2/D7r2 designed based on the 16S rDNA sequence of the cloned DNA fragment, positive amplifications were obtained from more than one hundred samples including symptomatic fruits and blotchy mottle leaves. Samples positive for phytoplasmas were negative for liberibacters, except for four samples, which were positive for both the phytoplasma and 'Candidatus Liberibacter asiaticus'. The phytoplasma was detected by electron microscopy in the sieve tubes of midribs from symptomatic leaves. These results show that a phytoplasma of group IX is associated with citrus HLB symptoms in northern, central, and southern SPs. This phytoplasma has very probably been transmitted to citrus from an external source of inoculum, but the putative insect vector is not yet known.

  9. The congruence subgroup problem

    Indian Academy of Sciences (India)

    Home; Journals; Proceedings – Mathematical Sciences; Volume 114; Issue 4. The Congruence Subgroup Problem. M S Raghunathan. Invited Articles Volume 114 ... Author Affiliations. M S Raghunathan1. School of Mathematics, Tata Institute of Fundamental Research, Homi Bhabha Road, Colaba, Mumbai 400 005, India ...

  10. Subgroups Among Opiate Addicts

    Science.gov (United States)

    Berzins, Juris I.; And Others

    1974-01-01

    The principal objective of the present investigation was to delineate homogeneous MMPI profile subgroups (types) through multivariate clustering procedures and to compare the derived (replicable) types on measures of the components of "sociopathy" as well as on other psychometric devices. (Author)

  11. In-Depth Transcriptome Sequencing of Mexican Lime Trees Infected with Candidatus Phytoplasma aurantifolia.

    Directory of Open Access Journals (Sweden)

    Mohsen Mardi

    Full Text Available Witches' broom disease of acid lime greatly affects the production of Mexican lime in Iran. It is caused by a phytoplasma (Candidatus Phytoplasma aurantifolia. However, the molecular mechanisms that underlie phytoplasma pathogenicity and the mode of interactions with host plants are largely unknown. Here, high-throughput transcriptome sequencing was conducted to explore gene expression signatures associated with phytoplasma infection in Mexican lime trees. We assembled 78,185 unique transcript sequences (unigenes with an average length of 530 nt. Of these, 41,805 (53.4% were annotated against the NCBI non-redundant (nr protein database using a BLASTx search (e-value ≤ 1e-5. When the abundances of unigenes in healthy and infected plants were compared, 2,805 transcripts showed significant differences (false discovery rate ≤ 0.001 and log2 ratio ≥ 1.5. These differentially expressed genes (DEGs were significantly enriched in 43 KEGG metabolic and regulatory pathways. The up-regulated DEGs were mainly categorized into pathways with possible implication in plant-pathogen interaction, including cell wall biogenesis and degradation, sucrose metabolism, secondary metabolism, hormone biosynthesis and signalling, amino acid and lipid metabolism, while down-regulated DEGs were predominantly enriched in ubiquitin proteolysis and oxidative phosphorylation pathways. Our analysis provides novel insight into the molecular pathways that are deregulated during the host-pathogen interaction in Mexican lime trees infected by phytoplasma. The findings can be valuable for unravelling the molecular mechanisms of plant-phytoplasma interactions and can pave the way for engineering lime trees with resistance to witches' broom disease.

  12. Ultrastructural changes in aster yellows phytoplasma affected Limonium sinuatum Mill. plants II. Pathology of cortex parenchyma cells

    Directory of Open Access Journals (Sweden)

    Anna Rudzińska-Langwald

    2014-01-01

    Full Text Available In Limonium sinuatum Mill, plants with severe symptoms of aster yellows infection phytoplasmas were present not only in the phloem but also in some cortex parenchymas cells. These parenchyma cells were situated at some distance from the conducting bundles. The phytoplasmas were observed directly in parenchyma cells cytoplasm. The number of phytoplasmas present in each selected cell varies. The cells with a small number of phytoplasmas show little pathological changes compared with the unaffected cells of the same zone of the stem as well with the cells of healthy plants. The cells filled with a number of phytoplasmas had their protoplast very much changed. The vacuole was reduced and in the cytoplasm a reduction of the number of ribosomes was noted and regions of homogenous structure appeared. Mitochondria were moved in the direction of the tonoplast and plasma membrane. Compared to the cells unaffected by phytoplasma, the mitochondria were smaller and had an enlarged cristae internal space. The chloroplasts from affected cells had a very significant reduction in size and the tylacoids system had disappeared. The role of these changes for creating phytoplasma friendly enviroment is discused.

  13. Analysis of phytoplasma-responsive sRNAs provide insight into the pathogenic mechanisms of mulberry yellow dwarf disease

    Science.gov (United States)

    Gai, Ying-Ping; Li, Yi-Qun; Guo, Fang-Yue; Yuan, Chuan-Zhong; Mo, Yao-Yao; Zhang, Hua-Liang; Wang, Hong; Ji, Xian-Ling

    2014-06-01

    The yellow dwarf disease associated with phytoplasmas is one of the most devastating diseases of mulberry and the pathogenesis involved in the disease is poorly understood. To analyze the molecular mechanisms mediating gene expression in mulberry-phytoplasma interaction, the comprehensive sRNA changes of mulberry leaf in response to phytoplasma-infection were examined. A total of 164 conserved miRNAs and 23 novel miRNAs were identified, and 62 conserved miRNAs and 13 novel miRNAs were found to be involved in the response to phytoplasma-infection. Meanwhile, target genes of the responsive miRNAs were identified by sequencing of the degradome library. In addition, the endogenous siRNAs were sequenced, and their expression profiles were characterized. Interestingly, we found that phytoplasma infection induced the accumulation of mul-miR393-5p which was resulted from the increased transcription of MulMIR393A, and mul-miR393-5p most likely initiate the biogenesis of siRNAs from TIR1 transcript. Based on the results, we can conclude that phytoplasma-responsive sRNAs modulate multiple hormone pathways and play crucial roles in the regulation of development and metabolism. These responsive sRNAs may work cooperatively in the response to phytoplasma-infection and be responsible for some symptoms in the infected plants.

  14. Molecular diagnostic tools for detection and differentiation of phytoplasmas based on chaperonin-60 reveal differences in host plant infection patterns.

    Directory of Open Access Journals (Sweden)

    Tim J Dumonceaux

    Full Text Available Phytoplasmas ('Candidatus Phytoplasma' spp. are insect-vectored bacteria that infect a wide variety of plants, including many agriculturally important species. The infections can cause devastating yield losses by inducing morphological changes that dramatically alter inflorescence development. Detection of phytoplasma infection typically utilizes sequences located within the 16S-23S rRNA-encoding locus, and these sequences are necessary for strain identification by currently accepted standards for phytoplasma classification. However, these methods can generate PCR products >1400 bp that are less divergent in sequence than protein-encoding genes, limiting strain resolution in certain cases. We describe a method for accessing the chaperonin-60 (cpn60 gene sequence from a diverse array of 'Ca.Phytoplasma' spp. Two degenerate primer sets were designed based on the known sequence diversity of cpn60 from 'Ca.Phytoplasma' spp. and used to amplify cpn60 gene fragments from various reference samples and infected plant tissues. Forty three cpn60 sequences were thereby determined. The cpn60 PCR-gel electrophoresis method was highly sensitive compared to 16S-23S-targeted PCR-gel electrophoresis. The topology of a phylogenetic tree generated using cpn60 sequences was congruent with that reported for 16S rRNA-encoding genes. The cpn60 sequences were used to design a hybridization array using oligonucleotide-coupled fluorescent microspheres, providing rapid diagnosis and typing of phytoplasma infections. The oligonucleotide-coupled fluorescent microsphere assay revealed samples that were infected simultaneously with two subtypes of phytoplasma. These tools were applied to show that two host plants, Brassica napus and Camelina sativa, displayed different phytoplasma infection patterns.

  15. DNA Barcoding for Identification of "Candidatus Phytoplasmas" Using a Fragment of the Elongation Factor Tu Gene

    DEFF Research Database (Denmark)

    Makarova, Olga; Contaldo, Nicoletta; Paltrinieri, Samanta

    2012-01-01

    /Principal Findings We designed a new set of primers and amplified a 420–444 bp fragment of tuf from all 91 phytoplasmas strains tested (16S rRNA groups -I through -VII, -IX through -XII, -XV, and -XX). Comparison of NJ trees constructed from the tuf barcode and a 1.2 kbp fragment of the 16S ribosomal gene revealed...

  16. On the alleged origin of geminiviruses from extrachromosomal DNAs of phytoplasmas

    Directory of Open Access Journals (Sweden)

    Noris Emanuela

    2011-06-01

    Full Text Available Abstract Background Several phytoplasmas, wall-less phloem limited plant pathogenic bacteria, have been shown to contain extrachromosomal DNA (EcDNA molecules encoding a replication associated protein (Rep similar to that of geminiviruses, a major group of single stranded (ss DNA plant viruses. On the basis of that observation and of structural similarities between the capsid proteins of geminiviruses and the Satellite tobacco necrosis virus, it has been recently proposed that geminiviruses evolved from phytoplasmal EcDNAs by acquiring a capsid protein coding gene from a co-invading plant RNA virus. Results Here we show that this hypothesis has to be rejected because (i the EcDNA encoded Rep is not of phytoplasmal origin but has been acquired by phytoplasmas through horizontal transfer from a geminivirus or its ancestor; and (ii the evolution of geminivirus capsid protein in land plants implies missing links, while the analysis of metagenomic data suggests an alternative scenario implying a more ancient evolution in marine environments. Conclusion The hypothesis of geminiviruses evolving in plants from DNA molecules of phytoplasma origin contrasts with other findings. An alternative scenario concerning the origin and spread of Rep coding phytoplasmal EcDNA is presented and its implications on the epidemiology of phytoplasmas are discussed.

  17. Diverse phytoplasmas associated with diseases in various crops in Russia - pathogens and vectors

    Science.gov (United States)

    Over a long-term survey (2006-2014), we detected that at least 22 species of cultivated crops from 10 families (Amaranthaceae, Apiaceae, Asteraceae, Brassicaceae, Cucurbitaceae, Fabaceae, Vitaceae, Poaceae, Rosaceae, Solanaceae) were infected with phytoplasma. Most of the plant species are herbaceou...

  18. Napier grass stunt disease prevalence, incidence, severity and genetic variability of the associated phytoplasma in Uganda

    DEFF Research Database (Denmark)

    Kawube, Geofrey; Talwana, Herbert; Nicolaisen, Mogens

    2015-01-01

    of 298 Napier grass fields were visited and NGSD status visually assessed and 1192 samples collected for identification and confirmation of the phytoplasma by polymerase chain reaction (PCR) assays using universal primers P1/P6 nested with R16F2n/R16R2n and, tuf primers 890/340 nested with 835 and 400...

  19. Maize redness in Serbia caused by stolbur phytoplasma is transmitted by Reptalus panzeri

    Science.gov (United States)

    Maize redness (MR) causes midrib, leaf and stalk reddening and abnormal ear development in maize in Serbia, Romania and Bulgaria. High populations of the ciixid Reptalus panzeri were found in MR affected maize fields in the southern Banat region of Serbia in 2005 and 2006, and stolbur phytoplasma w...

  20. First report of BLTVA phytoplasma in Capsicum annuum and Circulifer tenellus in Mexico

    Science.gov (United States)

    Pepper (Capsicum annuum) plants in Durango and Zacatecas, Mexico, in September and October, 2014, had small, chlorotic, curled leaves, plant stunting, and/or big bud symptoms characteristic of phytoplasma infection (Lee et al. 2004). Samples from symptomatic pepper fields included 33 collected near...

  1. Candidatus Phytoplasma malaysianum, a novel taxon associated with virescence and phyllody of Madagascar periwinkle (Catharanthus roseus)

    Science.gov (United States)

    This study addressed the taxonomic position and group classification of a phytoplasma responsible for virescence and phyllody symptoms in naturally diseased Madagascar periwinkle plants in western Malaysia. Unique regions in the 16S rRNA gene from the Malaysian periwinkle virescence (MaPV) phytopla...

  2. Apple proliferation phytoplasma influences the pattern of plant volatiles emitted depending on pathogen virulence

    Directory of Open Access Journals (Sweden)

    Margit eRid

    2016-01-01

    Full Text Available Apple proliferation (AP and pear decline (PD are the most severe diseases in pome fruit growing areas. AP-infected trees show typical symptoms such as witches’ broom, enlarged stipules, tasteless and dwarf fruits. PD-infected pears show a progressive weakening, reduced terminal growth, smaller fruits and die within weeks (quick decline or years (slow decline. The diseases are caused by the cell-wall lacking bacteria Candidatus Phytoplasma mali (AP phytoplasma and Ca. P. pyri (PD phytoplasma, respectively. In previous studies it has been shown that AP-infected apple trees emitted higher amounts of the sesquiterpene β-caryophyllene, an attractant of the insect vector Cacopsylla picta (Hemiptera: Psyllidae, thereby facilitating the dispersal of AP phytoplasma. In the present study, volatile organic compounds (VOCs occurring in the headspace of plants infected with Ca. P. mali strains causing different severity of symptoms in apple plants were collected, analyzed and identified. Headspace samples from healthy and AP-infected model plant tobacco (Nicotiana occidentalis and apple (Malus domestica as well as from healthy and PD-infected pear (Pyrus communis were investigated via thermodesorption and GC-MS analysis. Significantly higher concentrations of ethyl benzoate were produced in all phytoplasma-infected plants compared to healthy ones and an as yet unidentified sesquiterpene differed between the odor bouquets of healthy and by Ca. P. mali infected tobacco plants. Additionally, statistically significant higher amounts of both compounds were measured in the headspace of plants infected by the virulent AP strain. In apple, significantly higher concentrations of ethyl benzoate and methyl salicylate were observed for trees infected with strains of Ca. P. mali. Ethyl benzoate was also detected in the headspace of pear trees infected with Ca. P. pyri.

  3. Comparative analysis of the peanut witches'-broom phytoplasma genome reveals horizontal transfer of potential mobile units and effectors.

    Science.gov (United States)

    Chung, Wan-Chia; Chen, Ling-Ling; Lo, Wen-Sui; Lin, Chan-Pin; Kuo, Chih-Horng

    2013-01-01

    Phytoplasmas are a group of bacteria that are associated with hundreds of plant diseases. Due to their economical importance and the difficulties involved in the experimental study of these obligate pathogens, genome sequencing and comparative analysis have been utilized as powerful tools to understand phytoplasma biology. To date four complete phytoplasma genome sequences have been published. However, these four strains represent limited phylogenetic diversity. In this study, we report the shotgun sequencing and evolutionary analysis of a peanut witches'-broom (PnWB) phytoplasma genome. The availability of this genome provides the first representative of the 16SrII group and substantially improves the taxon sampling to investigate genome evolution. The draft genome assembly contains 13 chromosomal contigs with a total size of 562,473 bp, covering ∼90% of the chromosome. Additionally, a complete plasmid sequence is included. Comparisons among the five available phytoplasma genomes reveal the differentiations in gene content and metabolic capacity. Notably, phylogenetic inferences of the potential mobile units (PMUs) in these genomes indicate that horizontal transfer may have occurred between divergent phytoplasma lineages. Because many effectors are associated with PMUs, the horizontal transfer of these transposon-like elements can contribute to the adaptation and diversification of these pathogens. In summary, the findings from this study highlight the importance of improving taxon sampling when investigating genome evolution. Moreover, the currently available sequences are inadequate to fully characterize the pan-genome of phytoplasmas. Future genome sequencing efforts to expand phylogenetic diversity are essential in improving our understanding of phytoplasma evolution.

  4. 'Candidatus Phytoplasma phoenicium' associated with almond witches'-broom disease: from draft genome to genetic diversity among strain populations.

    Science.gov (United States)

    Quaglino, Fabio; Kube, Michael; Jawhari, Maan; Abou-Jawdah, Yusuf; Siewert, Christin; Choueiri, Elia; Sobh, Hana; Casati, Paola; Tedeschi, Rosemarie; Lova, Marina Molino; Alma, Alberto; Bianco, Piero Attilio

    2015-07-30

    Almond witches'-broom (AlmWB), a devastating disease of almond, peach and nectarine in Lebanon, is associated with 'Candidatus Phytoplasma phoenicium'. In the present study, we generated a draft genome sequence of 'Ca. P. phoenicium' strain SA213, representative of phytoplasma strain populations from different host plants, and determined the genetic diversity among phytoplasma strain populations by phylogenetic analyses of 16S rRNA, groEL, tufB and inmp gene sequences. Sequence-based typing and phylogenetic analysis of the gene inmp, coding an integral membrane protein, distinguished AlmWB-associated phytoplasma strains originating from diverse host plants, whereas their 16S rRNA, tufB and groEL genes shared 100 % sequence identity. Moreover, dN/dS analysis indicated positive selection acting on inmp gene. Additionally, the analysis of 'Ca. P. phoenicium' draft genome revealed the presence of integral membrane proteins and effector-like proteins and potential candidates for interaction with hosts. One of the integral membrane proteins was predicted as BI-1, an inhibitor of apoptosis-promoting Bax factor. Bioinformatics analyses revealed the presence of putative BI-1 in draft and complete genomes of other 'Ca. Phytoplasma' species. The genetic diversity within 'Ca. P. phoenicium' strain populations in Lebanon suggested that AlmWB disease could be associated with phytoplasma strains derived from the adaptation of an original strain to diverse hosts. Moreover, the identification of a putative inhibitor of apoptosis-promoting Bax factor (BI-1) in 'Ca. P. phoenicium' draft genome and within genomes of other 'Ca. Phytoplasma' species suggested its potential role as a phytoplasma fitness-increasing factor by modification of the host-defense response.

  5. Subgrouping Automata: automatic sequence subgrouping using phylogenetic tree-based optimum subgrouping algorithm.

    Science.gov (United States)

    Seo, Joo-Hyun; Park, Jihyang; Kim, Eun-Mi; Kim, Juhan; Joo, Keehyoung; Lee, Jooyoung; Kim, Byung-Gee

    2014-02-01

    Sequence subgrouping for a given sequence set can enable various informative tasks such as the functional discrimination of sequence subsets and the functional inference of unknown sequences. Because an identity threshold for sequence subgrouping may vary according to the given sequence set, it is highly desirable to construct a robust subgrouping algorithm which automatically identifies an optimal identity threshold and generates subgroups for a given sequence set. To meet this end, an automatic sequence subgrouping method, named 'Subgrouping Automata' was constructed. Firstly, tree analysis module analyzes the structure of tree and calculates the all possible subgroups in each node. Sequence similarity analysis module calculates average sequence similarity for all subgroups in each node. Representative sequence generation module finds a representative sequence using profile analysis and self-scoring for each subgroup. For all nodes, average sequence similarities are calculated and 'Subgrouping Automata' searches a node showing statistically maximum sequence similarity increase using Student's t-value. A node showing the maximum t-value, which gives the most significant differences in average sequence similarity between two adjacent nodes, is determined as an optimum subgrouping node in the phylogenetic tree. Further analysis showed that the optimum subgrouping node from SA prevents under-subgrouping and over-subgrouping. Copyright © 2013. Published by Elsevier Ltd.

  6. Peanut witches' broom (PnWB) phytoplasma-mediated leafy flower symptoms and abnormal vascular bundles development.

    Science.gov (United States)

    Liu, Chi-Te; Huang, Hsin-Mei; Hong, Syuan-Fei; Kuo-Huang, Ling-Long; Yang, Chiao-Yin; Lin, Yen-Yu; Lin, Chan-Pin; Lin, Shih-Shun

    2015-01-01

    The peanut witches' broom (PnWB) phytoplasma causes virescence symptoms such as phyllody (leafy flower) in infected peanuts. However, the obligate nature of phytoplasma limits the study of host-pathogen interactions, and the detailed anatomy of PnWB-infected plants has yet to be reported. Here, we demonstrate that 4',6'-diamidino-2-phenylindole (DAPI) staining can be used to track PnWB infection. The DAPI-stained phytoplasma cells were observed in phloem/internal phloem tissues, and changes in vascular bundle morphology, including increasing pith rays and thinner cell walls in the xylem, were found. We also discerned the cell types comprising PnWB in infected sieve tube members. These results suggest that the presence of PnWB in phloem tissue facilitates the transmission of phytoplasma via sap-feeding insect vectors. In addition, PnWB in sieve tube members and changes in vascular bundle morphology might strongly promote the ability of phytoplasmas to assimilate nutrients. These data will help further an understanding of the obligate life cycle and host-pathogen interactions of phytoplasma.

  7. Correspondence between flowers and leaves in terpenoid indole alkaloid metabolism of the phytoplasma-infected Catharanthus roseus plants.

    Science.gov (United States)

    Srivastava, Suchi; Pandey, Richa; Kumar, Sushil; Nautiyal, Chandra Shekhar

    2014-11-01

    Several plants of Catharanthus roseus cv 'leafless inflorescence (lli)' showing phenotype of phytoplasma infection were observed for symptoms of early flowering, virescence, phyllody, and apical clustering of branches. Symptomatic plants were studied for the presence/absence and identity of phytoplasma in flowers. Transcription levels of several genes involved in plants' metabolism and development, accumulation of pharmaceutically important terpenoid indole alkaloids in flowers and leaves and variation in the root-associated microbial flora were examined. The expression profile of 12 genes studied was semi-quantitatively similar in control leaves and phytoplasma-infected leaves and flowers, in agreement with the symptoms of virescence and phyllody in phytoplasma-infected plants. The flowers of phytoplasma-infected plants possessed the TIA profile of leaves and accumulated catharanthine, vindoline, and vincristine and vinblastine in higher concentrations than leaves. The roots of the infected plants displayed lower microbial diversity than those of normal plants. In conclusion, phytoplasma affected the biology of C. roseus lli plants multifariously, it reduced the differences between the metabolite accumulates of the leaves and flowers and restrict the microbial diversity of rhizosphere.

  8. Finite groups all of whose minimal subgroups are NE-subgroups

    Indian Academy of Sciences (India)

    subgroup of . In this article, we investigate the structure of under the assumption that subgroups of prime order are *-subgroups of . The finite groups, all of whose minimal subgroups of the generalized Fitting subgroup are *-subgroups ...

  9. Development of biomarkers and a diagnostic tool for investigation of coinfections by and interactions between potato purple top and potato witches’-broom phytoplasmas in tomato

    Science.gov (United States)

    Columbia Basin potato purple top (PPT) phytoplasma and Alaska potato witches’-broom (PWB) phytoplasma are two closely-related but mutually distinct pathogenic bacteria that infect potato and other vegetable crops. Inhabiting phloem sieve elements and being transmitted by phloem-feeding insect vecto...

  10. Evaluation of anti-phytoplasma properties of surfactin and tetracycline towards lime witches' broom disease using real-time PCR.

    Science.gov (United States)

    Askari, Najmeh; Salehi Jouzani, Gholamreza; Mousivand, Maryam; Foroutan, A; Hagh Nazari, Ali; Abbasalizadeh, Saeed; Soheilivand, Saeed; Mardi, M

    2011-01-01

    The anti-phytoplasma activities of surfactin (derived from Iranian native Bacillus subtilis isolates) and tetracycline towards Candidatus "Phytoplasma aurantifolia", the agent of lime Witches' broom disease, were investigated. HPLC was used to quantify the surfactin production in four previously characterized native surfactin-producing strains, and the one producing the highest amount of surfactin (about 1,500 mg/l) was selected and cultivated following optimized production and extraction protocols. Different combinations of purified surfactin and commercial tetracycline were injected into artificially phytoplasmainfected Mexican lime seedlings using a syringe injection system. An absolute quantitative real-time PCR system was developed to monitor the phytoplasma population shifts in the lime phloem during 3 months following the injections. The results revealed that the injections of surfactin or tetracycline had a significant inhibitory effect on Candidatus "P. aurantifolia". However, the combined treatment with both surfactin and tetracycline (1:1) resulted in the highest inhibition due to a synergic effect, which suppressed the phytoplasma population from about 2×10(5) to less than 10 phytoplasma units/g plant tissue.

  11. Phytoplasma-Responsive microRNAs Modulate Hormonal, Nutritional, and Stress Signalling Pathways in Mexican Lime Trees.

    Directory of Open Access Journals (Sweden)

    Farveh Ehya

    Full Text Available Witches' broom disease of Mexican lime (Citrus aurantifolia L., which is associated to the phytoplasma 'Candidatus Phytoplasma aurantifolia', is a devastating disease that results in significant economic losses. Plants adapt to biotic stresses by regulating gene expression at the transcriptional and post-transcriptional levels. MicroRNAs (miRNAs are a recently identified family of molecules that regulate plant responses to environmental stresses through post-transcriptional gene silencing.Using a high-throughput approach to sequence small RNAs, we compared the expression profiles of miRNAs in healthy Mexican lime trees and in plants infected with 'Ca. P. aurantifolia'.Our results demonstrated the involvement of different miRNAs in the response of Mexican lime trees to infection by 'Ca. P. aurantifolia'. We identified miRNA families that are expressed differentially upon infection with phytoplasmas. Most of the miRNAs had variants with small sequence variations (isomiRs, which are expressed differentially in response to pathogen infection.It is likely that the miRNAs that are expressed differentially in healthy and phytoplasma-infected Mexican lime trees are involved in coordinating the regulation of hormonal, nutritional, and stress signalling pathways, and the complex interactions between them. Future research to elucidate the roles of these miRNAs should improve our understanding of the level of diversity of specific plant responses to phytoplasmas.

  12. Phytoplasma-Responsive microRNAs Modulate Hormonal, Nutritional, and Stress Signalling Pathways in Mexican Lime Trees.

    Science.gov (United States)

    Ehya, Farveh; Monavarfeshani, Aboozar; Mohseni Fard, Ehsan; Karimi Farsad, Laleh; Khayam Nekouei, Mojtaba; Mardi, Mohsen; Salekdeh, Ghasem Hosseini

    2013-01-01

    Witches' broom disease of Mexican lime (Citrus aurantifolia L.), which is associated to the phytoplasma 'Candidatus Phytoplasma aurantifolia', is a devastating disease that results in significant economic losses. Plants adapt to biotic stresses by regulating gene expression at the transcriptional and post-transcriptional levels. MicroRNAs (miRNAs) are a recently identified family of molecules that regulate plant responses to environmental stresses through post-transcriptional gene silencing. Using a high-throughput approach to sequence small RNAs, we compared the expression profiles of miRNAs in healthy Mexican lime trees and in plants infected with 'Ca. P. aurantifolia'. Our results demonstrated the involvement of different miRNAs in the response of Mexican lime trees to infection by 'Ca. P. aurantifolia'. We identified miRNA families that are expressed differentially upon infection with phytoplasmas. Most of the miRNAs had variants with small sequence variations (isomiRs), which are expressed differentially in response to pathogen infection. It is likely that the miRNAs that are expressed differentially in healthy and phytoplasma-infected Mexican lime trees are involved in coordinating the regulation of hormonal, nutritional, and stress signalling pathways, and the complex interactions between them. Future research to elucidate the roles of these miRNAs should improve our understanding of the level of diversity of specific plant responses to phytoplasmas.

  13. RNA-Seq profile of flavescence dorée phytoplasma in grapevine.

    Science.gov (United States)

    Abbà, Simona; Galetto, Luciana; Carle, Patricia; Carrère, Sébastien; Delledonne, Massimo; Foissac, Xavier; Palmano, Sabrina; Veratti, Flavio; Marzachì, Cristina

    2014-12-11

    The phytoplasma-borne disease flavescence dorée is still a threat to European viticulture, despite mandatory control measures and prophylaxis against the leafhopper vector. Given the economic importance of grapevine, it is essential to find alternative strategies to contain the spread, in order to possibly reduce the current use of harmful insecticides. Further studies of the pathogen, the vector and the mechanisms of phytoplasma-host interactions could improve our understanding of the disease. In this work, RNA-Seq technology followed by three de novo assembly strategies was used to provide the first comprehensive transcriptomics landscape of flavescence dorée phytoplasma (FD) infecting field-grown Vitis vinifera leaves. With an average of 8300 FD-mapped reads per library, we assembled 347 sequences, corresponding to 215 annotated genes, and identified 10 previously unannotated genes, 15 polycistronic transcripts and three genes supposedly localized in the gaps of the FD92 draft genome. Furthermore, we improved the annotation of 44 genes with the addition of 5'/3' untranslated regions. Functional classification revealed that the most expressed genes were either related to translation and protein biosynthesis or hypothetical proteins with unknown function. Some of these hypothetical proteins were predicted to be secreted, so they could be bacterial effectors with a potential role in modulating the interaction with the host plant. Interestingly, qRT-PCR validation of the RNA-Seq expression values confirmed that a group II intron represented the FD genomic region with the highest expression during grapevine infection. This mobile element may contribute to the genomic plasticity that is necessary for the phytoplasma to increase its fitness and endorse host-adaptive strategies. The RNA-Seq technology was successfully applied for the first time to analyse the FD global transcriptome profile during grapevine infection. Our results provided new insights into the

  14. The linear chromosome of the plant-pathogenic mycoplasma 'Candidatus Phytoplasma mali'

    Directory of Open Access Journals (Sweden)

    Migdoll Alexander M

    2008-06-01

    Full Text Available Abstract Background Phytoplasmas are insect-transmitted, uncultivable bacterial plant pathogens that cause diseases in hundreds of economically important plants. They represent a monophyletic group within the class Mollicutes (trivial name mycoplasmas and are characterized by a small genome with a low GC content, and the lack of a firm cell wall. All mycoplasmas, including strains of 'Candidatus (Ca. Phytoplasma asteris' and 'Ca. P. australiense', examined so far have circular chromosomes, as is the case for almost all walled bacteria. Results Our work has shown that 'Ca. Phytoplasma mali', the causative agent of apple proliferation disease, has a linear chromosome. Linear chromosomes were also identified in the closely related provisional species 'Ca. P. pyri' and 'Ca. P. prunorum'. The chromosome of 'Ca. P. mali' strain AT is 601,943 bp in size and has a GC content of 21.4%. The chromosome is further characterized by large terminal inverted repeats and covalently closed hairpin ends. Analysis of the protein-coding genes revealed that glycolysis, the major energy-yielding pathway supposed for 'Ca. P. asteris', is incomplete in 'Ca. P. mali'. Due to the apparent lack of other metabolic pathways present in mycoplasmas, it is proposed that maltose and malate are utilized as carbon and energy sources. However, complete ATP-yielding pathways were not identified. 'Ca. P. mali' also differs from 'Ca. P. asteris' by a smaller genome, a lower GC content, a lower number of paralogous genes, fewer insertions of potential mobile DNA elements, and a strongly reduced number of ABC transporters for amino acids. In contrast, 'Ca. P. mali' has an extended set of genes for homologous recombination, excision repair and SOS response than 'Ca. P. asteris'. Conclusion The small linear chromosome with large terminal inverted repeats and covalently closed hairpin ends, the extremely low GC content and the limited metabolic capabilities reflect unique features of 'Ca

  15. Differentiation and classification of phytoplasmas in the pigeon pea witches'-broom group (16SrIX): an update based on multiple gene sequence analysis.

    Science.gov (United States)

    Lee, I-M; Bottner-Parker, K D; Zhao, Y; Bertaccini, A; Davis, R E

    2012-09-01

    The pigeon pea witches'-broom phytoplasma group (16SrIX) comprises diverse strains that cause numerous diseases in leguminous trees and herbaceous crops, vegetables, a fruit, a nut tree and a forest tree. At least 14 strains have been reported worldwide. Comparative phylogenetic analyses of the highly conserved 16S rRNA gene and the moderately conserved rplV (rpl22)-rpsC (rps3) and secY genes indicated that the 16SrIX group consists of at least six distinct genetic lineages. Some of these lineages cannot be readily differentiated based on analysis of 16S rRNA gene sequences alone. The relative genetic distances among these closely related lineages were better assessed by including more variable genes [e.g. ribosomal protein (rp) and secY genes]. The present study demonstrated that virtual RFLP analyses using rp and secY gene sequences allowed unambiguous identification of such lineages. A coding system is proposed to designate each distinct rp and secY subgroup in the 16SrIX group.

  16. Cytogenetic Prognostication Within Medulloblastoma Subgroups

    Science.gov (United States)

    Shih, David J.H.; Northcott, Paul A.; Remke, Marc; Korshunov, Andrey; Ramaswamy, Vijay; Kool, Marcel; Luu, Betty; Yao, Yuan; Wang, Xin; Dubuc, Adrian M.; Garzia, Livia; Peacock, John; Mack, Stephen C.; Wu, Xiaochong; Rolider, Adi; Morrissy, A. Sorana; Cavalli, Florence M.G.; Jones, David T.W.; Zitterbart, Karel; Faria, Claudia C.; Schüller, Ulrich; Kren, Leos; Kumabe, Toshihiro; Tominaga, Teiji; Shin Ra, Young; Garami, Miklós; Hauser, Peter; Chan, Jennifer A.; Robinson, Shenandoah; Bognár, László; Klekner, Almos; Saad, Ali G.; Liau, Linda M.; Albrecht, Steffen; Fontebasso, Adam; Cinalli, Giuseppe; De Antonellis, Pasqualino; Zollo, Massimo; Cooper, Michael K.; Thompson, Reid C.; Bailey, Simon; Lindsey, Janet C.; Di Rocco, Concezio; Massimi, Luca; Michiels, Erna M.C.; Scherer, Stephen W.; Phillips, Joanna J.; Gupta, Nalin; Fan, Xing; Muraszko, Karin M.; Vibhakar, Rajeev; Eberhart, Charles G.; Fouladi, Maryam; Lach, Boleslaw; Jung, Shin; Wechsler-Reya, Robert J.; Fèvre-Montange, Michelle; Jouvet, Anne; Jabado, Nada; Pollack, Ian F.; Weiss, William A.; Lee, Ji-Yeoun; Cho, Byung-Kyu; Kim, Seung-Ki; Wang, Kyu-Chang; Leonard, Jeffrey R.; Rubin, Joshua B.; de Torres, Carmen; Lavarino, Cinzia; Mora, Jaume; Cho, Yoon-Jae; Tabori, Uri; Olson, James M.; Gajjar, Amar; Packer, Roger J.; Rutkowski, Stefan; Pomeroy, Scott L.; French, Pim J.; Kloosterhof, Nanne K.; Kros, Johan M.; Van Meir, Erwin G.; Clifford, Steven C.; Bourdeaut, Franck; Delattre, Olivier; Doz, François F.; Hawkins, Cynthia E.; Malkin, David; Grajkowska, Wieslawa A.; Perek-Polnik, Marta; Bouffet, Eric; Rutka, James T.; Pfister, Stefan M.; Taylor, Michael D.

    2014-01-01

    Purpose Medulloblastoma comprises four distinct molecular subgroups: WNT, SHH, Group 3, and Group 4. Current medulloblastoma protocols stratify patients based on clinical features: patient age, metastatic stage, extent of resection, and histologic variant. Stark prognostic and genetic differences among the four subgroups suggest that subgroup-specific molecular biomarkers could improve patient prognostication. Patients and Methods Molecular biomarkers were identified from a discovery set of 673 medulloblastomas from 43 cities around the world. Combined risk stratification models were designed based on clinical and cytogenetic biomarkers identified by multivariable Cox proportional hazards analyses. Identified biomarkers were tested using fluorescent in situ hybridization (FISH) on a nonoverlapping medulloblastoma tissue microarray (n = 453), with subsequent validation of the risk stratification models. Results Subgroup information improves the predictive accuracy of a multivariable survival model compared with clinical biomarkers alone. Most previously published cytogenetic biomarkers are only prognostic within a single medulloblastoma subgroup. Profiling six FISH biomarkers (GLI2, MYC, chromosome 11 [chr11], chr14, 17p, and 17q) on formalin-fixed paraffin-embedded tissues, we can reliably and reproducibly identify very low-risk and very high-risk patients within SHH, Group 3, and Group 4 medulloblastomas. Conclusion Combining subgroup and cytogenetic biomarkers with established clinical biomarkers substantially improves patient prognostication, even in the context of heterogeneous clinical therapies. The prognostic significance of most molecular biomarkers is restricted to a specific subgroup. We have identified a small panel of cytogenetic biomarkers that reliably identifies very high-risk and very low-risk groups of patients, making it an excellent tool for selecting patients for therapy intensification and therapy de-escalation in future clinical trials. PMID

  17. Coconut lethal yellowing diseases: a phytoplasma threat to palms of global economic and social significance

    Directory of Open Access Journals (Sweden)

    Gurr M Geoff

    2016-10-01

    Full Text Available The recent discovery of Bogia Coconut Syndrome in Papua New Guinea is the first report of a lethal yellowing disease (LYD in Oceania. Numerous outbreaks of LYDs of coconut have been recorded in the Caribbean and Africa since the late 19th century and have caused the death of millions of palms across several continents during the 20th century. Despite the severity of economic losses, it was only in the 1970s that the causes of LYDs were identified as phytoplasmas, a group of insect-transmitted bacteria associated with diseases in many other economically important crop species. Since the development of polymerase chain reaction (PCR technology, knowledge of LYDs epidemiology, ecology and vectors has grown rapidly. There is no economically viable treatment for LYDs and vector-based management is hampered by the fact that vectors have been positively identified in very few cases despite many attempted transmission trials. Some varieties and hybrids of coconut palm are known to be less susceptible to LYD but none are completely resistant. Optimal and current management of LYD is through strict quarantine, prompt detection and destruction of symptomatic palms, and replanting with less susceptible varieties or crop species. Advances in technology such as loop mediated isothermal amplification (LAMP for detection and tracking of phytoplasma DNA in plants and insects, remote sensing for identifying symptomatic palms, and the advent of clustered regularly interspaced short palindromic repeats (CRISPR-based tools for gene editing and plant breeding are likely to allow rapid progress in taxonomy as well as understanding and managing LYD phytoplasma pathosystems.

  18. Soft n-Ary Subgroups

    Directory of Open Access Journals (Sweden)

    D.R. Prince Williams

    2015-09-01

    Full Text Available Soft set theory plays a vital role in solving many complicated problems with inherited uncertainty. An n-ary algebraic systems is a generalization of algebraic structures and it is the most natural way for the further development, deeper understanding of their properties. In this paper, we apply soft set theory to an n-ary algebraic systems and introduce the notions of soft n-ary groups and soft n-ary subgroups. Further, some operations on soft sets are extended to the former. Finally, we provide the characterization of soft n-ary subgroups over an n-ary group (G,f and study their related properties.

  19. On Cosets and Normal Subgroups

    OpenAIRE

    B. O. ONASANYA; S.A.Ilori

    2014-01-01

    The paper [5] has worked on fuzzy cosets and fuzzy normal subgroups of a group, [8] has extended the idea to fuzzy middle coset. In addition to what has been done, we make a link between fuzzy coset and fuzzy middle coset and investigate some more properties of the fuzzy middle coset. [7] made attempt with some results needing adjustment. [2], [8] and [9] have shown that if f 2 F(Sn), the set of all fuzzy subgroups of Sn, is such that Imf has the highest order and f is constant on the conjuga...

  20. 'Candidatus Phytoplasma tamaricis', a novel taxon discovered in witches'-broom diseased salt cedar (Tamarix chinensis Lour.)

    Science.gov (United States)

    Salt cedar trees with pronounced witches’-broom symptoms were observed in their natural habitat in China. 16S rRNA gene sequences unique to phytoplasmas were detected in every DNA sample extracted from stem and leaf tissues of the symptomatic trees, revealing a direct association between phytoplasm...

  1. Morphological changes of Paulownia seedlings infected phytoplasmas reveal the genes associated with witches' broom through AFLP and MSAP.

    Science.gov (United States)

    Cao, Xibing; Fan, Guoqiang; Zhao, Zhenli; Deng, Minjie; Dong, Yanpeng

    2014-01-01

    Paulownia witches' broom (PaWB) caused by phytoplasma might result in devastating damage to the growth and wood production of Paulownia. To study the effect of phytoplasma on DNA sequence and to discover the genes related to PaWB occurrence, DNA polymorphisms and DNA methylation levels and patterns in PaWB seedlings, the ones treated with various concentration of methyl methane sulfonate (MMS) and healthy seedlings were investigated with amplified fragment length polymorphism (AFLP) and methylation-sensitive amplification polymorphism (MSAP). Our results indicated that PaWB seedlings recovered a normal morphology, similar to healthy seedlings, after treatment with more than 20 mg · L-1 MMS; Phytoplasma infection did not change the Paulownia genomic DNA sequence at AFLP level, but changed the global DNA methylation levels and patterns; Genes related to PaWB were discovered through MSAP and validated using quantitative real-time PCR (qRT-PCR). These results implied that changes of DNA methylation levels and patterns were closely related to the morphological changes of seedlings infected with phytoplasmas.

  2. Population genetic analysis reveals a low level of genetic diversity of 'Candidatus Phytoplasma aurantifolia' causing witches' broom disease in lime.

    Science.gov (United States)

    Al-Abadi, Shaikha Y; Al-Sadi, Abdullah M; Dickinson, Matthew; Al-Hammadi, Mohammed S; Al-Shariqi, Rashid; Al-Yahyai, Rashid A; Kazerooni, Elham A; Bertaccini, Assunta

    2016-01-01

    Witches' broom disease of lime (WBDL) is a serious phytoplasma disease of acid lime in Oman, the UAE and Iran. Despite efforts to study it, no systemic study attempted to characterize the relationship among the associated phytoplasma, 'Candidatus Phytoplasma aurantifolia', from the three countries. This study utilized sequences of the 16S rRNA, imp and secA genes to characterize 57 strains collected from Oman (38), the UAE (9) and Iran (10). Phylogenetic analysis based on the 16S rRNA gene showed that the 57 strains shared 98.5-100 % nucleotide similarity to each other and to strains of 'Ca. P. aurantifolia' available in GenBank. The level of genetic diversity was low based on the 16S rRNA (0-0.011), imp (0-0.002) and secA genes (0-0.015). The presence of low level of diversity among phytoplasma strains from Oman, the UAE and Iran can be explained by the movement of infected lime seedlings from one country to another through trading and exchange of infected plants. The study discusses implication of the findings on WBDL spread and management.

  3. Endophytic bacterial community living in roots of healthy and 'Candidatus Phytoplasma mali'-infected apple (Malus domestica, Borkh.) trees.

    Science.gov (United States)

    Bulgari, Daniela; Bozkurt, Adem I; Casati, Paola; Cağlayan, Kadriye; Quaglino, Fabio; Bianco, Piero A

    2012-11-01

    'Candidatus Phytoplasma mali', the causal agent of apple proliferation (AP) disease, is a quarantine pathogen controlled by chemical treatments against insect vectors and eradication of diseased plants. In accordance with the European Community guidelines, novel strategies should be developed for sustainable management of plant diseases by using resistance inducers (e.g. endophytes). A basic point for the success of this approach is the study of endophytic bacteria associated with plants. In the present work, endophytic bacteria living in healthy and 'Ca. Phytoplasma mali'-infected apple trees were described by cultivation-dependent and independent methods. 16S rDNA sequence analysis showed the presence of the groups Proteobacteria, Acidobacteria, Bacteroidetes, Actinobacteria, Chlamydiae, and Firmicutes. In detail, library analyses underscored 24 and 17 operational taxonomic units (OTUs) in healthy and infected roots, respectively, with a dominance of Betaproteobacteria. Moreover, differences in OTUs number and in CFU/g suggested that phytoplasmas could modify the composition of endophytic bacterial communities associated with infected plants. Intriguingly, the combination of culturing methods and cloning analysis allowed the identification of endophytic bacteria (e.g. Bacillus, Pseudomonas, and Burkholderia) that have been reported as biocontrol agents. Future research will investigate the capability of these bacteria to control 'Ca. Phytoplasma mali' in order to develop sustainable approaches for managing AP.

  4. Morphological changes of Paulownia seedlings infected phytoplasmas reveal the genes associated with witches' broom through AFLP and MSAP.

    Directory of Open Access Journals (Sweden)

    Xibing Cao

    Full Text Available Paulownia witches' broom (PaWB caused by phytoplasma might result in devastating damage to the growth and wood production of Paulownia. To study the effect of phytoplasma on DNA sequence and to discover the genes related to PaWB occurrence, DNA polymorphisms and DNA methylation levels and patterns in PaWB seedlings, the ones treated with various concentration of methyl methane sulfonate (MMS and healthy seedlings were investigated with amplified fragment length polymorphism (AFLP and methylation-sensitive amplification polymorphism (MSAP. Our results indicated that PaWB seedlings recovered a normal morphology, similar to healthy seedlings, after treatment with more than 20 mg · L-1 MMS; Phytoplasma infection did not change the Paulownia genomic DNA sequence at AFLP level, but changed the global DNA methylation levels and patterns; Genes related to PaWB were discovered through MSAP and validated using quantitative real-time PCR (qRT-PCR. These results implied that changes of DNA methylation levels and patterns were closely related to the morphological changes of seedlings infected with phytoplasmas.

  5. ‘Candidatus Phytoplasma hispanicum’, a novel taxon associated with Mexican periwinkle virescence disease of Catharanthus roseus

    Science.gov (United States)

    Mexican periwinkle virescence (MPV) phytoplasma was originally discovered in diseased plants of Madagascar periwinkle (Catharanthus roseus) in Yucatán, Mexico. On the basis of results from RFLP analysis of PCR-amplified 16S rRNA gene sequences, strain MPV was previously classified as the first know...

  6. Phytoplasma Effector SAP54 Induces Indeterminate Leaf-Like Flower Development in Arabidopsis Plants1[C][W][OA

    Science.gov (United States)

    MacLean, Allyson M.; Sugio, Akiko; Makarova, Olga V.; Findlay, Kim C.; Grieve, Victoria M.; Tóth, Réka; Nicolaisen, Mogens; Hogenhout, Saskia A.

    2011-01-01

    Phytoplasmas are insect-transmitted bacterial plant pathogens that cause considerable damage to a diverse range of agricultural crops globally. Symptoms induced in infected plants suggest that these phytopathogens may modulate developmental processes within the plant host. We report herein that Aster Yellows phytoplasma strain Witches’ Broom (AY-WB) readily infects the model plant Arabidopsis (Arabidopsis thaliana) ecotype Columbia, inducing symptoms that are characteristic of phytoplasma infection, such as the production of green leaf-like flowers (virescence and phyllody) and increased formation of stems and branches (witches’ broom). We found that the majority of genes encoding secreted AY-WB proteins (SAPs), which are candidate effector proteins, are expressed in Arabidopsis and the AY-WB insect vector Macrosteles quadrilineatus (Hemiptera; Cicadellidae). To identify which of these effector proteins induce symptoms of phyllody and virescence, we individually expressed the effector genes in Arabidopsis. From this screen, we have identified a novel AY-WB effector protein, SAP54, that alters floral development, resulting in the production of leaf-like flowers that are similar to those produced by plants infected with this phytoplasma. This study offers novel insight into the effector profile of an insect-transmitted plant pathogen and reports to our knowledge the first example of a microbial pathogen effector protein that targets flower development in a host. PMID:21849514

  7. Use of quantitative real time PCR for a genome-wide study of AYWB phytoplasma gene expression in plant and insect hosts

    DEFF Research Database (Denmark)

    Makarova, Olga; MacLean, Allyson M.; Hogenhout, Saskia A.

    2011-01-01

    Phytoplasmas are obligate parasites of plants and insects and cause significant crop yield losses worldwide. A number of microarray gene expression studies have been performed to understand better the effects of phytoplasma infection on plant physiology. However, little effort has been made...... this technique for reliable gene expression quantification of phytoplasmas on a large scale. In our experimental setup, 242 genes of aster yellows phytoplasma strain witches' broom (AY-WB) were tested for differences in expression in plant and insect host environments, and were shown to be predominantly...... expressed in the plant or insect hosts. In silico operon prediction corroborated the experimental data. Our findings suggest that the delta delta Ct method can be used to study the physiology of this pathogen...

  8. Hopf algebras and congruence subgroups

    CERN Document Server

    Sommerhauser, Yorck

    2007-01-01

    We prove that the kernel of the natural action of the modular group on the center of the Drinfel'd double of a semisimple Hopf algebra is a congruence subgroup. To do this, we introduce a class of generalized Frobenius-Schur indicators and endow it with an action of the modular group that is compatible with the original one.

  9. Erratum The congruence subgroup problem

    Indian Academy of Sciences (India)

    R. Narasimhan (Krishtel eMaging) 1461 1996 Oct 15 13:05:22

    . 299–308). The congruence subgroup problem. M S RAGHUNATHAN. There is unfortunately an error in the paper cited above in the very first page. We correct this error (which does not materially affect the rest of the paper in any way) below.

  10. Phytoplasma infection of a tropical root crop triggers bottom-up cascades by favoring generalist over specialist herbivores.

    Directory of Open Access Journals (Sweden)

    Kris A G Wyckhuys

    Full Text Available Global interest on plant-microbe-insect interactions is rapidly growing, revealing the multiple ways in which microorganisms mediate plant-herbivore interactions. Phytopathogens regularly alter whole repertoires of plant phenotypic traits, and bring about shifts in key chemical or morphological characteristics of plant hosts. Pathogens can also cause cascading effects on higher trophic levels, and eventually shape entire plant-associated arthropod communities. We tested the hypothesis that a Candidatus Phytoplasma causing cassava witches' broom (CWB on cassava (Manihot esculenta Grantz is altering species composition of invasive herbivores and their associated parasitic hymenopterans. We conducted observational studies in cassava fields in eastern Cambodia to assess the effect of CWB infection on abundance of specialist and generalist mealybugs (Homoptera: Pseudococcidae, and associated primary and hyper-parasitoid species. CWB infection positively affects overall mealybug abundance and species richness at a plant- and field-level, and disproportionately favors a generalist mealybug over a specialist feeder. CWB phytoplasma infection led to increased parasitoid richness and diversity, with richness of 'comparative' specialist taxa being the most significantly affected. Parasitism rate did not differ among infected and uninfected plants, and mealybug host suppression was not impacted. CWB phytoplasma modifies host plant quality for sap-feeding homopterans, differentially affects success rates of two invasive species, and generates niche opportunities for higher trophic orders. By doing so, a Candidatus phytoplasma affects broader food web structure and functioning, and assumes the role of an ecosystem engineer. Our work unveils key facets of phytoplasma ecology, and sheds light upon complex multi-trophic interactions mediated by an emerging phytopathogen. These findings have further implications for invasion ecology and management.

  11. Phytoplasma infection of a tropical root crop triggers bottom-up cascades by favoring generalist over specialist herbivores

    Science.gov (United States)

    Graziosi, Ignazio; Burra, Dharani Dhar; Walter, Abigail Jan

    2017-01-01

    Global interest on plant-microbe-insect interactions is rapidly growing, revealing the multiple ways in which microorganisms mediate plant-herbivore interactions. Phytopathogens regularly alter whole repertoires of plant phenotypic traits, and bring about shifts in key chemical or morphological characteristics of plant hosts. Pathogens can also cause cascading effects on higher trophic levels, and eventually shape entire plant-associated arthropod communities. We tested the hypothesis that a Candidatus Phytoplasma causing cassava witches’ broom (CWB) on cassava (Manihot esculenta Grantz) is altering species composition of invasive herbivores and their associated parasitic hymenopterans. We conducted observational studies in cassava fields in eastern Cambodia to assess the effect of CWB infection on abundance of specialist and generalist mealybugs (Homoptera: Pseudococcidae), and associated primary and hyper-parasitoid species. CWB infection positively affects overall mealybug abundance and species richness at a plant- and field-level, and disproportionately favors a generalist mealybug over a specialist feeder. CWB phytoplasma infection led to increased parasitoid richness and diversity, with richness of ‘comparative’ specialist taxa being the most significantly affected. Parasitism rate did not differ among infected and uninfected plants, and mealybug host suppression was not impacted. CWB phytoplasma modifies host plant quality for sap-feeding homopterans, differentially affects success rates of two invasive species, and generates niche opportunities for higher trophic orders. By doing so, a Candidatus phytoplasma affects broader food web structure and functioning, and assumes the role of an ecosystem engineer. Our work unveils key facets of phytoplasma ecology, and sheds light upon complex multi-trophic interactions mediated by an emerging phytopathogen. These findings have further implications for invasion ecology and management. PMID:28813469

  12. Analysis of expressed genes of the bacterium 'Candidatus phytoplasma Mali' highlights key features of virulence and metabolism.

    Directory of Open Access Journals (Sweden)

    Christin Siewert

    Full Text Available 'Candidatus Phytoplasma mali' is a phytopathogenic bacterium of the family Acholeplasmataceae assigned to the class Mollicutes. This causative agent of the apple proliferation colonizes in Malus domestica the sieve tubes of the plant phloem resulting in a range of symptoms such as witches'--broom formation, reduced vigor and affecting size and quality of the crop. The disease is responsible for strong economical losses in Europe. Although the genome sequence of the pathogen is available, there is only limited information on expression of selected genes and metabolic key features that have not been examined on the transcriptomic or proteomic level so far. This situation is similar to many other phytoplasmas. In the work presented here, RNA-Seq and mass spectrometry shotgun techniques were applied on tissue samples from Nicotiana occidentalis infected by 'Ca. P. mali' strain AT providing insights into transcriptome and proteome of the pathogen. Data analysis highlights expression of 208 genes including 14 proteins located in the terminal inverted repeats of the linear chromosome. Beside a high portion of house keeping genes, the recently discussed chaperone GroES/GroEL is expressed. Furthermore, gene expression involved in formation of a type IVB and of the Sec-dependent secretion system was identified as well as the highly expressed putative pathogenicity-related SAP11-like effector protein. Metabolism of phytoplasmas depends on the uptake of spermidine/putescine, amino acids, co-factors, carbohydrates and in particular malate/citrate. The expression of these transporters was confirmed and the analysis of the carbohydrate cycle supports the suggested alternative energy-providing pathway for phytoplasmas releasing acetate and providing ATP. The phylogenetic analyses of malate dehydrogenase and acetate kinase in phytoplasmas show a closer relatedness to the Firmicutes in comparison to Mycoplasma species indicating an early divergence of the

  13. Multiplex Real-Time qPCR Assay for Simultaneous and Sensitive Detection of Phytoplasmas in Sesame Plants and Insect Vectors.

    Directory of Open Access Journals (Sweden)

    Cengiz Ikten

    Full Text Available Phyllody, a destructive and economically important disease worldwide caused by phytoplasma infections, is characterized by the abnormal development of floral structures into stunted leafy parts and contributes to serious losses in crop plants, including sesame (Sesamum indicum L.. Accurate identification, differentiation, and quantification of phyllody-causing phytoplasmas are essential for effective management of this plant disease and for selection of resistant sesame varieties. In this study, a diagnostic multiplex qPCR assay was developed using TaqMan® chemistry based on detection of the 16S ribosomal RNA gene of phytoplasmas and the 18S ribosomal gene of sesame. Phytoplasma and sesame specific primers and probes labeled with different fluorescent dyes were used for simultaneous amplification of 16SrII and 16SrIX phytoplasmas in a single tube. The multiplex real-time qPCR assay allowed accurate detection, differentiation, and quantification of 16SrII and 16SrIX groups in 109 sesame plant and 92 insect vector samples tested. The assay was found to have a detection sensitivity of 1.8 x 102 and 1.6 x 102 DNA copies for absolute quantification of 16SrII and 16SrIX group phytoplasmas, respectively. Relative quantification was effective and reliable for determination of phyllody phytoplasma DNA amounts normalized to sesame DNA in infected plant tissues. The development of this qPCR assay provides a method for the rapid measurement of infection loads to identify resistance levels of sesame genotypes against phyllody phytoplasma disease.

  14. Multiplex Real-Time qPCR Assay for Simultaneous and Sensitive Detection of Phytoplasmas in Sesame Plants and Insect Vectors.

    Science.gov (United States)

    Ikten, Cengiz; Ustun, Rustem; Catal, Mursel; Yol, Engin; Uzun, Bulent

    2016-01-01

    Phyllody, a destructive and economically important disease worldwide caused by phytoplasma infections, is characterized by the abnormal development of floral structures into stunted leafy parts and contributes to serious losses in crop plants, including sesame (Sesamum indicum L.). Accurate identification, differentiation, and quantification of phyllody-causing phytoplasmas are essential for effective management of this plant disease and for selection of resistant sesame varieties. In this study, a diagnostic multiplex qPCR assay was developed using TaqMan® chemistry based on detection of the 16S ribosomal RNA gene of phytoplasmas and the 18S ribosomal gene of sesame. Phytoplasma and sesame specific primers and probes labeled with different fluorescent dyes were used for simultaneous amplification of 16SrII and 16SrIX phytoplasmas in a single tube. The multiplex real-time qPCR assay allowed accurate detection, differentiation, and quantification of 16SrII and 16SrIX groups in 109 sesame plant and 92 insect vector samples tested. The assay was found to have a detection sensitivity of 1.8 x 102 and 1.6 x 102 DNA copies for absolute quantification of 16SrII and 16SrIX group phytoplasmas, respectively. Relative quantification was effective and reliable for determination of phyllody phytoplasma DNA amounts normalized to sesame DNA in infected plant tissues. The development of this qPCR assay provides a method for the rapid measurement of infection loads to identify resistance levels of sesame genotypes against phyllody phytoplasma disease.

  15. Biological Effects of Weak Electromagnetic Field on Healthy and Infected Lime (Citrus aurantifolia Trees with Phytoplasma

    Directory of Open Access Journals (Sweden)

    Fatemeh Abdollahi

    2012-01-01

    Full Text Available Exposure to electromagnetic fields (EMF has become an issue of concern for a great many people and is an active area of research. Phytoplasmas, also known as mycoplasma-like organisms, are wall-less prokaryotes that are pathogens of many plant species throughout the world. Effects of electromagnetic fields on the changes of lipid peroxidation, content of H2O2, proline, protein, and carbohydrates were investigated in leaves of two-year-old trees of lime (Citrus aurantifolia infected by the Candidatus Phytoplasma aurantifoliae. The healthy and infected plants were discontinuously exposed to a 10 KHz quadratic EMF with maximum power of 9 W for 5 days, each 5 h, at 25°C. Fresh and dry weight of leaves, content of MDA, proline, and protein increased in both healthy and infected plants under electromagnetic fields, compared with those of the control plants. Electromagnetic fields decreased hydrogen peroxide and carbohydrates content in both healthy and infected plants compared to those of the controls.

  16. Biological effects of weak electromagnetic field on healthy and infected lime (Citrus aurantifolia) trees with phytoplasma.

    Science.gov (United States)

    Abdollahi, Fatemeh; Niknam, Vahid; Ghanati, Faezeh; Masroor, Faribors; Noorbakhsh, Seyyed Nasr

    2012-01-01

    Exposure to electromagnetic fields (EMF) has become an issue of concern for a great many people and is an active area of research. Phytoplasmas, also known as mycoplasma-like organisms, are wall-less prokaryotes that are pathogens of many plant species throughout the world. Effects of electromagnetic fields on the changes of lipid peroxidation, content of H(2)O(2), proline, protein, and carbohydrates were investigated in leaves of two-year-old trees of lime (Citrus aurantifolia) infected by the Candidatus Phytoplasma aurantifoliae. The healthy and infected plants were discontinuously exposed to a 10 KHz quadratic EMF with maximum power of 9 W for 5 days, each 5 h, at 25 °C. Fresh and dry weight of leaves, content of MDA, proline, and protein increased in both healthy and infected plants under electromagnetic fields, compared with those of the control plants. Electromagnetic fields decreased hydrogen peroxide and carbohydrates content in both healthy and infected plants compared to those of the controls.

  17. Proteomic analysis of the Mexican lime tree response to "Candidatus Phytoplasma aurantifolia" infection.

    Science.gov (United States)

    Taheri, Farzan; Nematzadeh, Ghorbanali; Zamharir, Maryam Ghayeb; Nekouei, Mojtaba Khayam; Naghavi, Mohammadreza; Mardi, Mohsen; Salekdeh, Ghasem Hosseini

    2011-11-01

    "Candidatus Phytoplasma aurantifolia" is the causative agent of witches' broom disease in the Mexican lime tree (Citrus aurantifolia L.), and is responsible for major tree losses in Southern Iran and Oman. The pathogen is strictly biotrophic, and, therefore, completely dependent on living host cells for its survival. The molecular basis of compatibility and disease development in this system is poorly understood. We applied a proteomics approach to analyse gene expression in Mexican limes infected with "Ca. Phytoplasma aurantifolia". Leaf samples were collected from healthy and infected plants and were analysed using 2-DE coupled with MS. Among 800 leaf proteins that were detected reproducibly in eight biological replicates of healthy and eight biological replicates of infected plants, 55 showed a significant response to the disease. MS resulted in identification of 39 regulated proteins, which included proteins that were involved in oxidative stress defence, photosynthesis, metabolism, and the stress response. Our results provide the first proteomic view of the molecular basis of the infection process and identify genes that could help inhibit the effects of the pathogen. This journal is © The Royal Society of Chemistry 2011

  18. Finite groups all of whose minimal subgroups are NE∗ -subgroups

    Indian Academy of Sciences (India)

    We prove the following theorem which is an improvement of a recent result due to Asaad and Ramadan (see Theorem 1.1 of [2]). Hence, Q8 will denote the quaternion group of order 8 and a group G is called Q8-free if no quotient group of any subgroup of G is isomorphic to Q8. Throughout this paper, L will denote the class.

  19. Intertumoral Heterogeneity within Medulloblastoma Subgroups.

    Science.gov (United States)

    Cavalli, Florence M G; Remke, Marc; Rampasek, Ladislav; Peacock, John; Shih, David J H; Luu, Betty; Garzia, Livia; Torchia, Jonathon; Nor, Carolina; Morrissy, A Sorana; Agnihotri, Sameer; Thompson, Yuan Yao; Kuzan-Fischer, Claudia M; Farooq, Hamza; Isaev, Keren; Daniels, Craig; Cho, Byung-Kyu; Kim, Seung-Ki; Wang, Kyu-Chang; Lee, Ji Yeoun; Grajkowska, Wieslawa A; Perek-Polnik, Marta; Vasiljevic, Alexandre; Faure-Conter, Cecile; Jouvet, Anne; Giannini, Caterina; Nageswara Rao, Amulya A; Li, Kay Ka Wai; Ng, Ho-Keung; Eberhart, Charles G; Pollack, Ian F; Hamilton, Ronald L; Gillespie, G Yancey; Olson, James M; Leary, Sarah; Weiss, William A; Lach, Boleslaw; Chambless, Lola B; Thompson, Reid C; Cooper, Michael K; Vibhakar, Rajeev; Hauser, Peter; van Veelen, Marie-Lise C; Kros, Johan M; French, Pim J; Ra, Young Shin; Kumabe, Toshihiro; López-Aguilar, Enrique; Zitterbart, Karel; Sterba, Jaroslav; Finocchiaro, Gaetano; Massimino, Maura; Van Meir, Erwin G; Osuka, Satoru; Shofuda, Tomoko; Klekner, Almos; Zollo, Massimo; Leonard, Jeffrey R; Rubin, Joshua B; Jabado, Nada; Albrecht, Steffen; Mora, Jaume; Van Meter, Timothy E; Jung, Shin; Moore, Andrew S; Hallahan, Andrew R; Chan, Jennifer A; Tirapelli, Daniela P C; Carlotti, Carlos G; Fouladi, Maryam; Pimentel, José; Faria, Claudia C; Saad, Ali G; Massimi, Luca; Liau, Linda M; Wheeler, Helen; Nakamura, Hideo; Elbabaa, Samer K; Perezpeña-Diazconti, Mario; Chico Ponce de León, Fernando; Robinson, Shenandoah; Zapotocky, Michal; Lassaletta, Alvaro; Huang, Annie; Hawkins, Cynthia E; Tabori, Uri; Bouffet, Eric; Bartels, Ute; Dirks, Peter B; Rutka, James T; Bader, Gary D; Reimand, Jüri; Goldenberg, Anna; Ramaswamy, Vijay; Taylor, Michael D

    2017-06-12

    While molecular subgrouping has revolutionized medulloblastoma classification, the extent of heterogeneity within subgroups is unknown. Similarity network fusion (SNF) applied to genome-wide DNA methylation and gene expression data across 763 primary samples identifies very homogeneous clusters of patients, supporting the presence of medulloblastoma subtypes. After integration of somatic copy-number alterations, and clinical features specific to each cluster, we identify 12 different subtypes of medulloblastoma. Integrative analysis using SNF further delineates group 3 from group 4 medulloblastoma, which is not as readily apparent through analyses of individual data types. Two clear subtypes of infants with Sonic Hedgehog medulloblastoma with disparate outcomes and biology are identified. Medulloblastoma subtypes identified through integrative clustering have important implications for stratification of future clinical trials. Copyright © 2017 Elsevier Inc. All rights reserved.

  20. Identification of genes differentially expressed during interaction of Mexican lime tree infected with "Candidatus Phytoplasma aurantifolia"

    Directory of Open Access Journals (Sweden)

    Nekouei Mojtaba

    2011-01-01

    Full Text Available Abstract Background "Candidatus Phytoplasma aurantifolia", is the causative agent of witches' broom disease in Mexican lime trees (Citrus aurantifolia L., and is responsible for major losses of Mexican lime trees in Southern Iran and Oman. The pathogen is strictly biotrophic, and thus is completely dependent on living host cells for its survival. The molecular basis of compatibility and disease development in this system is poorly understood. Therefore, we have applied a cDNA- amplified fragment length polymorphism (AFLP approach to analyze gene expression in Mexican lime trees infected by "Ca. Phytoplasma aurantifolia". Results We carried out cDNA-AFLP analysis on grafted infected Mexican lime trees of the susceptible cultivar at the representative symptoms stage. Selective amplifications with 43 primer combinations allowed the visualisation of 55 transcript-derived fragments that were expressed differentially between infected and non-infected leaves. We sequenced 51 fragments, 36 of which were identified as lime tree transcripts after homology searching. Of the 36 genes, 70.5% were down-regulated during infection and could be classified into various functional groups. We showed that Mexican lime tree genes that were homologous to known resistance genes tended to be repressed in response to infection. These included the genes for modifier of snc1 and autophagy protein 5. Furthermore, down-regulation of genes involved in metabolism, transcription, transport and cytoskeleton was observed, which included the genes for formin, importin β 3, transducin, L-asparaginase, glycerophosphoryl diester phosphodiesterase, and RNA polymerase β. In contrast, genes that encoded a proline-rich protein, ubiquitin-protein ligase, phosphatidyl glycerol specific phospholipase C-like, and serine/threonine-protein kinase were up-regulated during the infection. Conclusion The present study identifies a number of candidate genes that might be involved in the

  1. Identification of genes differentially expressed during interaction of Mexican lime tree infected with "Candidatus Phytoplasma aurantifolia".

    Science.gov (United States)

    Zamharir, Maryam Ghayeb; Mardi, Mohsen; Alavi, Seyed Mohammad; Hasanzadeh, Nader; Nekouei, Mojtaba Khayyam; Zamanizadeh, Hamid Reza; Alizadeh, Ali; Salekdeh, Ghasem Hoseini

    2011-01-01

    "Candidatus Phytoplasma aurantifolia", is the causative agent of witches' broom disease in Mexican lime trees (Citrus aurantifolia L.), and is responsible for major losses of Mexican lime trees in Southern Iran and Oman. The pathogen is strictly biotrophic, and thus is completely dependent on living host cells for its survival. The molecular basis of compatibility and disease development in this system is poorly understood. Therefore, we have applied a cDNA- amplified fragment length polymorphism (AFLP) approach to analyze gene expression in Mexican lime trees infected by "Ca. Phytoplasma aurantifolia". We carried out cDNA-AFLP analysis on grafted infected Mexican lime trees of the susceptible cultivar at the representative symptoms stage. Selective amplifications with 43 primer combinations allowed the visualisation of 55 transcript-derived fragments that were expressed differentially between infected and non-infected leaves. We sequenced 51 fragments, 36 of which were identified as lime tree transcripts after homology searching. Of the 36 genes, 70.5% were down-regulated during infection and could be classified into various functional groups. We showed that Mexican lime tree genes that were homologous to known resistance genes tended to be repressed in response to infection. These included the genes for modifier of snc1 and autophagy protein 5. Furthermore, down-regulation of genes involved in metabolism, transcription, transport and cytoskeleton was observed, which included the genes for formin, importin β 3, transducin, L-asparaginase, glycerophosphoryl diester phosphodiesterase, and RNA polymerase β. In contrast, genes that encoded a proline-rich protein, ubiquitin-protein ligase, phosphatidyl glycerol specific phospholipase C-like, and serine/threonine-protein kinase were up-regulated during the infection. The present study identifies a number of candidate genes that might be involved in the interaction of Mexican lime trees with "Candidatus Phytoplasma

  2. Subgroup Achievement and Gap Trends: Massachusetts, 2010

    Science.gov (United States)

    Center on Education Policy, 2010

    2010-01-01

    This paper profiles the student subgroup achievement and gap trends in Massachusetts for 2010. In grade 8 (the only grade in which subgroup trends were analyzed by achievement level), Massachusetts showed across-the-board gains--improvements in both reading and math at the basic, proficient and advanced levels for all racial/ethnic subgroups, low…

  3. Subgroup Achievement and Gap Trends: Kentucky, 2010

    Science.gov (United States)

    Center on Education Policy, 2010

    2010-01-01

    This paper profiles the student subgroup achievement and gap trends in Kentucky for 2010. In grade 8 (the only grade in which subgroup trends were analyzed by achievement level), Kentucky showed mostly gains in both reading and math at the basic, proficient, and advanced levels for racial/ethnic subgroups, low income students, and boys and girls.…

  4. Integrated management of phytoplasma diseases in pome fruit: an overview of efficacy results of IPM insecticides against pear Psylla (Cacopsylla pyri).

    Science.gov (United States)

    Bangels, E; Peusens, G; Beliën, T

    2010-01-01

    Phytoplasmas are plant pathogenic mollicutes that cause devastating diseases in various crops worldwide. The closely related pome fruit tree phytoplasmas Candidatus Phytoplasma mali and Candidatus Phytoplasma pyri are the causal agents of apple proliferation and pear decline, respectively. They can be transmitted from tree to tree by Psyllidae. As pear suckers (Cacopsylla pyri) are widely considered to be the most important pest in pear orchards, a good control of this insect vector is a key element for limiting the natural spread of pear decline. Efficient control relies on a perfect tuning of treatment schedules, taking into account efficacies of (at preferably) low-impact insecticides and side-(repellent)-effects of alternative products (e.g. kaolin, mineral oils and fungicides), the optimal positioning of these crop protection agents, and the best possible presence of beneficial predators. The department of Zoology of the pcfruit vzw research institute (Belgium) has a long tradition of executing insecticide field trials according to EPPO guidelines. Here, we present an overview of the results of a selection of IPM-compatible insecticides (abamectin, spirotetramat, thiacloprid, spinosad, spirodiclofen), tested in efficacy trials against pear Psylla on different life stages during the last decade. Based on these results and monitoring data of pest and beneficial biology, we additionally propose optimal pear Psylla control schedules which allow to reduce the number of (phytoplasma harbouring) psyllids in integrated systems to a minimum.

  5. Research methods for subgrouping low back pain

    DEFF Research Database (Denmark)

    Kent, Peter; Keating, Jennifer L; Leboeuf-Yde, Charlotte

    2010-01-01

    There is considerable clinician and researcher interest in whether the outcomes for patients with low back pain, and the efficiency of the health systems that treat them, can be improved by 'subgrouping research'. Subgrouping research seeks to identify subgroups of people who have clinically...... studies (a method framework). The aims of this debate article are: (1) to present a method framework to inform the design and evaluation of subgrouping research in low back pain, (2) to describe method options when investigating prognostic effects or subgroup treatment effects, and (3) to discuss...

  6. First report of 16SrII-C subgroup phytoplasma causing phyllody and witches’-broom disease in Soybean in Tanzania

    NARCIS (Netherlands)

    Murithi, H.; Owati, A.; Madata, C.S.; Joosten, M.; Beed, F.; Lava Kumar, P.

    2015-01-01

    Soybean production in Tanzania is steadily increasing, driven by growing demand from feed and livestock producers and also for human consumption. Soybean production area has increased from 795 ha in 2003 to 4,100 ha in 2013 (FAO 2014). Major soybean production is in the Morogro, Ruvuma, Iringa, and

  7. Analyses of the 16S-23S intergenic region of the phytoplasma causing the sugarcane white leaf disease in Yunnan Province, China

    OpenAIRE

    Wang, Xiao-Yan; Li, Wen-Feng; Huang, Ying-Kun; Zhang, Rong-Yue; Luo, Zhi-Ming; Shan, Hong-Li; Yin, Jiong; Shen, Ke; Jia, Ying-Ming; Bai, Zhi-Gang

    2014-01-01

    Sugarcane white leaf (SCWL) is an important disease caused by a phytoplasma. In Baoshan, Yunnan, China, SCWL was firstly observed in 2012, and has extended its area of occurrence to 600 hm² . Up to 52% of the plants may become diseased in a field and even complete loss of cane yield may result in the heavily infected fields, posing a serious threat to Yunnan sugar industry. To ascertain the causal agent of suspected SCWL disease in Yunnan, nested PCR using two sets of phytoplasma primer pairs...

  8. [Complete sequence of a full-length DNA and molecular characterization of one plasmid from chinaberry (Melia azedarach Z) witches'-broom phytoplasma].

    Science.gov (United States)

    Song, Chuansheng; Lin, Caili; Tian, Guozhong; Zhao, Wenjun; Zhu, Shuifang; Mou, Haiqing; Hu, Jiaxu; Wang, Xizhuo; Guo, Minwei

    2011-09-01

    To clone plasmid from chinaberry witches'-broom phytoplasma and analyse its molecular characterization. Fragments of one plasmid (pCWBFq) in chinaberry witches'-broom phytoplasma-Fuqing strain (CWBFq) were amplified with primer pairs which were designed according to plasmid sequences published on NCBI. Transmembrane domain and subcellular localization predictions of proteins encoded by the plasmid pCWBFq as well as phylogenetic analysis among the plasmid sequences were completed by using bioinformatic softwares. Southern blot analysis was performed to detect the plasmids existed in CWBFq and several other phytoplasmas with the pCWBFq repA probe. One complete plasmid was sequenced from CWBFq. pCWBFq comprised 4446 bp and had a nucleotide content of 73.5% A + T and encoded six proteins. Protein P2, P3, P4 and P5 of pCWBFq contained 3, 2, 1 and 2 tranmembrane domains respectively, and their predicted signal peptide values were 0.989, 0.505, 0.918 and 0.914 respectively. Homologous comparison showed that RepA homology between pCWBFq and other phytoplasmas was between 9.6% -85.6% , however, the homology of different SSB proteins was between 74.0% - 89.4%. Southern blotting with pCWBFq repA probe confirmed the existence of the plasmids in CWBFq. In addition, The hybridizations occurred with paulownia witches'-broom phytoplasma-Nanyang strain (PaWBNy), periwinkle virescence phytoplasma-Hainan stanin (PeVHn), chinaberry witches'-broom phytoplasma-Fuzhou strain (CWBFz) and mulberry dwarf phytoplasma - Puyang strain (MDPy), whereas, no hybridizarions occurred with jujube witches'-broom phytoplasma-Beijing strain (JWBBj), cherry lethal yellows phytoplasma-Xichang strain (CLYXc) and Bischofia polycarpa witches'-broom phytoplasma-Nanchang strain (BiWBNc). The plasmid encoded a replication associated protein (RepA) and a single-stranded DNA binding protein (SSB), which were for the replication of plasmid. Four putative proteins encoded by the plasmid were predicted to contain

  9. A gene expression analysis of cell wall biosynthetic genes in Malus x domestica infected by 'Candidatus Phytoplasma mali'.

    Science.gov (United States)

    Guerriero, Gea; Giorno, Filomena; Ciccotti, Anna Maria; Schmidt, Silvia; Baric, Sanja

    2012-11-01

    Apple proliferation (AP) represents a serious threat to several fruit-growing areas and is responsible for great economic losses. Several studies have highlighted the key role played by the cell wall in response to pathogen attack. The existence of a cell wall integrity signaling pathway which senses perturbations in the cell wall architecture upon abiotic/biotic stresses and activates specific defence responses has been widely demonstrated in plants. More recently a role played by cell wall-related genes has also been reported in plants infected by phytoplasmas. With the aim of shedding light on the cell wall response to AP disease in the economically relevant fruit-tree Malus × domestica Borkh., we investigated the expression of the cellulose (CesA) and callose synthase (CalS) genes in different organs (i.e., leaves, roots and branch phloem) of healthy and infected symptomatic outdoor-grown trees, sampled over the course of two time points (i.e., spring and autumn 2011), as well as in in vitro micropropagated control and infected plantlets. A strong up-regulation in the expression of cell wall biosynthetic genes was recorded in roots from infected trees. Secondary cell wall CesAs showed up-regulation in the phloem tissue from branches of infected plants, while either a down-regulation of some genes or no major changes were observed in the leaves. Micropropagated plantlets also showed an increase in cell wall-related genes and constitute a useful system for a general assessment of gene expression analysis upon phytoplasma infection. Finally, we also report the presence of several 'knot'-like structures along the roots of infected apple trees and discuss the occurrence of this interesting phenotype in relation to the gene expression results and the modalities of phytoplasma diffusion.

  10. A gene expression analysis of cell wall biosynthetic genes in Malus × domestica infected by ‘Candidatus Phytoplasma mali’

    Science.gov (United States)

    Guerriero, Gea; Giorno, Filomena; Ciccotti, Anna Maria; Schmidt, Silvia; Baric, Sanja

    2016-01-01

    Apple proliferation (AP) represents a serious threat to several fruit-growing areas and is responsible for great economic losses. Several studies have highlighted the key role played by the cell wall in response to pathogen attack. The existence of a cell wall integrity signaling pathway which senses perturbations in the cell wall architecture upon abiotic/biotic stresses and activates specific defence responses has been widely demonstrated in plants. More recently a role played by cell wall-related genes has also been reported in plants infected by phytoplasmas. With the aim of shedding light on the cell wall response to AP disease in the economically relevant fruit-tree Malus × domestica Borkh., we investigated the expression of the cellulose (CesA) and callose synthase (CalS) genes in different organs (i.e., leaves, roots and branch phloem) of healthy and infected symptomatic outdoor-grown trees, sampled over the course of two time points (i.e., spring and autumn 2011), as well as in in vitro micropropagated control and infected plantlets. A strong up-regulation in the expression of cell wall biosynthetic genes was recorded in roots from infected trees. Secondary cell wall CesAs showed up-regulation in the phloem tissue from branches of infected plants, while either a down-regulation of some genes or no major changes were observed in the leaves. Micropropagated plantlets also showed an increase in cell wall-related genes and constitute a useful system for a general assessment of gene expression analysis upon phytoplasma infection. Finally, we also report the presence of several ‘knot’-like structures along the roots of infected apple trees and discuss the occurrence of this interesting phenotype in relation to the gene expression results and the modalities of phytoplasma diffusion. PMID:23086810

  11. Subgroup Achievement and Gap Trends: Delaware

    Science.gov (United States)

    Center on Education Policy, 2010

    2010-01-01

    In grade 8 (the only grade in which subgroup trends were analyzed by achievement level), Delaware students showed consistent gains in math at the basic, proficient, and advanced levels for racial/ethnic subgroups, low income students, and boys and girls. There were mixed results in reading. Achievement gaps narrowed in both reading and math in…

  12. Subgroup Achievement and Gap Trends: Maine

    Science.gov (United States)

    Center on Education Policy, 2010

    2010-01-01

    In grade 8 (the only grade in which subgroup trends were analyzed by achievement level), Maine students had across-the-board gains. There were improvements in both reading and math at the basic, proficient and advanced levels for the subgroups large enough to count, which were white students, low income students, and boys and girls. Results on…

  13. Subgroup Achievement and Gap Trends: Illinois

    Science.gov (United States)

    Center on Education Policy, 2010

    2010-01-01

    In grade 8 (the only grade in which subgroup trends were analyzed by achievement level), Illinois students showed mostly gains in both reading and math at the basic, proficient, and advanced levels for racial/ethnic subgroups, low income students, and boys and girls. There was mixed progress made in narrowing achievement gaps in reading and math…

  14. Subgroup Achievement and Gap Trends: Florida

    Science.gov (United States)

    Center on Education Policy, 2010

    2010-01-01

    In grade 8 (the only grade in which subgroup trends were analyzed by achievement level), Florida students showed gains almost across the board in both reading and math at the basic, proficient, and advanced levels for racial/ethnic subgroups, low income students, and boys and girls. Progress has been made in narrowing achievement gaps in both…

  15. ∗-supplemented subgroups of finite groups

    Indian Academy of Sciences (India)

    supplemented maximal and minimal subgroups of Sylow subgroups of finite groups, Proc. Amer. Math. Soc. 132(8) (2004) 2197–2204. [17] Wang Y, Wei H and Li Y, A generalization of Kramer's theorem and its applications,. Bull. Austral. Math.

  16. Existence of a dictatorial subgroup in social choice with independent subgroup utility scales, an alternative proof

    NARCIS (Netherlands)

    Khmelnitskaya, Anna Borisovna; van Deemen, Adrian; Rusinowska, Agnieszka

    2010-01-01

    Social welfare orderings for different scales of individual utility measurement in distinct population subgroups are studied. In Khmelnitskaya (2000), employing the continuous version of Arrow’s impossibility theorem, it was shown that for combinations of independent subgroups scales every

  17. Universal detection of phytoplasmas and Xylella spp. by TaqMan singleplex and multiplex real-time PCR with dual priming oligonucleotides.

    Directory of Open Access Journals (Sweden)

    Takao Ito

    Full Text Available Phytoplasmas and Xylella spp. are bacteria that cause many economically important plant diseases worldwide. TaqMan probe-based quantitative real-time polymerase chain reaction (qPCR assays have been utilized to universally detect phytoplasmas or Xylella fastidiosa. To develop a superior universal qPCR method, we used a dual priming oligonucleotide (DPO with two annealing sites as a reverse primer to target the well-conserved bacterial 16S rDNA. The new qPCR assays universally detected various species of phytoplasmas and subspecies of X. fastidiosa as well as Xylella taiwanensis, and generally showed superior threshold cycle values when amplifying specific or non-specific products compared to current universal qPCR assays. The proposed qPCR assays were integrated to develop a multiplex qPCR assay that simultaneously detected phytoplasmas, Xylella spp., and an internal plant DNA positive control within 1 hour. This assay could detect a minimum of ten bacterial cells and was compatible with crude extractions used in the rapid screening of various plants. The amplicons were of sufficient lengths to be directly sequenced for preliminary identification, and the primers could be used in universal conventional PCR assays. Additionally, reverse DPO primers can be utilized to improve other probe-based qPCR assays.

  18. The effects of status on subgroup relations.

    Science.gov (United States)

    Hornsey, Matthew J; Hogg, Michael A

    2002-06-01

    Two experiments were conducted to assess the impact of status differentials on subgroup attitudes and behaviours. In Experiment 1, 73 math-science students were led to believe they had higher or lower status than humanities students. They then performed a non-interactive decision-making task during which they were categorized exclusively as a university student (superordinate condition), or as a university student and math-science student simultaneously (subgroups condition). Experiment 2 (N = 98) differed from Experiment 1 in that perceptions of relative subgroup status were measured rather than manipulated. Consistent with social identity theory, subgroup members tended to categorize themselves more at the superordinate (university) level the lower status they considered their subgroup to be. In Experiment 2, a series of interactions also emerged, showing that status and inter-subgroup bias were positively related when the participants had been categorized exclusively at the superordinate level. When superordinate and subgroup identities were activated simultaneously, perceptions of status had no effect on levels of bias. The results were interpreted in terms of participants' needs for identity enhancement and identity distinctiveness.

  19. Identifying Tinnitus Subgroups With Cluster Analysis

    Science.gov (United States)

    Tyler, Richard; Coelho, Claudia; Tao, Pan; Ji, Haihong; Noble, William; Gehringer, Anne; Gogel, Stephanie

    2009-01-01

    Purpose We believe it is important to uncover tinnitus subgroups to identify subsets of patients most likely to benefit from different treatments. We review strategies for subgrouping based on etiology, subjective reports, the audiogram, psychoacoustics, imaging, and cluster analysis. Method Preliminary results of a 2-step cluster analysis based on 246 participants from whom we had 26 categorical and 25 continuous variables were determined. Results A 4-cluster solution suggested the following subgroups: (a) constant distressing tinnitus, (b) varying tinnitus that is worse in noise, (c) tinnitus patients who are copers and whose tinnitus is not influenced by touch (somatic modulation), and (d) tinnitus patients who are copers but whose tinnitus is worse in quiet environments. Conclusions Subgroups of tinnitus patients can be identified by using statistical approaches. The subgroups we identify here represent a preliminary attempt at identifying such patients. One next step would be to explore clinical trials of tinnitus treatments based on subgroup analyses or on using subgroups in the selection criteria. PMID:19056922

  20. Identification of subgroups among fibromyalgia patients

    Directory of Open Access Journals (Sweden)

    D. Chaleil

    2012-09-01

    Full Text Available This paper presents some hypotheses concerning the identification of homogeneous subgroups among fibromyalgia (FM patients in order to improve the management of the disease. It also reviews the available literature about this subject. Three methods for subgrouping are discussed according to clinical features, biomarkers, and gait analysis. Clinical subgrouping based on cluster analysis has been used for the identification of homogeneous subgroups of patients and, more recently, homogeneous clinical features. So far, longitudinal studies using clinical subgroups to direct treatment and predict outcome are still required. Biomarkers in FM, which is a neurobiological disease, are of promising interest, nevertheless currently, none of them can be used to subgroup FM patients. Due to the fact that cortical and subcortical mechanisms of gait control share some cognitive functions which are involved in FM, gait markers have been proposed to evaluate and to subgroup FM patients, in clinical settings. Three out of 4 core FM symptoms are linked to gait markers. Kinesia measured by means of cranio-caudal power is correlated to pain, and could be proposed to assess pain behavior (kinesiophobia. Stride frequency, which is linked to physical component, allows the identification of a hyperkinetic subgroup. Moreover, SF has been correlated to fatigue during the 6 minute walking test. Stride regularity, which expresses the unsteadiness of gait, is correlated to cognitive dysfunction in FM. Decreased stride regularity allows the recognition of a homogeneous subgroup characterized by an increased anxiety and depression, and decreased cognitive functions. These results need further studies to be validated and so used in the daily clinical practice.

  1. SUBGR: A Program to Generate Subgroup Data for the Subgroup Resonance Self-Shielding Calculation

    Energy Technology Data Exchange (ETDEWEB)

    Kim, Kang Seog [Oak Ridge National Lab. (ORNL), Oak Ridge, TN (United States)

    2016-06-06

    The Subgroup Data Generation (SUBGR) program generates subgroup data, including levels and weights from the resonance self-shielded cross section table as a function of background cross section. Depending on the nuclide and the energy range, these subgroup data can be generated by (a) narrow resonance approximation, (b) pointwise flux calculations for homogeneous media; and (c) pointwise flux calculations for heterogeneous lattice cells. The latter two options are performed by the AMPX module IRFFACTOR. These subgroup data are to be used in the Consortium for Advanced Simulation of Light Water Reactors (CASL) neutronic simulator MPACT, for which the primary resonance self-shielding method is the subgroup method.

  2. Isolation and characterization of the ATP-binding cassette (ABC) transporter system genes from loofah witches' broom phytoplasma.

    Science.gov (United States)

    Huang, Chun-Lin; Ho, Kuo-Chieh

    2007-10-01

    A clone containing a 3903 bp EcoRI-restriction fragment was obtained from a lambda(ZAP) genomic library of loofah witches' broom (LfWB) phytoplasma by plaque hybridization using a PCR fragment as a probe. Sequence analysis revealed that this fragment contained three open reading frames (ORFs). The deduced amino acid sequences of ORF 1 and ORF 2 showed a high homology with the ATP-binding proteins of the ABC transporter system genes of prokaryotes and eukaryotes, and encoded proteins with a molecular mass of 36 and 30 kDa, respectively. Based on amino acid sequence similarity, secondary structure, hydrophilicity and a signal peptide sequence at the N-terminus, we predicted that ORF 3 might encode a specific solute-binding prolipoprotein of the ABC transporter system with a molecular mass of 62 kDa. The cleavage site of this prolipoprotein signal peptide was similar to those of gram-positive bacteria. In addition to nutrient uptake, ABC transporter systems of bacteria also play a role in signal transduction, drug-resistance and perhaps virulence. The possible implications of the system to the survival and the pathogenesis of phytoplasma were discussed.

  3. Involvement of plasma membrane peroxidases and oxylipin pathway in the recovery from phytoplasma disease in apple (Malus domestica).

    Science.gov (United States)

    Patui, Sonia; Bertolini, Alberto; Clincon, Luisa; Ermacora, Paolo; Braidot, Enrico; Vianello, Angelo; Zancani, Marco

    2013-06-01

    Apple trees (Malus domestica Borkh.) may be affected by apple proliferation (AP), caused by 'Candidatus Phytoplasma mali'. Some plants can spontaneously recover from the disease, which implies the disappearance of symptoms through a phenomenon known as recovery. In this article it is shown that NAD(P)H peroxidases of leaf plasma membrane-enriched fractions exhibited a higher activity in samples from both AP-diseased and recovered plants. In addition, an increase in endogenous SA was characteristic of the symptomatic plants, since its content increased in samples obtained from diseased apple trees. In agreement, phenylalanine ammonia lyase (PAL) activity, a key enzyme of the phenylpropanoid pathway, was increased too. Jasmonic acid (JA) increased only during recovery, in a phase subsequent to the pathological state, and in concomitance to a decline of salicylic acid (SA). Oxylipin pathway, responsible for JA synthesis, was not induced during the development of AP-disease, but it appeared to be stimulated when the recovery occurred. Accordingly, lipoxygenase (LOX) activity, detected in plasma membrane-enriched fractions, showed an increase in apple leaves obtained from recovered plants. This enhancement was paralleled by an increase of hydroperoxide lyase (HPL) activity, detected in leaf microsomes, albeit the latter enzyme was activated in either the disease or recovery conditions. Hence, a reciprocal antagonism between SA- and JA-pathways could be suggested as an effective mechanism by which apple plants react to phytoplasma invasions, thereby providing a suitable defense response leading to the establishment of the recovery phenomenon. Copyright © Physiologia Plantarum 2012.

  4. Effect of phytoplasma infection on the activity of peroxidase, β-1,3 glucanase and chitinase in corn plants

    Directory of Open Access Journals (Sweden)

    Ana Carolina Bruno Junqueira

    2011-12-01

    Full Text Available In the present work we studied the effect of inoculating corn plants with the maize bushy stunt phytoplasma on the activity of the enzymes peroxidase, β-1,3 glucanase and chitinase. The experiments were carried out inside a greenhouse. Plants of a resistant and a susceptible corn hybrid were inoculated by using infective Dalbulus maidis leafhoppers 10 days after sowing. When symptoms started to appear, leaf samples were collected at different periods to quantify enzyme activity. The results showed an increase in the activity of the three enzymes in inoculated plants of both hybrids. In general, the values observed for the level of the different enzymes were higher in the susceptible hybrid when compared to the resistant one. Thus, the increases in peroxidase, β-1,3 glucanase and chitinase levels in inoculated plants are evidence of changes in the host metabolism caused by the phytoplasma. On the other hand, since the increases could not be correlated with plant resistance further studies are needed to explain such changes.

  5. Genetic and molecular alterations across medulloblastoma subgroups.

    Science.gov (United States)

    Skowron, Patryk; Ramaswamy, Vijay; Taylor, Michael D

    2015-10-01

    Medulloblastoma is the most common malignant brain tumour diagnosed in children. Over the last few decades, advances in radiation and chemotherapy have significantly improved the odds of survival. Nevertheless, one third of all patients still succumb to their disease, and many long-term survivors are afflicted with neurocognitive sequelae. Large-scale multi-institutional efforts have provided insight into the transcriptional and genetic landscape of medulloblastoma. Four distinct subgroups of medulloblastoma have been identified, defined by distinct transcriptomes, genetics, demographics and outcomes. Integrated genomic profiling of each of these subgroups has revealed distinct genetic alterations, driving pathways and in some instances cells of origin. In this review, we highlight, in a subgroup-specific manner, our current knowledge of the genetic and molecular alterations in medulloblastoma and underscore the possible avenues for future therapeutic intervention.

  6. On Preferential sylow fuzzy subgroups | Makamba | Quaestiones ...

    African Journals Online (AJOL)

    In this paper, for a prime p, we propose some plausible denitions for the notion of Sylow fuzzy p-subgroup of a nite group. We derive a number of results for nite fuzzy groups using one of the proposed denitions. We also discuss some of the relationships between various proposed denitions for suitability, including the crisp ...

  7. Zero-sum problems with subgroup weights

    Indian Academy of Sciences (India)

    In this note, we generalize some theorems on zero-sums with weights from [1], [4] and [5] in two directions. In particular, we consider Z Z p d for a general and subgroups of Z p ∗ as weights. Author Affiliations. S D Adhikari1 A A Ambily2 B Sury2. Harish-Chandra Research Institute, Chhatnag Road, Jhunsi, Allahabad 211 ...

  8. Interpretation of Subgroup Effects in Published Trials

    DEFF Research Database (Denmark)

    Hancock, Mark J; Kjær, Per; Korsholm, Lars

    2013-01-01

    that report on treatment effect modifiers (subgroups) for specific physical therapy interventions. The key messages are: (1) point estimates of treatment modifier effect size (interaction effect) and their confidence intervals can be calculated using group-level data when individual patient-level data...

  9. Phytoplasma Effector SAP54 Hijacks Plant Reproduction by Degrading MADS-box Proteins and Promotes Insect Colonization in a RAD23-Dependent Manner

    Science.gov (United States)

    MacLean, Allyson M.; Orlovskis, Zigmunds; Kowitwanich, Krissana; Zdziarska, Anna M.; Angenent, Gerco C.; Immink, Richard G. H.; Hogenhout, Saskia A.

    2014-01-01

    Pathogens that rely upon multiple hosts to complete their life cycles often modify behavior and development of these hosts to coerce them into improving pathogen fitness. However, few studies describe mechanisms underlying host coercion. In this study, we elucidate the mechanism by which an insect-transmitted pathogen of plants alters floral development to convert flowers into vegetative tissues. We find that phytoplasma produce a novel effector protein (SAP54) that interacts with members of the MADS-domain transcription factor (MTF) family, including key regulators SEPALLATA3 and APETALA1, that occupy central positions in the regulation of floral development. SAP54 mediates degradation of MTFs by interacting with proteins of the RADIATION SENSITIVE23 (RAD23) family, eukaryotic proteins that shuttle substrates to the proteasome. Arabidopsis rad23 mutants do not show conversion of flowers into leaf-like tissues in the presence of SAP54 and during phytoplasma infection, emphasizing the importance of RAD23 to the activity of SAP54. Remarkably, plants with SAP54-induced leaf-like flowers are more attractive for colonization by phytoplasma leafhopper vectors and this colonization preference is dependent on RAD23. An effector that targets and suppresses flowering while simultaneously promoting insect herbivore colonization is unprecedented. Moreover, RAD23 proteins have, to our knowledge, no known roles in flower development, nor plant defence mechanisms against insects. Thus SAP54 generates a short circuit between two key pathways of the host to alter development, resulting in sterile plants, and promotes attractiveness of these plants to leafhopper vectors helping the obligate phytoplasmas reproduce and propagate (zombie plants). PMID:24714165

  10. Generation and expression in plants of a single-chain variable fragment antibody against the immunodominant membrane protein of Candidatus phytoplasma aurantifolia.

    Science.gov (United States)

    Shahryari, F; Safarnejad, M R; Shams-Bakhsh, M; Schillberg, S; Nölke, G

    2013-08-01

    Witches' broom of lime is a disease caused by Candidatus Phytoplasma aurantifolia, which represents the most significant global threat to the production of lime trees (Citrus aurantifolia). Conventional disease management strategies have shown little success, and new approaches based on genetic engineering need to be considered. The expression of recombinant antibodies and fragments thereof in plant cells is a powerful approach that can be used to suppress plant pathogens. We have developed a single-chain variable fragment antibody (scFvIMP6) against the immunodominant membrane protein (IMP) of witches' broom phytoplasma and expressed it in different plant cell compartments. We isolated scFvIMP6 from a naïve scFv phage display library and expressed it in bacteria to demonstrate its binding activity against both recombinant IMP and intact phytoplasma cells. The expression of scFvIMP6 in plants was evaluated by transferring the scFvIMP6 cDNA to plant expression vectors featuring constitutive or phloem specific promoters in cassettes with or without secretion signals, therefore causing the protein to accumulate either in the cytosol or apoplast. All constructs were transiently expressed in Nicotiana benthamiana by agroinfiltration, and antibodies of the anticipated size were detected by immunoblotting. Plant-derived scFvIMP6 was purified by affinity chromatography, and specific binding to recombinant IMP was demonstrated by enzyme-linked immunosorbent assay. Our results indicate that scFvIMP6 binds with high activity and can be used for the detection of Ca. Phytoplasma aurantifolia and is also a suitable candidate for stable expression in lime trees to suppress witches' broom of lime.

  11. Phytoplasma effector SAP54 hijacks plant reproduction by degrading MADS-box proteins and promotes insect colonization in a RAD23-dependent manner.

    Directory of Open Access Journals (Sweden)

    Allyson M MacLean

    2014-04-01

    Full Text Available Pathogens that rely upon multiple hosts to complete their life cycles often modify behavior and development of these hosts to coerce them into improving pathogen fitness. However, few studies describe mechanisms underlying host coercion. In this study, we elucidate the mechanism by which an insect-transmitted pathogen of plants alters floral development to convert flowers into vegetative tissues. We find that phytoplasma produce a novel effector protein (SAP54 that interacts with members of the MADS-domain transcription factor (MTF family, including key regulators SEPALLATA3 and APETALA1, that occupy central positions in the regulation of floral development. SAP54 mediates degradation of MTFs by interacting with proteins of the RADIATION SENSITIVE23 (RAD23 family, eukaryotic proteins that shuttle substrates to the proteasome. Arabidopsis rad23 mutants do not show conversion of flowers into leaf-like tissues in the presence of SAP54 and during phytoplasma infection, emphasizing the importance of RAD23 to the activity of SAP54. Remarkably, plants with SAP54-induced leaf-like flowers are more attractive for colonization by phytoplasma leafhopper vectors and this colonization preference is dependent on RAD23. An effector that targets and suppresses flowering while simultaneously promoting insect herbivore colonization is unprecedented. Moreover, RAD23 proteins have, to our knowledge, no known roles in flower development, nor plant defence mechanisms against insects. Thus SAP54 generates a short circuit between two key pathways of the host to alter development, resulting in sterile plants, and promotes attractiveness of these plants to leafhopper vectors helping the obligate phytoplasmas reproduce and propagate (zombie plants.

  12. Phytoplasma Effector SAP54 Hijacks Plant Reproduction by Degrading MADS-box Proteins and Promotes Insect Colonization in a RAD23-Dependent Manner

    OpenAIRE

    Allyson M MacLean; Zigmunds Orlovskis; Krissana Kowitwanich; Zdziarska, Anna M.; Angenent, Gerco C.; Immink, Richard G. H.; Hogenhout, Saskia A.

    2014-01-01

    Pathogens that rely upon multiple hosts to complete their life cycles often modify behavior and development of these hosts to coerce them into improving pathogen fitness. However, few studies describe mechanisms underlying host coercion. In this study, we elucidate the mechanism by which an insect-transmitted pathogen of plants alters floral development to convert flowers into vegetative tissues. We find that phytoplasma produce a novel effector protein (SAP54) that interacts with members of ...

  13. Plant-Pathogen Interaction-Related MicroRNAs and Their Targets Provide Indicators of Phytoplasma Infection in Paulownia tomentosa × Paulownia fortunei.

    Directory of Open Access Journals (Sweden)

    Guoqiang Fan

    Full Text Available Paulownia witches' broom (PaWB caused by a phytoplasma, has caused extensive losses in the yields of paulownia timber and resulted in significant economic losses. However, the molecular mechanisms in Paulownia that underlie the phytoplasma stress are poorly characterized. In this study, we use an Illumina platform to sequence four small RNA libraries and four degradome sequencing libraries derived from healthy, PaWB-infected, and PaWB-infected 15 mg·L-1 and 30 mg·L-1 methyl methane sulfonate (MMS-treated plants. In total, 125 conserved and 118 novel microRNAs (miRNAs were identified and 33 miRNAs responsive to PaWB disease were discovered. Furthermore, 166 target genes for 18 PaWB disease-related miRNAs were obtained, and found to be involved in plant-pathogen interaction and plant hormone signal transduction metabolic pathways. Eleven miRNAs and target genes responsive to PaWB disease were examined by a quantitative real-time PCR approach. Our findings will contribute to studies on miRNAs and their targets in Paulownia, and provide new insights to further understand plant-phytoplasma interactions.

  14. Gene expression and biochemical changes of carbohydrate metabolism in in vitro micro-propagated apple plantlets infected by 'Candidatus Phytoplasma mali'.

    Science.gov (United States)

    Giorno, Filomena; Guerriero, Gea; Biagetti, Matteo; Ciccotti, Anna Maria; Baric, Sanja

    2013-09-01

    'Candidatus Phytoplasma mali' (Ca. P. mali) is the disease agent causing apple proliferation (AP), which has detrimental effects on production in many apple growing areas of Central and Southern Europe. The present study investigated transcriptional and biochemical changes related to the sugar metabolism as well as expression of pathogenesis-related (PR) protein genes in in vitro micro-propagated AP-infected and healthy control plantlets with the aim of shedding light on host plant response to 'Ca. P. mali' infection. Expression changes between infected and control plantlets were detected by quantitative real-time PCR analysis. The most significant transcriptional changes were observed for genes coding for pathogenesis-related proteins and for heat shock protein 70, as well as for some genes related to the sugar metabolism, such as a sorbitol transporter (SOT5), hexokinase, sucrose-phosphate synthase or granule bound starch synthase. Furthermore, biochemical analyses revealed that infected plantlets were characterized by a significant accumulation of starch and sucrose, while hexoses, such as glucose and fructose, and sorbitol were present at lower concentrations. In summary, the present analysis provides an overview of a gene set that is involved in response to phytoplasma infection and, therefore, it may help for a better understanding of the molecular mechanisms involved in phytoplasma-host plant interaction in apple. Copyright © 2013 Elsevier Masson SAS. All rights reserved.

  15. Topological groups with dense compactly generated subgroups

    Directory of Open Access Journals (Sweden)

    Hiroshi Fujita

    2002-04-01

    Full Text Available A topological group G is: (i compactly generated if it contains a compact subset algebraically generating G, (ii -compact if G is a union of countably many compact subsets, (iii 0-bounded if arbitrary neighborhood U of the identity element of G has countably many translates xU that cover G, and (iv finitely generated modulo open sets if for every non-empty open subset U of G there exists a finite set F such that F  U algebraically generates G. We prove that: (1 a topological group containing a dense compactly generated subgroup is both 0-bounded and finitely generated modulo open sets, (2 an almost metrizable topological group has a dense compactly generated subgroup if and only if it is both 0-bounded and finitely generated modulo open sets, and (3 an almost metrizable topological group is compactly generated if and only if it is -compact and finitely generated modulo open sets.

  16. Factorizing profinite groups into two Abelian subgroups

    Directory of Open Access Journals (Sweden)

    Wolfgang Herfort

    2013-03-01

    Full Text Available We prove that the class of profinite groups $G$ that have a factorization $G=AB$with $A$ and $B$ abelian closed subgroups, is closed under taking strict projective limits.This is a generalization of a recent result by K.H.~Hofmann and F.G.~Russo.As an application we reprove their generalization of Iwasawa's structure theorem forquasihamiltonian pro-$p$ groups.

  17. MPACT Subgroup Self-Shielding Efficiency Improvements

    Energy Technology Data Exchange (ETDEWEB)

    Stimpson, Shane [Oak Ridge National Lab. (ORNL), Oak Ridge, TN (United States); Liu, Yuxuan [Univ. of Michigan, Ann Arbor, MI (United States); Collins, Benjamin S. [Oak Ridge National Lab. (ORNL), Oak Ridge, TN (United States); Clarno, Kevin T. [Oak Ridge National Lab. (ORNL), Oak Ridge, TN (United States)

    2016-08-31

    Recent developments to improve the efficiency of the MOC solvers in MPACT have yielded effective kernels that loop over several energy groups at once, rather that looping over one group at a time. These kernels have produced roughly a 2x speedup on the MOC sweeping time during eigenvalue calculation. However, the self-shielding subgroup calculation had not been reevaluated to take advantage of these new kernels, which typically requires substantial solve time. The improvements covered in this report start by integrating the multigroup kernel concepts into the subgroup calculation, which are then used as the basis for further extensions. The next improvement that is covered is what is currently being termed as “Lumped Parameter MOC”. Because the subgroup calculation is a purely fixed source problem and multiple sweeps are performed only to update the boundary angular fluxes, the sweep procedure can be condensed to allow for the instantaneous propagation of the flux across a spatial domain, without the need to sweep along all segments in a ray. Once the boundary angular fluxes are considered to be converged, an additional sweep that will tally the scalar flux is completed. The last improvement that is investigated is the possible reduction of the number of azimuthal angles per octant in the shielding sweep. Typically 16 azimuthal angles per octant are used for self-shielding and eigenvalue calculations, but it is possible that the self-shielding sweeps are less sensitive to the number of angles than the full eigenvalue calculation.

  18. The ergodic theory of lattice subgroups

    CERN Document Server

    Gorodnik, Alexander

    2010-01-01

    The results established in this book constitute a new departure in ergodic theory and a significant expansion of its scope. Traditional ergodic theorems focused on amenable groups, and relied on the existence of an asymptotically invariant sequence in the group, the resulting maximal inequalities based on covering arguments, and the transference principle. Here, Alexander Gorodnik and Amos Nevo develop a systematic general approach to the proof of ergodic theorems for a large class of non-amenable locally compact groups and their lattice subgroups. Simple general conditions on the spectral theory of the group and the regularity of the averaging sets are formulated, which suffice to guarantee convergence to the ergodic mean

  19. Subgrouping the autism "spectrum": reflections on DSM-5.

    Directory of Open Access Journals (Sweden)

    Meng-Chuan Lai

    Full Text Available DSM-5 has moved autism from the level of subgroups ("apples and oranges" to the prototypical level ("fruit". But making progress in research, and ultimately improving clinical practice, will require identifying subgroups within the autism spectrum.

  20. Notes on relatively hyperbolic groups and relatively quasiconvex subgroups

    OpenAIRE

    Matsuda, Yoshifumi; Oguni, Shin-ichi; Yamagata, Saeko

    2013-01-01

    We define relatively quasiconvex subgroups of relatively hyperbolic groups in the sense of Osin and show that such subgroups have expected properties. Also we state several definitions equivalent to the definition of relatively hyperbolic groups in the sense of Osin.

  1. Additive subgroups of topological vector spaces

    CERN Document Server

    Banaszczyk, Wojciech

    1991-01-01

    The Pontryagin-van Kampen duality theorem and the Bochner theorem on positive-definite functions are known to be true for certain abelian topological groups that are not locally compact. The book sets out to present in a systematic way the existing material. It is based on the original notion of a nuclear group, which includes LCA groups and nuclear locally convex spaces together with their additive subgroups, quotient groups and products. For (metrizable, complete) nuclear groups one obtains analogues of the Pontryagin duality theorem, of the Bochner theorem and of the Lévy-Steinitz theorem on rearrangement of series (an answer to an old question of S. Ulam). The book is written in the language of functional analysis. The methods used are taken mainly from geometry of numbers, geometry of Banach spaces and topological algebra. The reader is expected only to know the basics of functional analysis and abstract harmonic analysis.

  2. Can the tinnitus spectrum identify tinnitus subgroups?

    Directory of Open Access Journals (Sweden)

    Karin M Heijneman

    2013-01-01

    Full Text Available The tinnitus spectrum is a psycho-acoustic metric of tinnitus. Previous work found a tight relation between the spectrum and the tone audiogram. This suggests that the spectrum and the audiogram provide essentially the same information, and the added value of the spectrum is limited. In order to test whether the spectrum shows tinnitus characteristics that cannot be inferred from the audiogram, we re-examined the relation between the tinnitus spectrum and the tone audiogram, in a group of 80 tinnitus patients. We defined three subgroups of patients, using the shape of their tinnitus spectrum: (1 patients with a spectrum, monotonously increasing with frequency (2 patients with a distinct peak in their spectrum, (3 all other patients. Patients in group 3 typically showed low frequency tinnitus spectra. In all three groups, the largest hearing loss was at high frequencies (>2 kHz. The mean audiograms of group 1 and 2 were remarkably similar; group 3 had an additional hearing loss for the lower frequencies (<2 kHz. The three groups did not differ with respect to age, sex, or tinnitus questionnaire outcomes. In subgroups 2 and 3, the shape of the spectrum clearly differed from that of the tone audiogram. In other words, the spectrum technique provided information that could not have been obtained by tone audiometry alone. Therefore, the spectrum measurement may develop into a technique that can differentiate between classes of tinnitus. This may eventually contribute to the effective management of tinnitus, as various classes of tinnitus may require different therapeutic interventions.

  3. Genome-Wide Identification and Analysis of MicroRNAs Involved in Witches’-Broom Phytoplasma Response in Ziziphus jujuba

    Science.gov (United States)

    Shao, Fenjuan; Zhang, Qian; Liu, Hongwei; Lu, Shanfa; Qiu, Deyou

    2016-01-01

    MicroRNAs (miRNAs) play an important role in responding to biotic and abiotic stresses in plants. Jujube witches’-broom a phytoplasma disease of Ziziphus jujuba is prevalent in China and is a serious problem to the industry. However, the molecular mechanism of the disease is poorly understood. In this study, genome-wide identification and analysis of microRNAs in response to witches’-broom was performed. A total of 85 conserved miRNA unique sequences belonging to 32 miRNA families and 24 novel miRNA unique sequences, including their complementary miRNA* strands were identified from small RNA libraries derived from a uninfected and witches’-broom infected Z. jujuba plant. Differentially expressed miRNAs associated with Jujube witches’-broom disease were investigated between the two libraries, and 12 up-regulated miRNAs and 10 down- regulated miRNAs identified with more than 2 fold changes. Additionally, 40 target genes of 85 conserved miRNAs and 49 target genes of 24 novel miRNAs were predicted and their putative functions assigned. Using the modified 5’-RACE method, we confirmed that SPL and MYB were cleaved by miR156 and miR159, respectively. Our results provide insight into the molecular mechanisms of witches’-broom disease in Z. jujuba. PMID:27824938

  4. Genome-Wide Identification and Analysis of MicroRNAs Involved in Witches'-Broom Phytoplasma Response in Ziziphus jujuba.

    Science.gov (United States)

    Shao, Fenjuan; Zhang, Qian; Liu, Hongwei; Lu, Shanfa; Qiu, Deyou

    2016-01-01

    MicroRNAs (miRNAs) play an important role in responding to biotic and abiotic stresses in plants. Jujube witches'-broom a phytoplasma disease of Ziziphus jujuba is prevalent in China and is a serious problem to the industry. However, the molecular mechanism of the disease is poorly understood. In this study, genome-wide identification and analysis of microRNAs in response to witches'-broom was performed. A total of 85 conserved miRNA unique sequences belonging to 32 miRNA families and 24 novel miRNA unique sequences, including their complementary miRNA* strands were identified from small RNA libraries derived from a uninfected and witches'-broom infected Z. jujuba plant. Differentially expressed miRNAs associated with Jujube witches'-broom disease were investigated between the two libraries, and 12 up-regulated miRNAs and 10 down- regulated miRNAs identified with more than 2 fold changes. Additionally, 40 target genes of 85 conserved miRNAs and 49 target genes of 24 novel miRNAs were predicted and their putative functions assigned. Using the modified 5'-RACE method, we confirmed that SPL and MYB were cleaved by miR156 and miR159, respectively. Our results provide insight into the molecular mechanisms of witches'-broom disease in Z. jujuba.

  5. Subgroup analysis in burnout : Relations between fatigue, anxiety, and depression.

    NARCIS (Netherlands)

    van Dam, A.

    2016-01-01

    Several authors have suggested that burned out patients do not form a homogeneous group and that subgroups should be considered. The identification of these subgroups may contribute to a better understanding of the burnout construct and lead to more specific therapeutic interventions. Subgroup

  6. Characterization of Direct Current-Electrical Penetration Graph Waveforms and Correlation With the Probing Behavior of Matsumuratettix hiroglyphicus (Hemiptera: Cicadellidae), the Insect Vector of Sugarcane White Leaf Phytoplasma.

    Science.gov (United States)

    Roddee, J; Kobori, Y; Yorozuya, H; Hanboonsong, Y

    2017-06-01

    The leafhopper Matsumuratettix hiroglyphicus (Matsumura) (Hemiptera: Cicadellidae) is an important vector of phytoplasma causing white leaf disease in sugarcane. Thus, the aim of our study was to understand and describe the stylet-probing activities of this vector while feeding on sugarcane plants, by using direct current (DC) electrical penetration graph (EPG) monitoring. The EPG signals were classified into six distinct waveforms, according to amplitude, frequency, voltage level, and electrical origin of the observed traces during stylet penetration into the host plant tissues (probing). These six EPG waveforms of probing behavior comprise no stylet penetration (NP); stylet pathway through epidermis, mesophyll, and parenchymal cells (waveform A); contact at the bundle sheath layer (waveform B); salivation into phloem sieve elements (waveform C); phloem sap ingestion (waveform D); and short ingestion time of xylem sap (waveform E). The above waveform patterns were correlated with histological data of salivary sheath termini in plant tissue generated from insect stylet tips. The key findings of this study were that M. hiroglyphicus ingests the phloem sap at a relatively higher rate and for longer duration from any other cell type, suggesting that M. hiroglyphicus is mainly a phloem-feeder. Quantitative comparison of probing behavior revealed that females typically probe more frequently and longer in the phloem than males. Thus, females may acquire and inoculate greater amounts of phytoplasma than males, enhancing the efficiency of phytoplasma transmission and potentially exacerbating disease spreading. Overall, our study provides basic information on the probing behavior and transmission mechanism of M. hiroglyphicus. © The Authors 2017. Published by Oxford University Press on behalf of Entomological Society of America. All rights reserved. For Permissions, please email: journals.permissions@oup.com.

  7. Clinical Subgroups in Bilateral Meniere Disease

    Science.gov (United States)

    Frejo, Lidia; Soto-Varela, Andres; Santos-Perez, Sofía; Aran, Ismael; Batuecas-Caletrio, Angel; Perez-Guillen, Vanesa; Perez-Garrigues, Herminio; Fraile, Jesus; Martin-Sanz, Eduardo; Tapia, Maria C.; Trinidad, Gabriel; García-Arumi, Ana María; González-Aguado, Rocío; Espinosa-Sanchez, Juan M.; Marques, Pedro; Perez, Paz; Benitez, Jesus; Lopez-Escamez, Jose A.

    2016-01-01

    Meniere disease (MD) is a heterogeneous clinical condition characterized by sensorineural hearing loss, episodic vestibular symptoms, and tinnitus associated with several comorbidities, such as migraine or autoimmune disorders (AD). The frequency of bilateral involvement may range from 5 to 50%, and it depends on the duration of the disease. We have performed a two-step cluster analysis in 398 patients with bilateral MD (BMD) to identify the best predictors to define clinical subgroups with a potential different etiology to improve the phenotyping of BMD and to develop new treatments. We have defined five clinical variants in BMD. Group 1 is the most frequently found, includes 46% of patients, and is defined by metachronic hearing loss without migraine and without AD. Group 2 is found in 17% of patients, and it is defined by synchronic hearing loss without migraine or AD. Group 3, with 13% of patients, is characterized by familial MD, while group 4, that includes 12% of patients, is associated by the presence of migraine in all cases. Group 5 is found in 11% of patients and is defined by AD. This approach can be helpful in selecting patients for genetic and clinical research. However, further studies will be required to improve the phenotyping in these clinical variants for a better understanding of the diverse etiological factors contributing to BMD. PMID:27822199

  8. A Rapid Protocol of Crude RNA/DNA Extraction for RT-qPCR Detection and Quantification of 'Candidatus Phytoplasma prunorum'.

    Directory of Open Access Journals (Sweden)

    Stefano Minguzzi

    Full Text Available Many efforts have been made to develop a rapid and sensitive method for phytoplasma and virus detection. Taking our cue from previous works, different rapid sample preparation methods have been tested and applied to Candidatus Phytoplasma prunorum ('Ca. P. prunorum' detection by RT-qPCR. A duplex RT-qPCR has been optimized using the crude sap as a template to simultaneously amplify a fragment of 16S rRNA of the pathogen and 18S rRNA of the host plant. The specific plant 18S rRNA internal control allows comparison and relative quantification of samples. A comparison between DNA and RNA contribution to qPCR detection is provided, showing higher contribution of the latter. The method presented here has been validated on more than a hundred samples of apricot, plum and peach trees. Since 2013, this method has been successfully applied to monitor 'Ca. P. prunorum' infections in field and nursery. A triplex RT-qPCR assay has also been optimized to simultaneously detect 'Ca. P. prunorum' and Plum pox virus (PPV in Prunus.

  9. Report of the Production and Delivery Subgroup

    Energy Technology Data Exchange (ETDEWEB)

    Glass, R; Zalesky, R

    2004-11-01

    The Production and Delivery Subgroup was tasked with evaluating the various options that could be used for hydrogen production and delivery in terms of availability/industry readiness, technical and economic barriers, and environmental considerations. Hydrogen can be produced using a variety of feedstocks and conversion technologies. The feedstock options include water, natural gas, coal, petroleum, methanol, ethanol, biomass, and organic waste streams. Ultimately, using these domestic resources we will be able to produce all the hydrogen we will need for the complete conversion of our transportation infrastructure. The various conversion technologies include electrolysis, reforming (principally of natural gas, but also ethanol and methanol), photobiological and photoelectrochemical, biofermentation, pyrolysis and gasification of biomass and coal, high temperature thermochemical, and catalytic membranes. All of these production technologies are being actively researched by DOE's Office of Hydrogen, Fuel Cells and Infrastructure Technologies (HFCIT); and other offices within DOE support work that complements the HFCIT Program activities. In addition, private industry is also dedicating significant resources to these efforts. In establishing the California Hydrogen Highway Network (CA H2 Net) we must utilize both distributed (that is, hydrogen that is produced at the point of use) as well as centralized production of hydrogen. Because of technical and economic barriers, most of the technologies for hydrogen production listed above will not become practical for either mode of hydrogen production in large quantities until at least the 2015-2030 timeframe. In the near term, that is, the transitional period between now and 2010 when we will establish a widely available hydrogen fueling infrastructure in California, the distributed production options of reforming and electrolysis will play the dominant role. In addition, production of hydrogen at centralized plants

  10. Toward immunomodulation of witches broom disease of lime (WBDL) by targeting immunodominant membrane protein (IMP) of candidatus Phytoplasma aurantifolia.

    Science.gov (United States)

    Shahryari, F; Safarnejad, M R; Shams-Bakhsh, M; Jouzani, G R Salehi

    2010-01-01

    The witches' broom disease of lime (WBDL) caused by Candidatus Phytoplasma aurantifolia is the most devastating disease of acidian lime in southern part of Iran as it destroy thousands of trees yearly throughout these regions. Traditional methods such as eradication of infected trees and insect vector control have shown limited effect on this case. Therefore, alternative approaches such as plantibody-mediated resistance, have been considered. Throughout present study we prepared sufficient amount of antigen that is required for generation of specific monoclonal recombinant antibodies against Immunodominant membrane protein (IMP) which will be exploited for plantibody-mediated resistance approach. The gene encoding IMP protein was obtained by PCR amplification using specific primers and DNA extracted from the infected plants. Amplified fragment was then inserted into T/A cloning vector. Intact clones containing the right sequence was selected after digestion, PCR amplification and subsequent sequencing analysis. IMP encoding region having the right sequence was sub-cloned into pET28a bacterial expression vector. Large scale expression of His tagged recombinant protein was performed in the BL21-de3 strain of E. coli and purification under native conditions was carried out through immobilized metal ion affinity chromatography (IMAC) in a column containing Ni-NTA agarose beads. Successful expression and purification steps were confirmed by SDS-PAGE and western blotting analyses. The results obtained indicated the successful production of about 18 mg purified recombinant IMP protein with a low level of contamination in one liter cultured medium. Finally the purified protein was dialyzed in phosphate saline buffer and applied for immunization of mice.

  11. Personalized dementia care: proven effectiveness of psychosocial interventions in subgroups

    NARCIS (Netherlands)

    van Mierlo, L.D.; van der Roest, H.G.; Meiland, F.J.M.; Dröes, R.M.

    2010-01-01

    Many psychosocial intervention studies report effects in subgroups of people with dementia. Insight into the characteristics of these subgroups is important for care practice. This study reviews personal characteristics of people with dementia (living in the community or in an institution) that are

  12. Subgroup Achievement and Gap Trends: District of Columbia

    Science.gov (United States)

    Center on Education Policy, 2010

    2010-01-01

    The District's demographics are such that achievement trends could only be determined for African American, male and female, and low income subgroups. In grade 8 (the only grade in which subgroup trends were analyzed by achievement level), Washington, DC students showed gains in both reading and math at the basic, proficient, and advanced levels…

  13. Identifying subgroups of patients using latent class analysis

    DEFF Research Database (Denmark)

    Nielsen, Anne Mølgaard; Kent, Peter; Hestbæk, Lise

    2017-01-01

    BACKGROUND: Heterogeneity in patients with low back pain (LBP) is well recognised and different approaches to subgrouping have been proposed. Latent Class Analysis (LCA) is a statistical technique that is increasingly being used to identify subgroups based on patient characteristics. However, as ...

  14. A Systematic Approach to Subgroup Classification in Intellectual Disability

    Science.gov (United States)

    Schalock, Robert L.; Luckasson, Ruth

    2015-01-01

    This article describes a systematic approach to subgroup classification based on a classification framework and sequential steps involved in the subgrouping process. The sequential steps are stating the purpose of the classification, identifying the classification elements, using relevant information, and using clearly stated and purposeful…

  15. Characteristic properties of large subgroups in primary abelian groups

    Indian Academy of Sciences (India)

    R. Narasimhan (Krishtel eMaging) 1461 1996 Oct 15 13:05:22

    Invariant properties of large subgroups. We start with some extensions of totally projective p-groups, namely: 1. p-torsion A-groups. Several details on A-groups appear in [7]. For example, any p- torsion abelian A-group is an isotype subgroup of a totally projective p-group with special properties described in [7]. Theorem 1.

  16. Multiplicity-adjusted semiparametric benefiting subgroup identification in clinical trials.

    Science.gov (United States)

    Schnell, Patrick M; Müller, Peter; Tang, Qi; Carlin, Bradley P

    2018-02-01

    Background A recent focus in the health sciences has been the development of personalized medicine, which includes determining the population for which a given treatment is effective. Due to limited data, identifying the true benefiting population is a challenging task. To tackle this difficulty, the credible subgroups approach provides a pair of bounding subgroups for the true benefiting subgroup, constructed so that one is contained by the benefiting subgroup while the other contains the benefiting subgroup with high probability. However, the method has so far only been developed for parametric linear models. Methods In this article, we develop the details required to follow the credible subgroups approach in more realistic settings by considering nonlinear and semiparametric regression models, supported for regulatory science by conditional power simulations. We also present an improved multiple testing approach using a step-down procedure. We evaluate our approach via simulations and apply it to data from four trials of Alzheimer's disease treatments carried out by AbbVie. Results Semiparametric modeling yields credible subgroups that are more robust to violations of linear treatment effect assumptions, and careful choice of the population of interest as well as the step-down multiple testing procedure result in a higher rate of detection of benefiting types of patients. The approach allows us to identify types of patients that benefit from treatment in the Alzheimer's disease trials. Conclusion Attempts to identify benefiting subgroups of patients in clinical trials are often met with skepticism due to a lack of multiplicity control and unrealistically restrictive assumptions. Our proposed approach merges two techniques, credible subgroups, and semiparametric regression, which avoids these problems and makes benefiting subgroup identification practical and reliable.

  17. The use of high-throughput small RNA sequencing reveals differentially expressed microRNAs in response to aster yellows phytoplasma-infection in Vitis vinifera cv. 'Chardonnay'.

    Science.gov (United States)

    Snyman, Marius C; Solofoharivelo, Marie-Chrystine; Souza-Richards, Rose; Stephan, Dirk; Murray, Shane; Burger, Johan T

    2017-01-01

    Phytoplasmas are cell wall-less plant pathogenic bacteria responsible for major crop losses throughout the world. In grapevine they cause grapevine yellows, a detrimental disease associated with a variety of symptoms. The high economic impact of this disease has sparked considerable interest among researchers to understand molecular mechanisms related to pathogenesis. Increasing evidence exist that a class of small non-coding endogenous RNAs, known as microRNAs (miRNAs), play an important role in post-transcriptional gene regulation during plant development and responses to biotic and abiotic stresses. Thus, we aimed to dissect complex high-throughput small RNA sequencing data for the genome-wide identification of known and novel differentially expressed miRNAs, using read libraries constructed from healthy and phytoplasma-infected Chardonnay leaf material. Furthermore, we utilised computational resources to predict putative miRNA targets to explore the involvement of possible pathogen response pathways. We identified multiple known miRNA sequence variants (isomiRs), likely generated through post-transcriptional modifications. Sequences of 13 known, canonical miRNAs were shown to be differentially expressed. A total of 175 novel miRNA precursor sequences, each derived from a unique genomic location, were predicted, of which 23 were differentially expressed. A homology search revealed that some of these novel miRNAs shared high sequence similarity with conserved miRNAs from other plant species, as well as known grapevine miRNAs. The relative expression of randomly selected known and novel miRNAs was determined with real-time RT-qPCR analysis, thereby validating the trend of expression seen in the normalised small RNA sequencing read count data. Among the putative miRNA targets, we identified genes involved in plant morphology, hormone signalling, nutrient homeostasis, as well as plant stress. Our results may assist in understanding the role that miRNA pathways play

  18. A comparison of five recursive partitioning methods to find person subgroups involved in meaningful treatment-subgroup interactions

    NARCIS (Netherlands)

    Doove, L. L.; Dusseldorp, E.; Van Deun, K.; Van Mechelen, I.

    2014-01-01

    In case multiple treatment alternatives are available for some medical problem, the detection of treatment–subgroup interactions (i.e., relative treatment effectiveness varying over subgroups of persons) is of key importance for personalized medicine and the development of optimal treatment

  19. G-protein coupled receptor expression patterns delineate medulloblastoma subgroups

    Science.gov (United States)

    2013-01-01

    Background Medulloblastoma is the most common malignant brain tumor in children. Genetic profiling has identified four principle tumor subgroups; each subgroup is characterized by different initiating mutations, genetic and clinical profiles, and prognoses. The two most well-defined subgroups are caused by overactive signaling in the WNT and SHH mitogenic pathways; less is understood about Groups 3 and 4 medulloblastoma. Identification of tumor subgroup using molecular classification is set to become an important component of medulloblastoma diagnosis and staging, and will likely guide therapeutic options. However, thus far, few druggable targets have emerged. G-protein coupled receptors (GPCRs) possess characteristics that make them ideal targets for molecular imaging and therapeutics; drugs targeting GPCRs account for 30-40% of all current pharmaceuticals. While expression patterns of many proteins in human medulloblastoma subgroups have been discerned, the expression pattern of GPCRs in medulloblastoma has not been investigated. We hypothesized that analysis of GPCR expression would identify clear subsets of medulloblastoma and suggest distinct GPCRs that might serve as molecular targets for both imaging and therapy. Results Our study found that medulloblastoma tumors fall into distinct clusters based solely on GPCR expression patterns. Normal cerebellum clustered separately from the tumor samples. Further, two of the tumor clusters correspond with high fidelity to the WNT and SHH subgroups of medulloblastoma. Distinct over-expressed GPCRs emerge; for example, LGR5 and GPR64 are significantly and uniquely over-expressed in the WNT subgroup of tumors, while PTGER4 is over-expressed in the SHH subgroup. Uniquely under-expressed GPCRs were also observed. Our key findings were independently validated using a large international dataset. Conclusions Our results identify GPCRs with potential to act as imaging and therapeutic targets. Elucidating tumorigenic pathways

  20. Demonstration of Microbial Subgroups among Normal Vaginal Microbiota Data

    OpenAIRE

    Lee, M.-L. T.

    2011-01-01

    In this study we identified subgroups of observations relating to the healthy vaginal microbiota. This microbiota resides in a dynamic environment that undergoes cyclic change during the menstrual cycle. Cluster analysis procedures were applied to divide a set of 226 normal microbiota observations into groups. Three subgroups containing 100, 65, and 61 observations were identified. Plots of principal components determined by canonical analysis were obtained to demonstrate graphically the clus...

  1. On T-Characterized Subgroups of Compact Abelian Groups

    Directory of Open Access Journals (Sweden)

    Saak Gabriyelyan

    2015-06-01

    Full Text Available A sequence \\(\\{ u_n \\}_{n\\in \\omega}\\ in abstract additively-written Abelian group \\(G\\ is called a \\(T\\-sequence if there is a Hausdorff group topology on \\(G\\ relative to which \\(\\lim_n u_n =0\\. We say that a subgroup \\(H\\ of an infinite compact Abelian group \\(X\\ is \\(T\\-characterized if there is a \\(T\\-sequence \\(\\mathbf{u} =\\{ u_n \\}\\ in the dual group of \\(X\\, such that \\(H=\\{ x\\in X: \\; (u_n, x\\to 1 \\}\\. We show that a closed subgroup \\(H\\ of \\(X\\ is \\(T\\-characterized if and only if \\(H\\ is a \\(G_\\delta\\-subgroup of \\(X\\ and the annihilator of \\(H\\ admits a Hausdorff minimally almost periodic group topology. All closed subgroups of an infinite compact Abelian group \\(X\\ are \\(T\\-characterized if and only if \\(X\\ is metrizable and connected. We prove that every compact Abelian group \\(X\\ of infinite exponent has a \\(T\\-characterized subgroup, which is not an \\(F_{\\sigma}\\-subgroup of \\(X\\, that gives a negative answer to Problem 3.3 in Dikranjan and Gabriyelyan (Topol. Appl. 2013, 160, 2427–2442.

  2. A Bayesian subgroup analysis using collections of ANOVA models.

    Science.gov (United States)

    Liu, Jinzhong; Sivaganesan, Siva; Laud, Purushottam W; Müller, Peter

    2017-07-01

    We develop a Bayesian approach to subgroup analysis using ANOVA models with multiple covariates, extending an earlier work. We assume a two-arm clinical trial with normally distributed response variable. We also assume that the covariates for subgroup finding are categorical and are a priori specified, and parsimonious easy-to-interpret subgroups are preferable. We represent the subgroups of interest by a collection of models and use a model selection approach to finding subgroups with heterogeneous effects. We develop suitable priors for the model space and use an objective Bayesian approach that yields multiplicity adjusted posterior probabilities for the models. We use a structured algorithm based on the posterior probabilities of the models to determine which subgroup effects to report. Frequentist operating characteristics of the approach are evaluated using simulation. While our approach is applicable in more general cases, we mainly focus on the 2 × 2 case of two covariates each at two levels for ease of presentation. The approach is illustrated using a real data example. © 2017 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  3. Subgroup Analysis in Burnout: Relations Between Fatigue, Anxiety, and Depression

    Science.gov (United States)

    van Dam, Arno

    2016-01-01

    Several authors have suggested that burned out patients do not form a homogeneous group and that subgroups should be considered. The identification of these subgroups may contribute to a better understanding of the burnout construct and lead to more specific therapeutic interventions. Subgroup analysis may also help clarify whether burnout is a distinct entity and whether subgroups of burnout overlap with other disorders such as depression and chronic fatigue syndrome. In a group of 113 clinically diagnosed burned out patients, levels of fatigue, depression, and anxiety were assessed. In order to identify possible subgroups, we performed a two-step cluster analysis. The analysis revealed two clusters that differed from one another in terms of symptom severity on the three aforementioned measures. Depression appeared to be the strongest predictor of group membership. These results are considered in the light of the scientific debate on whether burnout can be distinguished from depression and whether burnout subtyping is useful. Finally, implications for clinical practice and future research are discussed. PMID:26869983

  4. Subgroup analysis in burnout: relations between fatigue, anxiety and depression

    Directory of Open Access Journals (Sweden)

    Arno eVan Dam

    2016-02-01

    Full Text Available Several authors have suggested that burned out patients do not form a homogeneous group and that subgroups should be considered. The identification of these subgroups may contribute to a better understanding of the burnout construct and lead to more specific therapeutic interventions. Subgroup analysis may also help clarify whether burnout is a distinct entity and whether subgroups of burnout overlap with other disorders such as depression and chronic fatigue syndrome. In a group of 113 clinically-diagnosed burned out patients, levels of fatigue, depression and anxiety were assessed. In order to identify possible subgroups, we performed a two-step cluster analysis. The analysis revealed two clusters that differed from one another in terms of symptom severity on the three aforementioned measures. Depression appeared to be the strongest predictor of group membership. These results are considered in the light of the scientific debate on whether burnout can be distinguished from depression and whether burnout subtyping is useful. Finally, implications for clinical practice and future research are discussed.

  5. Cluster analysis of clinical data identifies fibromyalgia subgroups.

    Directory of Open Access Journals (Sweden)

    Elisa Docampo

    Full Text Available INTRODUCTION: Fibromyalgia (FM is mainly characterized by widespread pain and multiple accompanying symptoms, which hinder FM assessment and management. In order to reduce FM heterogeneity we classified clinical data into simplified dimensions that were used to define FM subgroups. MATERIAL AND METHODS: 48 variables were evaluated in 1,446 Spanish FM cases fulfilling 1990 ACR FM criteria. A partitioning analysis was performed to find groups of variables similar to each other. Similarities between variables were identified and the variables were grouped into dimensions. This was performed in a subset of 559 patients, and cross-validated in the remaining 887 patients. For each sample and dimension, a composite index was obtained based on the weights of the variables included in the dimension. Finally, a clustering procedure was applied to the indexes, resulting in FM subgroups. RESULTS: VARIABLES CLUSTERED INTO THREE INDEPENDENT DIMENSIONS: "symptomatology", "comorbidities" and "clinical scales". Only the two first dimensions were considered for the construction of FM subgroups. Resulting scores classified FM samples into three subgroups: low symptomatology and comorbidities (Cluster 1, high symptomatology and comorbidities (Cluster 2, and high symptomatology but low comorbidities (Cluster 3, showing differences in measures of disease severity. CONCLUSIONS: We have identified three subgroups of FM samples in a large cohort of FM by clustering clinical data. Our analysis stresses the importance of family and personal history of FM comorbidities. Also, the resulting patient clusters could indicate different forms of the disease, relevant to future research, and might have an impact on clinical assessment.

  6. Tracking cohesive subgroups over time in inferred social networks

    Science.gov (United States)

    Chin, Alvin; Chignell, Mark; Wang, Hao

    2010-04-01

    As a first step in the development of community trackers for large-scale online interaction, this paper shows how cohesive subgroup analysis using the Social Cohesion Analysis of Networks (SCAN; Chin and Chignell 2008) and Data-Intensive Socially Similar Evolving Community Tracker (DISSECT; Chin and Chignell 2010) methods can be applied to the problem of identifying cohesive subgroups and tracking them over time. Three case studies are reported, and the findings are used to evaluate how well the SCAN and DISSECT methods work for different types of data. In the largest of the case studies, variations in temporal cohesiveness are identified across a set of subgroups extracted from the inferred social network. Further modifications to the DISSECT methodology are suggested based on the results obtained. The paper concludes with recommendations concerning further research that would be beneficial in addressing the community tracking problem for online data.

  7. Young children with language difficulties: a dimensional approach to subgrouping.

    Science.gov (United States)

    Jansen, Rianne; Ceulemans, Eva; Grauwels, Jolien; Maljaars, Jarymke; Zink, Inge; Steyaert, Jean; Noens, Ilse

    2013-11-01

    A dimensional approach was used to create bottom-up constructed subgroups that captured the behavioral heterogeneity in 36 Dutch-speaking children with language difficulties. Four subgroups were delineated based upon differences in cognitive ability, symbol understanding, joint attention and autism spectrum disorder related characteristics. Children with a different developmental disorder were found within a single cluster. Therefore, the results of this study suggest that bottom-up constructed subgroups might capture the heterogeneous behavioral profiles of young children with developmental difficulties in a more meaningful way. Furthermore, joint attention and symbol understanding seem important skills to assess in young children presenting with language difficulties. Copyright © 2013 Elsevier Ltd. All rights reserved.

  8. Differential distributions of Synechococcus subgroups across the California Current System.

    Directory of Open Access Journals (Sweden)

    Ryan William Paerl

    2011-04-01

    Full Text Available Synechococcus is an abundant marine cyanobacterial genus composed of different populations that vary physiologically. Synechococcus narB gene sequences (encoding for nitrate reductase in cyanobacteria obtained previously from isolates and the environment (e.g. North Pacific Gyre Station ALOHA, Hawaii or Monterey Bay, California were used to develop quantitative PCR (qPCR assays. These qPCR assays were used to quantify populations from specific narB phylogenetic clades across the California Current System (CCS, a region composed of dynamic zones between a coastal-upwelling zone and the oligotrophic Pacific Ocean. Targeted populations (narB subgroups had different biogeographic patterns across the CCS, which appear to be driven by environmental conditions. Subgroups C_C1, D_C1 and D_C2 were abundant in coastal-upwelling to coastal-transition zone waters with relatively high to intermediate ammonium, nitrate and chl. a concentrations. Subgroups A_C1 and F_C1 were most abundant in coastal-transition zone waters with intermediate nutrient concentrations. E_O1 and G_O1 were most abundant at different depths of oligotrophic open-ocean waters (either in the upper mixed layer or just below. E_O1, A_C1 and F_C1 distributions differed from other narB subgroups and likely possess unique ecologies enabling them to be most abundant in waters between coastal and open-ocean waters. Different CCS zones possessed distinct Synechococcus communities. Core California Current (CC water possessed low numbers of narB subgroups relative to counted Synechococcus cells, and coastal-transition waters contained high abundances of Synechococcus cells and total number of narB subgroups. The presented biogeographic data provides insight on the distributions and ecologies of Synechococcus present in an eastern boundary current system.

  9. Discrete neurocognitive subgroups in fully or partially remitted bipolar disorder

    DEFF Research Database (Denmark)

    Jensen, Johan Høy; Knorr, Ulla; Vinberg, Maj

    2016-01-01

    significance difference pairwise comparison. RESULTS: Three discrete neurocognitive subgroups were detected: one that was cognitively intact (46.1%), one that was selectively impaired with deficits in processing speed (32.6%), and one that was globally impaired across verbal learning, working memory......, and executive skills (21.2%). The globally and selectively impaired subgroups were characterized by greater perceived stress and subjective cognitive complaints, poorer work and social adjustment, and reduced quality of life compared to patients who were cognitively intact. LIMITATIONS: The study design...

  10. Latino Male Ethnic Subgroups: Patterns in College Enrollment and Degree Completion

    Science.gov (United States)

    Ponjuan, Luis; Palomin, Leticia; Calise, Angela

    2015-01-01

    This chapter examines Latino male ethnic subgroups and their college enrollment and degree completion patterns. The chapter also offers recommendations to improve Latino male ethnic subgroups' educational achievement.

  11. A comparison of subgroup analyses in grant applications and publications.

    NARCIS (Netherlands)

    Boonacker, C.W.; Hoes, A.W.; Liere-Visser, K. van; Schilder, A.G.M.; Rovers, M.M.

    2011-01-01

    In this paper, the authors compare subgroup analyses as outlined in grant applications and their related publications. Grants awarded by the Netherlands Organization for Health Research and Development (ZonMw) from 2001 onward that were finalized before March 1, 2010, were studied. Of the 79 grant

  12. Heterogeneity in response during multisystemic therapy: Exploring subgroups and predictors

    NARCIS (Netherlands)

    Mertens, E.C.A.; Dekovic, M.; Asscher, J.J.; Manders, W.A.

    2017-01-01

    Multiple studies have shown that Multisystemic Therapy (MST) is, at group level, an effective treatment for adolescents showing serious externalizing problem behavior. The current study expands previous research on MST by, first, examining whether subgroups of participants who respond differently to

  13. Heterogeneity in response during Multisystemic Therapy : Exploring subgroups and predictors

    NARCIS (Netherlands)

    Mertens, E.C.A.; Dekovic, M.; Asscher, J.J.; Manders, W.A.

    2017-01-01

    Multiple studies have shown that Multisystemic Therapy (MST) is, at group level, an effective treatment for adolescents showing serious externalizing problem behavior. The current study expands previous research on MST by, first, examining whether subgroups of participants who respond differently to

  14. Practical Algorithms for Subgroup Detection in Covert Networks

    DEFF Research Database (Denmark)

    Memon, Nasrullah; Wiil, Uffe Kock; Qureshi, Pir Abdul Rasool

    2010-01-01

    In this paper, we present algorithms for subgroup detection and demonstrated them with a real-time case study of USS Cole bombing terrorist network. The algorithms are demonstrated in an application by a prototype system. The system finds associations between terrorist and terrorist organisations...

  15. Active medulloblastoma enhancers reveal subgroup-specific cellular origins

    Science.gov (United States)

    Lin, Charles Y.; Erkek, Serap; Tong, Yiai; Yin, Linlin; Federation, Alexander J.; Zapatka, Marc; Haldipur, Parthiv; Kawauchi, Daisuke; Risch, Thomas; Warnatz, Hans-Jörg; Worst, Barbara C.; Ju, Bensheng; Orr, Brent A.; Zeid, Rhamy; Polaski, Donald R.; Segura-Wang, Maia; Waszak, Sebastian M.; Jones, David T.W.; Kool, Marcel; Hovestadt, Volker; Buchhalter, Ivo; Sieber, Laura; Johann, Pascal; Chavez, Lukas; Gröschel, Stefan; Ryzhova, Marina; Korshunov, Andrey; Chen, Wenbiao; Chizhikov, Victor V.; Millen, Kathleen J.; Amstislavskiy, Vyacheslav; Lehrach, Hans; Yaspo, Marie-Laure; Eils, Roland; Lichter, Peter; Korbel, Jan O.; Pfister, Stefan M.; Bradner, James E.; Northcott, Paul A.

    2016-01-01

    Summary Medulloblastoma is a highly malignant paediatric brain tumour, often inflicting devastating consequences on the developing child. Genomic studies have revealed four distinct molecular subgroups with divergent biology and clinical behaviour. An understanding of the regulatory circuitry governing the transcriptional landscapes of medulloblastoma subgroups, and how this relates to their respective developmental origins, is lacking. Using H3K27ac and BRD4 ChIP-Seq, coupled with tissue-matched DNA methylation and transcriptome data, we describe the active cis-regulatory landscape across 28 primary medulloblastoma specimens. Analysis of differentially regulated enhancers and super-enhancers reinforced inter-subgroup heterogeneity and revealed novel, clinically relevant insights into medulloblastoma biology. Computational reconstruction of core regulatory circuitry identified a master set of transcription factors, validated by ChIP-Seq, that are responsible for subgroup divergence and implicate candidate cells-of-origin for Group 4. Our integrated analysis of enhancer elements in a large series of primary tumour samples reveals insights into cis-regulatory architecture, unrecognized dependencies, and cellular origins. PMID:26814967

  16. Notes on discrete subgroups of Möbius transformations

    Indian Academy of Sciences (India)

    Abstract. Jørgensen's inequality gives a necessary condition for a nonelementary two generator subgroup of SL(2, C) to be discrete. By embedding SL(2, C) into. ˆU(1, 1; H), we obtain a new type of Jørgensen's inequality, which is in terms of the coefficients of involved isometries. We provide an example to show that this ...

  17. On approximation of Lie groups by discrete subgroups

    Indian Academy of Sciences (India)

    voila.fr; salah.suissi@yahoo.fr. MS received 11 August 2012; revised 27 January 2013. Abstract. A locally compact group G is said to be approximated by discrete sub- groups (in the sense of Tôyama) if there is a sequence of discrete subgroups ...

  18. Depression in later life : three etiologically different subgroups

    NARCIS (Netherlands)

    Van den Berg, M.D.; Oldehinkel, A.J.; Bouhuys, A.L.; Brilman, E.I.; Beekman, A.T.F.; Ormel, J.

    Background: Various studies support the notion that early onset depression and late onset depression have different etiological pathways. Late onset depression has been found to be a heterogeneous group. This study attempts to divide the late onset group in two subgroups with different aetiology and

  19. Detection of Problem Gambler Subgroups Using Recursive Partitioning

    Science.gov (United States)

    Markham, Francis; Young, Martin; Doran, Bruce

    2013-01-01

    The multivariate socio-demographic risk factors for problem gambling have been well documented. While this body of research is valuable in determining risk factors aggregated across various populations, the majority of studies tend not to specifically identify particular subgroups of problem gamblers based on the interaction between variables. The…

  20. Differences in Psychosocial Predictors of Obesity Among LGBT Subgroups.

    Science.gov (United States)

    Warren, Jacob C; Smalley, K Bryant; Barefoot, K Nikki

    2016-08-01

    The purpose of the current study was to examine the overall presence of and differences in rates of overweight/obesity among a large, nationally diverse sample of lesbian, gay, bisexual, transgender (LGBT)-identified individuals (i.e., cisgender lesbians, cisgender gay men, cisgender bisexual women, cisgender bisexual men, transgender women, and transgender men) and to identify specific psychosocial predictors of obesity within each of the six LGBT subgroups. A total of 2702 LGBT-identified participants participated in the online study. Participants completed a series of demographic questions (including weight and height) and the Depression Anxiety Stress Scale 21. The percentage of participants who were overweight/obese did not differ significantly across LGBT subgroups, with 61.1% of the total sample being overweight/obese. However, the percentage of participants who self-reported body mass indexes in the obese range differed significantly across the six LGBT subgroups, with the highest prevalence in transgender men (46.0%). In addition, the predictors of obesity varied by subgroup, with age a significant predictor for cisgender lesbians, cisgender gay men, and cisgender bisexual women, relationship status for cisgender bisexual women, employment status for both cisgender gay men and cisgender bisexual women, education level for cisgender lesbians, and depression, anxiety, and stress for cisgender gay men. None of the examined psychosocial factors emerged as predictors of obesity for cisgender bisexual men, transgender women, or transgender men. These findings suggest that there are substantial variations in the presence and predictors of obesity across LGBT subgroups that support the need for culturally tailored healthy weight promotion efforts within the LGBT community.

  1. Clinical implications of medulloblastoma subgroups: incidence of CSF diversion surgery.

    Science.gov (United States)

    Schneider, Christian; Ramaswamy, Vijay; Kulkarni, Abhaya V; Rutka, James T; Remke, Marc; Tabori, Uri; Hawkins, Cynthia; Bouffet, Eric; Taylor, Michael D

    2015-03-01

    While medulloblastoma was initially thought to comprise a single homogeneous entity, it is now accepted that it in fact comprises 4 discrete subgroups, each with its own distinct demographics, clinical presentation, transcriptomics, genetics, and outcome. Hydrocephalus is a common complication of medulloblastoma and not infrequently requires CSF diversion. The authors report the incidence of CSF diversion surgery in each of the subgroups of medulloblastoma (Wnt, Shh, Group 3, and Group 4). The medical and imaging records for patients who underwent surgery for medulloblastoma at The Hospital for Sick Children were retrospectively reviewed. The primary outcome was the requirement for CSF diversion surgery either before or within 60 days of tumor resection. The modified Canadian Preoperative Prediction Rule for Hydrocephalus (mCPPRH) was compared among subgroups. Of 143 medulloblastoma patients, treated from 1991 to 2013, sufficient data were available for 130 patients (15 with Wnt, 30 with Shh, 30 with Group 3, and 55 with Group 4 medulloblastomas). Of these, 28 patients (22%) ultimately underwent CSF diversion surgery: 0% with Wnt, 29% with Shh, 29% with Group 3, and 43% with Group 4 tumors. Patients in the Wnt subgroup had a lower incidence of CSF diversion than all other patients combined (p = 0.04). Wnt patients had a lower mCPPRH score (lower risk of CSF diversion, p = 0.045), were older, had smaller ventricles at diagnosis, and had no leptomeningeal metastases. The overall rate of CSF diversion surgery for Shh, Group 3, and Group 4 medulloblastomas is around 30%, but no patients in the present series with a Wnt medulloblastoma required shunting. The low incidence of hydrocephalus in patients with Wnt medulloblastoma likely reflects both host factors (age) and disease factors (lack of metastases). The absence of hydrocephalus in patients with Wnt medulloblastomas likely contributes to their excellent rate of survival and may also contribute to a higher quality

  2. Cluster Analysis of Clinical Data Identifies Fibromyalgia Subgroups

    Science.gov (United States)

    Docampo, Elisa; Collado, Antonio; Escaramís, Geòrgia; Carbonell, Jordi; Rivera, Javier; Vidal, Javier; Alegre, José

    2013-01-01

    Introduction Fibromyalgia (FM) is mainly characterized by widespread pain and multiple accompanying symptoms, which hinder FM assessment and management. In order to reduce FM heterogeneity we classified clinical data into simplified dimensions that were used to define FM subgroups. Material and Methods 48 variables were evaluated in 1,446 Spanish FM cases fulfilling 1990 ACR FM criteria. A partitioning analysis was performed to find groups of variables similar to each other. Similarities between variables were identified and the variables were grouped into dimensions. This was performed in a subset of 559 patients, and cross-validated in the remaining 887 patients. For each sample and dimension, a composite index was obtained based on the weights of the variables included in the dimension. Finally, a clustering procedure was applied to the indexes, resulting in FM subgroups. Results Variables clustered into three independent dimensions: “symptomatology”, “comorbidities” and “clinical scales”. Only the two first dimensions were considered for the construction of FM subgroups. Resulting scores classified FM samples into three subgroups: low symptomatology and comorbidities (Cluster 1), high symptomatology and comorbidities (Cluster 2), and high symptomatology but low comorbidities (Cluster 3), showing differences in measures of disease severity. Conclusions We have identified three subgroups of FM samples in a large cohort of FM by clustering clinical data. Our analysis stresses the importance of family and personal history of FM comorbidities. Also, the resulting patient clusters could indicate different forms of the disease, relevant to future research, and might have an impact on clinical assessment. PMID:24098674

  3. Evidência molecular da ocorrência de um fitoplasma associado ao lenho mole da macieira Molecular evidence for an association of a phytoplasma with apple rubbery wood

    Directory of Open Access Journals (Sweden)

    Luiz Fernando Caldeira Ribeiro

    2007-03-01

    Full Text Available O lenho mole da macieira é uma doença relevante em diversas partes do mundo. Sintomas típicos desta doença têm sido observados em pomares instalados em estados do sul do território brasileiro desde a década de oitenta. Enxertia tem revelado a natureza infecciosa da doença e a observação de corpúsculos filamentosos no floema tem evidenciado possível associação com fitoplasma. No presente trabalho plantas com sintomas de lenho mole foram coletadas em pomar comercial, visando demonstrar a presença de fitoplasma em tecido doente, bem como identificar molecularmente este fitoplasma. Através do emprego de duplo PCR com iniciadores universais R16mF2/R1 e R16F2n/R2, fitoplasma foi consistentemente detectado em plantas sintomáticas. A identificação conduzida com duplo PCR usando-se iniciadores específicos R16(IIIF2/R demonstrou que o fitoplasma detectado pertencia ao grupo 16SrIII. Análises de RFLP conduzidas com as endonucleases AluI, KpnI, HinfI, HpaII, MseI, RsaI e SauIIIA confirmaram que o fitoplasma era um representante típico do grupo 16SrIII. A detecção e identificação molecular se constitui numa forte evidência que um fitoplasma está associado ao lenho mole da macieira no Brasil, complementando os trabalhos realizados anteriormente com transmissão por enxertia e observação por microscopia eletrônica .Apple rubbery wood is an important disease occurring worldwide. Typical symptoms have been observed since 80' decade in orchards located in the South part of Brazil. In previous studies, grafting has evidenciated that the disease had infeccious etiology and visualization of filamentous bodies inside phloem had indicated that a phytoplasma could be associated with the disease. In the present study, plants with symptoms of rubbery wood were sampled in a commercial orchard in order to demonstrate the presence of phytoplasma in infected tissue and to identify molecularly that the organism. Using nested PCR with universal

  4. Metabolic Consequences of Infection of Grapevine (Vitis vinifera L.) cv. “Modra frankinja” with Flavescence Dorée Phytoplasma

    Science.gov (United States)

    Prezelj, Nina; Covington, Elizabeth; Roitsch, Thomas; Gruden, Kristina; Fragner, Lena; Weckwerth, Wolfram; Chersicola, Marko; Vodopivec, Maja; Dermastia, Marina

    2016-01-01

    Flavescence dorée, caused by the quarantine phytoplasma FDp, represents the most devastating of the grapevine yellows diseases in Europe. In an integrated study we have explored the FDp–grapevine interaction in infected grapevines of cv. “Modra frankinja” under natural conditions in the vineyard. In FDp-infected leaf vein-enriched tissues, the seasonal transcriptional profiles of 14 genes selected from various metabolic pathways showed an FDp-specific plant response compared to other grapevine yellows and uncovered a new association of the SWEET17a vacuolar transporter of fructose with pathogens. Non-targeted metabolome analysis from leaf vein-enriched tissues identified 22 significantly changed compounds with increased levels during infection. Several metabolites corroborated the gene expression study. Detailed investigation of the dynamics of carbohydrate metabolism revealed significant accumulation of sucrose and starch in the mesophyll of FDp-infected leaves, as well as significant up-regulation of genes involved in their biosynthesis. In addition, infected leaves had high activities of ADP-glucose pyrophosphorylase and, more significantly, sucrose synthase. The data support the conclusion that FDp infection inhibits phloem transport, resulting in accumulation of carbohydrates and secondary metabolites that provoke a source-sink transition and defense response status. PMID:27242887

  5. Molecular typing of 'bois noir' phytoplasma strains in the Chianti Classico area (Tuscany, central Italy) and their association with symptom severity in Vitis vinifera L. cv. Sangiovese.

    Science.gov (United States)

    Pierro, Roberto; Passera, Alessandro; Panattoni, Alessandra; Casati, Paola; Luvisi, Andrea; Rizzo, Domenico; Bianco, Piero Attilio; Quaglino, Fabio; Materazzi, Alberto

    2017-10-13

    Bois Noir (BN) is the most widespread disease of the grapevine yellows complex in the Euro-Mediterranean area. BN is caused by 'Candidatus Phytoplasma solani' (BNp), transmitted from herbaceous plants to grapevine by polyphagous insect vectors. In this study, genetic diversity among BNp strains, their prevalence and possible association with grapevine symptom severity were investigated in a Sangiovese clone organic vineyard, in the Chianti Classico area (Tuscany). Field surveys over two years revealed a range of symptom severity on grapevine and an increase of BN incidence. TaqMan allelic discrimination assay detected only tufB-type b among BNp strains, suggesting the prevalence of the bindweed-related ecology. Nucleotide sequence analyses of vmp1 and stamp genes identified 12 vmp1 and 16 stamp sequence variants, showing an overall positive selection for such genes. The prevalent genotype was Vm43/St10, reported for the first time in this study and closely related to strains identified only in the French Eastern Pyrenees. BNp strains, identified in the examined vineyard and mostly grouped in separate bindweed-related phylogenetic clusters, showed statistically significant differences in their distribution in grapevines exhibiting distinct symptom severity. These results suggest the possible occurrence of a range of virulence within BNp strain populations in the Chianti Classico area.

  6. Combined group ECC protection and subgroup parity protection

    Science.gov (United States)

    Gara, Alan G.; Chen, Dong; Heidelberger, Philip; Ohmacht, Martin

    2013-06-18

    A method and system are disclosed for providing combined error code protection and subgroup parity protection for a given group of n bits. The method comprises the steps of identifying a number, m, of redundant bits for said error protection; and constructing a matrix P, wherein multiplying said given group of n bits with P produces m redundant error correction code (ECC) protection bits, and two columns of P provide parity protection for subgroups of said given group of n bits. In the preferred embodiment of the invention, the matrix P is constructed by generating permutations of m bit wide vectors with three or more, but an odd number of, elements with value one and the other elements with value zero; and assigning said vectors to rows of the matrix P.

  7. Fast determination of structurally cohesive subgroups in large networks.

    Science.gov (United States)

    Sinkovits, Robert S; Moody, James; Oztan, B Tolga; White, Douglas R

    2016-11-01

    Structurally cohesive subgroups are a powerful and mathematically rigorous way to characterize network robustness. Their strength lies in the ability to detect strong connections among vertices that not only have no neighbors in common, but that may be distantly separated in the graph. Unfortunately, identifying cohesive subgroups is a computationally intensive problem, which has limited empirical assessments of cohesion to relatively small graphs of at most a few thousand vertices. We describe here an approach that exploits the properties of cliques, k-cores and vertex separators to iteratively reduce the complexity of the graph to the point where standard algorithms can be used to complete the analysis. As a proof of principle, we apply our method to the cohesion analysis of a 29,462-vertex biconnected component extracted from a 128,151-vertex co-authorship data set.

  8. Distinguishing between Subgroups of Adolescents Who Self-Harm

    Science.gov (United States)

    Hargus, Emily; Hawton, Keith; Rodham, Karen

    2009-01-01

    The differences in factors associated with subgroups of adolescents in the continuum of deliberate self-harm (DSH) phenomena were investigated. In an anonymous self-report survey of 6,020 adolescents aged 15 and 16 years, 3.2% of adolescents (5.3% females, 1.3% males) reported DSH with intent to die, 2.8% (4.3% females; 1.5% males) reported DSH…

  9. Microscopic colitis: clinical findings, topography and persistence of histopathological subgroups.

    Science.gov (United States)

    Bjørnbak, C; Engel, P J H; Nielsen, P L; Munck, L K

    2011-11-01

    Uncertainty remains on topography and persistence of histological subgroups of microscopic colitis (MC). To assess longitudinal clinical, endoscopic, histological, and therapeutic description of MC subgroups including patients with incomplete findings of MC (MCi). Retrospective review of a consecutive cohort with MC and histological reassessment of MCi. Clinical characteristics of 168 patients with lymphocytic colitis (LC), 270 with collagenous colitis (CC) and 101 with MCi were similar. At colonoscopy 95% (95% CI: 91-98%) of CC and 98% (93-100%) of LC cases had diagnostic histopathology of MC in both left and right colon. Eight and three patients had characteristics of MC only in the left and right colon, respectively. Histology findings resembling coexistence of the other MC subtype was present in 48% (40-55%) with CC and 24% (18-31%) with LC. A first diagnosis of MC was made in 49 (30%) of 164 patients only at repeat endoscopy. Another 34 of 115 (30%) with MC in the first endoscopy did not fulfil the MC criteria at repeat endoscopy. Only seven cases had a primary endoscopy without histopathological abnormalities. Fifteen percentage of MCi were reclassified as MC. Ileal inflammation was present in 33 of 81 patients. Budesonide was efficacious in all MC subgroups irrespective of bile acid malabsorption. Clinical characteristics of microscopic colitis subgroups are indistinguishable. Biopsies from the left colon suffice to exclude microscopic colitis, and the histological diagnosis of microscopic colitis is inconsistent over time. Ileal inflammation is common. The term microscopic colitis should perhaps be considered one clinical entity and include lymphocytic colitis, collagenous colitis, and incomplete findings of microscopic colitis. © 2011 Blackwell Publishing Ltd.

  10. Pain and Fatigue Variability Patterns Distinguish Subgroups of Fibromyalgia Patients.

    Science.gov (United States)

    Bartley, Emily J; Robinson, Michael E; Staud, Roland

    2017-12-15

    The current study examined between- and within-subject variability in pain-related symptoms as predictors of pain and fatigue, and identified patient subgroups based upon symptom variability characteristics. Two hundred and fifty-six fibromyalgia (FM) patients completed daily diaries up to a period of 154 days and reported on symptoms of pain intensity, pain unpleasantness, fatigue, anxiety, and depressed mood. Measures of health status, quality of life, and somatic symptoms were obtained at baseline, and hierarchical linear modeling and cluster analyses were employed. Significant intra- and inter-individual variability in daily FM symptoms was observed. Higher levels of pain were associated with greater fluctuations in pain unpleasantness, fatigue, and depressed mood. Similar effects were observed for fatigue and individual variability in anxiety also emerged as a robust predictor. Three FM subgroups were revealed: low variability in symptoms (Cluster 1), high symptom variability (Cluster 2), and a mixed variability group characterized by low fluctuation in pain unpleasantness; moderate pain, fatigue, and depressed mood variability; and high anxiety variability (Cluster 3). Cluster 3 exhibited lower social functioning and higher levels of pain, compared to Cluster 1. These findings support the dynamic nature of FM pain and suggest the presence of FM subgroups based upon variation in mood and pain symptomatology. Fibromyalgia patients display significant intra- and inter-individual variability in pain, mood, and fatigue. Subgroups in mood and pain-related variability emerged, with phenotypic clusters differing across levels of pain intensity and social functioning. Better understanding of the processes impacting pain variability may facilitate targeted treatments for the control of pain. Copyright © 2017. Published by Elsevier Inc.

  11. Irreducible almost simple subgroups of classical algebraic groups

    CERN Document Server

    Burness, Timothy C; Marion, Claude; Testerman, Donna M

    2015-01-01

    Let G be a simple classical algebraic group over an algebraically closed field K of characteristic p\\geq 0 with natural module W. Let H be a closed subgroup of G and let V be a nontrivial p-restricted irreducible tensor indecomposable rational KG-module such that the restriction of V to H is irreducible. In this paper the authors classify the triples (G,H,V) of this form, where V \

  12. Distinct Histomorphology in Molecular Subgroups of Glioblastomas in Young Patients.

    Science.gov (United States)

    Neumann, Julia E; Dorostkar, Mario M; Korshunov, Andrey; Mawrin, Christian; Koch, Arend; Giese, Armin; Schüller, Ulrich

    2016-05-01

    Glioblastomas (GBMs) are malignant brain tumors that can be divided into different molecular subtypes based on genetics, global gene expression, and methylation patterns. Among these subgroups, "IDH" GBMs carry mutations within IDH1 or IDH2 The "K27" and "G34" subgroups are characterized by distinct mutations within Histone 3 (H3). These subtypes can be identified by sequencing methods and are particularly found in younger patients. To determine whether the molecular subtypes correlate with distinct histological features among the diverse histologic patterns of GBM, we performed a blinded assessment of the histology of GBMs of 77 patients ≤30 years old at the time of biopsy. The tumors were of the following molecular subtypes: IDH (n = 12), H3 K27M (n = 25), H3 G34R (n = 12), or no IDH/H3 mutations (n = 28). Of IDH-mutated cases, 75% had microcystic features or gemistocytic tumor cells. K27 GBMs had higher cell densities and pronounced nuclear pleomorphism, with 28% harboring tumor giant cells. All G34 GBMs had variable extents of a poorly differentiated/primitive neuroectodermal tumor-like morphology. GBMs without IDH/H3 mutations had foci of epitheliod-appearing cells. Thus, molecular GBM subgroups are associated with distinct histological patterns, suggesting that morphological features reflect the specific underlying molecular genetic abnormalities. © 2016 American Association of Neuropathologists, Inc. All rights reserved.

  13. Gambaran Populasi Golongan Darah Subgroup A (A1, A2 di PMI Kulon Progo

    Directory of Open Access Journals (Sweden)

    Hieronymus Rayi Prasetya

    2017-08-01

    Full Text Available Subgroup A1 and A2 are the most important in the blood group A. Subgroup A1 has the A antigen more than A2 subgroup, the A2 subgroup can cause misidentification of blood group due to poor A antigen and genetic variation possessed. Misidentification of the blood group will increase the risk of transfusion reactions. This research aims to describe the A1 and A2 subgroup population in Kulon Progo district. This study was conducted with a cross sectional sampling technique. The sample in this study were taken from donors of blood group A in Kulon Progo Red Cross. Identification of A1 and A2 subgroup is done by using lectin (Dolichos biflorus extract. The result of the examination of 53 samples showed that 96,2% was A1 subgroup and 3,8% was A2 subgroup. Key words : Subgroup A1, Subgroup A2, Population, Kulon Progo

  14. Informant discrepancy defines discrete, clinically useful autism spectrum disorder subgroups.

    Science.gov (United States)

    Lerner, Matthew D; De Los Reyes, Andres; Drabick, Deborah A G; Gerber, Alan H; Gadow, Kenneth D

    2017-07-01

    Discrepancy between informants (parents and teachers) in severity ratings of core symptoms commonly arise when assessing autism spectrum disorder (ASD). Whether such discrepancy yields unique information about the ASD phenotype and its clinical correlates has not been examined. We examined whether degree of discrepancy between parent and teacher ASD symptom ratings defines discrete, clinically meaningful subgroups of youth with ASD using an efficient, cost-effective procedure. Children with ASD (N = 283; 82% boys; M age  = 10.5 years) were drawn from a specialty ASD clinic. Parents and teachers provided ratings of the three core DSM-IV-TR domains of ASD symptoms (communication, social, and perseverative behavior) with the Child and Adolescent Symptom Inventory-4R (CASI-4R). External validators included child psychotropic medication status, frequency of ASD-relevant school-based services, and the Autism Diagnostic Observation Schedule (ADOS-2). Four distinct subgroups emerged that ranged from large between-informant discrepancy (informant-specific) to relative lack of discrepancy (i.e. informant agreement; cross-situational): Moderate Parent/Low Teacher or Low Parent/Moderate Teacher Severity (Discrepancy), and Moderate or High Symptom Severity (Agreement). Subgroups were highly distinct (mean probability of group assignment = 94%). Relative to Discrepancy subgroups, Agreement subgroups were more likely to receive psychotropic medication, school-based special education services, and an ADOS-2 diagnosis. These differential associations would not have been identified based solely on CASI-4R scores from one informant. The degree of parent-teacher discrepancy about ASD symptom severity appears to provide more clinically useful information than reliance on a specific symptom domain or informant, and thus yields an innovative, cost-effective approach to assessing functional impairment. This conclusion stands in contrast to existing symptom clustering approaches in

  15. Subgroup Analysis of Trials Is Rarely Easy (SATIRE: a study protocol for a systematic review to characterize the analysis, reporting, and claim of subgroup effects in randomized trials

    Directory of Open Access Journals (Sweden)

    Malaga German

    2009-11-01

    Full Text Available Abstract Background Subgroup analyses in randomized trials examine whether effects of interventions differ between subgroups of study populations according to characteristics of patients or interventions. However, findings from subgroup analyses may be misleading, potentially resulting in suboptimal clinical and health decision making. Few studies have investigated the reporting and conduct of subgroup analyses and a number of important questions remain unanswered. The objectives of this study are: 1 to describe the reporting of subgroup analyses and claims of subgroup effects in randomized controlled trials, 2 to assess study characteristics associated with reporting of subgroup analyses and with claims of subgroup effects, and 3 to examine the analysis, and interpretation of subgroup effects for each study's primary outcome. Methods We will conduct a systematic review of 464 randomized controlled human trials published in 2007 in the 118 Core Clinical Journals defined by the National Library of Medicine. We will randomly select journal articles, stratified in a 1:1 ratio by higher impact versus lower impact journals. According to 2007 ISI total citations, we consider the New England Journal of Medicine, JAMA, Lancet, Annals of Internal Medicine, and BMJ as higher impact journals. Teams of two reviewers will independently screen full texts of reports for eligibility, and abstract data, using standardized, pilot-tested extraction forms. We will conduct univariable and multivariable logistic regression analyses to examine the association of pre-specified study characteristics with reporting of subgroup analyses and with claims of subgroup effects for the primary and any other outcomes. Discussion A clear understanding of subgroup analyses, as currently conducted and reported in published randomized controlled trials, will reveal both strengths and weaknesses of this practice. Our findings will contribute to a set of recommendations to optimize

  16. A 6-gene signature identifies four molecular subgroups of neuroblastoma

    LENUS (Irish Health Repository)

    Abel, Frida

    2011-04-14

    Abstract Background There are currently three postulated genomic subtypes of the childhood tumour neuroblastoma (NB); Type 1, Type 2A, and Type 2B. The most aggressive forms of NB are characterized by amplification of the oncogene MYCN (MNA) and low expression of the favourable marker NTRK1. Recently, mutations or high expression of the familial predisposition gene Anaplastic Lymphoma Kinase (ALK) was associated to unfavourable biology of sporadic NB. Also, various other genes have been linked to NB pathogenesis. Results The present study explores subgroup discrimination by gene expression profiling using three published microarray studies on NB (47 samples). Four distinct clusters were identified by Principal Components Analysis (PCA) in two separate data sets, which could be verified by an unsupervised hierarchical clustering in a third independent data set (101 NB samples) using a set of 74 discriminative genes. The expression signature of six NB-associated genes ALK, BIRC5, CCND1, MYCN, NTRK1, and PHOX2B, significantly discriminated the four clusters (p < 0.05, one-way ANOVA test). PCA clusters p1, p2, and p3 were found to correspond well to the postulated subtypes 1, 2A, and 2B, respectively. Remarkably, a fourth novel cluster was detected in all three independent data sets. This cluster comprised mainly 11q-deleted MNA-negative tumours with low expression of ALK, BIRC5, and PHOX2B, and was significantly associated with higher tumour stage, poor outcome and poor survival compared to the Type 1-corresponding favourable group (INSS stage 4 and\\/or dead of disease, p < 0.05, Fisher\\'s exact test). Conclusions Based on expression profiling we have identified four molecular subgroups of neuroblastoma, which can be distinguished by a 6-gene signature. The fourth subgroup has not been described elsewhere, and efforts are currently made to further investigate this group\\'s specific characteristics.

  17. Pathogen-Induced Leaf Chlorosis: Products of Chlorophyll Breakdown Found in Degreened Leaves of Phytoplasma-Infected Apple (Malus × domestica Borkh.) and Apricot (Prunus armeniaca L.) Trees Relate to the Pheophorbide a Oxygenase/Phyllobilin Pathway.

    Science.gov (United States)

    Mittelberger, Cecilia; Yalcinkaya, Hacer; Pichler, Christa; Gasser, Johanna; Scherzer, Gerhard; Erhart, Theresia; Schumacher, Sandra; Holzner, Barbara; Janik, Katrin; Robatscher, Peter; Müller, Thomas; Kräutler, Bernhard; Oberhuber, Michael

    2017-04-05

    Phytoplasmoses such as apple proliferation (AP) and European stone fruit yellows (ESFY) cause severe economic losses in fruit production. A common symptom of both phytoplasma diseases is early yellowing or leaf chlorosis. Even though chlorosis is a well-studied symptom of biotic and abiotic stresses, its biochemical pathways are hardly known. In particular, in this context, a potential role of the senescence-related pheophorbide a oxygenase/phyllobilin (PaO/PB) pathway is elusive, which degrades chlorophyll (Chl) to phyllobilins (PBs), most notably to colorless nonfluorescent Chl catabolites (NCCs). In this work, we identified the Chl catabolites in extracts of healthy senescent apple and apricot leaves. In extracts of apple tree leaves, a total of 12 Chl catabolites were detected, and in extracts of leaves of the apricot tree 16 Chl catabolites were found. The seven major NCC fractions in the leaves of both fruit tree species were identical and displayed known structures. All of the major Chl catabolites were also found in leaf extracts from AP- or ESFY-infected trees, providing the first evidence that the PaO/PB pathway is relevant also for pathogen-induced chlorosis. This work supports the hypothesis that Chl breakdown in senescence and phytoplasma infection proceeds via a common pathway in some members of the Rosaceae family.

  18. High-throughput transcriptome analysis of the leafy flower transition of Catharanthus roseus induced by peanut witches'-broom phytoplasma infection.

    Science.gov (United States)

    Liu, Li-Yu Daisy; Tseng, Hsin-I; Lin, Chan-Pin; Lin, Yen-Yu; Huang, Yuan-Hung; Huang, Chien-Kang; Chang, Tean-Hsu; Lin, Shih-Shun

    2014-05-01

    Peanut witches'-broom (PnWB) phytoplasma are obligate bacteria that cause leafy flower symptoms in Catharanthus roseus. The PnWB-mediated leafy flower transitions were studied to understand the mechanisms underlying the pathogen-host interaction; however, our understanding is limited because of the lack of information on the C. roseus genome. In this study, the whole-transcriptome profiles from healthy flowers (HFs) and stage 4 (S4) PnWB-infected leafy flowers of C. roseus were investigated using next-generation sequencing (NGS). More than 60,000 contigs were generated using a de novo assembly approach, and 34.2% of the contigs (20,711 genes) were annotated as putative genes through name-calling, open reading frame determination and gene ontology analyses. Furthermore, a customized microarray based on this sequence information was designed and used to analyze samples further at various stages of PnWB infection. In the NGS profile, 87.8% of the genes showed expression levels that were consistent with those in the microarray profiles, suggesting that accurate gene expression levels can be detected using NGS. The data revealed that defense-related and flowering gene expression levels were altered in S4 PnWB-infected leafy flowers, indicating that the immunity and reproductive stages of C. roseus were compromised. The network analysis suggested that the expression levels of >1,000 candidate genes were highly associated with CrSVP1/2 and CrFT expression, which might be crucial in the leafy flower transition. In conclusion, this study provides a new perspective for understanding plant pathology and the mechanisms underlying the leafy flowering transition caused by host-pathogen interactions through analyzing bioinformatics data obtained using a powerful, rapid high-throughput technique.

  19. Suppression of aggressive strains of 'Candidatus phytoplasma mali' by mild strains in Catharanthus roseus and Nicotiana occidentalis and indication of similar action in apple trees.

    Science.gov (United States)

    Schneider, Bernd; Sule, Sandor; Jelkmann, Wilhelm; Seemüller, Erich

    2014-05-01

    To study antagonistic interactions of 'Candidatus Phytoplasma mali' strains, graft inoculation of Catharanthus roseus and Nicotiana occidentalis was performed with mild strains 1/93Vin and 1/93Tab as suppressors and three aggressive strains as challengers. Inoculation of the suppressors was carried out in either the cross-protection modus prior to grafting of the challengers or by co-inoculating suppressors and challengers. Monitoring using multiplex real-time polymerase chain reaction assays revealed that, in long-term cross-protection trials with C. roseus, suppressor 1/93Vin was present in all root and randomly collected stem samples over the entire observation period. In contrast, the challengers were never detected in such stem samples and rarely in the roots. Following simultaneous inoculation, the suppressor successively colonized all stem and root regions whereas detection of challenger AT steadily decreased. However, this strain remained detectable in up to 13 and 27% of stem and root samples, respectively. The cross-protection trials with N. occidentalis yielded results similar to that of the cross-protection experiments with C. roseus. Comparison of the symptomatology of infected apple trees with the presence of putatively suppressive strains indicated that suppression of severe strains also occurs in apple. Phylogenetic analysis using a variable fragment of AAA+ ATPase gene AP460 of 'Ca. P. mali' revealed that suppressors 1/93Vin and 1/93Tab, together with several other mild strains maintained in apple, cluster distantly from obviously nonsuppressive strains that were predominantly highly virulent.

  20. AKT pathway genes define 5 prognostic subgroups in glioblastoma.

    Directory of Open Access Journals (Sweden)

    Anna Joy

    Full Text Available Activity of GFR/PI3K/AKT pathway inhibitors in glioblastoma clinical trials has not been robust. We hypothesized variations in the pathway between tumors contribute to poor response. We clustered GBM based on AKT pathway genes and discovered new subtypes then characterized their clinical and molecular features. There are at least 5 GBM AKT subtypes having distinct DNA copy number alterations, enrichment in oncogenes and tumor suppressor genes and patterns of expression for PI3K/AKT/mTOR signaling components. Gene Ontology terms indicate a different cell of origin or dominant phenotype for each subgroup. Evidence suggests one subtype is very sensitive to BCNU or CCNU (median survival 5.8 vs. 1.5 years; BCNU/CCNU vs other treatments; respectively. AKT subtyping advances previous approaches by revealing additional subgroups with unique clinical and molecular features. Evidence indicates it is a predictive marker for response to BCNU or CCNU and PI3K/AKT/mTOR pathway inhibitors. We anticipate Akt subtyping may help stratify patients for clinical trials and augment discovery of class-specific therapeutic targets.

  1. AKT Pathway Genes Define 5 Prognostic Subgroups in Glioblastoma

    Science.gov (United States)

    Smirnov, Ivan; Reiser, Mark; Misra, Anjan; Shapiro, William R.; Mills, Gordon B.; Kim, Seungchan; Feuerstein, Burt G.

    2014-01-01

    Activity of GFR/PI3K/AKT pathway inhibitors in glioblastoma clinical trials has not been robust. We hypothesized variations in the pathway between tumors contribute to poor response. We clustered GBM based on AKT pathway genes and discovered new subtypes then characterized their clinical and molecular features. There are at least 5 GBM AKT subtypes having distinct DNA copy number alterations, enrichment in oncogenes and tumor suppressor genes and patterns of expression for PI3K/AKT/mTOR signaling components. Gene Ontology terms indicate a different cell of origin or dominant phenotype for each subgroup. Evidence suggests one subtype is very sensitive to BCNU or CCNU (median survival 5.8 vs. 1.5 years; BCNU/CCNU vs other treatments; respectively). AKT subtyping advances previous approaches by revealing additional subgroups with unique clinical and molecular features. Evidence indicates it is a predictive marker for response to BCNU or CCNU and PI3K/AKT/mTOR pathway inhibitors. We anticipate Akt subtyping may help stratify patients for clinical trials and augment discovery of class-specific therapeutic targets. PMID:24984002

  2. Evaluation of Lymphocyte Subgroups in Children With Down Syndrome.

    Science.gov (United States)

    Yılmaz, Cahide; Doğan, Murat; Başarslan, Fatmagül; Yılmaz, Nebi; Yuca, Sevil; Bulan, Keziban; Kaya, Avni; Çaksen, Hüseyin

    2015-09-01

    In this study, lymphocyte subgroups including blood CD3, CD4, CD8, CD4/CD8, CD19, and CD16.56 values were analyzed in children with Down syndrome (DS). The study includes 85 children with DS, followed at Department of Pediatrics, Faculty of Medicine, Yüzüncü Yil University and 64 healthy age-matched control participants. Blood CD3, CD4, CD8, CD4/CD8, CD19, and CD16.56 values were examined in both the groups. Significantly decreased blood CD3, CD4, and CD19 values were found in the study group (P < .05) when compared with the control group. In conclusion, we would like to emphasize that blood CD3, CD4, and CD19 levels were found to be decreased in children with DS. Based on these finding, we think that these decreased lymphocyte subgroups might be responsible for increased susceptibility to infections in children with DS. © The Author(s) 2013.

  3. AKT pathway genes define 5 prognostic subgroups in glioblastoma.

    Science.gov (United States)

    Joy, Anna; Ramesh, Archana; Smirnov, Ivan; Reiser, Mark; Misra, Anjan; Shapiro, William R; Mills, Gordon B; Kim, Seungchan; Feuerstein, Burt G

    2014-01-01

    Activity of GFR/PI3K/AKT pathway inhibitors in glioblastoma clinical trials has not been robust. We hypothesized variations in the pathway between tumors contribute to poor response. We clustered GBM based on AKT pathway genes and discovered new subtypes then characterized their clinical and molecular features. There are at least 5 GBM AKT subtypes having distinct DNA copy number alterations, enrichment in oncogenes and tumor suppressor genes and patterns of expression for PI3K/AKT/mTOR signaling components. Gene Ontology terms indicate a different cell of origin or dominant phenotype for each subgroup. Evidence suggests one subtype is very sensitive to BCNU or CCNU (median survival 5.8 vs. 1.5 years; BCNU/CCNU vs other treatments; respectively). AKT subtyping advances previous approaches by revealing additional subgroups with unique clinical and molecular features. Evidence indicates it is a predictive marker for response to BCNU or CCNU and PI3K/AKT/mTOR pathway inhibitors. We anticipate Akt subtyping may help stratify patients for clinical trials and augment discovery of class-specific therapeutic targets.

  4. Discovery-based protein expression profiling identifies distinct subgroups and pathways in leiomyosarcomas

    DEFF Research Database (Denmark)

    Kirik, Ufuk; Hansson, Karin; Krogh, Morten

    2014-01-01

    subgroups within the leiomyosarcomas with distinct protein expression patterns. Pathways analysis indicates that key biologic nodes like apoptosis, cytoskeleton remodeling, and telomere regulation are differentially regulated among these subgroups. Finally, investigating the similarities between protein...

  5. An overview of statistical planning to address subgroups in confirmatory clinical trials.

    Science.gov (United States)

    Koch, Gary G; Schwartz, Todd A

    2014-01-01

    The effects of treatments within demographic and clinical subgroups of patients are of major interest in most confirmatory clinical trials. Potential factors for defining subgroups include gender, age, disease severity, and geographic region. A major statistical issue for the interpretation of treatment comparisons for subgroups is whether the role of a subgroup is inferential, supportive, or exploratory through respectively corresponding to a primary, key secondary, or hypothesis-generating assessment. This article discusses statistical planning to control type 1 error for the multiple comparisons that correspond to the scope of prespecified inferential subgroups, and it provides some suggestions for addressing the type 2 error that can pertain to prespecified supportive subgroups. Treatment comparisons for exploratory subgroups without a priori specification should always have a very cautious interpretation that accounts for how random variation can influence their pattern of results, although the suggested methods for supportive subgroups can be helpful in this light.

  6. Cumulative subgroup analysis to reduce waste in clinical research for individualised medicine.

    Science.gov (United States)

    Song, Fujian; Bachmann, Max O

    2016-12-15

    Although subgroup analyses in clinical trials may provide evidence for individualised medicine, their conduct and interpretation remain controversial. Subgroup effect can be defined as the difference in treatment effect across patient subgroups. Cumulative subgroup analysis refers to a series of repeated pooling of subgroup effects after adding data from each of related trials chronologically, to investigate the accumulating evidence for subgroup effects. We illustrated the clinical relevance of cumulative subgroup analysis in two case studies using data from published individual patient data (IPD) meta-analyses. Computer simulations were also conducted to examine the statistical properties of cumulative subgroup analysis. In case study 1, an IPD meta-analysis of 10 randomised trials (RCTs) on beta blockers for heart failure reported significant interaction of treatment effects with baseline rhythm. Cumulative subgroup analysis could have detected the subgroup effect 15 years earlier, with five fewer trials and 71% less patients, than the IPD meta-analysis which first reported it. Case study 2 involved an IPD meta-analysis of 11 RCTs on treatments for pulmonary arterial hypertension that reported significant subgroup effect by aetiology. Cumulative subgroup analysis could have detected the subgroup effect 6 years earlier, with three fewer trials and 40% less patients than the IPD meta-analysis. Computer simulations have indicated that cumulative subgroup analysis increases the statistical power and is not associated with inflated false positives. To reduce waste of research data, subgroup analyses in clinical trials should be more widely conducted and adequately reported so that cumulative subgroup analyses could be timely performed to inform clinical practice and further research.

  7. Does a subgroup of postpolio patients need different management?

    Science.gov (United States)

    Bridgens, Ruth

    2015-07-01

    Throughout the 30 years of postpolio syndrome (PPS) research, there have been many puzzling anomalies in the data and not enough information to make sense of them. It is therefore welcome that Winberg et al have examined physical activity in relation to life satisfaction, sex and age. They hypothesized that activity would decrease with age and found the opposite. This result is not so surprising as Ostlund et al found that vitality was associated with older age and that younger age was associated with more pain, increasing physical fatigue, decreasing sleep quality and reducing activity. This commentary will examine past postpolio research with unexpected results in order to describe a subgroup of patients who may be more susceptible to overusing muscles and have particular exercise and activity needs. Copyright © 2015 Elsevier Inc. All rights reserved.

  8. Pain Drawings Improve Subgrouping of Low Back Pain Patients.

    Science.gov (United States)

    Hüllemann, Philipp; Keller, Thomas; Kabelitz, Maria; Freynhagen, Rainer; Tölle, Thomas; Baron, Ralf

    2017-03-01

    Subgrouping of low back pain (LBP) patients may be improved when pain drawings are combined with the painDETECT (PD-Q) questionnaire. We hypothesized that (1) different LBP subgroups determined by their pain radiation show different clinical patterns and (2) the occurrence of neuropathic symptoms depends on pain radiation. A total of 19,263 acute ( 3 months) LBP patients were allocated prospectively into 4 groups based on the location of pain drawings on a manikin and compared regarding neuropathic pain components, functionality, depression, pain intensity, and surgical interventions. All items were investigated at baseline and follow-up visits. Group I was composed of patients with axial LBP without radiating pain; group II, LBP with radiation into the thigh; group III, LBP with radiation into the shank; and group IV, LBP with radiation into the feet. Side-dependent pain radiation was assessed additionally. Depression, functionality, and pain intensity showed no clinically relevant differences, whereas PD-Q scores and the probability to rate positive for neuropathic pain increased with more distally radiating pain. Surgery and medication intake were most frequent in group IV. Follow-up analyses showed that only axial LBP became more neuropathic, whereas pain intensity decreased over time. Radicular patterns of pain drawings in LBP patients indicate severe pain conditions with the most neuropathic components, while axial LBP has the fewest. For the categorization of LBP, pain drawings help explain the underlying mechanism of pain, which might further improve mechanism-based treatment when used in clinical routines and research. © 2016 World Institute of Pain.

  9. Dysexecutive versus amnestic Alzheimer disease subgroups: analysis of demographic, genetic, and vascular factors.

    Science.gov (United States)

    Mez, Jesse; Cosentino, Stephanie; Brickman, Adam M; Huey, Edward D; Manly, Jennifer J; Mayeux, Richard

    2013-01-01

    The objective of this study was to compare the demographic and vascular characteristics and APOE genotypes of a dysexecutive subgroup of Alzheimer disease (AD) with an amnestic subgroup of AD early in the disease course. A total of 2224 participants from the National Alzheimer's Coordinating Center database who carried a diagnosis of mild cognitive impairment (n=1188) or mild AD (clinical dementia rating ≤1) (n=1036) were included in this study. A subset of the mild cognitive impairment (n=61) and mild AD (n=79) participants underwent an autopsy. A dysexecutive subgroup (n=587) was defined as having executive performance >1 SD worse than memory performance, and an amnestic subgroup (n=549) was defined conversely. Among the autopsy subset, the odds of an AD pathologic diagnosis were compared in the 2 subgroups. The demographics, APOE[Latin Small Letter Open E]4 status, and vascular risk factors were compared in the 2 subgroups. Among the autopsy subset, the odds of having an AD pathologic diagnosis did not differ between the dysexecutive and amnestic subgroups. Under an additive model, participants in the dysexecutive subgroup possessed the APOE[Latin Small Letter Open E]4 allele less frequently compared with those in the amnestic subgroup. The dysexecutive subgroup had a history of hypertension less frequently compared with the amnestic subgroup. These distinct characteristics add to accumulating evidence that a dysexecutive subgroup of AD may have a unique underlying pathophysiology.

  10. How can latent trajectories of back pain be translated into defined subgroups?

    DEFF Research Database (Denmark)

    Kongsted, Alice; Hestbæk, Lise; Kent, Peter

    2017-01-01

    descriptive definitions, as a way to apply the same definitions of mutually exclusive subgroups across populations. In this study, we investigated if the course trajectories of two LBP cohorts fitted with previously suggested trajectory subgroup definitions, how distinctly different these subgroups were......BACKGROUND: Similar types of trajectory patterns have been identified by Latent Class Analyses (LCA) across multiple low back pain (LBP) cohorts, but these patterns are impractical to apply to new cohorts or individual patients. It would be useful to be able to identify trajectory subgroups from......, and if the subgroup definitions matched with LCA-derived patterns. METHODS: Weekly measures of LBP intensity and frequency during 1 year were available from two clinical cohorts. We applied definitions of 16 possible trajectory subgroups to these observations and calculated the prevalence of the subgroups...

  11. Topography and Volcanology of the Huangtsuishan Volcano Subgroup, Northern Taiwan

    Directory of Open Access Journals (Sweden)

    Yu-Ming Lai

    2010-01-01

    Full Text Available Combining the shaded relief topography model and the slope map from the Digital Terrain Model (DTM images, toporaphical map, field occurrences and petrography, the volcanic sequences of the Huangtsuishan Volcano Subgroup (HVS can be constructed. Two types of volcanic centers can be identified in this area. One is the Tachienhou volcanic dome, which may be located in the center of an older caldera. The other is the Huangtsui composite volcano, which is composed of interbedding lava flows and pyroclastic deposits with a volcanic crater named the Huangtsui pond at the summit. Eight lava plateaus radiated from Mts. Huangtsui and Tachienhou to the north and the east can be distinguished based on the DTM images. The volcanic deposits are comprised of four lithofacies, the lava flows, pyroclastic breccias, tuffs and lahars on the base of field occurrences. At least thirteen layers of lava flow, named the H1 to H13 can be recognized in the HVS and can be reconstructed and categorized into four stages. An old and large volcano erupted lava flows to form the products of stages one and two, then collapsed to form a caldera with a dome for the third stage. The latest stage of lava flow was poured out from the Huangtsui volcano, which formed a crater at the summit.

  12. Personality style and impulsivity as determinants of suicidal subgroups.

    Science.gov (United States)

    Fazaa, Norman; Page, Stewart

    2009-01-01

    Studies on suicide have often been inadequate in the sense of failing to understand or conceptualize the dynamics of suicidal behavior from a comprehensive theoretical basis. The aim of the present study was therefore to examine Blatt's theory of Dependent and Self-critical personality dimensions (Blatt, 1974, Blatt & Shichman, 1983) in the context of actual suicidal behavior, and also to utilize these dimensions to facilitate our understanding of suicidal action. Ninety-six undergraduate students who had attempted suicide in the past were administered a series of measures related to suicidal behavior, involving impulsivity, intent, and lethality. Participants were also identified as Dependent or Self-critical in their basic personality orientation. Dependents and Self-critics engaged in contrasting suicidal behaviors along several parameters, with Self-critical individuals generally posing greater risk. These differences were congruent with Blatt's theoretical framework. Implications for suicide risk assessment, management, and treatment are discussed, with special reference to the importance of identifying distinctive suicidal subgroups identified by Dependent and Self-critical personality dimensions.

  13. Evidence of separate subgroups of juvenile southern bluefin tuna.

    Science.gov (United States)

    Chambers, Mark S; Sidhu, Leesa A; O'Neill, Ben; Sibanda, Nokuthaba

    2017-11-01

    Archival tagging studies of southern bluefin tuna (SBT , Thunnus maccoyii) have revealed that juveniles residing in the Great Australian Bight (GAB) over the austral summer undertake seasonal cyclic migrations to the southeast Indian Ocean and the Tasman Sea during winter. However, there remains disagreement about the extent of mixing between juvenile SBT regularly caught by longline fleets south of Africa and those observed in the GAB. Some researchers have argued that archival tag recoveries indicate most juveniles reside in the GAB over the austral summer. Others have suggested that recoveries of conventional and archival tags are better explained by a juvenile population consisting of separate groups on the eastern and western sides of the Indian Ocean with limited intermixing. We present analyses of catch and tag recovery data and re-examine archival tagging studies. The evidence provided strongly favors the hypothesis of separate juvenile subgroups, or contingents, with limited intermixing. We draw some tentative conclusions about the nature of the putative contingents and discuss some implications of these findings for the interpretation of existing datasets and future research priorities. We also provide the first evidence that the migration choices of juveniles that summer in the GAB are influenced by fidelity to winter feeding grounds and suggest this helps explain the collapse of the surface fishery off New South Wales in the 1980s.

  14. Resonance Elastic Scattering and Interference Effects Treatments in Subgroup Method

    Directory of Open Access Journals (Sweden)

    Yunzhao Li

    2016-04-01

    Full Text Available Based on the resonance integral (RI tables produced by the NJOY program, the conventional subgroup method usually ignores both the resonance elastic scattering and the resonance interference effects. In this paper, on one hand, to correct the resonance elastic scattering effect, RI tables are regenerated by using the Monte Carlo code, OpenMC, which employs the Doppler broadening rejection correction method for the resonance elastic scattering. On the other hand, a fast resonance interference factor method is proposed to efficiently handle the resonance interference effect. Encouraging conclusions have been indicated by the numerical results. (1 For a hot full power pressurized water reactor fuel pin-cell, an error of about +200 percent mille could be introduced by neglecting the resonance elastic scattering effect. By contrast, the approach employed in this paper can eliminate the error. (2 The fast resonance interference factor method possesses higher precision and higher efficiency than the conventional Bondarenko iteration method. Correspondingly, if the fast resonance interference factor method proposed in this paper is employed, the kinf can be improved by ∼100 percent mille with a speedup of about 4.56.

  15. Matching mice to malignancy: molecular subgroups and models of medulloblastoma

    Science.gov (United States)

    Lau, Jasmine; Schmidt, Christin; Markant, Shirley L.; Taylor, Michael D.; Wechsler-Reya, Robert J.

    2012-01-01

    Introduction Medulloblastoma, the largest group of embryonal brain tumors, has historically been classified into five variants based on histopathology. More recently, epigenetic and transcriptional analyses of primary tumors have sub-classified medulloblastoma into four to six subgroups, most of which are incongruous with histopathological classification. Discussion Improved stratification is required for prognosis and development of targeted treatment strategies, to maximize cure and minimize adverse effects. Several mouse models of medulloblastoma have contributed both to an improved understanding of progression and to developmental therapeutics. In this review, we summarize the classification of human medulloblastoma subtypes based on histopathology and molecular features. We describe existing genetically engineered mouse models, compare these to human disease, and discuss the utility of mouse models for developmental therapeutics. Just as accurate knowledge of the correct molecular subtype of medulloblastoma is critical to the development of targeted therapy in patients, we propose that accurate modeling of each subtype of medulloblastoma in mice will be necessary for preclinical evaluation and optimization of those targeted therapies. PMID:22315164

  16. Challenges in identifying asthma subgroups using unsupervised statistical learning techniques.

    Science.gov (United States)

    Prosperi, Mattia C F; Sahiner, Umit M; Belgrave, Danielle; Sackesen, Cansin; Buchan, Iain E; Simpson, Angela; Yavuz, Tolga S; Kalayci, Omer; Custovic, Adnan

    2013-12-01

    Unsupervised statistical learning techniques, such as exploratory factor analysis (EFA) and hierarchical clustering (HC), have been used to identify asthma phenotypes, with partly consistent results. Some of the inconsistency is caused by the variable selection and demographic and clinical differences among study populations. To investigate the effects of the choice of statistical method and different preparations of data on the clustering results; and to relate these to disease severity. Several variants of EFA and HC were applied and compared using various sets of variables and different encodings and transformations within a dataset of 383 children with asthma. Variables included lung function, inflammatory and allergy markers, family history, environmental exposures, and medications. Clusters and original variables were related to asthma severity (logistic regression and Bayesian network analysis). EFA identified five components (eigenvalues ≥ 1) explaining 35% of the overall variance. Variations of the HC (as linkage-distance functions) did not affect the cluster inference; however, using different variable encodings and transformations did. The derived clusters predicted asthma severity less than the original variables. Prognostic factors of severity were medication usage, current symptoms, lung function, paternal asthma, body mass index, and age of asthma onset. Bayesian networks indicated conditional dependence among variables. The use of different unsupervised statistical learning methods and different variable sets and encodings can lead to multiple and inconsistent subgroupings of asthma, not necessarily correlated with severity. The search for asthma phenotypes needs more careful selection of markers, consistent across different study populations, and more cautious interpretation of results from unsupervised learning.

  17. Subgroup analyses in cost-effectiveness analyses to support health technology assessments.

    Science.gov (United States)

    Fletcher, Christine; Chuang-Stein, Christy; Paget, Marie-Ange; Reid, Carol; Hawkins, Neil

    2014-01-01

    'Success' in drug development is bringing to patients a new medicine that has an acceptable benefit-risk profile and that is also cost-effective. Cost-effectiveness means that the incremental clinical benefit is deemed worth paying for by a healthcare system, and it has an important role in enabling manufacturers to obtain new medicines to patients as soon as possible following regulatory approval. Subgroup analyses are increasingly being utilised by decision-makers in the determination of the cost-effectiveness of new medicines when making recommendations. This paper highlights the statistical considerations when using subgroup analyses to support cost-effectiveness for a health technology assessment. The key principles recommended for subgroup analyses supporting clinical effectiveness published by Paget et al. are evaluated with respect to subgroup analyses supporting cost-effectiveness. A health technology assessment case study is included to highlight the importance of subgroup analyses when incorporated into cost-effectiveness analyses. In summary, we recommend planning subgroup analyses for cost-effectiveness analyses early in the drug development process and adhering to good statistical principles when using subgroup analyses in this context. In particular, we consider it important to provide transparency in how subgroups are defined, be able to demonstrate the robustness of the subgroup results and be able to quantify the uncertainty in the subgroup analyses of cost-effectiveness. Copyright © 2014 John Wiley & Sons, Ltd.

  18. Stratification of randomization is not required for a pre-specified subgroup analysis.

    Science.gov (United States)

    Kaiser, Lee D

    2013-01-01

    Published literature and regulatory agency guidance documents provide conflicting recommendations as to whether a pre-specified subgroup analysis also requires for its validity that the study employ randomization that is stratified on subgroup membership. This is an important issue, as subgroup analyses are often required to demonstrate efficacy in the development of drugs with a companion diagnostic. Here, it is shown, for typical randomization methods, that the fraction of patients in the subgroup given experimental treatment matches, on average, the target fraction in the entire study. Also, mean covariate values are balanced, on average, between treatment arms in the subgroup, and it is argued that the variance in covariate imbalance between treatment arms in the subgroup is at worst only slightly increased versus a subgroup-stratified randomization method. Finally, in an analysis of variance setting, a least-squares treatment effect estimator within the subgroup is shown to be unbiased whether or not the randomization is stratified on subgroup membership. Thus, a requirement that a study be stratified on subgroup membership would place an artificial roadblock to innovation and the goals of personalized healthcare. Copyright © 2012 John Wiley & Sons, Ltd.

  19. Data processing of qualitative results from an interlaboratory comparison for the detection of "Flavescence dorée" phytoplasma: How the use of statistics can improve the reliability of the method validation process in plant pathology.

    Science.gov (United States)

    Chabirand, Aude; Loiseau, Marianne; Renaudin, Isabelle; Poliakoff, Françoise

    2017-01-01

    A working group established in the framework of the EUPHRESCO European collaborative project aimed to compare and validate diagnostic protocols for the detection of "Flavescence dorée" (FD) phytoplasma in grapevines. Seven molecular protocols were compared in an interlaboratory test performance study where each laboratory had to analyze the same panel of samples consisting of DNA extracts prepared by the organizing laboratory. The tested molecular methods consisted of universal and group-specific real-time and end-point nested PCR tests. Different statistical approaches were applied to this collaborative study. Firstly, there was the standard statistical approach consisting in analyzing samples which are known to be positive and samples which are known to be negative and reporting the proportion of false-positive and false-negative results to respectively calculate diagnostic specificity and sensitivity. This approach was supplemented by the calculation of repeatability and reproducibility for qualitative methods based on the notions of accordance and concordance. Other new approaches were also implemented, based, on the one hand, on the probability of detection model, and, on the other hand, on Bayes' theorem. These various statistical approaches are complementary and give consistent results. Their combination, and in particular, the introduction of new statistical approaches give overall information on the performance and limitations of the different methods, and are particularly useful for selecting the most appropriate detection scheme with regards to the prevalence of the pathogen. Three real-time PCR protocols (methods M4, M5 and M6 respectively developed by Hren (2007), Pelletier (2009) and under patent oligonucleotides) achieved the highest levels of performance for FD phytoplasma detection. This paper also addresses the issue of indeterminate results and the identification of outlier results. The statistical tools presented in this paper and their

  20. Data processing of qualitative results from an interlaboratory comparison for the detection of "Flavescence dorée" phytoplasma: How the use of statistics can improve the reliability of the method validation process in plant pathology.

    Directory of Open Access Journals (Sweden)

    Aude Chabirand

    Full Text Available A working group established in the framework of the EUPHRESCO European collaborative project aimed to compare and validate diagnostic protocols for the detection of "Flavescence dorée" (FD phytoplasma in grapevines. Seven molecular protocols were compared in an interlaboratory test performance study where each laboratory had to analyze the same panel of samples consisting of DNA extracts prepared by the organizing laboratory. The tested molecular methods consisted of universal and group-specific real-time and end-point nested PCR tests. Different statistical approaches were applied to this collaborative study. Firstly, there was the standard statistical approach consisting in analyzing samples which are known to be positive and samples which are known to be negative and reporting the proportion of false-positive and false-negative results to respectively calculate diagnostic specificity and sensitivity. This approach was supplemented by the calculation of repeatability and reproducibility for qualitative methods based on the notions of accordance and concordance. Other new approaches were also implemented, based, on the one hand, on the probability of detection model, and, on the other hand, on Bayes' theorem. These various statistical approaches are complementary and give consistent results. Their combination, and in particular, the introduction of new statistical approaches give overall information on the performance and limitations of the different methods, and are particularly useful for selecting the most appropriate detection scheme with regards to the prevalence of the pathogen. Three real-time PCR protocols (methods M4, M5 and M6 respectively developed by Hren (2007, Pelletier (2009 and under patent oligonucleotides achieved the highest levels of performance for FD phytoplasma detection. This paper also addresses the issue of indeterminate results and the identification of outlier results. The statistical tools presented in this paper

  1. Low Back Pain Subgroups using Fear-Avoidance Model Measures: Results of a Cluster Analysis

    Science.gov (United States)

    Beneciuk, Jason M.; Robinson, Michael E.; George, Steven Z.

    2012-01-01

    Objectives The purpose of this secondary analysis was to test the hypothesis that an empirically derived psychological subgrouping scheme based on multiple Fear-Avoidance Model (FAM) constructs would provide additional capabilities for clinical outcomes in comparison to a single FAM construct. Methods Patients (n = 108) with acute or sub-acute low back pain (LBP) enrolled in a clinical trial comparing behavioral physical therapy interventions to classification based physical therapy completed baseline questionnaires for pain catastrophizing (PCS), fear-avoidance beliefs (FABQ-PA, FABQ-W), and patient-specific fear (FDAQ). Clinical outcomes were pain intensity and disability measured at baseline, 4-weeks, and 6-months. A hierarchical agglomerative cluster analysis was used to create distinct cluster profiles among FAM measures and discriminant analysis was used to interpret clusters. Changes in clinical outcomes were investigated with repeated measures ANOVA and differences in results based on cluster membership were compared to FABQ-PA subgrouping used in the original trial. Results Three distinct FAM subgroups (Low Risk, High Specific Fear, and High Fear & Catastrophizing) emerged from cluster analysis. Subgroups differed on baseline pain and disability (p’s<.01) with the High Fear & Catastrophizing subgroup associated with greater pain than the Low Risk subgroup (p<.01) and the greatest disability (p’s<.05). Subgroup × time interactions were detected for both pain and disability (p’s<.05) with the High Fear & Catastrophizing subgroup reporting greater changes in pain and disability than other subgroups (p’s<.05). In contrast, FABQ-PA subgroups used in the original trial were not associated with interactions for clinical outcomes. Discussion These data suggest that subgrouping based on multiple FAM measures may provide additional information on clinical outcomes in comparison to determining subgroup status by FABQ-PA alone. Subgrouping methods for

  2. Subgroup report on hard x-ray microprobes

    Energy Technology Data Exchange (ETDEWEB)

    Ice, G.E. [Oak Ridge National Lab., TN (United States); Barbee, T.; Bionta, R. [Lawrence Livermore National Lab., CA (United States); Howells, M.; Thompson, A.C. [Lawrence Berkeley Lab., CA (United States); Yun, W. [Argonne National Lab., IL (United States)

    1994-09-01

    The increasing availability of synchrotron x-ray sources has stimulated the development of advanced hard x-ray (E{>=}5 keV) microprobes. New x-ray optics have been demonstrated which show promise for achieving intense submicron hard x-ray probes. These probes will be used for extraordinary elemental detection by x-ray fluorescence/absorption and for microdiffraction to identify phase and strain. The inherent elemental and crystallographic sensitivity of an x-ray microprobe and its inherently nondestructive and penetrating nature makes the development of an advanced hard x-ray microprobe an important national goal. In this workshop state-of-the-art hard x-ray microprobe optics were described and future directions were discussed. Gene Ice, Oak Ridge National Laboratory (ORNL), presented an overview of the current status of hard x-ray microprobe optics and described the use of crystal spectrometers to improve minimum detectable limits in fluorescent microprobe experiments. Al Thompson, Lawrence Berkeley Laboratory (LBL), described work at the Center for X-ray Optics to develop a hard x-ray microprobe based on Kirkpatrick-Baez (KB) optics. Al Thompson also showed the results of some experimental measurements with their KB optics. Malcolm Howells presented a method for bending elliptical mirrors and Troy Barbee commented on the use of graded d spacings to achieve highest efficiency in KB multilayer microfocusing. Richard Bionta, Lawrence Livermore National Laboratory (LLNL), described the development of the first hard x-ray zone plates and future promise of so called {open_quotes}jelly roll{close_quotes} or sputter slice zone plates. Wenbing Yun, Argonne National Laboratory (ANL), described characterization of jelly roll and lithographically produced zone plates and described the application of zone plates to focus extremely narrow bandwidths by nuclear resonance. This report summarizes the presentations of the workshop subgroup on hard x-ray microprobes.

  3. Balance Impairments in Different Subgroups of Patients With Migraine.

    Science.gov (United States)

    Carvalho, Gabriela F; Bonato, Paolo; Florencio, Lidiane L; Pinheiro, Carina F; Dach, Fabiola; Bigal, Marcelo E; Bevilaqua-Grossi, Debora

    2017-03-01

    Patients with migraine often experience balance impairments. However, the relationship between clinical features - like aura and chronicity - and the severity of balance impairments is not well established. The objective of this study was to assess balance impairments in different subgroups of migraine patients. One hundred five subjects diagnosed according to the ICHD-III were recruited in the study. They were uniformly distributed among three groups: migraine with aura, migraine without aura, and chronic migraine. Thirty-five controls were also recruited in the study. Balance impairments were assessed in all subjects via the modified Sensory Organization test and the Limits of Stability test. The results in the four groups were compared using ANCOVA tests with age, BMI, presence of dizziness, level of physical activity, time of migraine onset, and medication intake as covariates. Subjects in the migraine with aura and the chronic migraine groups showed poorer balance control than control subjects in three of the four conditions tested using the modified Sensory Organization test: FirmCE: CG: 1.5 cm2 , 95%CI 1.3 to 1.7; M: 2.1 cm2 , 95%CI 1.6 to 2.6; MA: 4.5 cm2 , 95%CI 3.2 to 5.8; CM: 4.5 cm2 , 95%CI 3.0 to 6.0; P migraine without aura group (P migraine groups were found in the reaction time, movement velocity, endpoint excursion, and maximal excursion parameters (P  .05). There is evidence of balance control impairments in subjects with all subtypes of migraine compared to control subjects. The presence of aura and frequent migraine attacks reflect negatively in the postural control performance and may have a significant clinical impact in patients with migraine that should be addressed with appropriate clinical interventions. © 2016 American Headache Society.

  4. Clinical and epidemiological features of acute infantile gastroenteritis associated with human rotavirus subgroups 1 and 2.

    OpenAIRE

    Uhnoo, I; Svensson, L

    1986-01-01

    During a prospective 1-year study rotavirus isolates from 169 children with gastroenteritis were investigated by polyacrylamide gel electrophoresis. A total of 118 (70%) of the strains analyzed contained sufficient viral nucleic acid to give visible electrophoretic patterns; 36% were identified as strains belonging to subgroup 1 (short patterns), and 64% were identified as strains belonging to subgroup 2 (long patterns). The two subgroups cocirculated at equal frequencies during the first 7 m...

  5. Developing the group mind through functional subgrouping: linking systems-centered training (SCT) and interpersonal neurobiology.

    Science.gov (United States)

    Gantt, Susan P; Agazarian, Yvonne M

    2010-10-01

    This article introduces the systems-centered concept of the "group mind" by linking systems-centered thinking and interpersonal neurobiology, building on Siegel's definition of mind as the process of regulating the flow of energy and information. Functional subgrouping, the systems-centered group method for resolving conflicts, discriminates and integrates the flow of energy and information within and between group members, subgroups, and the group-as-a-whole, thus potentiating survival, development, and transformation. This article uses the interpersonal neurobiological framework to discuss functional subgrouping as a tool for developing the group mind: considering how functional subgrouping facilitates emotional regulation, creates a secure relational context, and potentiates neural integration.

  6. Etiological Subgroups of Small-for-Gestational-Age: Differential Neurodevelopmental Outcomes.

    Directory of Open Access Journals (Sweden)

    Xiuhong Li

    Full Text Available It remains unclear why substantial variations in neurodevelopmental outcomes exist within small-for-gestational-age (SGA children. We prospectively compared 5-y neurodevelopmental outcomes across SGA etiological subgroups.Children born SGA (N = 1050 from U.S. Early Childhood Longitudinal Study-Birth Cohort (2001-2007 was divided into etiological subgroups by each of 7 well-established prenatal risk factors. We fit linear regression models to compare 5-y reading, math, gross motor and fine motor scores across SGA subgroups, adjusting for socio-demographic confounders.Compared to singleton SGA subgroup, multiple-birth SGA subgroup had lower mean reading (adjusted mean difference, -4.08 [95% confidence interval, -6.10, -2.06] and math (-2.22 [-3.61, -0.84] scores. These disadvantages in reading and math existed only among multiple-birth SGA subgroup without ovulation stimulation (reading, -4.50 [-6.64, -2.36]; math, -2.91 [-4.37, -1.44], but not among those with ovulation stimulation (reading, -2.33 [-6.24, 1.57]; math 0.63 [-1.86, 3.12]. Compared to singleton SGA subgroup without maternal smoking and inadequate gestational weight gain, singleton SGA subgroup with co-occurrence of maternal smoking and inadequate gestational weight gain (GWG had lower mean reading (-4.81 [-8.50, -1.12] and math (-2.95 [-5.51, -0.38] scores. These differences were not mediated by Apgar score.Multiple-birth SGA subgroups (vs. singleton SGA or singleton SGA subgroup with co-occurrence of smoking and inadequate GWG (vs. singleton SGA subgroup without maternal smoking and inadequate gestational weight gain have poorer cognitive development up to 5 y.

  7. Rapid, reliable, and reproducible molecular sub-grouping of clinical medulloblastoma samples.

    Science.gov (United States)

    Northcott, Paul A; Shih, David J H; Remke, Marc; Cho, Yoon-Jae; Kool, Marcel; Hawkins, Cynthia; Eberhart, Charles G; Dubuc, Adrian; Guettouche, Toumy; Cardentey, Yoslayma; Bouffet, Eric; Pomeroy, Scott L; Marra, Marco; Malkin, David; Rutka, James T; Korshunov, Andrey; Pfister, Stefan; Taylor, Michael D

    2012-04-01

    The diagnosis of medulloblastoma likely encompasses several distinct entities, with recent evidence for the existence of at least four unique molecular subgroups that exhibit distinct genetic, transcriptional, demographic, and clinical features. Assignment of molecular subgroup through routine profiling of high-quality RNA on expression microarrays is likely impractical in the clinical setting. The planning and execution of medulloblastoma clinical trials that stratify by subgroup, or which are targeted to a specific subgroup requires technologies that can be economically, rapidly, reliably, and reproducibly applied to formalin-fixed paraffin embedded (FFPE) specimens. In the current study, we have developed an assay that accurately measures the expression level of 22 medulloblastoma subgroup-specific signature genes (CodeSet) using nanoString nCounter Technology. Comparison of the nanoString assay with Affymetrix expression array data on a training series of 101 medulloblastomas of known subgroup demonstrated a high concordance (Pearson correlation r = 0.86). The assay was validated on a second set of 130 non-overlapping medulloblastomas of known subgroup, correctly assigning 98% (127/130) of tumors to the appropriate subgroup. Reproducibility was demonstrated by repeating the assay in three independent laboratories in Canada, the United States, and Switzerland. Finally, the nanoString assay could confidently predict subgroup in 88% of recent FFPE cases, of which 100% had accurate subgroup assignment. We present an assay based on nanoString technology that is capable of rapidly, reliably, and reproducibly assigning clinical FFPE medulloblastoma samples to their molecular subgroup, and which is highly suited for future medulloblastoma clinical trials.

  8. Identifying Changes in Youth's Subgroup Membership over Time Based on Their Targeted Communication about Substance Use with Parents and Friends

    Science.gov (United States)

    Kam, Jennifer A.

    2011-01-01

    Using latent class/transition analyses, this study: (a) identified subgroups of youth based on their targeted communication about substance use with parents and friends, (b) examined subgroup differences in substance use, and (c) considered changes in subgroup membership over four years. Among 5,874 youth, five subgroups emerged, with parents-only…

  9. Heterogeneity in chronic fatigue syndrome - empirically defined subgroups from the PACE trial.

    Science.gov (United States)

    Williams, T E; Chalder, T; Sharpe, M; White, P D

    2017-06-01

    Chronic fatigue syndrome is likely to be a heterogeneous condition. Previous studies have empirically defined subgroups using combinations of clinical and biological variables. We aimed to explore the heterogeneity of chronic fatigue syndrome. We used baseline data from the PACE trial, which included 640 participants with chronic fatigue syndrome. Variable reduction, using a combination of clinical knowledge and principal component analyses, produced a final dataset of 26 variables for 541 patients. Latent class analysis was then used to empirically define subgroups. The most statistically significant and clinically recognizable model comprised five subgroups. The largest, 'core' subgroup (33% of participants), had relatively low scores across all domains and good self-efficacy. A further three subgroups were defined by: the presence of mood disorders (21%); the presence of features of other functional somatic syndromes (such as fibromyalgia or irritable bowel syndrome) (21%); or by many symptoms - a group which combined features of both of the above (14%). The smallest 'avoidant-inactive' subgroup was characterized by physical inactivity, belief that symptoms were entirely physical in nature, and fear that they indicated harm (11%). Differences in the severity of fatigue and disability provided some discriminative validation of the subgroups. In addition to providing further evidence for the heterogeneity of chronic fatigue syndrome, the subgroups identified may aid future research into the important aetiological factors of specific subtypes of chronic fatigue syndrome and the development of more personalized treatment approaches.

  10. Quality-of-Life Differences among Diagnostic Subgroups of Children Receiving Ventilating Tubes for Otitis Media

    DEFF Research Database (Denmark)

    Heidemann, Christian Hamilton; Lauridsen, Henrik Hein; Kjeldsen, Anette Drøhse

    2015-01-01

    OBJECTIVE: The pathological picture may differ considerably between diagnostic subgroups of children with otitis media receiving ventilating tubes. The aims of this study are to investigate differences in quality of life among diagnostic subgroups of children treated with ventilating tubes and to...

  11. Orienting Schools toward Equity: Subgroup Accountability Pressure and School-Level Responses

    Science.gov (United States)

    Garver, Rachel

    2017-01-01

    This article examines school-level responses to subgroup accountability pressure through an ethnographic case study of a school cited for failing to make adequate yearly progress for student subgroups. Concerns about the calculations and measures used to derive the citation and reservations about acting on accountability data delegitimized the…

  12. Level of evidence for promising subgroup findings in an overall non-significant trial

    NARCIS (Netherlands)

    Tanniou, Julien; van der Tweel, Ingeborg|info:eu-repo/dai/nl/262684438; Teerenstra, S.; Roes, Kit C.B.|info:eu-repo/dai/nl/115147020

    2016-01-01

    In drug development and drug licensing, it sometimes occurs that a new drug does not demonstrate effectiveness for the full study population, but there appears to be benefit in a relevant, pre-defined subgroup. This raises the question, how strong the evidence from such a subgroup is, and which

  13. Measuring English Language Workplace Proficiency across Subgroups: Using CFA Models to Validate Test Score Interpretation

    Science.gov (United States)

    Yoo, Hanwook; Manna, Venessa F.

    2017-01-01

    This study assessed the factor structure of the Test of English for International Communication (TOEIC®) Listening and Reading test, and its invariance across subgroups of test-takers. The subgroups were defined by (a) gender, (b) age, (c) employment status, (d) time spent studying English, and (e) having lived in a country where English is the…

  14. Latent class analysis derived subgroups of low back pain patients - do they have prognostic capacity?

    DEFF Research Database (Denmark)

    Mølgaard Nielsen, Anne; Hestbaek, Lise; Vach, Werner

    2017-01-01

    BACKGROUND: Heterogeneity in patients with low back pain is well recognised and different approaches to subgrouping have been proposed. One statistical technique that is increasingly being used is Latent Class Analysis as it performs subgrouping based on pattern recognition with high accuracy. Pr...

  15. Affiliative Subgroups in Preschool Classrooms: Integrating Constructs and Methods from Social Ethology and Sociometric Traditions.

    Science.gov (United States)

    Santos, António J; Daniel, João R; Fernandes, Carla; Vaughn, Brian E

    2015-01-01

    Recent studies of school-age children and adolescents have used social network analyses to characterize selection and socialization aspects of peer groups. Fewer network studies have been reported for preschool classrooms and many of those have focused on structural descriptions of peer networks, and/or, on selection processes rather than on social functions of subgroup membership. In this study we started by identifying and describing different types of affiliative subgroups (HMP- high mutual proximity, LMP- low mutual proximity, and ungrouped children) in a sample of 240 Portuguese preschool children using nearest neighbor observations. Next, we used additional behavioral observations and sociometric data to show that HMP and LMP subgroups are functionally distinct: HMP subgroups appear to reflect friendship relations, whereas LMP subgroups appear to reflect common social goals, but without strong, within-subgroup dyadic ties. Finally, we examined the longitudinal implications of subgroup membership and show that children classified as HMP in consecutive years had more reciprocated friendships than did children whose subgroup classification changed from LMP or ungrouped to HMP. These results extend previous findings reported for North American peer groups.

  16. Caffeine for Apnea of Prematurity trial: benefits may vary in subgroups

    NARCIS (Netherlands)

    Davis, Peter G.; Schmidt, Barbara; Roberts, Robin S.; Doyle, Lex W.; Asztalos, Elizabeth; Haslam, Ross; Sinha, Sunil; Tin, Win; Schmidt, B.; D'Ilario, J.; Cairnie, J.; Dix, J.; Adams, B.; Faber, B.; Callanan, K.; Davis, N.; Duff, J.; Ford, G.; Golec, L.; Lacy, M.; Hohn, D.; Barnett, C.; Goodchildt, L.; Lontis, R.; Fraser, S.; Keng, J.; Saunders, K.; Opie, G.; Kelly, E.; Bairam, A.; Ferland, S.; Laperriere, L.; Bélanger, S.; St Amand, P.; Blayney, M.; Davis, D.; Frank, J.; Lemyre, L.; Solimano, A.; Singh, A.; Chalmers, M.; Ramsay, K.; Synnes, A.; Whitfield, M.; Rogers, M.; Tomlinson, J.; Offringa, M.; Nuytemans, D.; Vermeulen, E.; Kok, J.; van Wassenaer, A.; Arnon, S.; Chalaf, A.; Regev, R.; Netter, I.; Ohlsson, A.; Nesbitt, K.; O'Brien, K.; Hamilton, A. M.; Sankaran, K.; Morgan, S.; Proctor, P.; LaCorte, M.; LeBlanc, P.; Braithwaite, A.; Golan, A.; Barabi, T.; Goldstein, E.; Reynolds, G.; Dromgool, B.; Meskell, S.; McMillan, D.; Schaab, D.; Spellen, L.; Sauve, R.; Christianson, H.; Anseeuw-Deeks, D.; Alvaro, R.; Chiu, A.; Porter, C.; Turner, G.; Moddemann, D.; Granke, N.; Penner, K.; Mulder, T.; Ghys, A.; van der Hoeven, M.; Clarke, M.; Parfitt, J.; MacLean, H.; Nwaesei, C.; Kuhn, L.; Ryan, H.; Saunders, C.; Schulze, A.; Pudenz, P.; Muller, M.; Lagercrantz, H.; Bhiladvala, M.; Legneval, L.; Herlenius, E.; Matthew, D.; Amos, W.; Tulsiani, S.; Tan-Dy, C.; Turner, M.; Shinwell, E.; Levine, R.; Juster-Reicher, A.; Barrington, K.; Kokkotis, T.; Khairy, M.; Grier, P.; Vachon, J.; Tin, W.; Fritz, S.; Walti, H.; Royer, D.; Halliday, H.; Millar, D.; Berry, A.; Mayes, C.; Cummings, C.; Fahnenstich, H.; Philipp, K.; Tillmann, B.; Weber, P.; Canning, R.; Wariyar, U.; Embleton, N.; Bucher, H.-U.; Fauchere, J.-C.; Pfister, R.; Launoy, V.; Huppi, P.; Poets, C.; Urschitz-Duprat, P.; Davis, P.; Doyle, L. W.; Gent, M.; Fraser, W.; Hey, E.; Perlman, M.; Thorpe, K.; Gray, S.; Roberts, R. S.; Chambers, C.; Costantini, L.; McGean, L.; Scapinello, L.

    2010-01-01

    OBJECTIVE: To determine whether the benefits of caffeine vary in three subgroups of 2006 participants in the Caffeine for Apnea of Prematurity (CAP) trial. STUDY DESIGN: Post-hoc subgroup analyses were performed on the basis of: (1) indication for commencement of study drug: treat apnea, prevent

  17. Nilpotency and Theory of L-Subgroups of an L-Group

    Directory of Open Access Journals (Sweden)

    Naseem Ajmal

    2014-03-01

    Full Text Available In this paper, the notion of commutator is modified and extended to L-setting. Also, the notion of descending central series is introduced which is used to formulate the important notion of nilpotent L-subgroup of an L-group. Moreover, the level subset characterization for the notion of nilpotent L-subgroup is provided.

  18. Subgrouping of Readers Based on Performance Measures: A Latent Profile Analysis

    Science.gov (United States)

    Wolff, Ulrika

    2010-01-01

    By using latent profile analysis eight stable and interpretable subgroups of readers were identified. The basis for subgrouping was different performance measures with four aspects of reading in focus: reading of continuous texts, reading of document texts, word reading and reading speed. Participants were 9-year-old Swedish students included in…

  19. Identidade molecular dos fitoplasmas associados aos enfezamentos do tomateiro e da berinjela com base na análise do gene 16S rDNA Molecular identity of the phytoplasma associated to stunting of tomato and eggplant on the basis of analyses of the 16S rDNA

    Directory of Open Access Journals (Sweden)

    Ana Paula de Oliveira Amaral Mello

    2007-09-01

    Full Text Available Doenças de hortaliças de ocorrência no território brasileiro e em outras áreas do mundo têm sido associadas a diversos fitoplasmas. Na região de Piracicaba-SP e Bragança Paulista-SP, em plantas de tomate e berinjela foram observados sintomas típicos de enfezamento caracterizados por porte reduzido, clorose foliar, superbrotamento de ramos, desenvolvimento anormal do cálice, encurtamento de entre-nós, redução no tamanho de folhas, flores e frutos. Através de duplo PCR, utilizando os iniciadores R16 mF1/mR2 e R16 F2n/R2, fragmentos de DNA de 1,2 kb foram amplificados de amostras sintomáticas, demonstrando a presença de fitoplasma nos tecidos das plantas. O uso de iniciadores específicos demonstrou que estes fitoplasmas eram afiliados ao grupo 16SrIII. Análises de RFLP, usando as enzimas de restrição AluI, HpaII, KpnI, MboI, MseI e RsaI confirmaram que os fitoplasmas detectados eram representantes do grupo 16SrIII. Os fragmentos de DNA amplificados foram clonados em Escherichia coli, sequenciados e comparados, por homologia de seqüência, entre si e com outros fitoplasmas do grupo 16SrIII. Um índice de similaridade de seqüência acima de 95% foi encontrado quando seqüências dos fitoplasmas detectados em tomate e berinjela foram comparadas com aquelas de outros representantes do grupo 16SrIII. Um índice de 98-99% foi obtido quando seqüências dos fitoplasmas encontrados em tomate e berinjela foram comparadas entre si. Estes resultados evidenciaram que o enfezamento do tomateiro e da berinjela podem estar associados a um mesmo fitoplasma, com base na análise de seqüências do gene do 16S rDNA.Vegetable diseases occurring in the Brazilian territory and around the world have been associated with various phytoplasmas. In the region of Piracicaba-SP and Bragança-SP, in eggplant and tomato plants typical symptoms of stunting characterized by reduced canopy, leaf yellowing, proliferation of shoots, calix malformation

  20. Identification of subgroups of patients with low back pain using Latent Class Analysis

    DEFF Research Database (Denmark)

    Nielsen, Anne Mølgaard

    Low back pain (LBP) is a major global health problem but the evidence base available to inform clinical decision making and to provide prognostic information to patients, is less than ideal. Therefore, there is a need for further knowledge about this largely non‐specific condition. Within...... questionnaire and the clinicians’ findings on a standardised examination of the low back. By using pattern recognition, subgroups of patients were identified within which their responses and scores are similar, and therefore the patients are more alike within the subgroups than across the subgroups. Latent...... in the outcomes, their prognostic capacity was as high or higher than two existing subgrouping tools (STarT Back Tool and Quebec Task Force Classification), and three baseline characteristics (LBP intensity, leg pain intensity and pain‐related disability). In contrast, the novel subgroupings had a lower...

  1. Valid randomization-based p-values for partially post hoc subgroup analyses.

    Science.gov (United States)

    Lee, Joseph J; Rubin, Donald B

    2015-10-30

    By 'partially post-hoc' subgroup analyses, we mean analyses that compare existing data from a randomized experiment-from which a subgroup specification is derived-to new, subgroup-only experimental data. We describe a motivating example in which partially post hoc subgroup analyses instigated statistical debate about a medical device's efficacy. We clarify the source of such analyses' invalidity and then propose a randomization-based approach for generating valid posterior predictive p-values for such partially post hoc subgroups. Lastly, we investigate the approach's operating characteristics in a simple illustrative setting through a series of simulations, showing that it can have desirable properties under both null and alternative hypotheses. Copyright © 2015 John Wiley & Sons, Ltd.

  2. A method for identifying genetic heterogeneity within phenotypically defined disease subgroups.

    Science.gov (United States)

    Liley, James; Todd, John A; Wallace, Chris

    2017-02-01

    Many common diseases show wide phenotypic variation. We present a statistical method for determining whether phenotypically defined subgroups of disease cases represent different genetic architectures, in which disease-associated variants have different effect sizes in two subgroups. Our method models the genome-wide distributions of genetic association statistics with mixture Gaussians. We apply a global test without requiring explicit identification of disease-associated variants, thus maximizing power in comparison to standard variant-by-variant subgroup analysis. Where evidence for genetic subgrouping is found, we present methods for post hoc identification of the contributing genetic variants. We demonstrate the method on a range of simulated and test data sets, for which expected results are already known. We investigate subgroups of individuals with type 1 diabetes (T1D) defined by autoantibody positivity, establishing evidence for differential genetic architecture with positivity for thyroid-peroxidase-specific antibody, driven generally by variants in known T1D-associated genomic regions.

  3. Individualizing antipsychotic treatment selection in schizophrenia: characteristics of empirically derived patient subgroups.

    Science.gov (United States)

    Correll, C U; Cañas, F; Larmo, I; Levy, P; Montes, J-M; Fagiolini, A; Papageorgiou, G; Rossi, A; Sturlason, R; Zink, M

    2011-03-01

    Treatment of schizophrenia with antipsychotic drugs is frequently sub-optimal. One reason for this may be heterogeneity between patients with schizophrenia. The objectives of this study were to identify patient, disease and treatment attributes that are important for physicians in choosing an antipsychotic drug, and to identify empirically subgroups of patients who may respond differentially to antipsychotic drugs. The survey was conducted by structured interview of 744 randomly-selected psychiatrists in four European countries who recruited 3996 patients with schizophrenia. Information on 39 variables was collected. Multiple component analysis was used to identify dimensions that explained the variance between patients. Three axes, accounting for 99% of the variance, were associated with disease severity (64%), socioeconomic status (27%) and patient autonomy (8%). These dimensions discriminated between six discrete patient subgroups, identified using ascending hierarchical classification analysis. The six subgroups differed regarding educational level, illness severity, autonomy, symptom presentation, addictive behaviors, comorbidities and cardiometabolic risk factors. Subgroup 1 patients had moderately severe physician-rated disease and addictive behaviours (23.2%); Subgroup 2 patients were well-integrated and autonomous with mild to moderate disease (6.7%); Subgroup 3 patients were less well-integrated with mild to moderate disease, living alone (11.2%); Subgroup 4 patients were women with low education levels (5.4%), Subgroup 5 patients were young men with severe disease (36.8%); and Subgroup 6 patients were poorly-integrated with moderately severe disease, needing caregiver support (16.7%). The presence of these subgroups, which require confirmation and extension regarding potentially identifiable biological markers, may help individualizing treatment in patients with schizophrenia. Copyright © 2011 Elsevier Masson SAS. All rights reserved.

  4. Treatment effect heterogeneity for univariate subgroups in clinical trials: Shrinkage, standardization, or else.

    Science.gov (United States)

    Varadhan, Ravi; Wang, Sue-Jane

    2016-01-01

    Treatment effect heterogeneity is a well-recognized phenomenon in randomized controlled clinical trials. In this paper, we discuss subgroup analyses with prespecified subgroups of clinical or biological importance. We explore various alternatives to the naive (the traditional univariate) subgroup analyses to address the issues of multiplicity and confounding. Specifically, we consider a model-based Bayesian shrinkage (Bayes-DS) and a nonparametric, empirical Bayes shrinkage approach (Emp-Bayes) to temper the optimism of traditional univariate subgroup analyses; a standardization approach (standardization) that accounts for correlation between baseline covariates; and a model-based maximum likelihood estimation (MLE) approach. The Bayes-DS and Emp-Bayes methods model the variation in subgroup-specific treatment effect rather than testing the null hypothesis of no difference between subgroups. The standardization approach addresses the issue of confounding in subgroup analyses. The MLE approach is considered only for comparison in simulation studies as the "truth" since the data were generated from the same model. Using the characteristics of a hypothetical large outcome trial, we perform simulation studies and articulate the utilities and potential limitations of these estimators. Simulation results indicate that Bayes-DS and Emp-Bayes can protect against optimism present in the naïve approach. Due to its simplicity, the naïve approach should be the reference for reporting univariate subgroup-specific treatment effect estimates from exploratory subgroup analyses. Standardization, although it tends to have a larger variance, is suggested when it is important to address the confounding of univariate subgroup effects due to correlation between baseline covariates. The Bayes-DS approach is available as an R package (DSBayes). © 2015 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  5. Treatment effect heterogeneity for univariate subgroups in clinical trials: Shrinkage, standardization, or else

    Science.gov (United States)

    Varadhan, Ravi; Wang, Sue-Jane

    2016-01-01

    Treatment effect heterogeneity is a well-recognized phenomenon in randomized controlled clinical trials. In this paper, we discuss subgroup analyses with prespecified subgroups of clinical or biological importance. We explore various alternatives to the naive (the traditional univariate) subgroup analyses to address the issues of multiplicity and confounding. Specifically, we consider a model-based Bayesian shrinkage (Bayes-DS) and a nonparametric, empirical Bayes shrinkage approach (Emp-Bayes) to temper the optimism of traditional univariate subgroup analyses; a standardization approach (standardization) that accounts for correlation between baseline covariates; and a model-based maximum likelihood estimation (MLE) approach. The Bayes-DS and Emp-Bayes methods model the variation in subgroup-specific treatment effect rather than testing the null hypothesis of no difference between subgroups. The standardization approach addresses the issue of confounding in subgroup analyses. The MLE approach is considered only for comparison in simulation studies as the “truth” since the data were generated from the same model. Using the characteristics of a hypothetical large outcome trial, we perform simulation studies and articulate the utilities and potential limitations of these estimators. Simulation results indicate that Bayes-DS and Emp-Bayes can protect against optimism present in the naïve approach. Due to its simplicity, the naïve approach should be the reference for reporting univariate subgroup-specific treatment effect estimates from exploratory subgroup analyses. Standardization, although it tends to have a larger variance, is suggested when it is important to address the confounding of univariate subgroup effects due to correlation between baseline covariates. The Bayes-DS approach is available as an R package (DSBayes). PMID:26485117

  6. Chromosomal phylogeny of the Drosophila fasciola species subgroup revisited (Diptera, Drosophilidae

    Directory of Open Access Journals (Sweden)

    Nilda Maria Diniz

    2004-01-01

    Full Text Available The analysis of polytene chromosomes in 26 strains of seven species in the Drosophila fasciola subgroup, from several locations in Brazil, in addition to strains of two species belonging to the Drosophila mulleri subgroup (D. aldrichi and D. mulleri, enabled us to determine that the 3c inversion found in the latter species differ in one of its break points from that present in the species of the fasciola subgroup. Therefore, a change in the mulleri complex denomination from inversion 3c to inversion 3u is proposed. Accordingly, the fasciola subgroup is no longer a lesser phylogenetic part within the mulleri subgroup. Rather, it is directly related to the likely ancestor of the repleta group, called Primitive I. This information removes the main obstacle to considering the Drosophila fasciola subgroup as an ancestral group within the Drosophila repleta species group, according to the hypothesis of Throckmorton. Our data also support the conclusion that D. onca and D. carolinae are closely related species based on one new inversion in chromosome 4 (4f², in both species. D. fascioloides and D. ellisoni also form a pair of sister species based on the presence of fusions of chromosomes 2-4 and 3-5. D. rosinae is related only to the likely ancestor of the fasciola subgroup, where the 3c inversion was fixed.

  7. Patterns of subgrouping and spatial affiliation in a community of mantled howling monkeys (Alouatta palliata).

    Science.gov (United States)

    Bezanson, Michelle; Garber, Paul A; Murphy, John T; Premo, L S

    2008-03-01

    Studies of social affiliation and social spacing offer important insight into the dynamics of subgroup formation and social strategies in living primates. Among the 11 species in the genus Alouatta, mantled howlers (A. palliata) are the only species to consistently form large, stable social groups composed of several adult males and several adult females. In this study, we examine patterns of subgrouping, activity, and partner preferences in a troop of 26-29 wild mantled howling monkeys (including 12-13 marked individuals) inhabiting Isla de Ometepe, Nicaragua. During two study seasons in 2000 and 2001, we simultaneously monitored the size, composition, and activities of individuals in two to three different subgroups. A half-weight association index was used to calculate partner preferences and patterns of spatial association. Results indicate that our howler study troop fragmented into subgroups of 1-20 with subgroups averaging five and six individuals. Subgroup size and membership reflected individual patterns of social affiliation and social tolerance, and in general remained consistent across activities and from year to year. We also found evidence of cliques or social networks of three to four individuals embedded within larger subgroups. A small number of adult males appeared to play an important social role as the nucleus of clique formation. We argue that the persistence of strong male-male and male-female partner preferences in mantled howlers helps to explain the stability of relatively large multimale-multifemale groups.

  8. Generators for the l-torsion subgroup of Jacobians of Genus Two Curves

    DEFF Research Database (Denmark)

    Ravnshøj, Christian Robenhagen

    2008-01-01

    We give an explicit description of the matrix representation of the Frobenius endomorphism on the Jacobian of a genus two curve on the subgroup of l-torsion points. By using this description, we can describe the matrix representation of the Weil-pairing on the subgroup of l-torsion points...... explicitly. Finally, the explicit description of the Weil-pairing provides us with an efficient, probabilistic algorithm to find generators of the subgroup of l-torsion points on the Jacobian of a genus two curve....

  9. Debate: Subgroup analyses in clinical trials: fun to look at - but don't believe them!

    Directory of Open Access Journals (Sweden)

    Sleight Peter

    2000-07-01

    Full Text Available Abstract Analysis of subgroup results in a clinical trial is surprisingly unreliable, even in a large trial. This is the result of a combination of reduced statistical power, increased variance and the play of chance. Reliance on such analyses is likely to be more erroneous, and hence harmful, than application of the overall proportional (or relative result in the whole trial to the estimate of absolute risk in that subgroup. Plausible explanations can usually be found for effects that are, in reality, simply due to the play of chance. When clinicians believe such subgroup analyses, there is a real danger of harm to the individual patient.

  10. On the use of genetic programming for mining comprehensible rules in subgroup discovery.

    Science.gov (United States)

    Luna, José María; Romero, José Raúl; Romero, Cristóbal; Ventura, Sebastián

    2014-12-01

    This paper proposes a novel grammar-guided genetic programming algorithm for subgroup discovery. This algorithm, called comprehensible grammar-based algorithm for subgroup discovery (CGBA-SD), combines the requirements of discovering comprehensible rules with the ability to mine expressive and flexible solutions owing to the use of a context-free grammar. Each rule is represented as a derivation tree that shows a solution described using the language denoted by the grammar. The algorithm includes mechanisms to adapt the diversity of the population by self-adapting the probabilities of recombination and mutation. We compare the approach with existing evolutionary and classic subgroup discovery algorithms. CGBA-SD appears to be a very promising algorithm that discovers comprehensible subgroups and behaves better than other algorithms as measures by complexity, interest, and precision indicate. The results obtained were validated by means of a series of nonparametric tests.

  11. Team negotiation: social, epistemic, economic, and psychological consequences of subgroup conflict.

    Science.gov (United States)

    Halevy, Nir

    2008-12-01

    Large collectives (e.g., organizations, political parties, nations) are seldom unitary players. Rather, they consist of different subgroups that often have conflicting interests. Nonetheless, negotiation research consistently regards negotiating teams, who represent these collectives, as monolithic parties with uniform interests. This article integrates concepts from social psychology, management, political science, and behavioral game theory to explore the effects of subgroup conflict on team negotiation. Specifically, the present research introduced a conflict of interests within negotiating teams and investigated how this internal conflict affects the outcome of the negotiation between teams. An experiment with 80 four-person teams found that conflict between subgroups had a detrimental effect on the performance of negotiating teams. This research also employed a recent model of motivated information processing in groups to investigate possible processes underlying the effect of subgroup conflict on team negotiation.

  12. Manual therapy in osteoarthritis of the hip: outcome in subgroups of patients

    National Research Council Canada - National Science Library

    Hoeksma, H.L; Dekker, J; Ronday, H.K; Breedveld, F.C; Ende, van den, C.H.M

    2005-01-01

    OBJECTIVE: To investigate whether manual therapy has particular benefit in subgroups of patients defined on the basis of hip function, range of joint motion, pain and radiological deterioration. METHODS...

  13. Effects of hydroxyethyl starch in subgroups of patients with severe sepsis

    DEFF Research Database (Denmark)

    Müller, Rasmus G; Haase, Nicolai; Wetterslev, Jørn

    2013-01-01

    It has been speculated that certain subgroups of sepsis patients may benefit from treatment with hydroxyethyl starch (HES) 130/0.42, specifically in the earlier resuscitation of patients with more severely impaired circulation....

  14. Twelve-year trends in health insurance coverage among Latinos, by subgroup and immigration status.

    Science.gov (United States)

    Shah, N Sarita; Carrasquillo, Olveen

    2006-01-01

    We examine twelve-year trends in the Latino uninsured population by ethnic subgroup and immigration status. From 1993 to 1999, most Latino subgroups, particularly Puerto Ricans, had large decreases in Medicaid coverage. For some subgroups these were offset by increases in employer coverage, but not for Mexicans, resulting in a four-percentage-point increase in their uninsured population. During 2000-2004, Medicaid/SCHIP expansions benefited most subgroups and mitigated smaller losses in employer coverage. However, during 1993-2004, the percentage of noncitizen Latinos lacking coverage increased by several percentage points. This was attributable to Medicaid losses during 1993-1999 and losses in employer coverage during 2000-2004.

  15. Identification of atopic dermatitis subgroups in children from two longitudinal birth cohorts

    NARCIS (Netherlands)

    Paternoster, Lavinia; Savenije, Olga E M; Heron, Jon; Evans, David M; Vonk, Judith M; Brunekreef, Bert; Wijga, Alet H; Henderson, A John; Koppelman, Gerard H; Brown, Sara J

    2017-01-01

    BACKGROUND: Atopic dermatitis (AD) is a prevalent disease with variable natural history. Longitudinal birth cohort studies provide an opportunity to define subgroups based on disease trajectories, which may represent different genetic and environmental pathomechanisms. OBJECTIVE: To investigate the

  16. Novel molecular subgroups for clinical classification and outcome prediction in childhood medulloblastoma: a cohort study.

    Science.gov (United States)

    Schwalbe, Edward C; Lindsey, Janet C; Nakjang, Sirintra; Crosier, Stephen; Smith, Amanda J; Hicks, Debbie; Rafiee, Gholamreza; Hill, Rebecca M; Iliasova, Alice; Stone, Thomas; Pizer, Barry; Michalski, Antony; Joshi, Abhijit; Wharton, Stephen B; Jacques, Thomas S; Bailey, Simon; Williamson, Daniel; Clifford, Steven C

    2017-07-01

    International consensus recognises four medulloblastoma molecular subgroups: WNT (MBWNT), SHH (MBSHH), group 3 (MBGrp3), and group 4 (MBGrp4), each defined by their characteristic genome-wide transcriptomic and DNA methylomic profiles. These subgroups have distinct clinicopathological and molecular features, and underpin current disease subclassification and initial subgroup-directed therapies that are underway in clinical trials. However, substantial biological heterogeneity and differences in survival are apparent within each subgroup, which remain to be resolved. We aimed to investigate whether additional molecular subgroups exist within childhood medulloblastoma and whether these could be used to improve disease subclassification and prognosis predictions. In this retrospective cohort study, we assessed 428 primary medulloblastoma samples collected from UK Children's Cancer and Leukaemia Group (CCLG) treatment centres (UK), collaborating European institutions, and the UKCCSG-SIOP-PNET3 European clinical trial. An independent validation cohort (n=276) of archival tumour samples was also analysed. We analysed samples from patients with childhood medulloblastoma who were aged 0-16 years at diagnosis, and had central review of pathology and comprehensive clinical data. We did comprehensive molecular profiling, including DNA methylation microarray analysis, and did unsupervised class discovery of test and validation cohorts to identify consensus primary molecular subgroups and characterise their clinical and biological significance. We modelled survival of patients aged 3-16 years in patients (n=215) who had craniospinal irradiation and had been treated with a curative intent. Seven robust and reproducible primary molecular subgroups of childhood medulloblastoma were identified. MBWNT remained unchanged and each remaining consensus subgroup was split in two. MBSHH was split into age-dependent subgroups corresponding to infant (<4·3 years; MBSHH-Infant; n=65) and

  17. Discrete subgroups of adolescents diagnosed with borderline personality disorder: a latent class analysis of personality features.

    Science.gov (United States)

    Ramos, Vera; Canta, Guilherme; de Castro, Filipa; Leal, Isabel

    2014-08-01

    Research suggests that borderline personality disorder (BPD) can be diagnosed in adolescents and is marked by considerable heterogeneity. This study aimed to identify personality features characterizing adolescents with BPD and possible meaningful patterns of heterogeneity that could lead to personality subgroups. The authors analyzed data on 60 adolescents, ages 15 to 18 years, who met DSM criteria for a BPD diagnosis. The authors used latent class analysis (LCA) to identify subgroups based on the personality pattern scales from the Millon Adolescent Clinical Inventory (MACI). LCA indicated that the best-fitting solution was a two-class model, identifying two discrete subgroups of BPD adolescents that were described as internalizing and externalizing. The subgroups were then compared on clinical and sociodemographic variables, measures of personality dimensions, DSM BPD criteria, and perception of attachment styles. Adolescents with a BPD diagnosis constitute a heterogeneous group and vary meaningfully on personality features that can have clinical implications for treatment.

  18. TEST PREPARATION FOR THE GRE ANALYTICAL ABILITY MEASURE: DIFFERENTIAL EFFECTS FOR SUBGROUPS OF GRE TEST TAKERS

    National Research Council Canada - National Science Library

    Powers, Donald E

    1986-01-01

    ... on other sections of the GRE General Test. The results suggested little, if any, difference among subgroups of examinees with respect to their response to the particular kind of test preparation considered in the study...

  19. Incidence and follow-up of Braunwald subgroups in unstable angina pectoris

    NARCIS (Netherlands)

    A.J.M. van Miltenburg-van Zijl (Addy); M.L. Simoons (Maarten); R.J. Veerhoek (Rinus); P.M.M. Bossuyt (Patrick)

    1995-01-01

    textabstractObjectives. This study was performed to establish the prognosis of patients with unstable angina within the subgroups of the Braunwald classification. Background. Among many classifications of unstable angina, the Braunwald classification is frequently used. However, the incidence

  20. On s-semipermutable subgroups of finite groups and p-nilpotency

    Indian Academy of Sciences (India)

    Introduction. All groups considered in this paper are finite groups. Most of the notations are standard and can be found in [4] and [3]. Recall that a group H is said to be s-permutable (s-quasinormal) [6] in G if HP = PH for all Sylow subgroups P of G. A subgroup H of a group G is called s-semipermutable [2]. inGif it is ...

  1. Finite groups with the set of the number of subgroups of possible ...

    Indian Academy of Sciences (India)

    Recently, Chen et al. [3] determined the groups in which the number of subgroups of possible order is less than or equal to 3, but there exist some gaps in the proof of their theorem. If we denote by n(G) the set of the number of subgroups of possible order of a group G, then we can investigate the structure of G by n(G).

  2. A recursive formula for the number of intuitionistic fuzzy subgroups of a finite cyclic group

    Science.gov (United States)

    Chandni, Sharma, P. K.; Singh, Pushpinder; Singh, Manreet

    2017-07-01

    In this article, we have given an explicit recursive formula for the number of intuitionistic fuzzy subgroups of a finite cyclic group G = Zp1 × Zp ×………..×Zpm, where p1, p2, ….., pm are distinct prime numbers. A method for constructing an intuitionistic fuzzy subgroup of a given group in terms of double pinned flags is also proposed.

  3. Resolution and Characterization of Distinct cpn60-Based Subgroups of Gardnerella vaginalis in the Vaginal Microbiota

    Science.gov (United States)

    Paramel Jayaprakash, Teenus; Schellenberg, John J.; Hill, Janet E.

    2012-01-01

    Bacterial vaginosis (BV), characterized by a shift of the vaginal microbiota from a Lactobacillus-dominated community to a dense biofilm containing a complex mixture of organisms, is an important risk factor in poor reproductive health outcomes. The Nugent score, based on Gram stain, is used to diagnose BV and Gardnerella vaginalis abundance in the sample is one factor determining Nugent score. A high Nugent score is indicative of BV but does not always correspond to the presence of clinical symptoms. G. vaginalis is recognized as a heterogeneous group of organisms, which can also be part of the normal, healthy vaginal microbiome. In addition, asymptomatic BV and non-Gardnerella types of BV are being recognized. In an attempt to resolve the heterogeneous group of G. vaginalis, a phylogenetic tree of cpn60 universal target sequences from G. vaginalis isolates was constructed that indicates the existence of four subgroups of G. vaginalis. This subdivision, supported by whole genome similarity calculation of representative strains using JSpecies, demonstrates that these subgroups may represent different species. The cpn60 subgroupings did not correspond with the Piot biotyping scheme, but did show consistency with ARDRA genotyping and sialidase gene presence. Isolates from all four subgroups produced biofilm in vitro. We also investigated the distribution of G. vaginalis subgroups in vaginal samples from Kenyan women with Nugent scores consistent with BV, Intermediate and Normal microbiota (n = 44). All subgroups of G. vaginalis were detected in these women, with a significant difference (z = −3.372, n = 39, p = 0.001) in frequency of G. vaginalis subgroup B between BV and Normal groups. Establishment of a quantifiable relationship between G. vaginalis subgroup distribution and clinical status could have significant diagnostic implications. PMID:22900080

  4. Resolution and characterization of distinct cpn60-based subgroups of Gardnerella vaginalis in the vaginal microbiota.

    Directory of Open Access Journals (Sweden)

    Teenus Paramel Jayaprakash

    Full Text Available Bacterial vaginosis (BV, characterized by a shift of the vaginal microbiota from a Lactobacillus-dominated community to a dense biofilm containing a complex mixture of organisms, is an important risk factor in poor reproductive health outcomes. The Nugent score, based on Gram stain, is used to diagnose BV and Gardnerella vaginalis abundance in the sample is one factor determining Nugent score. A high Nugent score is indicative of BV but does not always correspond to the presence of clinical symptoms. G. vaginalis is recognized as a heterogeneous group of organisms, which can also be part of the normal, healthy vaginal microbiome. In addition, asymptomatic BV and non-Gardnerella types of BV are being recognized. In an attempt to resolve the heterogeneous group of G. vaginalis, a phylogenetic tree of cpn60 universal target sequences from G. vaginalis isolates was constructed that indicates the existence of four subgroups of G. vaginalis. This subdivision, supported by whole genome similarity calculation of representative strains using JSpecies, demonstrates that these subgroups may represent different species. The cpn60 subgroupings did not correspond with the Piot biotyping scheme, but did show consistency with ARDRA genotyping and sialidase gene presence. Isolates from all four subgroups produced biofilm in vitro. We also investigated the distribution of G. vaginalis subgroups in vaginal samples from Kenyan women with Nugent scores consistent with BV, Intermediate and Normal microbiota (n = 44. All subgroups of G. vaginalis were detected in these women, with a significant difference (z = -3.372, n = 39, p = 0.001 in frequency of G. vaginalis subgroup B between BV and Normal groups. Establishment of a quantifiable relationship between G. vaginalis subgroup distribution and clinical status could have significant diagnostic implications.

  5. Comparative review of some properties of fuzzy and anti fuzzy subgroups

    OpenAIRE

    B. O. ONASANYA

    2010-01-01

    This paper is to comparatively review some works in fuzzy and anti fuzzy group theory. The aim is to provide anti fuzzy versions of some existing theorems in fuzzy group theory and see how much similar they are to their fuzzy versions. The research therefore focuses on the properties of fuzzy subgroup, fuzzy cosets, fuzzy conjugacy and fuzzy normal subgroups of a group which are mimicked in anti fuzzy group theory.

  6. Delineation of motoneuron subgroups supplying individual eye muscles in the human oculomotor nucleus

    OpenAIRE

    Che Ngwa, Emmanuel; Zeeh, Christina; Messoudi, Ahmed; Büttner-Ennever, Jean A.; Horn, Anja K. E.

    2014-01-01

    The oculomotor nucleus (nIII) contains the motoneurons of medial, inferior, and superior recti (MR, IR, and SR), inferior oblique (IO), and levator palpebrae (LP) muscles. The delineation of motoneuron subgroups for each muscle is well-known in monkey, but not in human. We studied the transmitter inputs to human nIII and the trochlear nucleus (nIV), which innervates the superior oblique muscle (SO), to outline individual motoneuron subgroups. Parallel series of sections from human brainstems ...

  7. Delineation of motoneuron subgroups supplying individual eye muscles in the human oculomotor nucleus

    OpenAIRE

    Emmanuel eChe-Ngwa; Christina eZeeh; Christina eZeeh; Ahmed eMessoudi; Jean Alice Büttner-Ennever; Anja Kerstin Ellen Horn; Anja Kerstin Ellen Horn

    2014-01-01

    The oculomotor nucleus (nIII) contains the motoneurons of medial, inferior and superior recti (MR, IR, SR), inferior oblique (IO) and levator palpebrae (LP) muscles. The delineation of motoneuron subgroups for each muscle is well-known in monkey, but not in human. We studied the transmitter inputs to human nIII and the trochlear nucleus (nIV), which innervates the superior oblique muscle (SO), to outline individual motoneuron subgroups. Parallel series of sections from human brainstems were i...

  8. Are there distinct cognitive and motivational sub-groups of children with ADHD?

    Science.gov (United States)

    Lambek, Rikke; Sonuga-Barke, Edmund; Tannock, Rosemary; Sørensen, Anne Virring; Damm, Dorte; Thomsen, Per Hove

    2017-11-16

    Attention-deficit/hyperactivity disorder (ADHD) is proposed to be a neuropsychologically heterogeneous disorder that encompasses two distinct sub-groups, one with executive function (EF) deficits and one with delay aversion (DA). However, such claims have often been based on studies that have operationalized neuropsychological deficits using a categorical approach - using intuitive but rather arbitrary, clinical cut-offs. The current study applied an alternative empirical approach to sub-grouping in ADHD, latent profile analysis (LPA), and attempted to validate emerging subgroups through clinically relevant correlates. One-hundred medication-naïve children with ADHD and 96 typically developing children (6-14 years) completed nine EF and three DA tasks as well as an odor identification test. Parents and teachers provided reports of the children's behavior (ADHD and EF). Models of the latent structure of scores on EF and DA tests were contrasted using confirmatory factor analysis (CFA). LPA was carried out based on factor scores from the CFA and sub-groups were compared in terms of odor identification and behavior. A model with one DA and two EF factors best fit the data. LPA resulted in four sub-groups that differed in terms of general level of neuropsychological performance (ranging from high to very low), odor identification, and behavior. The sub-groups did not differ in terms of the relative EF and DA performance. Results in the ADHD group were replicated in the control group. While EF and DA appear to be dissociable constructs; they do not yield distinct sub-groups when sub-grouping is based on a statistical approach such as LPA.

  9. Classification of low back-related leg pain: do subgroups differ in disability and psychosocial factors?

    Science.gov (United States)

    Walsh, Jeremy; Hall, Toby

    2009-01-01

    It has been proposed that patients with low back-related leg pain can be classified according to pain mechanisms into four distinct subgroups: Central Sensitization (CS), Denervation (D), Peripheral Nerve Sensitization (PNS), and Musculoskeletal (M). The purpose of this study was to determine whether there were any differences in terms of disability and psychosocial factors between these four subgroups. Forty-five subjects with low back-related leg pain completed the Oswestry Disability Index, the hospital Anxiety and Depression Scale, and the Fear Avoidance Beliefs Questionnaire. Subsequently, an examiner blinded to the questionnaire results classified the subjects into one of the four subgroups, according to the findings of the self-administered Leeds Assessment of Neuropathic Signs and Symptoms questionnaire and a physical examination. It was found that the PNS subgroup had significantly greater disability compared to all other subgroups and significantly greater fear avoidance beliefs about physical activity compared to the CS and D subgroups. This highlights the importance of sub-classification but also the need to take into account disability and psychosocial factors in the management of low back-related leg pain.

  10. IGHV1, IGHV5 and IGHV7 subgroup genes in the rhesus macaque.

    Science.gov (United States)

    Bible, Jon M; Howard, Wendy; Robbins, Helena; Dunn-Walters, Deborah K

    2003-03-01

    The diversity of the antibody response is achieved, in part, by rearrangement of different immunoglobulin (Ig) genes. The Ig heavy chain is made up of a variable region (IGHV), a diversity region (IGHD) and a joining region (IGHJ). Human germline IGHV genes have been grouped into seven multigene subgroups. Size and usage of these subgroups is not equal, the IGHV3 subgroup is the most commonly used (36%), followed by IGHV1/7 (26%), then IGHV4, IGHV5, IGHV2, IGHV6 (15%, 12%, 4%, 3% respectively). The rhesus macaque (Macaca mulatta) is a useful non-human primate model for studies of infection and the database of germline Ig genes for the macaque is gradually growing to become a useful tool in the study of B-cell responses. The proportions of IGHV subgroup usage in the macaque are similar to those in man. Representatives from IGHV3 and IGHV4 subgroups for the macaque have been published, as have germline sequences of the IGHD and IGHJ genes. However, to date there have been no sequences published from the second largest IGHV subgroup, IGHV1. We report the isolation and sequencing of a genomic fragment containing an IGHV1 gene from the macaque. Polymerase chain reaction (PCR) primers designed from this sequence enabled us to amplify and sequence 25 new IGHV1 germline genes. We also isolated two IGHV7 genes, using the same primers, and two IGHV5 genes, using human IGHV5 primers.

  11. Presence of a Phytoplasma Associated with Witches’-Broom Disease in Ugni molinae Turcz. and Gaultheria phillyreifolia (Pers. Sleumer Determined by DAPI, PCR, and DNA Sequencing Presencia de un Fitoplasma Asociado a la Enfermedad de "Escoba de Bruja" en Ugni molinae Turcz. y Gaultheria phillyreifolia (Pers. Sleumer Determinado Mediante DAPI, PCR y Secuenciación de ADN

    Directory of Open Access Journals (Sweden)

    Nolberto Arismendi S

    2010-03-01

    Full Text Available Murta (Ugni molinae Turcz. and common chaura (Gaultheria phillyreifolia (Pers. Sleumer are native species of Chile. Plants of both species have shown over-branching like witches' broom. The causal agents of these symptoms in many plants are phytoplasma. To verify the presence of these microorganisms, DAPI (4',6-diamidino-2-phenylindole staining analysis and polymerase chain reaction (PCR were performed in symptomatic and asymptomatic plants. Positive PCR samples were sequenced to identify the pathogens involved. In individuals of both species with witches’ broom symptoms, DAPI staining showed fluorescent bodies in the phloem tissues, but not in asymptomatic plants. Verification by nested-PCR, phytoplasmatic DNA was amplified from diseased murta and chaura, but not in apparently healthy plants. Sequencing of amplified products allowed locating phytoplasma within the ash yellows group (16SrVII and related to Candidatus phytoplasma fraxini. This is the first report of phytoplasma in Chilean native species. Considering the diversity of plant species infected by the ash yellows group suggests that G. phillyreifolia and U. molinae could be a phytoplasma reservoir for other economically important agricultural crops.La murta (Ugni molinae Turcz. y la chaura común (Gaultheria phillyreifolia (Pers. Sleumer son especies nativas de Chile. En plantas de ambas especies se ha observado una sobre-ramificación de tipo "escoba de bruja". En muchas plantas los agentes causales de esta sintomatología son fitoplasmas. Para verificar la presencia de estos microorganismos se analizaron plantas con y sin síntomas mediante tinciones DAPI (4’,6-diamidino-2-fenilindol y reacción en cadena de la polimerasa (PCR. Muestras positivas en la PCR fueron secuenciadas para identificar al fitopatógeno implicado. En individuos de ambas especies con síntomas de escoba de bruja, la tinción DAPI permitió observar cuerpos fluorescentes en los tejidos del floema, situaci

  12. Pediatric RSV Infection During Two Winter Seasons in British Columbia: A Role for Subgroup Analysis in Young Children?

    Directory of Open Access Journals (Sweden)

    E Wilson

    1990-01-01

    Full Text Available Using a panel of eight monoclonal antibodies directed against the G, F and NP proteins of respiratory syncytial virus, 167 virus isolates from nasopharyngeal washing cultures at British Columbia Children’s Hospital during two consecutive epidemics were subgrouped. Slides made and frozen at the time of virus isolation or prepared from recovered frozen passage material, were assayed by indirect immunofluorescence. Of 85 strains tested in 1987–88, 54 (64% were subgroup A, and 31 (36% subgroup B. By contrast, of 82 strains tested in 1988–89 five (6% were subgroup A and 77 (94% subgroup B. Review of patient charts did not reveal significant differences in clinical course of patients infected with the two subgroups, but the risk of infection with subgroup A was significantly greater than the risk of subgroup B infection in younger patients.

  13. Gardnerella vaginalis Subgroups Defined by cpn60 Sequencing and Sialidase Activity in Isolates from Canada, Belgium and Kenya.

    Directory of Open Access Journals (Sweden)

    John J Schellenberg

    Full Text Available Increased abundance of Gardnerella vaginalis and sialidase activity in vaginal fluid is associated with bacterial vaginosis (BV, a common but poorly understood clinical entity associated with poor reproductive health outcomes. Since most women are colonized with G. vaginalis, its status as a normal member of the vaginal microbiota or pathogen causing BV remains controversial, and numerous classification schemes have been described. Since 2005, sequencing of the chaperonin-60 universal target (cpn60 UT has distinguished four subgroups in isolate collections, clone libraries and deep sequencing datasets. To clarify potential clinical and diagnostic significance of cpn60 subgroups, we undertook phenotypic and molecular characterization of 112 G. vaginalis isolates from three continents. A total of 36 subgroup A, 33 B, 35 C and 8 D isolates were identified through phylogenetic analysis of cpn60 sequences as corresponding to four "clades" identified in a recently published study, based on sequencing 473 genes across 17 isolates. cpn60 subgroups were compared with other previously described molecular methods for classification of Gardnerella subgroups, including amplified ribosomal DNA restriction analysis (ARDRA and real-time PCR assays designed to quantify subgroups in vaginal samples. Although two ARDRA patterns were observed in isolates, each was observed in three cpn60 subgroups (A/B/D and B/C/D. Real-time PCR assays corroborated cpn60 subgroups overall, but 13 isolates from subgroups A, B and D were negative in all assays. A putative sialidase gene was detected in all subgroup B, C and D isolates, but only in a single subgroup A isolate. In contrast, sialidase activity was observed in all subgroup B isolates, 3 (9% subgroup C isolates and no subgroup A or D isolates. These observations suggest distinct roles for G. vaginalis subgroups in BV pathogenesis. We conclude that cpn60 UT sequencing is a robust approach for defining G. vaginalis

  14. Gardnerella vaginalis Subgroups Defined by cpn60 Sequencing and Sialidase Activity in Isolates from Canada, Belgium and Kenya.

    Science.gov (United States)

    Schellenberg, John J; Paramel Jayaprakash, Teenus; Withana Gamage, Niradha; Patterson, Mo H; Vaneechoutte, Mario; Hill, Janet E

    2016-01-01

    Increased abundance of Gardnerella vaginalis and sialidase activity in vaginal fluid is associated with bacterial vaginosis (BV), a common but poorly understood clinical entity associated with poor reproductive health outcomes. Since most women are colonized with G. vaginalis, its status as a normal member of the vaginal microbiota or pathogen causing BV remains controversial, and numerous classification schemes have been described. Since 2005, sequencing of the chaperonin-60 universal target (cpn60 UT) has distinguished four subgroups in isolate collections, clone libraries and deep sequencing datasets. To clarify potential clinical and diagnostic significance of cpn60 subgroups, we undertook phenotypic and molecular characterization of 112 G. vaginalis isolates from three continents. A total of 36 subgroup A, 33 B, 35 C and 8 D isolates were identified through phylogenetic analysis of cpn60 sequences as corresponding to four "clades" identified in a recently published study, based on sequencing 473 genes across 17 isolates. cpn60 subgroups were compared with other previously described molecular methods for classification of Gardnerella subgroups, including amplified ribosomal DNA restriction analysis (ARDRA) and real-time PCR assays designed to quantify subgroups in vaginal samples. Although two ARDRA patterns were observed in isolates, each was observed in three cpn60 subgroups (A/B/D and B/C/D). Real-time PCR assays corroborated cpn60 subgroups overall, but 13 isolates from subgroups A, B and D were negative in all assays. A putative sialidase gene was detected in all subgroup B, C and D isolates, but only in a single subgroup A isolate. In contrast, sialidase activity was observed in all subgroup B isolates, 3 (9%) subgroup C isolates and no subgroup A or D isolates. These observations suggest distinct roles for G. vaginalis subgroups in BV pathogenesis. We conclude that cpn60 UT sequencing is a robust approach for defining G. vaginalis subgroups within the

  15. On the same side of the faultline: Inclusion in the leader’s subgroup and employee performance

    NARCIS (Netherlands)

    Meyer, B.; Shemla, M.; Li, J.; Wegge, J.

    Extending theory on faultlines and subgroups, we argue that faultlines splitting a team into homogeneous subgroups can have different effects on team members' individual performance, depending on different intra-subgroup processes. Specifically, we propose that the effect of faultline strength on

  16. Functional dyspepsia: relationship between clinical subgroups and Helicobacter pylori status in Western Turkey

    Directory of Open Access Journals (Sweden)

    M. Saruc

    2003-06-01

    Full Text Available The etiology of functional dyspepsia is not known. The objective of the present study was to determine the characteristics of functional dyspepsia in Western Turkey. We divided 900 patients with functional dyspepsia into three subgroups according to symptoms: ulcer-like (UL, 321 (35.6%, motility disorder-like (ML, 281 (31.2%, and the combination (C of these symptoms, 298 (33.1%. All patients were submitted to endoscopic evaluation, with two biopsies taken from the cardia and corpus, and four from the antrum of the stomach. All biopsy samples were studied for Helicobacter pylori (Hp density, chronic inflammation, activity, intestinal metaplasia, atrophy, and the presence of lymphoid aggregates by histological examination. One antral biopsy was used for the rapid urease test. Tissue cagA status was determined by PCR from an antral biopsy specimen by a random sampling method. We also determined the serum levels of tumor necrosis factor-alpha (TNF-alpha and gastrin by the same method. Data were analyzed statistically by the Kolmogorov-Smirnov test and by analysis of variance. Hp and cagA positivity was significantly higher in the UL subgroup than in the others. The patients in the ML subgroup had the lowest Hp and cagA positivity and Hp density. The ML subgroup also showed the lowest level of Hp-induced inflammation among all subgroups. The serum levels of TNF-alpha and gastrin did not reveal any difference between groups. Our findings show a poor association of Hp with the ML subgroup of functional dyspepsia, but a stronger association with the UL and C subgroups.

  17. Divide and Conquer: Sub-Grouping of ASD Improves ASD Detection Based on Brain Morphometry.

    Science.gov (United States)

    Katuwal, Gajendra J; Baum, Stefi A; Cahill, Nathan D; Michael, Andrew M

    2016-01-01

    Low success (ASD) classification using brain morphometry from the large multi-site ABIDE dataset and inconsistent findings on brain morphometric abnormalities in ASD can be attributed to the ASD heterogeneity. In this study, we show that ASD brain morphometry is highly heterogeneous, and demonstrate that the heterogeneity can be mitigated and classification improved if autism severity (AS), verbal IQ (VIQ) and age are used with morphometric features. Morphometric features from structural MRIs (sMRIs) of 734 males (ASD: 361, controls: 373) of ABIDE were derived using FreeSurfer. Applying the Random Forest classifier, an AUC of 0.61 was achieved. Adding VIQ and age to morphometric features, AUC improved to 0.68. Sub-grouping the subjects by AS, VIQ and age improved the classification with the highest AUC of 0.8 in the moderate-AS sub-group (AS = 7-8). Matching subjects on age and/or VIQ in each sub-group further improved the classification with the highest AUC of 0.92 in the low AS sub-group (AS = 4-5). AUC decreased with AS and VIQ, and was the lowest in the mid-age sub-group (13-18 years). The important features were mainly from the frontal, temporal, ventricular, right hippocampal and left amygdala regions. However, they highly varied with AS, VIQ and age. The curvature and folding index features from frontal, temporal, lingual and insular regions were dominant in younger subjects suggesting their importance for early detection. When the experiments were repeated using the Gradient Boosting classifier similar results were obtained. Our findings suggest that identifying brain biomarkers in sub-groups of ASD can yield more robust and insightful results than searching across the whole spectrum. Further, it may allow identification of sub-group specific brain biomarkers that are optimized for early detection and monitoring, increasing the utility of sMRI as an important tool for early detection of ASD.

  18. The interest of gait markers in the identification of subgroups among fibromyalgia patients.

    Science.gov (United States)

    Auvinet, Bernard; Chaleil, Denis; Cabane, Jean; Dumolard, Anne; Hatron, Pierre; Juvin, Robert; Lanteri-Minet, Michel; Mainguy, Yves; Negre-Pages, Laurence; Pillard, Fabien; Riviere, Daniel; Maugars, Yves-Michel

    2011-11-11

    Fibromyalgia (FM) is a heterogeneous syndrome and its classification into subgroups calls for broad-based discussion. FM subgrouping, which aims to adapt treatment according to different subgroups, relies in part, on psychological and cognitive dysfunctions. Since motor control of gait is closely related to cognitive function, we hypothesized that gait markers could be of interest in the identification of FM patients' subgroups. This controlled study aimed at characterizing gait disorders in FM, and subgrouping FM patients according to gait markers such as stride frequency (SF), stride regularity (SR), and cranio-caudal power (CCP) which measures kinesia. A multicentre, observational open trial enrolled patients with primary FM (44.1 ± 8.1 y), and matched controls (44.1 ± 7.3 y). Outcome measurements and gait analyses were available for 52 pairs. A 3-step statistical analysis was carried out. A preliminary single blind analysis using k-means cluster was performed as an initial validation of gait markers. Then in order to quantify FM patients according to psychometric and gait variables an open descriptive analysis comparing patients and controls were made, and correlations between gait variables and main outcomes were calculated. Finally using cluster analysis, we described subgroups for each gait variable and looked for significant differences in self-reported assessments. SF was the most discriminating gait variable (73% of patients and controls). SF, SR, and CCP were different between patients and controls. There was a non-significant association between SF, FIQ and physical components from Short-Form 36 (p = 0.06). SR was correlated to FIQ (p = 0.01) and catastrophizing (p = 0.05) while CCP was correlated to pain (p = 0.01). The SF cluster identified 3 subgroups with a particular one characterized by normal SF, low pain, high activity and hyperkinesia. The SR cluster identified 2 distinct subgroups: the one with a reduced SR was distinguished by high FIQ

  19. The interest of gait markers in the identification of subgroups among fibromyalgia patients

    Directory of Open Access Journals (Sweden)

    Auvinet Bernard

    2011-11-01

    Full Text Available Abstract Background Fibromyalgia (FM is a heterogeneous syndrome and its classification into subgroups calls for broad-based discussion. FM subgrouping, which aims to adapt treatment according to different subgroups, relies in part, on psychological and cognitive dysfunctions. Since motor control of gait is closely related to cognitive function, we hypothesized that gait markers could be of interest in the identification of FM patients' subgroups. This controlled study aimed at characterizing gait disorders in FM, and subgrouping FM patients according to gait markers such as stride frequency (SF, stride regularity (SR, and cranio-caudal power (CCP which measures kinesia. Methods A multicentre, observational open trial enrolled patients with primary FM (44.1 ± 8.1 y, and matched controls (44.1 ± 7.3 y. Outcome measurements and gait analyses were available for 52 pairs. A 3-step statistical analysis was carried out. A preliminary single blind analysis using k-means cluster was performed as an initial validation of gait markers. Then in order to quantify FM patients according to psychometric and gait variables an open descriptive analysis comparing patients and controls were made, and correlations between gait variables and main outcomes were calculated. Finally using cluster analysis, we described subgroups for each gait variable and looked for significant differences in self-reported assessments. Results SF was the most discriminating gait variable (73% of patients and controls. SF, SR, and CCP were different between patients and controls. There was a non-significant association between SF, FIQ and physical components from Short-Form 36 (p = 0.06. SR was correlated to FIQ (p = 0.01 and catastrophizing (p = 0.05 while CCP was correlated to pain (p = 0.01. The SF cluster identified 3 subgroups with a particular one characterized by normal SF, low pain, high activity and hyperkinesia. The SR cluster identified 2 distinct subgroups: the one with a

  20. Efficacy of Nintedanib in Idiopathic Pulmonary Fibrosis across Prespecified Subgroups in INPULSIS.

    Science.gov (United States)

    Costabel, Ulrich; Inoue, Yoshikazu; Richeldi, Luca; Collard, Harold R; Tschoepe, Inga; Stowasser, Susanne; Azuma, Arata

    2016-01-15

    In the two replicate, placebo-controlled, 52-week, phase III INPULSIS trials, nintedanib 150 mg twice daily significantly reduced the annual rate of decline in FVC, the primary endpoint, in subjects with idiopathic pulmonary fibrosis (IPF). It is unknown if this effect was uniform across all subjects treated with nintedanib. To investigate the potential association of demographic and clinical variables with the effect of nintedanib in subjects with IPF. Subgroup analyses of pooled data from the INPULSIS trials were prespecified. Subgroups were analyzed by sex, age (70%), baseline St. George's Respiratory Questionnaire (SGRQ) total score (≤40, >40), smoking status (never, ex/current), systemic corticosteroid use (yes/no), and bronchodilator use (yes/no). A total of 1,061 subjects were treated (nintedanib n = 638, placebo n = 423). There was no statistically significant difference in the effect of nintedanib for the primary endpoint or the key secondary endpoints of change from baseline in SGRQ total score or time to first acute exacerbation in any subgroup. Treatment effects for the key secondary endpoints seemed more pronounced in subjects with baseline FVC ≤70% predicted, because the majority of acute exacerbations and a greater deterioration in SGRQ total score occurred in placebo-treated subjects in this subgroup. Pooled data from the INPULSIS trials support a consistent effect of nintedanib across a range of IPF phenotypes by slowing disease progression across a number of prespecified subgroups.

  1. [Identification of subgroups with lower level of stroke knowledge using decision-tree analysis].

    Science.gov (United States)

    Kim, Hyun Kyung; Jeong, Seok Hee; Kang, Hyun Cheol

    2014-02-01

    This study was performed to explore levels of stroke knowledge and identify subgroups with lower levels of stroke knowledge among adults in Korea. A cross-sectional survey was used and data were collected in 2012. A national sample of 990 Koreans aged 20 to 74 years participated in this study. Knowledge of risk factors, warning signs, and first action for stroke were surveyed using face-to-face interviews. Descriptive statistics and decision tree analysis were performed using SPSS WIN 20.0 and Answer Tree 3.1. Mean score for stroke risk factor knowledge was 7.7 out of 10. The least recognized risk factor was diabetes and four subgroups with lower levels of knowledge were identified. Score for knowledge of stroke warning signs was 3.6 out of 6. The least recognized warning sign was sudden severe headache and six subgroups with lower levels of knowledge were identified. The first action for stroke was recognized by 65.7 percent of participants and four subgroups with lower levels of knowledge were identified. Multi-faceted education should be designed to improve stroke knowledge among Korean adults, particularly focusing on subgroups with lower levels of knowledge and less recognition of items in this study.

  2. Detecting treatment-subgroup interactions in clustered data with generalized linear mixed-effects model trees.

    Science.gov (United States)

    Fokkema, M; Smits, N; Zeileis, A; Hothorn, T; Kelderman, H

    2017-10-25

    Identification of subgroups of patients for whom treatment A is more effective than treatment B, and vice versa, is of key importance to the development of personalized medicine. Tree-based algorithms are helpful tools for the detection of such interactions, but none of the available algorithms allow for taking into account clustered or nested dataset structures, which are particularly common in psychological research. Therefore, we propose the generalized linear mixed-effects model tree (GLMM tree) algorithm, which allows for the detection of treatment-subgroup interactions, while accounting for the clustered structure of a dataset. The algorithm uses model-based recursive partitioning to detect treatment-subgroup interactions, and a GLMM to estimate the random-effects parameters. In a simulation study, GLMM trees show higher accuracy in recovering treatment-subgroup interactions, higher predictive accuracy, and lower type II error rates than linear-model-based recursive partitioning and mixed-effects regression trees. Also, GLMM trees show somewhat higher predictive accuracy than linear mixed-effects models with pre-specified interaction effects, on average. We illustrate the application of GLMM trees on an individual patient-level data meta-analysis on treatments for depression. We conclude that GLMM trees are a promising exploratory tool for the detection of treatment-subgroup interactions in clustered datasets.

  3. Somatosensory nociceptive characteristics differentiate subgroups in people with chronic low back pain: a cluster analysis.

    Science.gov (United States)

    Rabey, Martin; Slater, Helen; OʼSullivan, Peter; Beales, Darren; Smith, Anne

    2015-10-01

    The objectives of this study were to explore the existence of subgroups in a cohort with chronic low back pain (n = 294) based on the results of multimodal sensory testing and profile subgroups on demographic, psychological, lifestyle, and general health factors. Bedside (2-point discrimination, brush, vibration and pinprick perception, temporal summation on repeated monofilament stimulation) and laboratory (mechanical detection threshold, pressure, heat and cold pain thresholds, conditioned pain modulation) sensory testing were examined at wrist and lumbar sites. Data were entered into principal component analysis, and 5 component scores were entered into latent class analysis. Three clusters, with different sensory characteristics, were derived. Cluster 1 (31.9%) was characterised by average to high temperature and pressure pain sensitivity. Cluster 2 (52.0%) was characterised by average to high pressure pain sensitivity. Cluster 3 (16.0%) was characterised by low temperature and pressure pain sensitivity. Temporal summation occurred significantly more frequently in cluster 1. Subgroups were profiled on pain intensity, disability, depression, anxiety, stress, life events, fear avoidance, catastrophizing, perception of the low back region, comorbidities, body mass index, multiple pain sites, sleep, and activity levels. Clusters 1 and 2 had a significantly greater proportion of female participants and higher depression and sleep disturbance scores than cluster 3. The proportion of participants undertaking Low back pain, therefore, does not appear to be homogeneous. Pain mechanisms relating to presentations of each subgroup were postulated. Future research may investigate prognoses and interventions tailored towards these subgroups.

  4. Breast Cancer Prevalence and Mortality among Hispanic Subgroups in the United States, 2009–2013

    Directory of Open Access Journals (Sweden)

    Bijou R. Hunt

    2016-01-01

    Full Text Available Background. This paper presents data on breast cancer prevalence and mortality among US Hispanics and Hispanic subgroups, including Cuban, Mexican, Puerto Rican, Central American, and South American. Methods. Five-year average annual female breast cancer prevalence and mortality rates for 2009–2013 were examined using data from the National Health Interview Survey (prevalence and the National Center for Health Statistics and the American Community Survey (mortality rates. Results. Overall breast cancer prevalence among US Hispanic women was 1.03%. Although the estimates varied slightly by Hispanic subgroup, these differences were not statistically significant. The breast cancer mortality rate for Hispanics overall was 17.71 per 100,000 women. Higher rates were observed among Cubans (17.89, Mexicans (18.78, and Puerto Ricans (19.04, and a lower rate was observed among Central and South Americans (10.15. With the exception of the rate for Cubans, all Hispanic subgroup rates were statistically significantly different from the overall Hispanic rate. Additionally, all Hispanic subgroups rates were statistically significantly higher than the Central and South American rate. Conclusion. The data reveal significant differences in mortality across Hispanic subgroups. These data enable public health officials to develop targeted interventions to help lower breast cancer mortality among the highest risk populations.

  5. Fixed and Adaptive Parallel Subgroup-Specific Design for Survival Outcomes: Power and Sample Size

    Directory of Open Access Journals (Sweden)

    Miranta Antoniou

    2017-12-01

    Full Text Available Biomarker-guided clinical trial designs, which focus on testing the effectiveness of a biomarker-guided approach to treatment in improving patient health, have drawn considerable attention in the era of stratified medicine with many different designs being proposed in the literature. However, planning such trials to ensure they have sufficient power to test the relevant hypotheses can be challenging and the literature often lacks guidance in this regard. In this study, we focus on the parallel subgroup-specific design, which allows the evaluation of separate treatment effects in the biomarker-positive subgroup and biomarker-negative subgroup simultaneously. We also explore an adaptive version of the design, where an interim analysis is undertaken based on a fixed percentage of target events, with the option to stop each biomarker-defined subgroup early for futility or efficacy. We calculate the number of events and patients required to ensure sufficient power in each of the biomarker-defined subgroups under different scenarios when the primary outcome is time-to-event. For the adaptive version, stopping probabilities are also explored. Since multiple hypotheses are being tested simultaneously, and multiple interim analyses are undertaken, we also focus on controlling the overall type I error rate by way of multiplicity adjustment.

  6. Diversity among mandarin varieties and natural sub-groups in aroma volatiles compositions.

    Science.gov (United States)

    Goldenberg, Livnat; Yaniv, Yossi; Doron-Faigenboim, Adi; Carmi, Nir; Porat, Ron

    2016-01-15

    Mandarins constitute a large, diverse and important group within the Citrus family. Here, we analysed the aroma volatiles compositions of 13 mandarin varieties belonging to seven genetically different natural sub-groups that included common mandarin (C. reticulata Blanco), clementine (C. clementina Hort. ex. Tan), satsuma (C. unshiu Marcovitch), Mediterranean mandarin (C. deliciosa Tenore), King mandarin (C. nobilis Loureiro), and mandarin hybrids, such as tangor (C. reticulata × C. sinensis) and tangelo (C. reticulata × C. paradisi). We found that mandarin varieties among tangors ('Temple', 'Ortanique'), tangelos ('Orlando', 'Minneola') and King ('King') had more volatiles, at higher levels, and were richer in sesquiterpene and ester volatiles, than other varieties belonging to the sub-groups common mandarin ('Ora', 'Ponkan'), clementine ('Oroval', 'Caffin'), satsuma ('Okitsu', 'Owari') and Mediterranean mandarin ('Avana', 'Yusuf Efendi'). Hierarchical clustering and principal component analysis accurately differentiated between mandarin varieties and natural sub-groups according to their aroma-volatile profiles. Although we found wide differences in aroma-volatiles compositions among varieties belonging to different natural sub-groups, we detected only minor differences among varieties within any natural sub-group. These findings suggest that selecting appropriate parents would enable manipulation of aroma-volatile compositions in future mandarin breeding programmes. © 2015 Society of Chemical Industry.

  7. Are there distinct cognitive and motivational sub-groups of children with ADHD?

    DEFF Research Database (Denmark)

    Lambek, Rikke; Sonuga-Barke, Edmund; Tannock, Rosemary

    2017-01-01

    relevant correlates. One-hundred medication-naïve children with ADHD and 96 typically developing children (6–14 years) completed nine EF and three DA tasks as well as an odor identification test. Parents and teachers provided reports of the children's behavior (ADHD and EF). Models of the latent structure...... of scores on EF and DA tests were contrasted using confirmatory factor analysis (CFA). LPA was carried out based on factor scores from the CFA and sub-groups were compared in terms of odor identification and behavior. A model with one DA and two EF factors best fit the data. LPA resulted in four sub......-groups that differed in terms of general level of neuropsychological performance (ranging from high to very low), odor identification, and behavior. The sub-groups did not differ in terms of the relative EF and DA performance. Results in the ADHD group were replicated in the control group. While EF and DA appear...

  8. Identity practices, ingroup projection, and the evaluation of subgroups: a study among Turkish-Dutch Sunnis.

    Science.gov (United States)

    Lie, Jessamina Lih Yan; Verkuyten, Maykel

    2012-01-01

    This research focuses on religious subgroup evaluations by examining the attitude of Turkish-Dutch Sunni Muslims towards Alevi and Shiite Muslims. Following the Ingroup Projection Model, it was expected that Sunni participants who practice Islam will project their self-defining subgroup practices on the superordinate Muslim category, which will be related to more ingroup bias towards Alevis, a Muslim subgroup that performs different religious practices. Two studies yielded consistent evidence that practicing Islam increased ingroup bias towards Alevis. Furthermore, in Study 2, we found evidence that the effect of practicing Islam on ingroup bias was mediated by relative ingroup prototypicality (RIP). Moreover, practicing Islam did not affect RIP in relation to Shiites who perform the same religious practices that we examined. These findings support the Ingroup Projection Model.

  9. Eating disorder behavior and early maladaptive schemas in subgroups of eating disorders.

    Science.gov (United States)

    Unoka, Zsolt; Tölgyes, Tamás; Czobor, Pál; Simon, Lajos

    2010-06-01

    To examine relationship between Eating Disorder Behaviors (EDB) and Early Maladaptive Schemas (EMS) across eating disorder (ED) subgroups. EMS and ED behaviors were measured by Young Schema Questionnaire and Eating Behavior Severity Scale, respectively, among patients diagnosed with Restrictive or Binge/purging Anorexia, or bulimia nervosa. Canonical component analysis showed significant association between ED behaviors and EMSs. Canonical factor-pairs (EDB and EMS) revealed specific associations between certain patterns of EDBs, including binge-purging and physical exercise, and certain patterns of maladaptive cognitive schema, including Emotional deprivation, Abandonment, Enmeshments, Subjugation, and Emotional inhibition. ED subgroups significantly differred between the EMS and EDB canonical factors, respectively. Our findings indicate that EMS and EDB are associated, and that the factors that potentially mediate the association differ significantly among ED subgroups. These results are consistent with the notion that EMSs play a specific role in the development and maintenance of ED behaviors.

  10. Effect of Nintedanib in Subgroups of Idiopathic Pulmonary Fibrosis by Diagnostic Criteria.

    Science.gov (United States)

    Raghu, Ganesh; Wells, Athol U; Nicholson, Andrew G; Richeldi, Luca; Flaherty, Kevin R; Le Maulf, Florence; Stowasser, Susanne; Schlenker-Herceg, Rozsa; Hansell, David M

    2017-01-01

    In the absence of a surgical lung biopsy, patients diagnosed with idiopathic pulmonary fibrosis (IPF) in clinical practice could participate in the INPULSIS trials of nintedanib if they had honeycombing and/or traction bronchiectasis plus reticulation, without atypical features of usual interstitial pneumonia (UIP), on high-resolution computed tomography (HRCT). Thus, the patients in these trials represented patients with definite UIP and a large subgroup of patients with possible UIP. To investigate the potential impact of diagnostic subgroups on the progression of IPF and the effect of nintedanib. We conducted a post hoc subgroup analysis of patients with honeycombing on HRCT and/or confirmation of UIP by biopsy versus patients without either, using pooled data from the INPULSIS trials. Seven hundred twenty-three (68.1%) patients had honeycombing and/or biopsy, and 338 (31.9%) patients had no honeycombing or biopsy. In these subgroups, respectively, the adjusted annual rate of decline in FVC in patients treated with placebo was -225.7 and -221.0 ml/yr, and the nintedanib versus placebo difference in the adjusted annual rate of decline in FVC was 117.0 ml/yr (95% confidence interval, 76.3-157.8) and 98.9 ml/yr (95% confidence interval, 36.4-161.5). There was no significant treatment-by-subgroup interaction (P = 0.8139). Adverse events were similar between the subgroups. Patients with IPF diagnosed in clinical practice who had possible UIP with traction bronchiectasis on HRCT and had not undergone surgical lung biopsy had disease that progressed in a similar way, and responded similarly to nintedanib, to that of patients with honeycombing on HRCT and/or confirmation of UIP by biopsy.

  11. Subgroup and resistance analyses of raltegravir for resistant HIV-1 infection

    DEFF Research Database (Denmark)

    Cooper, David A; Steigbigel, Roy T; Gatell, Jose M

    2008-01-01

    conducted subgroup analyses of the data from week 48 in both studies according to baseline prognostic factors. Genotyping of the integrase gene was performed in raltegravir recipients who had virologic failure. RESULTS: Virologic responses to raltegravir were consistently superior to responses to placebo...... over placebo was shown in clinically relevant subgroups of patients, including those with baseline characteristics that typically predict a poor response to antiretroviral therapy: a high HIV-1 RNA level, low CD4 cell count, and low genotypic or phenotypic sensitivity score. (ClinicalTrials.gov numbers...

  12. Identification of a novel subgroup of Koala retrovirus from Koalas in Japanese zoos.

    Science.gov (United States)

    Shojima, Takayuki; Yoshikawa, Rokusuke; Hoshino, Shigeki; Shimode, Sayumi; Nakagawa, So; Ohata, Takuji; Nakaoka, Rie; Miyazawa, Takayuki

    2013-09-01

    We identified a new subgroup of koala retrovirus (KoRV), named KoRV-J, which utilizes thiamine transport protein 1 as a receptor instead of the Pit-1 receptor used by KoRV (KoRV-A). By subgroup-specific PCR, KoRV-J and KoRV-A were detected in 67.5 and 100% of koalas originating from koalas from northern Australia, respectively. Altogether, our results indicate that the invasion of the koala population by KoRV-J may have occurred more recently than invasion by KoRV-A.

  13. The Importance of Risk and Subgroup Analysis of Nonparticipants in a Geriatric Intervention Study

    DEFF Research Database (Denmark)

    Rosted, E.; Poulsen, Ingrid; Hendriksen, C

    2016-01-01

    Background. A major concern in intervention studies is the generalizability of the findings due to refusal of intended participants to actually take part. In studies including ill older people the number of those declining to participate may be large and the concern is therefore relevant...... randomized study. Conclusion. We recommend that intervention studies among older people or other fragile patient groups include analysis of relevant risk and subgroup analyses of refusers........ Objectives. To compare patients characteristics, rates of acute readmission, and mortality after one and six months among older persons who agreed and those who declined to participate in a randomized controlled trial and to describe subgroups of nonparticipants. Design. Comparative study based...

  14. The Importance of Risk and Subgroup Analysis of Nonparticipants in a Geriatric Intervention Study

    DEFF Research Database (Denmark)

    Rosted, E.; Poulsen, Ingrid; Hendriksen, C

    2016-01-01

    . Objectives. To compare patients characteristics, rates of acute readmission, and mortality after one and six months among older persons who agreed and those who declined to participate in a randomized controlled trial and to describe subgroups of nonparticipants. Design. Comparative study based...... on a randomized controlled trial. Setting. University hospital in the Capital Region of Denmark. Participants. Patients >70 years discharged home after a short Emergency Department stay. 399 were requested to participate; 271 consented, whereas 128 refused. Results. Refusers were more likely to be readmitted (p...... randomized study. Conclusion. We recommend that intervention studies among older people or other fragile patient groups include analysis of relevant risk and subgroup analyses of refusers....

  15. A comparison of three clustering methods for finding subgroups in MRI, SMS or clinical data

    DEFF Research Database (Denmark)

    Kent, Peter; Jensen, Rikke K; Kongsted, Alice

    2014-01-01

    intensity data collected for 52 weeks by text (SMS) messaging (n = 1,121 people), and the last dataset contained a range of clinical variables measured in low back pain patients (n = 543 people). Four artificial datasets (n = 1,000 each) containing subgroups of varying complexity were also analysed testing......BACKGROUND: There are various methodological approaches to identifying clinically important subgroups and one method is to identify clusters of characteristics that differentiate people in cross-sectional and/or longitudinal data using Cluster Analysis (CA) or Latent Class Analysis (LCA...

  16. Optimizing Subgroups Formation for E-MBMS Transmissions in LTE Networks

    Science.gov (United States)

    Algharem, M.; Omar, M. H.; Stiawan, D.; Budiarto, R.

    2017-04-01

    Long Term Evolution (LTE) network provides a high throughput with low latency which make it suitable for multicast and broadcast services. In Conventional Multicast Scheme (CMS), data is transmitted according to the user with worst channel condition which results in wasting network resources. To overcome the drawback of CMS, a new subgrouping mechanism is proposed to split the multicast group into several subgroups based on users channel quality. The performance of the proposed mechanism has been evaluated using LTE simulator. The simulation results show that the proposed mechanism increase the multicast performance compared to CMS in term of goodput and spectrum efficiency, while maintain fairness index of users in an acceptable level.

  17. Clinimetrics corner: choosing appropriate study designs for particular questions about treatment subgroups

    DEFF Research Database (Denmark)

    Kent, Peter; Hancock, Mark; Petersen, Ditte H.D

    2010-01-01

    , depending on the design of the trial. Objectives: This paper discusses the randomized controlled trial designs that are suitable to answer particular questions about treatment subgroups. It focuses on trial designs that are suitable to answer four questions: (1) 'Is the treatment effective in a pre...... that are inappropriate given the randomized controlled trial design used. The research design to choose, when developing a study protocol that investigates the effect of treatment subgroups, depends on the particular research question. Similarly, the inferences that can be drawn from an existing study will vary...

  18. Internalin profiling and multilocus sequence typing suggest four Listeria innocua subgroups with different evolutionary distances from Listeria monocytogenes

    Directory of Open Access Journals (Sweden)

    Wang Jun

    2010-03-01

    Full Text Available Abstract Background Ecological, biochemical and genetic resemblance as well as clear differences of virulence between L. monocytogenes and L. innocua make this bacterial clade attractive as a model to examine evolution of pathogenicity. This study was attempted to examine the population structure of L. innocua and the microevolution in the L. innocua-L. monocytogenes clade via profiling of 37 internalin genes and multilocus sequence typing based on the sequences of 9 unlinked genes gyrB, sigB, dapE, hisJ, ribC, purM, gap, tuf and betL. Results L. innocua was genetically monophyletic compared to L. monocytogenes, and comprised four subgroups. Subgroups A and B correlated with internalin types 1 and 3 (except the strain 0063 belonging to subgroup C and internalin types 2 and 4 respectively. The majority of L. innocua strains belonged to these two subgroups. Subgroup A harbored a whole set of L. monocytogenes-L. innocua common and L. innocua-specific internalin genes, and displayed higher recombination rates than those of subgroup B, including the relative frequency of occurrence of recombination versus mutation (ρ/θ and the relative effect of recombination versus point mutation (r/m. Subgroup A also exhibited a significantly smaller exterior/interior branch length ratio than expected under the coalescent model, suggesting a recent expansion of its population size. The phylogram based on the analysis with correction for recombination revealed that the time to the most recent common ancestor (TMRCA of L. innocua subgroups A and B were similar. Additionally, subgroup D, which correlated with internalin type 5, branched off from the other three subgroups. All L. innocua strains lacked seventeen virulence genes found in L. monocytogenes (except for the subgroup D strain L43 harboring inlJ and two subgroup B strains bearing bsh and were nonpathogenic to mice. Conclusions L. innocua represents a young species descending from L. monocytogenes and

  19. Internalin profiling and multilocus sequence typing suggest four Listeria innocua subgroups with different evolutionary distances from Listeria monocytogenes.

    Science.gov (United States)

    Chen, Jianshun; Chen, Qiaomiao; Jiang, Lingli; Cheng, Changyong; Bai, Fan; Wang, Jun; Mo, Fan; Fang, Weihuan

    2010-03-31

    Ecological, biochemical and genetic resemblance as well as clear differences of virulence between L. monocytogenes and L. innocua make this bacterial clade attractive as a model to examine evolution of pathogenicity. This study was attempted to examine the population structure of L. innocua and the microevolution in the L. innocua-L. monocytogenes clade via profiling of 37 internalin genes and multilocus sequence typing based on the sequences of 9 unlinked genes gyrB, sigB, dapE, hisJ, ribC, purM, gap, tuf and betL. L. innocua was genetically monophyletic compared to L. monocytogenes, and comprised four subgroups. Subgroups A and B correlated with internalin types 1 and 3 (except the strain 0063 belonging to subgroup C) and internalin types 2 and 4 respectively. The majority of L. innocua strains belonged to these two subgroups. Subgroup A harbored a whole set of L. monocytogenes-L. innocua common and L. innocua-specific internalin genes, and displayed higher recombination rates than those of subgroup B, including the relative frequency of occurrence of recombination versus mutation (rho/theta) and the relative effect of recombination versus point mutation (r/m). Subgroup A also exhibited a significantly smaller exterior/interior branch length ratio than expected under the coalescent model, suggesting a recent expansion of its population size. The phylogram based on the analysis with correction for recombination revealed that the time to the most recent common ancestor (TMRCA) of L. innocua subgroups A and B were similar. Additionally, subgroup D, which correlated with internalin type 5, branched off from the other three subgroups. All L. innocua strains lacked seventeen virulence genes found in L. monocytogenes (except for the subgroup D strain L43 harboring inlJ and two subgroup B strains bearing bsh) and were nonpathogenic to mice. L. innocua represents a young species descending from L. monocytogenes and comprises four subgroups: two major subgroups A and B

  20. Differences in end-range lumbar flexion during slumped sitting and forward bending between low back pain subgroups and genders

    Science.gov (United States)

    Hoffman, Shannon L.; Johnson, Molly B.; Zou, Dequan; Van Dillen, Linda R.

    2012-01-01

    Patterns of lumbar posture and motion are associated with low back pain (LBP). Research suggests LBP subgroups demonstrate different patterns during common tasks. This study assessed differences in end-range lumbar flexion during two tasks between two LBP subgroups classified according to the Movement System Impairment model. Additionally, the impact of gender differences on subgroup differences was assessed. Kinematic data were collected. Subjects in the Rotation (Rot) and Rotation with Extension (RotExt) LBP subgroups were asked to sit slumped and bend forward from standing. Lumbar end-range flexion was calculated. Subjects reported symptom behavior during each test. Compared to the RotExt subgroup, the Rot subgroup demonstrated greater end-range lumbar flexion during slumped sitting and a trend towards greater end-range lumbar flexion with forward bending. Compared to females, males demonstrated greater end-range lumbar flexion during slumped sitting and forward bending. A greater proportion of people in the Rot subgroup reported symptoms with each test compared to the RotExt subgroup. Males and females were equally likely to report symptoms with each test. Gender differences were not responsible for LBP subgroup differences. Subgrouping people with LBP provides insight into differences in lumbar motion within the LBP population. Results suggesting potential consistent differences across flexion-related tasks support the presence of stereotypical movement patterns that are related to LBP. PMID:22261650

  1. Differences in end-range lumbar flexion during slumped sitting and forward bending between low back pain subgroups and genders.

    Science.gov (United States)

    Hoffman, Shannon L; Johnson, Molly B; Zou, Dequan; Van Dillen, Linda R

    2012-04-01

    Patterns of lumbar posture and motion are associated with low back pain (LBP). Research suggests LBP subgroups demonstrate different patterns during common tasks. This study assessed differences in end-range lumbar flexion during two tasks between two LBP subgroups classified according to the Movement System Impairment model. Additionally, the impact of gender differences on subgroup differences was assessed. Kinematic data were collected. Subjects in the Rotation (Rot) and Rotation with Extension (RotExt) LBP subgroups were asked to sit slumped and bend forward from standing. Lumbar end-range flexion was calculated. Subjects reported symptom behaviour during each test. Compared to the RotExt subgroup, the Rot subgroup demonstrated greater end-range lumbar flexion during slumped sitting and a trend towards greater end-range lumbar flexion with forward bending. Compared to females, males demonstrated greater end-range lumbar flexion during slumped sitting and forward bending. A greater proportion of people in the Rot subgroup reported symptoms with each test compared to the RotExt subgroup. Males and females were equally likely to report symptoms with each test. Gender differences were not responsible for LBP subgroup differences. Subgrouping people with LBP provides insight into differences in lumbar motion within the LBP population. Results suggesting potential consistent differences across flexion-related tasks support the presence of stereotypical movement patterns that are related to LBP. Copyright © 2011 Elsevier Ltd. All rights reserved.

  2. High School Graduation Rates across English Learner Student Subgroups in Arizona. REL 2017-205

    Science.gov (United States)

    Huang, Min; Haas, Eric; Zhu, Niufeng; Tran, Loan

    2016-01-01

    Recent studies have documented differences in academic achievement between current and former English learner students. These differences validate calls for more focused analyses of achievement across English learner student subgroups. Specifically, there is interest in examining variation in academic success based on the amount of time a student…

  3. Bounds for the orders of the finite subgroups of G(k)

    OpenAIRE

    Serre, Jean-Pierre

    2010-01-01

    If k is a commutative field and G a reductive (connected) algebraic group over k, we give bounds for the orders of the finite subgroups of G(k); these bounds depends on the type of G and on the Galois groups of the cyclotomic extensions of k.

  4. Can I retake it? Exploring subgroup differences and criterion-related validity in promotion retesting.

    Science.gov (United States)

    Van Iddekinge, Chad H; Morgeson, Frederick P; Schleicher, Deidra J; Campion, Michael A

    2011-09-01

    Despite recent interest in the practice of allowing job applicants to retest, surprisingly little is known about how retesting affects 2 of the most critical factors on which staffing procedures are evaluated: subgroup differences and criterion-related validity. We examined these important issues in a sample of internal candidates who completed a job-knowledge test for a within-job promotion. This was a useful context for these questions because we had job-performance data on all candidates (N = 403), regardless of whether they passed or failed the promotion test (i.e., there was no direct range restriction). We found that retest effects varied by subgroup, such that females and younger candidates improved more upon retesting than did males and older candidates. There also was some evidence that Black candidates did not improve as much as did candidates from other racial groups. In addition, among candidates who retested, their retest scores were somewhat better predictors of subsequent job performance than were their initial test scores (rs = .38 vs. .27). The overall results suggest that retesting does not negatively affect criterion-related validity and may even enhance it. Furthermore, retesting may reduce the likelihood of adverse impact against some subgroups (e.g., female candidates) but increase the likelihood of adverse impact against other subgroups (e.g., older candidates). PsycINFO Database Record (c) 2011 APA, all rights reserved

  5. Psychosocial and Friendship Characteristics of Bully/Victim Subgroups in Korean Primary School Children

    Science.gov (United States)

    Shin, Yoolim

    2010-01-01

    This study investigated psychosocial and friendship characteristics of Korean children who engaged in bully/victim subgroups among their peer groups. The participants were 605 elementary school students in Bucheon City, Korea. The participants completed a peer nomination inventory as well as loneliness and social anxiety scales. Friendship quality…

  6. Using Social Network Analysis to Identify Sub-Groups in the Operating Room

    NARCIS (Netherlands)

    Listyowardojo, Tita A.; Steglich, Christian; Peuchen, Stephen; Johnson, Addie; de Waard, D.; Godthelp, J.; Kooi, F.L.; Brookhuis, K.A.

    2009-01-01

    The frequency with which operating room (OR) staff work together can impact patient safety because staff who often work together share a set of experiences which may enable them to anticipate each other’s actions and reactions in the future. Identifying sub-groups of staff who frequently work

  7. Patterns of alcohol use and consequences among empirically derived sexual minority subgroups.

    Science.gov (United States)

    Talley, Amelia E; Sher, Kenneth J; Steinley, Douglas; Wood, Phillip K; Littlefield, Andrew K

    2012-03-01

    The current study develops an empirically determined classification of sexual orientation developmental patterns based on participants' annual reports of self-identifications, sexual attractions, and sexual behaviors during the first 4 years of college. A secondary aim of the current work was to examine trajectories of alcohol involvement among identified subgroups. Data were drawn from a subsample of a longitudinal study of incoming first-time college students at a large, public university (n = 2,068). Longitudinal latent class analysis was used to classify sexual minority participants into empirically derived subgroups based on three self-reported facets of sexual orientation. Multivariate repeated-measures analyses were conducted to examine how trajectories of alcohol involvement varied by sexual orientation class membership. Four unique subclasses of sexual orientation developmental patterns were identified for males and females: one consistently exclusively heterosexual group and three sexual minority groups. Despite generally similar alcohol use patterns among subclasses, certain sexual minority subgroups reported elevated levels of alcohol-related negative consequences and maladaptive motivations for use throughout college compared with their exclusively heterosexual counterparts. Elevations in coping and conformity motivations for alcohol use were seen among those subgroups that also evidenced heightened negative alcohol-related consequences. Implications and limitations of the current work are discussed.

  8. Contents of Stereotypes toward Woman Subgroups: An Investigation in the Framework of Stereotype Content Model

    Directory of Open Access Journals (Sweden)

    Timucin Aktan

    2016-12-01

    Full Text Available The aim of the study was to investigate the stereotype contents toward woman subgroups and relate these contents to social-structural predictors and sexism. In this respect, 119 university students were recruited for the first study and they were asked to rate 10 woman subgroups in terms of their competence and warmth, and their status and competitiveness. Participants' level of sexism was also measured using ambivalent sexism scale. The findings of the first study revealed that competence and warmth were the two fundamental dimensions of the stereotype contents, these stereotypes could be depicted in three clusters, the content of many women stereotypes were mixed, and status was linked to competence and competition was related to lack of warmth. Besides replicating the main hypotheses of stereotype content model, the findings supported its two basic assumptions, i.e. negative stereotypes are not necessary to reveal stereotype clusters and personal stereotypes are more open to motivational concerns. Finally, sexism was related only with competition, but not with stereotype contents. Since, high competent / high warm cluster was not observed in the first study, the number of woman subgroups was increased in the second study. Thus, 86 university students were asked to rate 18 women subgroups on the scales used in the first study. Results replicated the findings of the first study, supporting the main hypothesis of stereotype content model. The findings of the studies were discussed in the light of relevant literature.

  9. Clinical trials with nested subgroups: Analysis, sample size determination and internal pilot studies.

    Science.gov (United States)

    Placzek, Marius; Friede, Tim

    2017-01-01

    The importance of subgroup analyses has been increasing due to a growing interest in personalized medicine and targeted therapies. Considering designs with multiple nested subgroups and a continuous endpoint, we develop methods for the analysis and sample size determination. First, we consider the joint distribution of standardized test statistics that correspond to each (sub)population. We derive multivariate exact distributions where possible, providing approximations otherwise. Based on these results, we present sample size calculation procedures. Uncertainties about nuisance parameters which are needed for sample size calculations make the study prone to misspecifications. We discuss how a sample size review can be performed in order to make the study more robust. To this end, we implement an internal pilot study design where the variances and prevalences of the subgroups are reestimated in a blinded fashion and the sample size is recalculated accordingly. Simulations show that the procedures presented here do not inflate the type I error significantly and maintain the prespecified power as long as the sample size of the smallest subgroup is not too small. We pay special attention to the case of small sample sizes and attain a lower boundary for the size of the internal pilot study.

  10. Structural Mobility, Exchange Mobility and Subgroup Consistent Mobility Measurement – US–German Mobility Measurements Revisited

    OpenAIRE

    Schluter, C.; D. VAN DE GAER

    2008-01-01

    We formalize the concept of structural mobility and use the framework of subgroup consistent mobility measurement to derive a relative and an absolute measure of mobility that is increasing both in upward structural mobility and exchange mobility. In our empirical illustration, we contribute substantively to the ongoing debate about mobility rankings between the USA and Germany.

  11. Perceived discrimination and chronic health in adults from nine ethnic subgroups in the USA.

    Science.gov (United States)

    Carlisle, Shauna K

    2015-01-01

    This comparative analysis examines the association between chronic cardiovascular, respiratory and pain conditions, race, ethnicity, nativity, length of residency, and perceived discrimination among three racial and nine ethnic subgroups of Asian Americans (Vietnamese, Filipino, and Chinese), Latino-American (Cuban, Portuguese, and Mexican), and Afro-Caribbean American (Haitian, Jamaican, and Trinidadian/Tobagonian) respondents. Analysis used weighted Collaborative Psychiatric Epidemiology Surveys-merged data from the National Latino and Asian American Study and the National Survey of American Life. Logistic regression analysis was conducted to determine which groups within the model were more likely to report perceived discrimination effects. Afro-Caribbean subgroups were more likely to report perceived discrimination than Asian American and Latino-American subgroups were. Logistic regression revealed a significant positive association with perceived discrimination and chronic pain only for Latino-American respondents. Significant differences in reports of perceived discrimination emerged by race and ethnicity. Caribbean respondents were more likely to report high levels of perceived discrimination; however, they showed fewer significant associations related to chronic health conditions compared to Asian Americans and Latino-Americans. Examination of perceived discrimination across ethnic subgroups reveals large variations in the relationship between chronic health and discrimination by race and ethnicity. Examining perceived discrimination by ethnicity may reveal more complex chronic health patterns masked by broader racial groupings.

  12. Manual therapy in osteoarthritis of the hip: outcome in subgroups of patients

    NARCIS (Netherlands)

    Hoeksma, H.L.; Dekker, J.; Ronday, H.K.; Breedveld, F.C.; Ende, van den C.H.M.

    2005-01-01

    OBJECTIVE: To investigate whether manual therapy has particular benefit in subgroups of patients defined on the basis of hip function, range of joint motion, pain and radiological deterioration. METHODS: The study was performed in the out-patient clinic of physical therapy of a large hospital. Data

  13. Manual therapy in osteoarthritis of the hip: outcome in specific subgroups of patients.

    NARCIS (Netherlands)

    Hoeksma, H.L.; Dekker, J.; Ronday, H.K.; Breedveld, F.C.; Ende, C.H.M. van den

    2005-01-01

    OBJECTIVE: To investigate whether manual therapy has particular benefit in subgroups of patients defined on the basis of hip function, range of joint motion, pain and radiological deterioration. METHODS: The study was performed in the out-patient clinic of physical therapy of a large hospital. Data

  14. Manual therapy in osteoarthritis of the hip: outcome in subgroups of patients

    NARCIS (Netherlands)

    Hoeksma, H.L.; Dekker, J.; Ronday, H.K.; Breedveld, F.C.; van den Ende, C.H.M.

    2005-01-01

    Objective. To investigate whether manual therapy has particular benefit in subgroups of patients defined on the basis of hip function, range of joint motion, pain and radiological deterioration. Methods. The study was performed in the out-patient clinic of physical therapy of a large hospital. Data

  15. Young People with Harmful Sexual Behaviour: Do Those with Learning Disabilities Form a Distinct Subgroup?

    Science.gov (United States)

    Almond, Louise; Giles, Susan

    2008-01-01

    The study examines 102 young people with Learning Disabilities (n = 51) and without a learning disability (NLD; n = 51) to explore ways in which LD young people with harmful sexual behaviours (HSB) should be recognized as a subgroup requiring specialized treatment and intervention. Throughout this comparison of perpetrator, victim and abuse…

  16. Hecke Eigenforms in the Cohomology of Congruence Subgroups of SL(3, Z)

    NARCIS (Netherlands)

    Geemen, Bert van; Kallen, Wilberd van der; Top, Jaap; Verberkmoes, Alain

    1997-01-01

    We list here Hecke eigenvalues of several automorphic forms for congruence subgroups of SL(3; Z). To compute such tables, we describe an algorithm that combines techniques developed previously with the Lenstra–Lenstra–Lovász algorithm. With our implementation of this new algorithm we were able to

  17. The Influence of Working Memory on Reading Growth in Subgroups of Children with Reading Disabilities

    Science.gov (United States)

    Swanson, H. Lee; Jerman, Olga

    2007-01-01

    This 3-year longitudinal study determined whether (a) subgroups of children with reading disabilities (RD) (children with RD only, children with both reading and arithmetic deficits, and low verbal IQ readers) and skilled readers varied in working memory (WM) and short-term memory (STM) growth and (b) whether growth in an executive system and/or a…

  18. Identification and Characterization of Unique Subgroups of Chronic Pain Individuals with Dispositional Personality Traits

    Directory of Open Access Journals (Sweden)

    S. Mehta

    2016-01-01

    Full Text Available Objective. The current study attempted to identify and characterize distinct CP subgroups based on their level of dispositional personality traits. The secondary objective was to compare the difference among the subgroups in mood, coping, and disability. Methods. Individuals with chronic pain were assessed for demographic, psychosocial, and personality measures. A two-step cluster analysis was conducted in order to identify distinct subgroups of patients based on their level of personality traits. Differences in clinical outcomes were compared using the multivariate analysis of variance based on cluster membership. Results. In 229 participants, three clusters were formed. No significant difference was seen among the clusters on patient demographic factors including age, sex, relationship status, duration of pain, and pain intensity. Those with high levels of dispositional personality traits had greater levels of mood impairment compared to the other two groups (p<0.05. Significant difference in disability was seen between the subgroups. Conclusions. The study identified a high risk group of CP individuals whose level of personality traits significantly correlated with impaired mood and coping. Use of pharmacological treatment alone may not be successful in improving clinical outcomes among these individuals. Instead, a more comprehensive treatment involving psychological treatments may be important in managing the personality traits that interfere with recovery.

  19. Identification and Characterization of Unique Subgroups of Chronic Pain Individuals with Dispositional Personality Traits.

    Science.gov (United States)

    Mehta, S; Rice, D; McIntyre, A; Getty, H; Speechley, M; Sequeira, K; Shapiro, A P; Morley-Forster, P; Teasell, R W

    2016-01-01

    Objective. The current study attempted to identify and characterize distinct CP subgroups based on their level of dispositional personality traits. The secondary objective was to compare the difference among the subgroups in mood, coping, and disability. Methods. Individuals with chronic pain were assessed for demographic, psychosocial, and personality measures. A two-step cluster analysis was conducted in order to identify distinct subgroups of patients based on their level of personality traits. Differences in clinical outcomes were compared using the multivariate analysis of variance based on cluster membership. Results. In 229 participants, three clusters were formed. No significant difference was seen among the clusters on patient demographic factors including age, sex, relationship status, duration of pain, and pain intensity. Those with high levels of dispositional personality traits had greater levels of mood impairment compared to the other two groups (p disability was seen between the subgroups. Conclusions. The study identified a high risk group of CP individuals whose level of personality traits significantly correlated with impaired mood and coping. Use of pharmacological treatment alone may not be successful in improving clinical outcomes among these individuals. Instead, a more comprehensive treatment involving psychological treatments may be important in managing the personality traits that interfere with recovery.

  20. The Measurement of Collaborative Culture in Secondary Schools: An Informal Subgroup Approach

    Science.gov (United States)

    Meredith, Chloé; Moolenaar, Nienke M.; Struyve, Charlotte; Vandecandelaere, Machteld; Gielen, Sarah; Kyndt, Eva

    2017-01-01

    Research on teacher collaboration underlines the importance of a collaborative culture for teachers' functioning. However, while scholars usually regard collaborative culture as a school team characteristic, this study argues that subgroups may be more meaningful units of analysis to conceptualize and assess teachers' perceptions of collaborative…

  1. Pooling of Individual Patient Data from Clinical Trials. Improvement of analyses of subgroups

    NARCIS (Netherlands)

    Koopman, L.

    2008-01-01

    Meta-analyses that use individual patient data (IPD), that is, the raw data of individual trials, rather than simply the overall results of each trial have been proposed as a major improvement in subgroup analyses. Since IPD meta-analyses often include more detailed data, they usually have greater

  2. Weinberg Angle Derivation from Discrete Subgroups of SU(2 and All That

    Directory of Open Access Journals (Sweden)

    Potter F.

    2015-01-01

    Full Text Available The Weinberg angle W of the Standard Model of leptons and quarks is derived from specific discrete (i.e., finite subgroups of the electroweak local gauge group SU(2 L U(1 Y . In addition, the cancellation of the triangle anomaly is achieved even when there are four quark families and three lepton families!

  3. Subgroup analyses of maraviroc in previously treated R5 HIV-1 infection

    NARCIS (Netherlands)

    Fätkenheuer, Gerd; Nelson, Mark; Lazzarin, Adriano; Konourina, Irina; Hoepelman, Andy I. M.; Lampiris, Harry; Hirschel, Bernard; Tebas, Pablo; Raffi, François; Trottier, Benoit; Bellos, Nicholaos; Saag, Michael; Cooper, David A.; Westby, Mike; Tawadrous, Margaret; Sullivan, John F.; Ridgway, Caroline; Dunne, Michael W.; Felstead, Steve; Mayer, Howard; van der Ryst, Elna; Angel, Jonathan; Conway, Brian; Gough, Kevin A.; Lalonde, Richard G.; Laplante, Francois; Leblanc, Roger P.; Montaner, Julio S. G.; Rachlis, Anita R.; Romanowski, Barbara; Rosser, Stuart J.; Rubinstein, Ethan; Shafran, Stephen David; Smaill, Fiona; Tremblay, Cecile; Trottier, Sylvie; Tsoukas, Christos; Walmsley, Sharon Lynn; Voskanian, Alen; Akil, Bisher; Arduino, Roberto Claudio; Asmuth, David; Beatty, George William; Becker, Stephen Lawrence; Bellos, Nicholaos C.; Blue, Sky Robert; Bolan, Robert Key; Brand, John D.; Burnazian, George Ghazaros; Burnside, Alfred F.; Campbell, Thomas B.; Campo, Rafael E.; Casey, Kathleen King; Cimoch, Paul Joseph; Cohen, Calvin J.; Coodley, Gregg Oscar; Corales, Roberto B.; DeJesus, Edwin; Diaz, Leslie E.; Drusano, George L.; Ernst, Jerome A.; Feinberg, Judith E.; Feldman, Lawrence Edward; Fine, Steven M.; Flamm, Jason Andrew; Follansbee, Stephen Eliot; Fralich, Todd Allen; Gallant, Emanuel; Godofsky, Eliot Warren; Green, Gary; Greiger-Zanlungo, Paula Rosa; Gripshover, Barbara Marie; Groger, Richard K.; Gulick, Roy; Hardy, William David; Hassler, Shawn K.; Haubrich, Richard Harold; Hauptman, Stephen P.; Henry, David Holden; Henry, William Keith; Hernandez, Jose Norberto; Hicks, Charles Byron; Horberg, Michael Alan; Jemsek, Joseph G.; Kelly, Allan Rowan; Kinder, Clifford A.; Klein, Daniel Benjamin; Kogelman, Laura; Lalezari, Jacob Paul; LaMarca, Anthony; Lampiris, Harry William; Leibowitz, Matthew; Leider, Jason Mark; Lennox, Jeffrey Lloyd; Liporace, Ralph; Martin, Harold Luther; Martinez-Bejar, Lucia M.; Martorell, Claudia; McGowan, Joseph P.; Mildvan, Donna; Miles, Steven; Mitsuyasu, Ronald Takeshi; Morales-Ramirez, Javier Osvaldo; Morris, Anne B.; Mounzer, Karam Chucri; Myers, Robert Anderson; Nadler, Jeffrey P.; Pearce, Daniel; Pierone, Gerald; Rashbaum, Bruce Stephen; Ravishankar, Jayashree; Redfield, Robert Ray; Reichman, Richard Craig; Robbins, William Jay; Roberts, Stockton Edward; Rodriguez, Jorge E.; Sathasivam, Kunthavi; Sax, Paul Edward; Schwartz, Lawrence E.; Segal-Maurer, Sorana; Sension, Michael Grant; Sepulveda-Arzola, Gladys E.; Skolnik, Paul Richard; Sloan, Louis Marshall; Smith, Robert P.; Sosman, James Michael; Stapleton, Jack Thomas; Steigbigel, Roy; Steinhart, Corklin R.; Sweet, Donna Elaine; Swindells, Susan; Thompson, Melanie Ann; Sisneros, Silver; Towner, William James; Gordon, Peter; Hawkins, Trevor N.; Wheeler, David Allen; Williams, Sally; Wilcox, Dean; Williams, Steven; Wills, Todd Stephen; Wohlfeiler, Michael Bruce; Wright, David; Xavier, Angela; Yangco, Bienvenido Gamulo; Zingman, Barry Stephen; Zorrilla, Carmen D.; Allworth, Anthony M.; Bloch, Mark T.; Bodsworth, Neil J.; Chuah, John; Cooper, David; Doong, Nicholas; Dwyer, Dominic; Gold, Julian; Hoy, Jennifer Frances; Moore, Richard J.; Roth, Norman J.; Workman, Cassy; Clumeck, Nathan; Dellot, Patricia; Goffard, Jean Christophe; Moutschen, Michel; Vandercam, Bernard C.; Vogelaers, Dirk; Bentata, Michele; Cotte, Laurent; Delfraissy, Jean-Francois; Durant, Jacques; Girard, Pierre-Marie; Hocqueloux, Laurent; Landman, Roland; Lafeuillade, Alain; Martin, Isabelle Poizot; Molina, Jean-Michel; Pialoux, Gilles; Piketty, Christophe; Raffi, Francois; Reynes, Jacques; Verdon, Renaud; Arasteh, Keikawus; Bogner, Johannes Richard; Brockmeyer, Norbert H.; Esser, Stefan; Goebel, Frank-Detlef; Harrer, Thomas; Kern, Peter; Knechten, Heribert; van Lunzen, Jan; Mueller, Markus; Mutz, Antonius; Oette, Mark; Plettenberg, Andreas; Rockstroh, Juergen; Rump, Jorg-Andres; Schmidt, Reinhold E.; Schneider, Lothar; Schuster, Dieter; Staszewski, Schlomo; Stellbrink, Hans-Juergen; Trein, Andreas; Weitner, Lutwinus; Aiuti, Fernando; Bassetti, Dante; Di Biagio, Antonio; Caramello, Pietro; Carosi, Giampiero; Esposito, Roberto; Leoncini, Francesco; Manconi, Paolo Emilio; Mazzotta, Francesco; Montella, Francesco; Raise, Enzo; Vullo, Vicenzo; Hoepelman, Ilja Mohandas; Perenboom, Rosalinde Maria; Prins, J. M.; Richter, Clemens; van der Ende, Marchina Elisabeth; Beniowski, Marek; Boron-Kaczmarska, Anna; Flisiak, Robert; Halota, Waldemar; Horban, Andrzej; Mach, Tomasz; Smiatacz, Tomasz; Lozano de Leon, Fernando; Viciana Fernandez, Pompeyo; Rubio Garcia, Rafael; Gatell Artigas, Jose Josep; Gonzalez Garcia, Juan Julian; Gutierrez, Felix; Gonzalez Lahoz, Juan; Iribarren Loyarte, Jose; Moreno, Santiago; Pulido Ortega, Federico; Domingo Pedrol, Pere; Rivero, Antonio; Clotet, Bonaventura; Sarria, Cristina; Gisslen, Magnus; Flamholc, Leo; Karlsson, Anders; Battegay, Manuel; Bernasconi, Enos; Cavassini, Matthias; Drechsler, Henning; Opravil, Milos; Vernazza, Pietro; Easterbrook, Philippa Jane; Fisher, Martin; Hay, Philip; Johnson, Margaret A.; Leen, Clifford L.; Nelson, Mark R.; Ong, Edmund; Weber, Jonathan N.; White, David J.; Wilkins, Edmund; Wiselka, Martin; Alvarez-Jacinto, Ana Maria; Antoniskis, Diana; Atkinson, Barbara A.; Berger, Daniel S.; Blick, Gary; Brenna, Robert Owen; Burack, Jeffrey Howard; Church, L. W. Preston; Clay, Patrick G.; Cook, Paul Peniston; Creticos, Catherine Maria; Daly, Patrick William; Feleke, Getachew; File, Thomas Mc Donald; Galpin, Jeffrey Eliot; Green, Stephen Lloyd; Haas, Frances Fae; Hanna, Barbara J.; Hsiao, Chiu-Bin; Hsu, Ricky K.; Jones, Robert S.; Kadlecik, Peter; Kalayjian, Robert Charles; Keller, Robert H.; Kerkar, Shubha; Koirala, Janak; Lai, Leon Liang-Yu; Lalla-Reddy, Sujata; Macarthur, Rodger David; Malanoski, Gregory John; Markowitz, Norman Peter; McLeroth, Patrick L.; McMeeking, Alexander A.; Miljkovic, Goran; Montana, John Buscemi; Nixon, Daniel Edward; Norris, Dorece G.; Penico, Jesse Pullen; Perez-Limonte, Leonel; Posorske, Lynette H.; Prelutsky, David James; Riddell, James; Rodwick, Barry Michael; Ruane, Peter Jerome; Sampson, James; Santiago, Steven; Seinfeld, Amy; Sharp, Victoria Lee; Shebib, Zaher; Tanner, Mark Leslie; Timpone, Joseph G.; Wade, Barbara H.; Wallach, Frances; Weinberg, Winkler; Zurawski, Christine

    2008-01-01

    BACKGROUND: We conducted subanalyses of the combined results of the Maraviroc versus Optimized Therapy in Viremic Antiretroviral Treatment-Experienced Patients (MOTIVATE) 1 and MOTIVATE 2 studies to better characterize the efficacy and safety of maraviroc in key subgroups of patients. METHODS: We

  4. Identification of a genomic subgroup of BK polyomavirus spread in European populations.

    Science.gov (United States)

    Ikegaya, Hiroshi; Saukko, Pekka J; Tertti, Risto; Metsärinne, Kaj P; Carr, Michael J; Crowley, Brendan; Sakurada, Koichi; Zheng, Huai-Ying; Kitamura, Tadaichi; Yogo, Yoshiaki

    2006-11-01

    BK polyomavirus (BKV) is highly prevalent in the human population, infecting children without obvious symptoms and persisting in the kidney in a latent state. In immunosuppressed patients, BKV is reactivated and excreted in urine. BKV isolates worldwide are classified into four serologically distinct subtypes, I-IV, with subtype I being the most frequently detected. Furthermore, subtype I is subdivided into subgroups based on genomic variations. In this study, the distribution patterns of the subtypes and subgroups of BKV were compared among four patient populations with various immunosuppressive states and of various ethnic backgrounds: (A) Finnish renal-transplant recipients; (B) Irish/English haematopoietic stem-cell transplant recipients with and without haemorrhagic cystitis; (C) Japanese renal-transplant recipients; and (D) Japanese bone-marrow transplant recipients. The typing sequences (287 bp) of BKV in population A were determined in this study; those in populations B-D have been reported previously. These sequences were subjected to phylogenetic and single nucleotide polymorphism analyses. Based on the results of these analyses, the BKV isolates in the four patient populations were classified into subtypes and subgroups. The incidence of subtype IV varied significantly among patient populations. Furthermore, the incidence of subgroup Ib-2 within subtype I was high in populations A and B, whereas that of Ic was high in populations C and D (PBKV DNA sequences supported the hypothesis that there is geographical separation of European and Asian BKV strains.

  5. On finite groups whose every proper normal subgroup is a union of ...

    Indian Academy of Sciences (India)

    R. Narasimhan (Krishtel eMaging) 1461 1996 Oct 15 13:05:22

    On finite groups whose every proper normal subgroup is a union of a given number of conjugacy classes. ALI REZA ASHRAFI and GEETHA VENKATARAMAN. ∗. Department of Mathematics, University of Kashan, Kashan, Iran. ∗. Department of Mathematics and Mathematical Sciences Foundation, St. Stephen's. College ...

  6. Contribution of Dietary Supplements to Nutritional Adequacy by Socioeconomic Subgroups in Adults of the United States

    Directory of Open Access Journals (Sweden)

    Jeffrey B. Blumberg

    2017-12-01

    Full Text Available Many Americans have inadequate intakes of several nutrients, and the Dietary Guidelines for Americans 2015–2020 identified vitamins A, C, D, and E, in addition to calcium, magnesium, iron, potassium, choline, and fiber as “underconsumed nutrients”. Based on nationally representative data on 10,698 adults from National Health and Nutrition Examination Surveys (NHANES, 2009–2012, assessments were made of socioeconomic differences, based on the Poverty Income Ratio (PIR, in terms of the association of dietary supplement use on nutrient intake and nutrient inadequacies. Compared to food alone, the use of any dietary supplement plus food was associated with significantly (p < 0.01 higher intakes of 15–16 of 19 nutrients examined in all socioeconomic groups; and significantly reduced rates of inadequacy for 10/17 nutrients in the subgroup PIR > 1.85 (not poor, but only 4–5/17 nutrients (calcium and vitamins A, C, D, E for the poor and nearly poor subgroups (PIR < 1.35 and PIR 1.35 to ≤1.85, respectively. An increased prevalence of intakes above the Tolerable Upper Intake Level (UL was seen for 3–9/13 nutrients, but all were less than 5% in the PIR subgroups. In conclusion, dietary supplement use was associated with an increased micronutrient intake, decreased inadequacies, and a slight increase in the prevalence of intakes above the UL, with greater benefits seen in the PIR > 1.85 subgroup.

  7. Identification of New World Quails Susceptible to Infection with Avian Leukosis Virus Subgroup J.

    Science.gov (United States)

    Plachý, Jiří; Reinišová, Markéta; Kučerová, Dana; Šenigl, Filip; Stepanets, Volodymyr; Hron, Tomáš; Trejbalová, Kateřina; Elleder, Daniel; Hejnar, Jiří

    2017-02-01

    The J subgroup of avian leukosis virus (ALV-J) infects domestic chickens, jungle fowl, and turkeys. This virus enters the host cell through a receptor encoded by the tvj locus and identified as Na+/H+ exchanger 1. The resistance to avian leukosis virus subgroup J in a great majority of galliform species has been explained by deletions or substitutions of the critical tryptophan 38 in the first extracellular loop of Na+/H+ exchanger 1. Because there are concerns of transspecies virus transmission, we studied natural polymorphisms and susceptibility/resistance in wild galliforms and found the presence of tryptophan 38 in four species of New World quails. The embryo fibroblasts of New World quails are susceptible to infection with avian leukosis virus subgroup J, and the cloned Na+/H+ exchanger 1 confers susceptibility on the otherwise resistant host. New World quails are also susceptible to new avian leukosis virus subgroup J variants but resistant to subgroups A and B and weakly susceptible to subgroups C and D of avian sarcoma/leukosis virus due to obvious defects of the respective receptors. Our results suggest that the avian leukosis virus subgroup J could be transmitted to New World quails and establish a natural reservoir of circulating virus with a potential for further evolution. Since its spread in broiler chickens in China and Southeast Asia in 2000, ALV-J remains a major enzootic challenge for the poultry industry. Although the virus diversifies rapidly in the poultry, its spillover and circulation in wild bird species has been prevented by the resistance of most species to ALV-J. It is, nevertheless, important to understand the evolution of the virus and its potential host range in wild birds. Because resistance to avian retroviruses is due particularly to receptor incompatibility, we studied Na+/H+ exchanger 1, the receptor for ALV-J. In New World quails, we found a receptor compatible with virus entry, and we confirmed the susceptibilities of four New

  8. Dietary and physical activity behaviors of New York City children from different ethnic minority subgroups.

    Science.gov (United States)

    Vangeepuram, Nita; Mervish, Nancy; Galvez, Maida P; Brenner, Barbara; Wolff, Mary S

    2012-01-01

    To examine racial/ethnic differences in diet and physical activity behaviors in ethnic minority New York City children. Cross-sectional data from a community-based study of 486 6- to 8-year-old children were used. Race/ethnicity was derived using a caregiver's report of child's race and Hispanic ancestry. Dietary intake was obtained by 24-hour diet recalls using the Nutrition Data System for Research. Physical activity was assessed with pedometers and caregiver interviews. We compared diet and activity measures across racial/ethnic subgroups using chi-square and analysis of variance tests. Multivariate analyses adjusted for age, gender, body mass index, and caregiver education (with breastfeeding history and total energy intake included in diet models). Participants (N = 486) were categorized as Mexican (29.4%), Dominican (8.4%), Puerto Rican (20.6%), other/mixed Hispanic (14.0%), or non-Hispanic black (27.6%). Obesity rates were lower in non-Hispanic blacks (18%) than in Hispanics (31%). Mexicans had the lowest obesity rates among Hispanic subgroups (25%), and Dominicans had the highest (39%). There were differences in mean daily servings of food groups, with Mexicans having healthier diets and Puerto Ricans and non-Hispanic Blacks having less healthy diets. Sedentary time was lower in Mexicans than in other groups in adjusted models. Examination of additional models, including home language, did not show significant differences in the estimates. Diet and activity behaviors varied across racial/ethnic subgroups. Specifically, Mexican children had healthier diets, the least amount of sedentary time, and the lowest rates of obesity among the Hispanic subgroups examined. Targeted interventions in ethnic subgroups may be warranted to address specific behaviors. Copyright © 2012 Academic Pediatric Association. Published by Elsevier Inc. All rights reserved.

  9. A Person-Centered Approach to Examining Heterogeneity and Subgroups Among Survivors of Sexual Assault

    Science.gov (United States)

    Masters, N. Tatiana; Stappenbeck, Cynthia A.; Kaysen, Debra; Kajumulo, Kelly F.; Davis, Kelly Cue; George, William H.; Norris, Jeanette; Heiman, Julia R.

    2015-01-01

    This study identified subgroups of female sexual assault survivors based on characteristics of their victimization experiences, validated the subgroup structure in a second cohort of women recruited identically to the first, and examined subgroups' differential associations with sexual risk/safety behavior, heavy episodic drinking (HED), psychological distress symptomatology, incarceration, transactional sex, and experiences with controlling and violent partners. The community sample consisted of 667 female survivors of adolescent or adult sexual assault who were 21 to 30 years old (M=24.78, SD=2.66). Eligibility criteria included having unprotected sex within the past year, other HIV/STI risk factors, and some experience with HED, but without alcohol problems or dependence. Latent class analyses (LCA) were used to identify subgroups of women with similar victimization experiences. Three groups were identified and validated across two cohorts of women using multiple-group LCA: Contact or Attempted assault (17% of the sample), Incapacitated assault (52%), and Forceful Severe assault (31%). Groups did not differ in their sexual risk/safety behavior. Women in the Forceful Severe category had higher levels of anxiety, depression, and trauma symptoms, higher proportions of incarceration and transactional sex, and more experiences with controlling and violent partners than did women in the other two groups. Women in the Forceful Severe category also reported a higher frequency of HED than women in the Incapacitated category. Different types of assault experiences appear to be differentially associated with negative outcomes. Understanding heterogeneity and subgroups among sexual assault survivors has implications for improving clinical care and contributing to recovery. PMID:26052619

  10. Leading Causes of Death among Asian American Subgroups (2003-2011.

    Directory of Open Access Journals (Sweden)

    Katherine G Hastings

    Full Text Available Our current understanding of Asian American mortality patterns has been distorted by the historical aggregation of diverse Asian subgroups on death certificates, masking important differences in the leading causes of death across subgroups. In this analysis, we aim to fill an important knowledge gap in Asian American health by reporting leading causes of mortality by disaggregated Asian American subgroups.We examined national mortality records for the six largest Asian subgroups (Asian Indian, Chinese, Filipino, Japanese, Korean, Vietnamese and non-Hispanic Whites (NHWs from 2003-2011, and ranked the leading causes of death. We calculated all-cause and cause-specific age-adjusted rates, temporal trends with annual percent changes, and rate ratios by race/ethnicity and sex. Rankings revealed that as an aggregated group, cancer was the leading cause of death for Asian Americans. When disaggregated, there was notable heterogeneity. Among women, cancer was the leading cause of death for every group except Asian Indians. In men, cancer was the leading cause of death among Chinese, Korean, and Vietnamese men, while heart disease was the leading cause of death among Asian Indians, Filipino and Japanese men. The proportion of death due to heart disease for Asian Indian males was nearly double that of cancer (31% vs. 18%. Temporal trends showed increased mortality of cancer and diabetes in Asian Indians and Vietnamese; increased stroke mortality in Asian Indians; increased suicide mortality in Koreans; and increased mortality from Alzheimer's disease for all racial/ethnic groups from 2003-2011. All-cause rate ratios revealed that overall mortality is lower in Asian Americans compared to NHWs.Our findings show heterogeneity in the leading causes of death among Asian American subgroups. Additional research should focus on culturally competent and cost-effective approaches to prevent and treat specific diseases among these growing diverse populations.

  11. Delineation of motoneuron subgroups supplying individual eye muscles in the human oculomotor nucleus.

    Science.gov (United States)

    Che Ngwa, Emmanuel; Zeeh, Christina; Messoudi, Ahmed; Büttner-Ennever, Jean A; Horn, Anja K E

    2014-01-01

    The oculomotor nucleus (nIII) contains the motoneurons of medial, inferior, and superior recti (MR, IR, and SR), inferior oblique (IO), and levator palpebrae (LP) muscles. The delineation of motoneuron subgroups for each muscle is well-known in monkey, but not in human. We studied the transmitter inputs to human nIII and the trochlear nucleus (nIV), which innervates the superior oblique muscle (SO), to outline individual motoneuron subgroups. Parallel series of sections from human brainstems were immunostained for different markers: choline acetyltransferase combined with glutamate decarboxylase (GAD), calretinin (CR) or glycine receptor. The cytoarchitecture was visualized with cresyl violet, Gallyas staining and expression of non-phosphorylated neurofilaments. Apart from nIV, seven subgroups were delineated in nIII: the central caudal nucleus (CCN), a dorsolateral (DL), dorsomedial (DM), central (CEN), and ventral (VEN) group, the nucleus of Perlia (NP) and the non-preganglionic centrally projecting Edinger-Westphal nucleus (EWcp). DL, VEN, NP, and EWcp were characterized by a strong supply of GAD-positive terminals, in contrast to DM, CEN, and nIV. CR-positive terminals and fibers were confined to CCN, CEN, and NP. Based on location and histochemistry of the motoneuron subgroups in monkey, CEN is considered as the SR and IO motoneurons, DL and VEN as the B- and A-group of MR motoneurons, respectively, and DM as IR motoneurons. A good correlation between monkey and man is seen for the CR input, which labels only motoneurons of eye muscles participating in upgaze (SR, IO, and LP). The CCN contained LP motoneurons, and nIV those of SO. This study provides a map of the individual subgroups of motoneurons in human nIII for the first time, and suggests that NP may contain upgaze motoneurons. Surprisingly, a strong GABAergic input to human MR motoneurons was discovered, which is not seen in monkey and may indicate a functional oculomotor specialization.

  12. Serological relationships among subgroups in bovine viral diarrhea virus genotype 1 (BVDV-1).

    Science.gov (United States)

    Alpay, Gizem; Yeşilbağ, Kadir

    2015-01-30

    Bovine viral diarrhea virus (BVDV) has various economic impacts associated with diarrhea, poor performance, an increase in the frequency of other infections and lethal outcomes. Both genotypes, namely BVDV-1 and BVDV-2, as well as different subgroups within these genotypes have been reported worldwide. Understanding the serological differences among the BVDV subgroups is important for disease epidemiology and prevention as well as vaccination programs. The aim of this study was to determine the serological relatedness among the subgroups in BVDV-1. For that purpose, sheep hyperimmune sera were collected against representative strains from 6 of the subgroups of BVDV-1 (BVDV-1a, -1b, -1d, -1f, -1h and -1l). The serum samples that gave the peak antibody titer to the homologous strains were used to perform cross neutralization assays. The highest homologous antibody titer (1:5160) was obtained against BVDV-1h. Regarding the cross neutralizing (heterologous) antibodies, the lowest titer (1:20) was produced by the BVDV-1f antiserum against the BVDV-1a and BVDV1-b viruses. The highest cross neutralizing titer (1:2580) achieved by the BVDV-1h antiserum was against the BVDV-1b strain. The cross neutralization results indicated particular serological differences between the recently described subgroup (BVDV-1l) and BVDV-1a/-1b, which are widely used in commercial vaccines. Considering the cross neutralization titers, it is concluded that selected BVDV-1l and BVDV-1h strains can be used for the development of diagnostic and control tools. Copyright © 2014 Elsevier B.V. All rights reserved.

  13. The efficacy of natalizumab in patients with relapsing multiple sclerosis: subgroup analyses of AFFIRM and SENTINEL.

    LENUS (Irish Health Repository)

    Hutchinson, Michael

    2012-02-01

    The AFFIRM and SENTINEL studies showed that natalizumab was effective both as monotherapy and in combination with interferon beta (IFNbeta)-1a in patients with relapsing multiple sclerosis (MS). Further analyses of AFFIRM and SENTINEL data were conducted to determine the efficacy of natalizumab in prespecified patient subgroups according to baseline characteristics: relapse history 1 year before randomization (1, 2, > or = 3), Expanded Disability Status Scale score (< or = 3.5, > 3.5), number of T2 lesions (< 9, > or = 9), presence of gadolinium-enhancing (Gd+) lesions (0, > or = 1), age (< 40, > or = 40) and gender (male, female). A post hoc analysis was conducted to determine the efficacy of natalizumab in patients with highly active disease (i. e., > or = 2 relapses in the year before study entry and > or = 1 Gd+ lesion at study entry). In both AFFIRM and SENTINEL studies natalizumab reduced the annualized relapse rates across all subgroups (except the small subgroups with < 9 baseline T2 lesions) over 2 years. In AFFIRM, natalizumab significantly reduced the risk of sustained disability progression in most subgroups. In SENTINEL, natalizumab significantly reduced the risk of sustained disability progression in the following subgroups: > or = 9 T2 lesions at baseline, > or = 1 Gd+ lesions at baseline, female patients and patients < 40 years of age. Natalizumab reduced the risk of disability progression by 64 % and relapse rate by 81 % in treatment- naive patients with highly active disease and by 58 % and 76 %, respectively, in patients with highly active disease despite IFNbeta-1a treatment. These results indicate that natalizumab is effective in reducing disability progression and relapses in patients with relapsing MS, particularly in patients with highly active disease.

  14. Diagnostic accuracy of digital versus film mammography: exploratory analysis of selected population subgroups in DMIST.

    Science.gov (United States)

    Pisano, Etta D; Hendrick, R Edward; Yaffe, Martin J; Baum, Janet K; Acharyya, Suddhasatta; Cormack, Jean B; Hanna, Lucy A; Conant, Emily F; Fajardo, Laurie L; Bassett, Lawrence W; D'Orsi, Carl J; Jong, Roberta A; Rebner, Murray; Tosteson, Anna N A; Gatsonis, Constantine A

    2008-02-01

    To retrospectively compare the accuracy of digital versus film mammography in population subgroups of the Digital Mammographic Imaging Screening Trial (DMIST) defined by combinations of age, menopausal status, and breast density, by using either biopsy results or follow-up information as the reference standard. DMIST included women who underwent both digital and film screening mammography. Institutional review board approval at all participating sites and informed consent from all participating women in compliance with HIPAA was obtained for DMIST and this retrospective analysis. Areas under the receiver operating characteristic curve (AUCs) for each modality were compared within each subgroup evaluated (age or= 65 years, dense vs nondense breasts at mammography, and pre- or perimenopausal vs postmenopausal status for the two younger age cohorts [10 new subgroups in toto]) while controlling for multiple comparisons (P film vs both vs neither), mammographic lesion type (mass, calcifications, or other), digital machine type, mammographic and pathologic size and diagnosis, existence of prior mammographic study at time of interpretation, months since prior mammographic study, and compressed breast thickness. Thirty-three centers enrolled 49 528 women. Breast cancer status was determined for 42,760 women, the group included in this study. Pre- or perimenopausal women younger than 50 years who had dense breasts at film mammography comprised the only subgroup for which digital mammography was significantly better than film (AUCs, 0.79 vs 0.54; P = .0015). Breast Imaging Reporting and Data System-based sensitivity in this subgroup was 0.59 for digital and 0.27 for film mammography. AUCs were not significantly different in any of the other subgroups. For women aged 65 years or older with fatty breasts, the AUC showed a nonsignificant tendency toward film being better than digital mammography (AUCs, 0.88 vs 0.70; P = .0025). Digital mammography performed significantly better

  15. Procedural justice and social regulation across group boundaries: does subgroup identity undermine relationship-based governance?

    Science.gov (United States)

    Huo, Yuen J

    2003-03-01

    The relational model of authority suggests that people are inclined to accept the decisions of ethnic outgroup authorities when they identify with a superordinate category they share with the authority, and when the authority satisfies their relational justice concerns. Using responses from a random sample of African Americans, Latinos, and Whites about their cross-ethnic interactions with legal authorities, the findings indicated that those who are highly identified with the superordinate category of America indicate greater reliance on relational concerns and less on instrumental concerns when evaluating the authority's decision. In contrast, identification with one's ethnic subgroup did not moderate the linkage between relational concerns and acceptance. Across all ethnic groups, there were positive rather than negative correlations between measures of American and ethnic identity. Together, these findings indicate that subgroup identity does not undermine the relational basis of social regulation and that relationship-based governance is compatible with multiculturalism.

  16. Automatically high precision manufacturing technology for micro-optic subgroups; Techical Digest

    Science.gov (United States)

    Sure, Thomas; Guyenot, Volker; Gerhardt, Michael

    2005-05-01

    To realize the image quality of high end objectives, e. g. high NA microscope objectives working in the DUV spectral region the subgroups have to be manufactured with a mechanical precision which is difficult to achieve cost effectively. For high end microscope objectives the accuracy of the diameter of the lens mount must be within 1 µm, the run-out must be met within 1 µm and the distance of the lens vertex relative to the shoulder of the mount must fit within 1 µm. To realize the required precision, today various measurement techniques and production processes are used. Picking up the subgroups on different machining tools and measurement systems will loosen the accuracy. Here, we present the concept and the layout of a new manufacturing tool where we implemented the different measurement techniques in one CNC machining center.

  17. Subgroup Benchmark Calculations for the Intra-Pellet Nonuniform Temperature Cases

    Energy Technology Data Exchange (ETDEWEB)

    Kim, Kang Seog [Oak Ridge National Lab. (ORNL), Oak Ridge, TN (United States); Jung, Yeon Sang [Seoul National Univ. (Korea, Republic of); Liu, Yuxuan [Univ. of Michigan, Ann Arbor, MI (United States); Joo, Han Gyu [Seoul National Univ. (Korea, Republic of)

    2016-08-01

    A benchmark suite has been developed by Seoul National University (SNU) for intrapellet nonuniform temperature distribution cases based on the practical temperature profiles according to the thermal power levels. Though a new subgroup capability for nonuniform temperature distribution was implemented in MPACT, no validation calculation has been performed for the new capability. This study focuses on bench-marking the new capability through a code-to-code comparison. Two continuous-energy Monte Carlo codes, McCARD and CE-KENO, are engaged in obtaining reference solutions, and the MPACT results are compared to the SNU nTRACER using a similar cross section library and subgroup method to obtain self-shielded cross sections.

  18. Exceptional quantum subgroups for the rank two Lie algebras B2 and G2

    CERN Document Server

    Coquereaux, R; Tahri, E H

    2010-01-01

    Exceptional modular invariants for the Lie algebras B2 (at levels 2,3,7,12) and G2 (at levels 3,4) can be obtained from conformal embeddings. We determine the associated alge bras of quantum symmetries and discover or recover, as a by-product, the graphs describing exceptional quantum subgroups of type B2 or G2 which encode their module structure over the associated fusion category. Global dimensions are given.

  19. Non-specific chronic low back pain: differences in spinal kinematics in subgroups during functional tasks.

    Science.gov (United States)

    Hemming, Rebecca; Sheeran, Liba; van Deursen, Robert; Sparkes, Valerie

    2017-07-21

    A multidimensional classification approach suggests that motor control impairment subgroups exist in non-specific chronic low back pain (NSCLBP). Differences in sitting lumbar posture have been identified between two such subgroups [flexion pattern (FP) and active extension pattern (AEP)] and healthy individuals; however, functional spinal movement has not been explored. This study will evaluate whether NSCLBP subgroups exhibit regional spinal kinematic differences, compared to healthy individuals, during functional tasks. Observational, cross-sectional study design. Spinal kinematics of 50 NSCLBP subjects (27 FP, 23 AEP) and 28 healthy individuals were investigated using 3D motion analysis (Vicon™) during functional tasks [reaching upwards, step down, step up, lifting, and replacing a box, stand-to-sit, sit-to-stand, bending to retrieve (and returning from retrieving) a pen from the floor]. Mean sagittal angle for the total thoracic, total lumbar, upper thoracic, lower thoracic, upper lumbar, and lower lumbar regions between groups was compared. Significant differences were observed in lower thoracic and upper lumbar regions between NSCLBP subgroups during most tasks. Significant differences were observed between the FP and healthy group in the lower thoracic region during stand-to-sit-to-stand tasks and bending (and returning from) to retrieve a pen from the floor. All significant results demonstrated the FP group to operate in comparatively greater flexion. The thoraco-lumbar spine discriminated between FP and AEP, and FP and healthy groups during functional tasks. FP individuals demonstrated more kyphotic thoraco-lumbar postures, which may be pain provocative. No significant differences were observed between AEP and healthy groups, suggesting that alternative mechanisms may occur in AEP.

  20. Subgroup analysis of Asian patients in the INPULSIS® trials of nintedanib in idiopathic pulmonary fibrosis.

    Science.gov (United States)

    Taniguchi, Hiroyuki; Xu, Zuojun; Azuma, Arata; Inoue, Yoshikazu; Li, Huiping; Fujimoto, Tsuyoshi; Bailes, Zelie; Schlenker-Herceg, Rozsa; Kim, Dong S

    2016-11-01

    In the two-replicate randomized Phase III INPULSIS® trials in patients with idiopathic pulmonary fibrosis (IPF), nintedanib 150 mg bd significantly reduced the annual rate of decline in forced vital capacity (FVC) compared with placebo. The key secondary endpoints were time to first investigator-reported acute exacerbation and change from baseline in St George's Respiratory Questionnaire total score, both over 52 weeks. Here, we assessed the effect of nintedanib in Asian patients. Pre-specified subgroup analyses of the effect of nintedanib on the primary and key secondary endpoints in Asian versus White patients were undertaken based on pooled data from the two INPULSIS® trials. Safety data were analyzed descriptively. Of the treated patients, 322 were Asian (nintedanib n = 194; placebo n = 128) and 608 were White (nintedanib n = 360; placebo n = 248). In Asian patients, the nintedanib versus placebo difference in the adjusted annual rate of decline in FVC was 94.1 mL/year (95% CI: 33.7, 154.6). The treatment effect of nintedanib on the annual rate of decline in FVC in Asian and White patients was similar (treatment-by-subgroup interaction P = 0.72) and consistent with the overall population. No significant treatment-by-subgroup interaction was observed for the key secondary endpoints between Asian and White patients. In Asian patients, the most common adverse event in the nintedanib group was diarrhoea (56.2% of patients vs 15.6% for placebo). In pre-specified subgroup analyses of Asian versus White patients with IPF in the INPULSIS® trials, race did not influence the effect of nintedanib on disease progression. © 2016 Asian Pacific Society of Respirology.

  1. Page 1 Congruence subgroup problem 95 have Q = Inv'(Q) × G ...

    Indian Academy of Sciences (India)

    In particular, for T = 2), this topology is the trivial topology. -. We prove: Theorem 5.1. Let G be as above and assume that if G is a form of *As then it is isotropic at every finite completion. Let Tº ={v:v is a finite place of K and G(K) is compact}. Then, any non-central normal subgroup of G(K) is T-adically closed. In particular, for.

  2. Pain Sensitivity Subgroups in Individuals With Spine Pain: Potential Relevance to Short-Term Clinical Outcome

    Science.gov (United States)

    Bialosky, Joel E.; Robinson, Michael E.

    2014-01-01

    Background Cluster analysis can be used to identify individuals similar in profile based on response to multiple pain sensitivity measures. There are limited investigations into how empirically derived pain sensitivity subgroups influence clinical outcomes for individuals with spine pain. Objective The purposes of this study were: (1) to investigate empirically derived subgroups based on pressure and thermal pain sensitivity in individuals with spine pain and (2) to examine subgroup influence on 2-week clinical pain intensity and disability outcomes. Design A secondary analysis of data from 2 randomized trials was conducted. Methods Baseline and 2-week outcome data from 157 participants with low back pain (n=110) and neck pain (n=47) were examined. Participants completed demographic, psychological, and clinical information and were assessed using pain sensitivity protocols, including pressure (suprathreshold pressure pain) and thermal pain sensitivity (thermal heat threshold and tolerance, suprathreshold heat pain, temporal summation). A hierarchical agglomerative cluster analysis was used to create subgroups based on pain sensitivity responses. Differences in data for baseline variables, clinical pain intensity, and disability were examined. Results Three pain sensitivity cluster groups were derived: low pain sensitivity, high thermal static sensitivity, and high pressure and thermal dynamic sensitivity. There were differences in the proportion of individuals meeting a 30% change in pain intensity, where fewer individuals within the high pressure and thermal dynamic sensitivity group (adjusted odds ratio=0.3; 95% confidence interval=0.1, 0.8) achieved successful outcomes. Limitations Only 2-week outcomes are reported. Conclusions Distinct pain sensitivity cluster groups for individuals with spine pain were identified, with the high pressure and thermal dynamic sensitivity group showing worse clinical outcome for pain intensity. Future studies should aim to confirm

  3. Mindfulness and Emotional Outcomes: Identifying Subgroups of College Students using Latent Profile Analysis

    OpenAIRE

    Pearson, Matthew R.; Lawless, Adrienne K.; Brown, David B.; Bravo, Adrian J.

    2015-01-01

    In non-meditating samples, distinct facets of mindfulness are found to be negatively correlated, preventing the meaningful creation of a total mindfulness score. The present study used person-centered analyses to distinguish subgroups of college students based on their mindfulness scores, which allows the examination of individuals who are high (or low) on all facets of mindfulness. Using the Lo-Mendell-Rubin Adjusted LRT test, we settled on a 4-class solution that included a high mindfulness...

  4. Which subgroups of fire fighters are more prone to work-related diminished health requirements?

    Science.gov (United States)

    Plat, Marie-Christine J; Frings-Dresen, Monique H W; Sluiter, Judith K

    2012-10-01

    To determine whether certain subgroups of fire fighters are prone to work-related diminished health requirements. The health requirements for fire-fighting were tested in a workers' health surveillance (WHS) setting. These health requirements included psychological, physical and sense-related components as well as cardiovascular risk factors. The odds ratio (OR) and 95% confidence interval (95% CI) for the presence of the diminished health requirements were calculated for the subgroups of gender, professionalism and age. The prevalence of diminished psychological requirements was equivalent among the subgroups, and no significant high-risk group was identified. As compared to men fire fighters, women fire fighters were more likely to have diminished physical requirements (OR 28.5; 95% CI 12.1-66.9) and less likely to have cardiovascular risk factors (OR 0.3; 0.1-0.5). As compared to volunteer fire fighters, professionals were less likely to have diminished physical requirements (OR 0.5; 0.3-0.9), but professionals had a higher prevalence of cardiovascular risk factors with an odds ratio of 1.9 (1.1-3.2). As compared to the youngest fire fighters, the oldest fire fighters were more likely to have diminished sense-related requirements (OR 7.1; 3.4-15.2); a similar comparison could be made between oldest and middle-aged fire fighters (OR 5.1; 2.5-10.5). In addition, the oldest fire fighters were more likely to have cardiovascular risk factors when compared to the youngest (OR 4.4; 1.7-11.1) and to the middle-aged fire fighters (OR 3.1; 1.2-7.9). Subgroups (gender, professionalism and age) of fire fighters are prone to at least one specific work-related diminished health requirement. Therefore, parts of the WHS could be applied with more attention to these high-risk groups.

  5. Identification of Responders to Amiodarone: Subgroup Analysis of the EMIAT Study

    OpenAIRE

    Kehl, Victoria; Ulm, Kurt; Schmidt, G; Barthel, P.; Malik, Marek

    2003-01-01

    Clinical trials often judge the efficacy of a new treatment by comparing the survival patterns of patients who are randomly assigned to undergo the new or a standard/placebo treatment. Usually, the entire groups are analyzed, although certain subgroups of patients may react differently to the new treatment than others. Some patients taking the new treatment might benefit from it (the positive responders) while others may be harmed by it (the negative responders). We applied a newly developed ...

  6. Evolutionary Dynamics of Male Reproductive Genes in the Drosophila virilis Subgroup

    OpenAIRE

    Yasir H. Ahmed-Braimah; Unckless, Robert L.; Clark, Andrew G.

    2017-01-01

    Postcopulatory sexual selection (PCSS) is a potent evolutionary force that can drive rapid changes of reproductive genes within species, and thus has the potential to generate reproductive incompatibilities between species. Male seminal fluid proteins (SFPs) are major players in postmating interactions, and are important targets of PCSS in males. The virilis subgroup of Drosophila exhibits strong interspecific gametic incompatibilities, and can serve as a model to study the genetic basis of P...

  7. Restriction of complementary series representations of $O(1,N)$ to symmetric subgroups

    DEFF Research Database (Denmark)

    Möllers, Jan; Oshima, Yoshiki

    2012-01-01

    is given by a direct integral of principal series representations whereas the discrete part consists of finitely many complementary series representations. The explicit Plancherel formula is computed on the Fourier transformed side of the non-compact realization of the complementary series by using......We find the complete branching law for the restriction of complementary series representations of $O(1,n+1)$ to the symmetric subgroup $O(1,m+1)\\times O(n-m)$, $0\\leq m

  8. Restriction of complementary series representations of O(1,N) to symmetric subgroups

    DEFF Research Database (Denmark)

    Möllers, Jan; Oshima, Yoshiki

    by a direct integral of principal series representations whereas the discrete part consists of finitely many complementary series representations. The explicit Plancherel formula is computed on the Fourier transformed side of the non-compact realization of the complementary series by using the spectral......We find the complete branching law for the restriction of complementary series representations of O(1, n+1) to the symmetric subgroup O(1,m+1)× O(n − m), 0 m

  9. Centralizers of maximal regular subgroups in simple Lie groups and relative congruence classes of representations

    Energy Technology Data Exchange (ETDEWEB)

    Larouche, M [Departement de Mathematiques et Statistique, Universite de Montreal, 2920 chemin de la Tour, Montreal, Quebec H3T 1J4 (Canada); Lemire, F W [Department of Mathematics, University of Windsor, Windsor, Ontario (Canada); Patera, J, E-mail: larouche@dms.umontreal.ca, E-mail: lemire@uwindsor.ca, E-mail: patera@crm.umontreal.ca [Centre de Recherches Mathematiques, Universite de Montreal, CP 6128-Centre ville, Montreal, Quebec H3C 3J7 (Canada)

    2011-10-14

    In this paper, we present a new, uniform and comprehensive description of centralizers of the maximal regular subgroups in compact simple Lie groups of all types and ranks. The centralizer is either a direct product of finite cyclic groups, a continuous group of rank 1, or a product, not necessarily direct, of a continuous group of rank 1 with a finite cyclic group. Explicit formulas for the action of such centralizers on irreducible representations of the simple Lie algebras are given. (paper)

  10. Caffeine for Apnea of Prematurity trial: benefits may vary in subgroups.

    Science.gov (United States)

    Davis, Peter G; Schmidt, Barbara; Roberts, Robin S; Doyle, Lex W; Asztalos, Elizabeth; Haslam, Ross; Sinha, Sunil; Tin, Win

    2010-03-01

    To determine whether the benefits of caffeine vary in three subgroups of 2006 participants in the Caffeine for Apnea of Prematurity (CAP) trial. Post-hoc subgroup analyses were performed on the basis of: (1) indication for commencement of study drug: treat apnea, prevent apnea, or facilitate extubation; (2) positive pressure ventilation (PPV) at randomization: endotracheal tube (ETT), noninvasive ventilation, or none; and (3) timing of commencement of study drug: early or late (3 days). Outcomes assessed were those showing treatment effects in the original analyses. We investigated the consistency of caffeine effects by using regression models that incorporated treatment/subgroup factor interactions. There was little evidence of a differential treatment effect of caffeine in subgroups defined by the clinical indication for starting study drug. The size and direction of the caffeine effect on death or disability differed depending on PPV at randomization (P = .03). Odds ratios (95% CI) were: no support, 1.32 (0.81-2.14); noninvasive support, 0.73 (0.52-1.03); and ETT, 0.73 (0.57-0.94). Adjustment for baseline factors strengthened this effect (P = .02). Starting caffeine early resulted in larger reductions in days of respiratory support. Postmenstrual age at time of discontinuing PPV was shorter with earlier treatment (P = .01). Mean differences (95% CI) were: early, 1.35 weeks (0.90-1.81); and late 0.55 weeks (-0.11-0.99). Adjustment for baseline factors weakened this effect (P = .03). There is evidence of variable beneficial effects of caffeine. Infants receiving respiratory support appeared to derive more neurodevelopmental benefits from caffeine than infants not receiving support. Earlier initiation of caffeine may be associated with a greater reduction in time on ventilation. Copyright 2010 Mosby, Inc. All rights reserved.

  11. Twitch and nontwitch motoneuron subgroups in the oculomotor nucleus of monkeys receive different afferent projections.

    Science.gov (United States)

    Wasicky, Richard; Horn, Anja K E; Büttner-Ennever, Jean A

    2004-11-08

    Motoneurons in the primate oculomotor nucleus can be divided into two categories, those supplying twitch muscle fibers and those supplying nontwitch muscle fibers. Recent studies have shown that twitch motoneurons lie within the classical oculomotor nucleus (nIII), and nontwitch motoneurons lie around the borders. Nontwitch motoneurons of medial and inferior rectus are in the C group dorsomedial to nIII, whereas those of inferior oblique and superior rectus lie near the midline are in the S group. In this anatomical study, afferents to the twitch and nontwitch subgroups of nIII have been anterogradely labeled by injections of tritiated leucine into three areas and compared. 1) Abducens nucleus injections gave rise to silver grain deposits over all medial rectus subgroups, both twitch and nontwitch. 2) Laterally placed vestibular complex injections that included the central superior vestibular nucleus labeled projections only in twitch motoneuron subgroups. However, injections into the parvocellular medial vestibular nucleus (mvp), or Y group, resulted in labeled terminals over both twitch and nontwitch motoneurons. 3) Pretectal injections that included the nucleus of the optic tract (NOT), and the olivary pretectal nucleus (OLN), labeled terminals only over nontwitch motoneurons, in the contralateral C group and in the S group. Our study demonstrates that twitch and nontwitch motoneuron subgroups do not receive identical afferent inputs. They can be controlled either in parallel, or independently, suggesting that they have basically different functions. We propose that twitch motoneurons primarily drive eye movements and nontwitch motoneurons the tonic muscle activity, as in gaze holding and vergence, possibly involving a proprioceptive feedback system. 2004 Wiley-Liss, Inc.

  12. [Association between anxiety and quality of life in different subgroups irritable bowel syndrome].

    Science.gov (United States)

    Fosado-Gayosso, M; Casillas-Guzmán, G B; Serralde-Zúñiga, A E; Pérez-Hernández, J L; Higuera-de la Tijera, M F; Pérez-Torres, E; Abdo-Francis, J M

    2011-01-01

    Irritable Bowel Syndrome (IBS) is a frequent functional digestive disorder. Several studies have established the relationship between IBS and anxiety. Also it has been described a negative impact on quality of life in patients who suffer it, but in our country none of these studies have used ROME III criteria for evaluation. To know the frequency of anxiety in the different subgroups of IBS and its impact on quality of life. The study was conducted in patients who attended for first time to the outpatient clinic of our hospital for ten months. Adult patients who met the criteria of IBS were included. We applied the SF-36 quality of life questionnaire and the Hamilton anxiety scale. One hundred and two patients who met for IBS criteria were included, of which 85% had anxiety. The IBS-C was the most frequent subgroup. Divided by subgroups, found that 52%, 85.1%, 90% and 80.9% had anxiety for IBS-C, IBS-D, IBS-M and IBS-NC respectively, without significant difference between groups. Patients with anxiety had lower quality of life scores in the categories of physical health, mental health and change in the state of health, (54.2 ± 18 vs. 72 ± 16, 52.8 ± 20 vs. 74 ± 14, 48 ± 28 vs. 59 ± 32) with respect to those who have no anxiety (p anxiety was not associated to any subgroup in particular of IBS, the presence of this influenced adversely and significantly on the quality of life of patients who suffer it.

  13. Exercise challenge in Gulf War Illness reveals two subgroups with altered brain structure and function.

    Directory of Open Access Journals (Sweden)

    Rakib U Rayhan

    Full Text Available Nearly 30% of the approximately 700,000 military personnel who served in Operation Desert Storm (1990-1991 have developed Gulf War Illness, a condition that presents with symptoms such as cognitive impairment, autonomic dysfunction, debilitating fatigue and chronic widespread pain that implicate the central nervous system. A hallmark complaint of subjects with Gulf War Illness is post-exertional malaise; defined as an exacerbation of symptoms following physical and/or mental effort. To study the causal relationship between exercise, the brain, and changes in symptoms, 28 Gulf War veterans and 10 controls completed an fMRI scan before and after two exercise stress tests to investigate serial changes in pain, autonomic function, and working memory. Exercise induced two clinical Gulf War Illness subgroups. One subgroup presented with orthostatic tachycardia (n = 10. This phenotype correlated with brainstem atrophy, baseline working memory compensation in the cerebellar vermis, and subsequent loss of compensation after exercise. The other subgroup developed exercise induced hyperalgesia (n = 18 that was associated with cortical atrophy and baseline working memory compensation in the basal ganglia. Alterations in cognition, brain structure, and symptoms were absent in controls. Our novel findings may provide an understanding of the relationship between the brain and post-exertional malaise in Gulf War Illness.

  14. Kuwaiti population subgroup of nomadic Bedouin ancestry—Whole genome sequence and analysis

    Directory of Open Access Journals (Sweden)

    Sumi Elsa John

    2015-03-01

    Full Text Available Kuwaiti native population comprises three distinct genetic subgroups of Persian, “city-dwelling” Saudi Arabian tribe, and nomadic “tent-dwelling” Bedouin ancestry. Bedouin subgroup is characterized by presence of 17% African ancestry; it owes it origin to nomadic tribes of the deserts of Arabian Peninsula and North Africa. By sequencing whole genome of a Kuwaiti male from this subgroup at 41X coverage, we report 3,752,878 SNPs, 411,839 indels, and 8451 structural variations. Neighbor-joining tree, based on shared variant positions carrying disease-risk alleles between the Bedouin and other continental genomes, places Bedouin genome at the nexus of African, Asian, and European genomes in concordance with geographical location of Kuwait and Peninsula. In congruence with participant's medical history for morbid obesity and bronchial asthma, risk alleles are seen at deleterious SNPs associated with obesity and asthma. Many of the observed deleterious ‘novel’ variants lie in genes associated with autosomal recessive disorders characteristic of the region.

  15. Pharmacotherapy effectiveness for clinical subgroups among children and adolescents with early onset schizophrenia.

    Science.gov (United States)

    Jerrell, Jeanette M; McIntyre, Roger S; Deroche, Chelsea B

    2017-03-01

    This study aims to determine the effectiveness of pharmacotherapies among children and adolescents diagnosed with early onset schizophrenia subgrouped according to their co-occurring psychiatric disorders. A retrospective cohort design was employed, using South Carolina's (USA) Medicaid claims dataset covering outpatient and inpatient medical services, between January, 1999 and December, 2013 to identify patients ≤17 years of age. Random effects regression analyses assessed differential changes in acute psychiatric service utilization over time across the 3 subgroups associated with antipsychotic, mood stabilizer, psychostimulant, or antidepressant pharmacotherapy. For patients with schizophrenia and comorbid mood disorders or emotional dysregulation (Cluster 1), or schizophrenia and severe cognitive impairments (Cluster 2), those treated with monotherapy second-generation antipsychotics (SGAs) over time demonstrated consistently lower use of acute psychiatric treatment services as did those coprescribed mood stabilizers, primarily lithium, or anticonvulsants. In all clusters, including the relatively homogenous subgroup of patients with early onset schizophrenia and few comorbid disorders, acute psychiatric service utilization was significantly higher and more variable over time for those prescribed multiple SGAs. Regardless of the specific constellation of symptoms and comorbid disorders targeted, the coprescription of multiple SGAs was not effective over time in stabilizing children and adolescents outside of acute care settings. Copyright © 2017 John Wiley & Sons, Ltd.

  16. Prospective effects of hearing status on loneliness and depression in older persons: identification of subgroups.

    Science.gov (United States)

    Pronk, Marieke; Deeg, Dorly J H; Smits, Cas; van Tilburg, Theo G; Kuik, Dirk J; Festen, Joost M; Kramer, Sophia E

    2011-12-01

    To determine the possible longitudinal relationships between hearing status and depression, and hearing status and loneliness in the older population. Multiple linear regression analyses were used to assess the associations between baseline hearing and 4-year follow-up of depression, social loneliness, and emotional loneliness. Hearing was measured both by self-report and a speech-in-noise test. Each model was corrected for age, gender, hearing aid use, baseline wellbeing, and relevant confounders. Subgroup effects were tested using interaction terms. We used data from two waves of the Longitudinal Aging Study Amsterdam (2001-02 and 2005-06, ages 63-93). Sample sizes were 996 (self-report (SR) analyses) and 830 (speech-in-noise test (SNT) analyses). Both hearing measures showed significant adverse associations with both loneliness measures (p loneliness model) and men (SR and SNT-emotional loneliness model). No significant effects appeared for depression. We found significant adverse effects of poor hearing on emotional and social loneliness for specific subgroups of older persons. Future research should confirm the subgroup effects and may contribute to the development of tailored prevention and intervention programs.

  17. Facilitation of the Estuary/Ocean Subgroup for Research, Monitoring, and Evaluation, FY06 Annual Report

    Energy Technology Data Exchange (ETDEWEB)

    Johnson, Gary E.

    2006-10-03

    This annual report is a deliverable for fiscal year 2006 (FY06) for Project 2002-077-00, Facilitation of the Estuary/Ocean Subgroup (EOS). The EOS is part of the research, monitoring, and evaluation (RME) effort the Action Agencies (Bonneville Power Administration, U.S. Army Corps of Engineers, U.S. Bureau of Reclamation) developed in response to the 2000 and 2004 Biological Opinions on operation of the Federal Columbia River Power System. The goal of the EOS project is to facilitate activities of the estuary/ocean RME subgroup as it coordinates implementation of the Estuary RME Plan. In FY06, EOS project accomplishments included: 1) subgroup meetings; 2) participation in the estuary work group of the Pacific Northwest Aquatic Monitoring Partnership; 3) project management via the project tracking system, PISCES; 4) quarterly project status reports; and 5) a major revision to the Estuary RME Plan (new version May 2006) based on comments by EOS members, the Independent Scientific Review Panel, and other reviewers. In the context of uncertainty about the direction of the federal RME due to litigation on the FCRPS Biological Opinion, FY06 activities for the EOS project resulted in expanded substantive coordination with other regional RME forums, project tracking infrastructure, and a new version of the Estuary RME Plan.

  18. Kuwaiti population subgroup of nomadic Bedouin ancestry-Whole genome sequence and analysis.

    Science.gov (United States)

    John, Sumi Elsa; Thareja, Gaurav; Hebbar, Prashantha; Behbehani, Kazem; Thanaraj, Thangavel Alphonse; Alsmadi, Osama

    2015-03-01

    Kuwaiti native population comprises three distinct genetic subgroups of Persian, "city-dwelling" Saudi Arabian tribe, and nomadic "tent-dwelling" Bedouin ancestry. Bedouin subgroup is characterized by presence of 17% African ancestry; it owes it origin to nomadic tribes of the deserts of Arabian Peninsula and North Africa. By sequencing whole genome of a Kuwaiti male from this subgroup at 41X coverage, we report 3,752,878 SNPs, 411,839 indels, and 8451 structural variations. Neighbor-joining tree, based on shared variant positions carrying disease-risk alleles between the Bedouin and other continental genomes, places Bedouin genome at the nexus of African, Asian, and European genomes in concordance with geographical location of Kuwait and Peninsula. In congruence with participant's medical history for morbid obesity and bronchial asthma, risk alleles are seen at deleterious SNPs associated with obesity and asthma. Many of the observed deleterious 'novel' variants lie in genes associated with autosomal recessive disorders characteristic of the region.

  19. Television viewing in low-income latino children: variation by ethnic subgroup and English proficiency.

    Science.gov (United States)

    Thompson, Darcy A; Matson, Pamela A; Ellen, Jonathan M

    2013-02-01

    Television viewing is associated with an increased risk for obesity in children. Latino children are at high risk for obesity and yet little is known about differences in television viewing habits within this population. The purpose of this study is to determine if hours of television viewed by young children with low-income Latina mothers differs by maternal ethnic subgroup and English language proficiency. This was a cross-sectional analysis of data from the Welfare, Children, & Families: A Three City Study. Participants were 422 low-income Latina mothers of Mexican and Puerto Rican descent with children ages 0-4 years old. The dependent variable was hours of daily television viewed by the child. The independent variable was maternal ethnic subgroup and English language proficiency. Analyses involved the use of multiple negative binomial regression models, which were adjusted for demographic variables. Multivariable regression analyses showed that compared to children with mothers of Mexican descent, children of mothers of Puerto Rican descent watch more daily television (television viewing (IRR=1.29, 95% CI 1.04, 1.61). No relationship was found for children of Puerto Rican descent. Child television viewing varies in low-income Latino children by maternal ethnic subgroup and English language proficiency. Interventionists must consider the varying sociocultural contexts of Latino children and their influence on television viewing.

  20. The Importance of Risk and Subgroup Analysis of Nonparticipants in a Geriatric Intervention Study

    Directory of Open Access Journals (Sweden)

    Elizabeth Rosted

    2016-01-01

    Full Text Available Background. A major concern in intervention studies is the generalizability of the findings due to refusal of intended participants to actually take part. In studies including ill older people the number of those declining to participate may be large and the concern is therefore relevant. Objectives. To compare patients characteristics, rates of acute readmission, and mortality after one and six months among older persons who agreed and those who declined to participate in a randomized controlled trial and to describe subgroups of nonparticipants. Design. Comparative study based on a randomized controlled trial. Setting. University hospital in the Capital Region of Denmark. Participants. Patients ≥70 years discharged home after a short Emergency Department stay. 399 were requested to participate; 271 consented, whereas 128 refused. Results. Refusers were more likely to be readmitted (p<0.001 or die (p=0.006. The largest subgroup of refusers described as “too ill” had the highest risk of readmission (OR = 3.00, 95% CI = 1.61–5.47, p=0.001 and of mortality within six months (OR = 3.50, 95% CI = 1.64–7.49, p=0.002. However, this seems not to have affected the results of our randomized study. Conclusion. We recommend that intervention studies among older people or other fragile patient groups include analysis of relevant risk and subgroup analyses of refusers.

  1. Patterns and Risk Factors of Soil-Transmitted Helminthiasis among Orang Asli Subgroups in Peninsular Malaysia

    Science.gov (United States)

    Ngui, Romano; Aziz, Shafie; Chua, Kek Heng; Aidil, Roslan Muhammad; Lee, Soo Ching; Tan, Tiong Kai; Sani, Mistam Mohd; Arine, Ahmad Fadzlun; Rohela, Mahmud; Lim, Yvonne A. L.

    2015-01-01

    A cross-sectional study was conducted to provide comprehensive data on the patterns and associated risk factors of soil-transmitted helminth (STH) infections among five Orang Asli subgroups in Peninsular Malaysia. The overall prevalence of STH infections was 59.9% (95% confidence interval [CI] = 56.1–63.7%). Trichuris trichiura (54.3%; 95% CI = 50.4–58.2%) was the predominant species followed by Ascaris lumbricoides (26.7%; 95% CI = 23.3–30.1%) and hookworm (9.1%; 95% CI = 6.9–11.3%). This study showed diversity for STH infections by subgroup with poverty and personal sanitary behavior as important risk factors for infection. Risk profile analyses indicating that Orang Kuala subgroup who has a generally well-developed infrastructure and better quality of life had a low rate of infection. There is a need for poverty reduction and promotion of deworming programs along with mass scale campaigns to create awareness about health and hygiene to reduce STH infections. PMID:26055746

  2. Efficacy of intravitreal ocriplasmin for treatment of vitreomacular adhesion: subgroup analyses from two randomized trials.

    Science.gov (United States)

    Haller, Julia A; Stalmans, Peter; Benz, Matthew S; Gandorfer, Arnd; Pakola, Stephen J; Girach, Aniz; Kampik, Anselm; Jaffe, Glenn J; Toth, Cynthia A

    2015-01-01

    To evaluate the efficacy of a single intravitreal injection of ocriplasmin 125 μg across relevant subpopulations of patients with symptomatic vitreomacular adhesion (VMA)/vitreomacular traction (VMT), including when associated with macular hole. Two multicenter, randomized, placebo-controlled, double-masked, 6-month studies. A total of 652 randomized patients (464 receiving ocriplasmin; 188 receiving placebo). A single intravitreal injection of ocriplasmin 125 μg or placebo in the study eye. Prespecified subgroup analyses were conducted to evaluate the effects on the proportion of patients with nonsurgical resolution of focal VMA at day 28, nonsurgical full-thickness macular hole (FTMH) closure at month 6, and categoric improvement in best-corrected visual acuity (BCVA) at month 6. Resolution of VMA at day 28 was achieved more often in younger patients (Treatment differences in favor of ocriplasmin were generally observed across each subgroup of subpopulations studied. Subgroup analyses confirmed the positive effect of ocriplasmin across relevant subpopulations. Copyright © 2015 American Academy of Ophthalmology. Published by Elsevier Inc. All rights reserved.

  3. Patterns and Risk Factors of Soil-Transmitted Helminthiasis Among Orang Asli Subgroups in Peninsular Malaysia.

    Science.gov (United States)

    Ngui, Romano; Aziz, Shafie; Chua, Kek Heng; Aidil, Roslan Muhammad; Lee, Soo Ching; Tan, Tiong Kai; Sani, Mistam Mohd; Arine, Ahmad Fadzlun; Rohela, Mahmud; Lim, Yvonne A L

    2015-08-01

    A cross-sectional study was conducted to provide comprehensive data on the patterns and associated risk factors of soil-transmitted helminth (STH) infections among five Orang Asli subgroups in Peninsular Malaysia. The overall prevalence of STH infections was 59.9% (95% confidence interval [CI] = 56.1-63.7%). Trichuris trichiura (54.3%; 95% CI = 50.4-58.2%) was the predominant species followed by Ascaris lumbricoides (26.7%; 95% CI = 23.3-30.1%) and hookworm (9.1%; 95% CI = 6.9-11.3%). This study showed diversity for STH infections by subgroup with poverty and personal sanitary behavior as important risk factors for infection. Risk profile analyses indicating that Orang Kuala subgroup who has a generally well-developed infrastructure and better quality of life had a low rate of infection. There is a need for poverty reduction and promotion of deworming programs along with mass scale campaigns to create awareness about health and hygiene to reduce STH infections. © The American Society of Tropical Medicine and Hygiene.

  4. A sensitive real-time PCR for detection and subgrouping of human respiratory syncytial virus.

    Science.gov (United States)

    Do, Lien Anh Ha; van Doorn, H Rogier; Bryant, Juliet E; Nghiem, My Ngoc; Nguyen Van, Vinh Chau; Vo, Cong Khanh; Nguyen, Minh Dung; Tran, Tinh Hien; Farrar, Jeremy; de Jong, Menno D

    2012-01-01

    Improved diagnostic tools for rapid detection, quantitation, and subgrouping of human respiratory syncytial virus (RSV) are needed to aid the development and evaluation of novel intervention strategies. A quantitative real-time RT-PCR using specific locked nucleic acid (LNA) probes was developed to identify RSV and to distinguish RSV subgroups A and B (RSV LNA assay). RSV subgroup diversity and the relationship between viral load and disease severity in confirmed RSV infections were also explored. 264 archived respiratory specimens from pediatric patients were tested in parallel using the commercial multiplex Seeplex™ RV detection kit (Seegene) and the novel RSV LNA assay. The LNA assay demonstrated a significantly higher sensitivity than Seeplex, improving overall detection rates from 24% (64/264) to 32% (84/264). Detection limits of 9.0×10(1) and 6.0×10(2)copies/mL were observed for RSV A and B, respectively. RSV A was detected in 53/84 (63%) cases, and 31/84 (37%) were positive for RSV B. This novel method offers a rapid, quantitative, highly specific and sensitive approach to laboratory diagnosis of RSV. Copyright © 2011 Elsevier B.V. All rights reserved.

  5. Personality does not distinguish people with fibromyalgia but identifies subgroups of patients.

    Science.gov (United States)

    Torres, Xavier; Bailles, Eva; Valdes, Manuel; Gutierrez, Fernando; Peri, Josep-Maria; Arias, Anna; Gomez, Emili; Collado, Antonio

    2013-01-01

    The objectives were to compare the personality of fibromyalgia (FM) patients with other chronic painful and nonpainful disorders considering the confusion due to psychopathology and to assess the clustering of FM patients according to their personality profile. Differences in the NEO Five-Factor Inventory between FM, non-FM chronic pain and drug-resistant epileptic patients were assessed including the confounding effect of demographics and psychopathological status by multivariate regression analysis. Clustering of FM patients was assessed by two-step cluster analysis. Differences in clinical severity and psychosocial problems between subgroups and their outcome 6 months after multidisciplinary treatment were assessed. The final sample comprised 874 patients. Once the effect of confounding variables was considered, clinically nonsignificant differences in personality were observed between groups. FM patients could, however, be grouped into two clusters. Cluster 1 was characterized by higher neuroticism and lower extraversion and showed a worse pretreatment clinical state including more psychosocial problems. In spite of having reached a wider general improvement at 6-month follow-up, Cluster 1 patients remained more anxious and depressed. Identifying personality-based subgroups of FM might allow implementing specific preventive strategies. FM treatment might be optimized by increasing medication compliance, improving therapeutic alliance and testing different therapeutic options and treatment sequencing for each personality subgroup. © 2013.

  6. 78 FR 37845 - Meeting of the Imperial Sand Dunes Recreation Area (ISDRA) Subgroup of the California Desert...

    Science.gov (United States)

    2013-06-24

    ... California Desert District Advisory Council SUMMARY: Notice is hereby given, in accordance with Public Laws 92-463 and 94-579, that the Imperial Sand Dunes Recreation Area Subgroup of the California Desert... filed in advance of the meeting for the California Desert District Advisory Council ISDRA Subgroup, c/o...

  7. Functional divergence of the NIP III subgroup proteins involved altered selective constraints and positive selection

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    Zhu Zhujun

    2010-11-01

    Full Text Available Abstract Background Nod26-like intrinsic proteins (NIPs that belong to the aquaporin superfamily are unique to plants. According to homology modeling and phylogenetic analysis, the NIP subfamily can be further divided into three subgroups with distinct biological functions (NIP I, NIP II, and NIP III. In some grasses, the NIP III subgroup proteins (NIP2s were demonstrated to be permeable to solutes with larger diameter, such as silicic acid and arsenous acids. However, to date there is no data-mining or direct experimental evidences for the permeability of such larger solutes for dicot NIP2s, although they exhibit similar three-dimensional structures as those in grasses. It is therefore intriguing to investigate the molecular mechanisms that drive the evolution of plant NIP2s. Results The NIP III subgroup is more ancient with a divergence time that predates the monocot-dicot split. The proliferation of NIP2 genes in modern grass species is primarily attributed to whole genome and segmental chromosomal duplication events. The structure of NIP2 genes is relatively conserved, possessing five exons and four introns. All NIP2s possess an ar/R filter consisting of G, S, G, and R, except for the cucumber CsNIP2;2, where a small G in the H2 is substituted with the bulkier C residue. Our maximum likelihood analysis revealed that NIP2s, especially the loop A (LA region, have undergone strong selective pressure for adaptive evolution. The analysis at the amino acid level provided strong statistical evidences for the functional divergence between monocot and dicot NIP III subgroup proteins. In addition, several SDPs (Specificity Determining Positions responsible for functional specificity were predicted. Conclusions The present study provides the first evidences of functional divergence between dicot and monocot NIP2s, and suggests that positive selection, as well as a radical shift of evolutionary rate at some critical amino acid sites is the primary

  8. Delineation of motoneuron subgroups supplying individual eye muscles in the human oculomotor nucleus

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    Emmanuel eChe-Ngwa

    2014-02-01

    Full Text Available The oculomotor nucleus (nIII contains the motoneurons of medial, inferior and superior recti (MR, IR, SR, inferior oblique (IO and levator palpebrae (LP muscles. The delineation of motoneuron subgroups for each muscle is well-known in monkey, but not in human. We studied the transmitter inputs to human nIII and the trochlear nucleus (nIV, which innervates the superior oblique muscle (SO, to outline individual motoneuron subgroups. Parallel series of sections from human brainstems were immunostained for different markers: acetylcholine transferase (ChAT combined with glutamate decarboxylase (GAD, calretinin (CR or glycine receptor (GlyR. The cytoarchitecture was visualized with Cresyl violet, Gallyas staining and expression of non-phosphorylated neurofilaments (NP-NF. Apart from nIV, seven subgroups were delineated in nIII: the central caudal nucleus (CCN, a dorsolateral (DL, dorsomedial (DM, central (CEN, and ventral group (VEN, the nucleus of Perlia (NP and the non-preganglionic centrally projecting Edinger-Westphal nucleus (EWcp. DL, VEN, NP and EWcp were characterized by a strong supply of GAD-positive terminals, in contrast to DM, CEN and nIV. CR-positive terminals and fibres were confined to CCN, CEN and NP. Based on location and histochemistry of the motoneuron subgroups in monkey, CEN is considered as the SR and IO motoneurons, DL and VEN as the B- and A-group of MR motoneurons, respectively, and DM as IR motoneurons. A good correlation between monkey and man is seen for the CR input, which labels only motoneurons of eye muscles participating in upgaze (SR, IO and LP. The CCN contained LP motoneurons, and nIV those of SO. This study provides a map of the individual subgroups of motoneurons in human nIII for the first time, and suggests that NP may contain upgaze motoneurons. Surprisingly, a strong GABAergic input to human MR motoneurons was discovered, which is not seen in monkey and may indicate a functional oculomotor specialization.

  9. Identification of Subgroups of Women with Carpal Tunnel Syndrome with Central Sensitization.

    Science.gov (United States)

    Fernández-de-Las-Peñas, César; Fernández-Muñoz, Juan J; Navarro-Pardo, Esperanza; da-Silva-Pocinho, Ricardo F; Ambite-Quesada, Silvia; Pareja, Juan A

    2016-09-01

    Identification of subjects with different sensitization mechanisms can help to identify better therapeutic strategies for carpal tunnel syndrome (CTS). The aim of the current study was to identify subgroups of women with CTS with different levels of sensitization. A total of 223 women with CTS were recruited. Self-reported variables included pain intensity, function, disability, and depression. Pressure pain thresholds (PPT) were assessed bilaterally over median, ulnar, and radial nerves, C5-C6 joint, carpal tunnel, and tibialis anterior to assess widespread pressure pain hyperalgesia. Heat (HPT) and cold (CPT) pain thresholds were also bilaterally assessed over the carpal tunnel and the thenar eminence to determine thermal pain hyperalgesia. Pinch grip force between the thumb and the remaining fingers was calculated to determine motor assessment. Subgroups were determined according to the status on a previous clinical prediction rule: PPT over the affected C5-C6 joint 66 points. The ANOVA showed that women within group 1 (positive rule, n = 60) exhibited bilateral widespread pressure hyperalgesia (P < 0.001) and bilateral thermal thresholds (P < 0.001) than those within group 2 (negative rule, n = 162). Women in group 1 also exhibited higher depression than those in group 2 (P = 0.023). No differences in self-reported variables were observed. This study showed that a clinical prediction rule originally developed for identifying women with CTS who are likely to respond favorably to manual physical therapy was able to identify women exhibiting higher widespread pressure hyper-sensitivity and thermal hyperalgesia. This subgroup of women with CTS exhibiting higher sensitization may need specific therapeutic programs. © 2016 American Academy of Pain Medicine. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.

  10. Disentangling Heterogeneity of Childhood Disruptive Behavior Problems Into Dimensions and Subgroups.

    Science.gov (United States)

    Bolhuis, Koen; Lubke, Gitta H; van der Ende, Jan; Bartels, Meike; van Beijsterveldt, Catharina E M; Lichtenstein, Paul; Larsson, Henrik; Jaddoe, Vincent W V; Kushner, Steven A; Verhulst, Frank C; Boomsma, Dorret I; Tiemeier, Henning

    2017-08-01

    Irritable and oppositional behaviors are increasingly considered as distinct dimensions of oppositional defiant disorder. However, few studies have explored this multidimensionality across the broader spectrum of disruptive behavior problems (DBPs). This study examined the presence of dimensions and distinct subgroups of childhood DBPs, and the cross-sectional and longitudinal associations between these dimensions. Using factor mixture models (FMMs), the presence of dimensions and subgroups of DBPs was assessed in the Generation R Study at ages 6 (n = 6,209) and 10 (n = 4,724) years. Replications were performed in two population-based cohorts (Netherlands Twin Registry, n = 4,402, and Swedish Twin Study of Child and Adolescent Development, n = 1,089) and a clinical sample (n = 1,933). We used cross-lagged modeling in the Generation R Study to assess cross-sectional and longitudinal associations between dimensions. DBPs were assessed using mother-reported responses to the Child Behavior Checklist. Empirically obtained dimensions of DBPs were oppositional behavior (age 6 years), disobedient behavior, rule-breaking behavior (age 10 years), physical aggression, and irritability (both ages). FMMs suggested that one-class solutions had the best model fit for all dimensions in all three population-based cohorts. Similar results were obtained in the clinical sample. All three dimensions, including irritability, predicted subsequent physical aggression (range, 0.08-0.16). This study showed that childhood DBPs should be regarded as a multidimensional phenotype rather than comprising distinct subgroups. Incorporating multidimensionality will improve diagnostic accuracy and refine treatment. Future studies need to address the biological validity of the DBP dimensions observed in this study; herein lies an important opportunity for neuroimaging and genetic measures. Copyright © 2017 American Academy of Child and Adolescent Psychiatry. Published by Elsevier Inc. All

  11. Dissociation between two subgroups of the suprachiasmatic nucleus affected by the number of damped oscillated neurons

    Science.gov (United States)

    Gu, Changgui; Yang, Huijie; Rohling, Jos HT

    2017-03-01

    In mammals, the main clock located in the suprachiasmatic nucleus (SCN) of the brain synchronizes the body rhythms to the environmental light-dark cycle. The SCN is composed of about 2 ×104 neurons which can be classified into three oscillatory phenotypes: self-sustained oscillators, damped oscillators, and arrhythmic neurons. Exposed to an artificial external light-dark cycle with a period of 22 h instead of 24 h , two subgroups of the SCN can become desynchronized (dissociated). The ventrolateral (VL) subgroup receives photic input and is entrained to the external cycle and a dorsomedial (DM) subgroup oscillates with its endogenous (i.e., free running) period and is synchronized to the external light-dark cycle through coupling from the VL. In the present study, we examined the effects of damped oscillatory neurons on the dissociation between VL and DM under an external 22 h cycle. We found that, with increasing numbers of damped oscillatory neurons located in the VL, the dissociation between the VL and DM emerges, but if these neurons are increasingly present in the DM the dissociation disappears. Hence, the damped oscillatory neurons in different subregions of the SCN play distinct roles in the dissociation between the two subregions of the SCN. This shows that synchrony between SCN subregions is affected by the number of damped oscillatory neurons and the location of these cells. We suggest that more knowledge on the number and the location of these cells may explain why some species do show a dissociation between the subregions and others do not, as the distribution of oscillatory types of neurons offers a plausible and novel candidate mechanism to explain heterogeneity.

  12. LIN28B overexpression defines a novel fetal-like subgroup of juvenile myelomonocytic leukemia.

    Science.gov (United States)

    Helsmoortel, Hetty H; Bresolin, Silvia; Lammens, Tim; Cavé, Hélène; Noellke, Peter; Caye, Aurélie; Ghazavi, Farzaneh; de Vries, Andrica; Hasle, Henrik; Labarque, Veerle; Masetti, Riccardo; Stary, Jan; van den Heuvel-Eibrink, Marry M; Philippé, Jan; Van Roy, Nadine; Benoit, Yves; Speleman, Frank; Niemeyer, Charlotte; Flotho, Christian; Basso, Giuseppe; Te Kronnie, Geertruy; Van Vlierberghe, Pieter; De Moerloose, Barbara

    2016-03-03

    Juvenile myelomonocytic leukemia (JMML) is a rare and aggressive stem cell disease of early childhood. RAS activation constitutes the core component of oncogenic signaling. In addition, leukemic blasts in one-fourth of JMML patients present with monosomy 7, and more than half of patients show elevated age-adjusted fetal hemoglobin (HbF) levels. Hematopoietic stem cell transplantation is the current standard of care and results in an event-free survival rate of 50% to 60%, indicating that novel molecular-driven therapeutic options are urgently needed. Using gene expression profiling in a series of 82 patient samples, we aimed at understanding the molecular biology behind JMML and identified a previously unrecognized molecular subgroup characterized by high LIN28B expression. LIN28B overexpression was significantly correlated with higher HbF levels, whereas patients with monosomy 7 seldom showed enhanced LIN28B expression. This finding gives a biological explanation of why patients with monosomy 7 are rarely diagnosed with high age-adjusted HbF levels. In addition, this new fetal-like JMML subgroup presented with reduced levels of most members of the let-7 microRNA family and showed characteristic overexpression of genes involved in fetal hematopoiesis and stem cell self-renewal. Lastly, high LIN28B expression was associated with poor clinical outcome in our JMML patient series but was not independent from other prognostic factors such as age and age-adjusted HbF levels. In conclusion, we identified elevated LIN28B expression as a hallmark of a novel fetal-like subgroup in JMML. © 2016 by The American Society of Hematology.

  13. Three subgroups of pain profiles identified in 227 women with arthritis: a latent class analysis.

    Science.gov (United States)

    de Luca, Katie; Parkinson, Lynne; Downie, Aron; Blyth, Fiona; Byles, Julie

    2017-03-01

    The objectives were to identify subgroups of women with arthritis based upon the multi-dimensional nature of their pain experience and to compare health and socio-demographic variables between subgroups. A latent class analysis of 227 women with self-reported arthritis was used to identify clusters of women based upon the sensory, affective, and cognitive dimensions of the pain experience. Multivariate multinomial logistic regression analysis was used to determine the relationship between cluster membership and health and sociodemographic characteristics. A three-class cluster model was most parsimonious. 39.5 % of women had a unidimensional pain profile; 38.6 % of women had moderate multidimensional pain profile that included additional pain symptomatology such as sensory qualities and pain catastrophizing; and 21.9 % of women had severe multidimensional pain profile that included prominent pain symptomatology such as sensory and affective qualities of pain, pain catastrophizing, and neuropathic pain. Women with severe multidimensional pain profile have a 30.5 % higher risk of poorer quality of life and a 7.3 % higher risk of suffering depression, and women with moderate multidimensional pain profile have a 6.4 % higher risk of poorer quality of life when compared to women with unidimensional pain. This study identified three distinct subgroups of pain profiles in older women with arthritis. Women had very different experiences of pain, and cluster membership impacted significantly on health-related quality of life. These preliminary findings provide a stronger understanding of profiles of pain and may contribute to the development of tailored treatment options in arthritis.

  14. Taxonomic boundaries, phylogenetic relationships and biogeography of the Drosophila willistoni subgroup (Diptera: Drosophilidae).

    Science.gov (United States)

    Robe, L J; Cordeiro, J; Loreto, E L S; Valente, V L S

    2010-06-01

    The Drosophila willistoni subgroup represents a complex with varying taxonomic levels. It encompasses D. willistoni and its five sibling species: D. equinoxialis, D. insularis, D. paulistorum, D. pavlovskiana and D. tropicalis. Of these, D. equinoxialis, D. tropicalis and D. willistoni present differentiation at subspecific level, whereas D. paulistorum represents a superspecies, formed by six semispecies. Despite this taxonomic and evolutionary complexity, many of these semi and subspecific taxa have not yet had their phylogenetic status tested in an explicitly molecular study. Aiming to contribute to the understanding of the evolution of this challenging group, we analyzed nucleotide sequences from two mitochondrial and four nuclear datasets, both individually and simultaneously, through different phylogenetic methods. High levels of incongruence were detected among partitions, especially concerning the mitochondrial sequences. As this incongruence was found to be statistically significant and robust to the use of different models and approaches, and basically restricted to mitochondrial loci, we suggest that it may stem mainly from hybridization-mediated asymmetrical introgression. Despite this, our nuclear data finally led to a phylogenetic hypothesis which further refines several aspects related to the willistoni subgroup phylogeny. In this respect, D. insularis, D. tropicalis, D. willistoni and D. equinoxialis successively branched off from the willistoni subgroup main stem, which recently subdivided to produce D. paulistorum and D. pavlovskiana. As regards the semispecies evolution, we found evidence of a recent diversification, which highly influenced the obtained results due to the associated small levels of genetic differentiation, further worsened by the possibly associated incompletely sorted ancestral polymorphisms and by the possibility of introgression. This study also raises the question of whether these semispecies are monophyletic at all. This

  15. Differential impact of supported housing on selected subgroups of homeless veterans with substance abuse histories.

    Science.gov (United States)

    O'Connell, Maria J; Kasprow, Wesley J; Rosenheck, Robert A

    2012-12-01

    Studies have demonstrated that supported housing is an effective intervention for individuals who are homeless and have a mental illness or substance use disorder. This study examined data from an experimental trial of the U.S. Department of Housing and Urban Development-Veterans Affairs Supported Housing (HUD-VASH) program to identify differences in the program's impact on subgroups defined by sociodemographic or clinical characteristics. Data were analyzed from 259 male homeless veterans with substance abuse problems who were randomly assigned to HUD-VASH (intensive case management [ICM] plus rent subsidy vouchers), ICM only, or treatment as usual between June 1992 and December 1995. Four subgroups were defined: African American versus Caucasian, younger versus older than 42.3 years, co-occurring diagnoses of mental illness versus diagnosis of a substance use disorder only, and active versus less active substance use upon program entry. Mixed models were used to identify significant interactions between HUD-VASH assignment and each subgroup. Compared with ICM alone, HUD-VASH was associated with more positive housing outcomes for Caucasians, veterans with co-occurring mental disorders, and veterans who were active substance users. HUD-VASH was associated with more positive socioclinical outcomes for African Americans. No differences were observed in housing or socioclinical outcomes as a function of age. Among homeless veterans with a substance use disorder, Caucasians and those with active substance use showed greater housing benefits than other veterans from HUD-VASH than from ICM alone. African Americans showed greater socioclinical benefit than Caucasians from HUD-VASH versus ICM. Interaction analysis deserves further study.

  16. Quality-of-Life Differences among Diagnostic Subgroups of Children Receiving Ventilating Tubes for Otitis Media.

    Science.gov (United States)

    Heidemann, Christian Hamilton; Lauridsen, Henrik Hein; Kjeldsen, Anette Drøhse; Faber, Christian Emil; Johansen, Eva Charlotte Jung; Godballe, Christian

    2015-10-01

    The pathological picture may differ considerably between diagnostic subgroups of children with otitis media receiving ventilating tubes. The aims of this study are to investigate differences in quality of life among diagnostic subgroups of children treated with ventilating tubes and to investigate possible predictors for clinical success. Longitudinal observational study. Secondary care units. Four hundred ninety-one families were enrolled in the study. The Otitis Media-6 questionnaire was applied in the assessment of child quality of life. Caregivers completed questionnaires at 7 time points from before treatment to 18-month follow-up. Logistic regression analysis was used to investigate possible predictors for clinical success. Response rates ranged from 96% to 81%; diagnostic distribution: 15% recurrent acute otitis media (rAOM), 47% otitis media with effusion (OME), and 38% mixed diagnosis of rAOM and OME (rAOM/OME). There were no significant differences between children diagnosed with rAOM and children diagnosed with rAOM/OME. However, these children had a significantly poorer quality of life at baseline compared with children diagnosed with only OME. Factors associated with clinical success included a diagnosis of rAOM, number of interrupted nights, physician visits, and canceled social activities due to OM. Results highlight the importance of distinguishing between diagnostic subgroups of children having ventilating tube treatment. A diagnosis of rAOM was found to predict baseline quality of life. Children with rAOM with or without OME were found to suffer significantly more than children with only OME before treatment. Factors associated with disease severity were found to predict clinical success. © American Academy of Otolaryngology-Head and Neck Surgery Foundation 2015.

  17. Somatosensory profiles in subgroups of patients with myogenic temporomandibular disorders and Fibromyalgia Syndrome.

    Science.gov (United States)

    Pfau, Doreen B; Rolke, Roman; Nickel, Ralf; Treede, Rolf-Detlef; Daublaender, Monika

    2009-12-15

    Some patients with myofascial pain from temporomandibular disorders (TMD) report pain in extra-trigeminal body regions. Our aim was to distinguish TMD as regional musculoskeletal pain syndrome (n=23) from a widespread pain syndrome (FMS; n=18) based on patients' tender point scores, pain drawings and quantitative sensory testing (QST) profiles. Referenced to 18 age- and gender-matched healthy subjects significant group differences for cold, pressure and pinprick pain thresholds, suprathreshold pinprick sensitivity and mechanical detection thresholds were found. Pain sensitivity in TMD patients ranged between those of FMS patients and healthy controls. The group of TMD patients was inhomogeneous with respect to their tender point count with an insensitive group (n=12) resembling healthy controls and a sensitive TMD group (n=9) resembling FMS patients. Nevertheless sensitive TMD patients did not fulfil diagnostic criteria for FMS in regard to widespread pain as shown by their pain drawings. TMD subgroups did not differ with respect to psychological parameters. The sensitive subgroup was more sensitive compared to healthy controls and to insensitive TMD patients in regard to their QST profile over all test areas as well as to their tenderness over orofacial muscles and trigeminal foramina. However, sensitive TMD patients had a short pain duration arguing against a transition from TMD to FMS over time. Data rather suggest an overlap in pathophysiology with FMS, e.g. a disturbance of central pain processing, in this subgroup of TMD patients. Those patients could be identified on the basis of their tender point count as an easy practicable screening tool.

  18. Baseline hospital performance and the impact of medical emergency teams: Modelling vs. conventional subgroup analysis

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    Hillman Ken

    2009-12-01

    Full Text Available Abstract Background To compare two approaches to the statistical analysis of the relationship between the baseline incidence of adverse events and the effect of medical emergency teams (METs. Methods Using data from a cluster randomized controlled trial (the MERIT study, we analysed the relationship between the baseline incidence of adverse events and its change from baseline to the MET activation phase using quadratic modelling techniques. We compared the findings with those obtained with conventional subgroup analysis. Results Using linear and quadratic modelling techniques, we found that each unit increase in the baseline incidence of adverse events in MET hospitals was associated with a 0.59 unit subsequent reduction in adverse events (95%CI: 0.33 to 0.86 after MET implementation and activation. This applied to cardiac arrests (0.74; 95%CI: 0.52 to 0.95, unplanned ICU admissions (0.56; 95%CI: 0.26 to 0.85 and unexpected deaths (0.68; 95%CI: 0.45 to 0.90. Control hospitals showed a similar reduction only for cardiac arrests (0.95; 95%CI: 0.56 to 1.32. Comparison using conventional subgroup analysis, on the other hand, detected no significant difference between MET and control hospitals. Conclusions Our study showed that, in the MERIT study, when there was dependence of treatment effect on baseline performance, an approach based on regression modelling helped illustrate the nature and magnitude of such dependence while sub-group analysis did not. The ability to assess the nature and magnitude of such dependence may have policy implications. Regression technique may thus prove useful in analysing data when there is a conditional treatment effect.

  19. Identification of novel vibration- and deflection-sensitive neuronal subgroups in Johnston’s organ of the fruit fly

    Directory of Open Access Journals (Sweden)

    Eriko eMatsuo

    2014-05-01

    Full Text Available The fruit fly Drosophila melanogaster responds behaviorally to sound, gravity, and wind. Johnston’s organ (JO at the antennal base serves as a sensory organ in the fruit fly to detect these mechanosensory stimuli. Among the five anatomically defined subgroups of sensory neurons in JO, subgroups A and B detect sound vibrations and subgroups C and E respond to static deflections, such as gravity and wind. The functions of subgroup-D JO neurons, however, remain unknown. In this study, we used molecular-genetic methods to explore the physiologic properties of subgroup-D JO neurons. Both vibrations and static deflection of the antennal receiver activated subgroup-D JO neurons. This finding clearly revealed that zone D in the antennal mechanosensory and motor center (AMMC, the projection target of subgroup-D JO neurons, is a primary center for antennal vibrations and deflection in the fly brain. We anatomically identified two types of interneurons downstream of subgroup-D JO neurons, AMMC LNs and AMMC D1 neurons. AMMC LNs are local neurons whose projections are confined within the AMMC, connecting zones B and D. On the other hand, AMMC D1 neurons have both local dendritic arborizations within the AMMC and descending projections to the thoracic ganglia, suggesting that AMMC D1 neurons are likely to relay information of the antennal movement detected by subgroup-D JO neurons from the AMMC directly to the thorax. Together, these findings provide a neural basis for how JO and its brain targets encode information of complex movements of the fruit fly antenna.

  20. Clustering Multiple Sclerosis Subgroups with Multifractal Methods and Self-Organizing Map Algorithm

    Science.gov (United States)

    Karaca, Yeliz; Cattani, Carlo

    Magnetic resonance imaging (MRI) is the most sensitive method to detect chronic nervous system diseases such as multiple sclerosis (MS). In this paper, Brownian motion Hölder regularity functions (polynomial, periodic (sine), exponential) for 2D image, such as multifractal methods were applied to MR brain images, aiming to easily identify distressed regions, in MS patients. With these regions, we have proposed an MS classification based on the multifractal method by using the Self-Organizing Map (SOM) algorithm. Thus, we obtained a cluster analysis by identifying pixels from distressed regions in MR images through multifractal methods and by diagnosing subgroups of MS patients through artificial neural networks.

  1. Fecal metagenomic profiles in subgroups of patients with myalgic encephalomyelitis/chronic fatigue syndrome.

    Science.gov (United States)

    Nagy-Szakal, Dorottya; Williams, Brent L; Mishra, Nischay; Che, Xiaoyu; Lee, Bohyun; Bateman, Lucinda; Klimas, Nancy G; Komaroff, Anthony L; Levine, Susan; Montoya, Jose G; Peterson, Daniel L; Ramanan, Devi; Jain, Komal; Eddy, Meredith L; Hornig, Mady; Lipkin, W Ian

    2017-04-26

    Myalgic encephalomyelitis/chronic fatigue syndrome (ME/CFS) is characterized by unexplained persistent fatigue, commonly accompanied by cognitive dysfunction, sleeping disturbances, orthostatic intolerance, fever, lymphadenopathy, and irritable bowel syndrome (IBS). The extent to which the gastrointestinal microbiome and peripheral inflammation are associated with ME/CFS remains unclear. We pursued rigorous clinical characterization, fecal bacterial metagenomics, and plasma immune molecule analyses in 50 ME/CFS patients and 50 healthy controls frequency-matched for age, sex, race/ethnicity, geographic site, and season of sampling. Topological analysis revealed associations between IBS co-morbidity, body mass index, fecal bacterial composition, and bacterial metabolic pathways but not plasma immune molecules. IBS co-morbidity was the strongest driving factor in the separation of topological networks based on bacterial profiles and metabolic pathways. Predictive selection models based on bacterial profiles supported findings from topological analyses indicating that ME/CFS subgroups, defined by IBS status, could be distinguished from control subjects with high predictive accuracy. Bacterial taxa predictive of ME/CFS patients with IBS were distinct from taxa associated with ME/CFS patients without IBS. Increased abundance of unclassified Alistipes and decreased Faecalibacterium emerged as the top biomarkers of ME/CFS with IBS; while increased unclassified Bacteroides abundance and decreased Bacteroides vulgatus were the top biomarkers of ME/CFS without IBS. Despite findings of differences in bacterial taxa and metabolic pathways defining ME/CFS subgroups, decreased metabolic pathways associated with unsaturated fatty acid biosynthesis and increased atrazine degradation pathways were independent of IBS co-morbidity. Increased vitamin B6 biosynthesis/salvage and pyrimidine ribonucleoside degradation were the top metabolic pathways in ME/CFS without IBS as well as in the

  2. Cost-Effectiveness of Endovascular Stroke Therapy: A Patient Subgroup Analysis From a US Healthcare Perspective.

    Science.gov (United States)

    Kunz, Wolfgang G; Hunink, M G Myriam; Sommer, Wieland H; Beyer, Sebastian E; Meinel, Felix G; Dorn, Franziska; Wirth, Stefan; Reiser, Maximilian F; Ertl-Wagner, Birgit; Thierfelder, Kolja M

    2016-11-01

    Endovascular therapy in addition to standard care (EVT+SC) has been demonstrated to be more effective than SC in acute ischemic large vessel occlusion stroke. Our aim was to determine the cost-effectiveness of EVT+SC depending on patients' initial National Institutes of Health Stroke Scale (NIHSS) score, time from symptom onset, Alberta Stroke Program Early CT Score (ASPECTS), and occlusion location. A decision model based on Markov simulations estimated lifetime costs and quality-adjusted life years (QALYs) associated with both strategies applied in a US setting. Model input parameters were obtained from the literature, including recently pooled outcome data of 5 randomized controlled trials (ESCAPE [Endovascular Treatment for Small Core and Proximal Occlusion Ischemic Stroke], EXTEND-IA [Extending the Time for Thrombolysis in Emergency Neurological Deficits-Intra-Arterial], MR CLEAN [Multicenter Randomized Clinical Trial of Endovascular Treatment for Acute Ischemic Stroke in the Netherlands], REVASCAT [Randomized Trial of Revascularization With Solitaire FR Device Versus Best Medical Therapy in the Treatment of Acute Stroke Due to Anterior Circulation Large Vessel Occlusion Presenting Within 8 Hours of Symptom Onset], and SWIFT PRIME [Solitaire With the Intention for Thrombectomy as Primary Endovascular Treatment]). Probabilistic sensitivity analysis was performed to estimate uncertainty of the model results. Net monetary benefits, incremental costs, incremental effectiveness, and incremental cost-effectiveness ratios were derived from the probabilistic sensitivity analysis. The willingness-to-pay was set to $50 000/QALY. Overall, EVT+SC was cost-effective compared with SC (incremental cost: $4938, incremental effectiveness: 1.59 QALYs, and incremental cost-effectiveness ratio: $3110/QALY) in 100% of simulations. In all patient subgroups, EVT+SC led to gained QALYs (range: 0.47-2.12), and mean incremental cost-effectiveness ratios were considered cost

  3. Tailoring the implementation of new biomarkers based on their added predictive value in subgroups of individuals.

    Directory of Open Access Journals (Sweden)

    A van Giessen

    Full Text Available The value of new biomarkers or imaging tests, when added to a prediction model, is currently evaluated using reclassification measures, such as the net reclassification improvement (NRI. However, these measures only provide an estimate of improved reclassification at population level. We present a straightforward approach to characterize subgroups of reclassified individuals in order to tailor implementation of a new prediction model to individuals expected to benefit from it.In a large Dutch population cohort (n = 21,992 we classified individuals to low (< 5% and high (≥ 5% fatal cardiovascular disease risk by the Framingham risk score (FRS and reclassified them based on the systematic coronary risk evaluation (SCORE. Subsequently, we characterized the reclassified individuals and, in case of heterogeneity, applied cluster analysis to identify and characterize subgroups. These characterizations were used to select individuals expected to benefit from implementation of SCORE.Reclassification after applying SCORE in all individuals resulted in an NRI of 5.00% (95% CI [-0.53%; 11.50%] within the events, 0.06% (95% CI [-0.08%; 0.22%] within the nonevents, and a total NRI of 0.051 (95% CI [-0.004; 0.116]. Among the correctly downward reclassified individuals cluster analysis identified three subgroups. Using the characterizations of the typically correctly reclassified individuals, implementing SCORE only in individuals expected to benefit (n = 2,707,12.3% improved the NRI to 5.32% (95% CI [-0.13%; 12.06%] within the events, 0.24% (95% CI [0.10%; 0.36%] within the nonevents, and a total NRI of 0.055 (95% CI [0.001; 0.123]. Overall, the risk levels for individuals reclassified by tailored implementation of SCORE were more accurate.In our empirical example the presented approach successfully characterized subgroups of reclassified individuals that could be used to improve reclassification and reduce implementation burden. In particular when newly

  4. Exhaled nitric oxide measure using multiple flows in clinically relevant subgroups of COPD

    DEFF Research Database (Denmark)

    Roberts, Nassim Bazeghi; Gerds, Thomas A; Budtz-Jørgensen, Esben

    2011-01-01

    Although there is widespread interest in fractional exhaled nitric oxide (FeNO) as a non-invasive, time and cost effective biomarker for assessing airway inflammation in chronic obstructive pulmonary disease (COPD), its usefulness is still controversial. We examined the FeNO levels in clinically...... (Caw). All patients had spirometry, assessment of symptoms with questionnaires and low-dose CT scan as well as assessment of weight and body composition. We examined the following subgroups of COPD: Patients with 1) Severe emphysema, 2) Chronic bronchitis, 3) Frequent exacerbations, 4) Loss of lean...

  5. Pain rating schema: three distinct subgroups of individuals emerge when rating mild, moderate, and severe pain

    Directory of Open Access Journals (Sweden)

    Frey-Law LA

    2013-12-01

    Full Text Available Laura A Frey-Law,1 Jennifer E Lee,2,3 Alex M Wittry,4 Myles Melyon5 1Department of Physical Therapy and Rehabilitation Science, The University of Iowa, Iowa City, IA, USA; 2Mount Mercy University, Department of Psychology, Cedar Rapids, IA, USA; ³College of Nursing, The University of Iowa, 4Department of Emergency Medicine, The University of Iowa Hospitals and Clinics, Iowa City, IA, USA; 5Midwestern University, Glendale, AZ, USA Background: While the validity of pain assessment has been well documented, the underlying schema (ie, organized, preconceived ideas of how individuals interpret numerical pain ratings is not well understood. This study's objectives were to examine numerical pain intensity ratings, from (0 to 10 cm on the visual analog scale [VAS] across multiple severities of commonly experienced acute pain conditions to determine whether the ratings differed between these pain conditions and/or between individuals. Methods: A community sample (N=365, 66% female rated their anticipated pain intensity (VAS for threshold, mild, moderate, severe, and tolerance level, using several common pain conditions: headache, toothache, joint injury, delayed-onset muscle soreness, burns, and “general pain.” Results: Cluster analysis revealed three subgroups of individuals, suggesting three types of underlying pain rating schema: 1 Low Rating subgroup (low VAS pain intensity ratings across all the pain severity categories; 2 Low/High Rating subgroup (low VAS pain intensity rating for mild, but high VAS pain intensity rating for severe pain; and 3 High Rating subgroup (high VAS pain intensity ratings across all the pain severity categories. Overall, differences between pain conditions were small: muscle soreness pain intensity was consistently rated lower than the other pain types across severities. The highest pain ratings varied between joint injury and general pain, depending on severity level. No effects of sex or current experience of pain

  6. Commognitive analysis of undergraduate mathematics students' first encounter with the subgroup test

    Science.gov (United States)

    Ioannou, Marios

    2017-08-01

    This study analyses learning aspects of undergraduate mathematics students' first encounter with the subgroup test, using the commognitive theoretical framework. It focuses on students' difficulties as these are related to the object-level and metalevel mathematical learning in group theory, and, when possible, highlights any commognitive conflicts. In the data analysis, one can identify three types of difficulties, relevant to object-level learning: namely regarding the frequently observed confusion between groups and sets, the object-level rules of visual mediators, and the object-level rules of contextual notions, such as permutations, exponentials, sets and matrices. In addition, data analysis suggests two types of difficulties, relevant to metalevel learning. The first refers to the actual proof that the three conditions of subgroup test hold, and the second is related to syntactic inaccuracies, incomplete argumentation and problematic use of visual mediators. Finally, this study suggests that there are clear links between object-level and metalevel learning, mainly due to the fact that objectification of the various relevant mathematical notions influences the endorsement of the governing metarules.

  7. Subgroup variations in bone mineral density response to zoledronic acid after hip fracture.

    Science.gov (United States)

    Magaziner, Jay S; Orwig, Denise L; Lyles, Kenneth W; Nordsletten, Lars; Boonen, Steven; Adachi, Jonathan D; Recknor, Chris; Colón-Emeric, Cathleen S; Mesenbrink, Peter; Bucci-Rechtweg, Christina; Su, Guoqin; Johnson, Rasheeda; Pieper, Carl F

    2014-12-01

    Minimizing post-fracture bone loss is an important aspect of recovery from hip fracture, and determination of factors that affect bone mineral density (BMD) response to treatment after hip fracture may assist in the development of targeted therapeutic interventions. A post hoc analysis of the HORIZON Recurrent Fracture Trial was done to determine the effect of zoledronic acid (ZOL) on total hip (TH) and femoral neck (FN) BMD in subgroups with low-trauma hip fracture. A total of 2127 patients were randomized (1:1) to yearly infusions of ZOL 5 mg (n = 1065) or placebo (n = 1062) within 90 days of operation for low-trauma hip fracture. The 1486 patients with a baseline and at least one post-baseline BMD assessment at TH or FN (ZOL = 745, placebo = 741) were included in the analyses. Percentage change from baseline in TH and FN BMD was assessed at months 12 and 24 and compared across subgroups of hip fracture patients. Percentage change from baseline in TH and FN BMD at months 12 and 24 was greater (p 6 weeks post-surgery; and for TH and FN BMD in patients with a history of one or more prior fractures. All interactions were limited to the first 12 months after treatment with none observed for the 24-month comparisons. (Clinical trial registration number NCT00046254.) © 2014 American Society for Bone and Mineral Research.

  8. Subgrouping siblings of people with autism: Identifying the broader autism phenotype

    Science.gov (United States)

    Allison, Carrie; Smith, Paula; Watson, Peter; Auyeung, Bonnie; Ring, Howard; Baron‐Cohen, Simon

    2015-01-01

    We investigate the broader autism phenotype (BAP) in siblings of individuals with autism spectrum conditions (ASC). Autistic traits were measured in typical controls (n = 2,000), siblings (n = 496), and volunteers with ASC (n = 2,322) using the Autism‐Spectrum Quotient (AQ), both self‐report and parent‐report versions. Using cluster analysis of AQ subscale scores, two sibling subgroups were identified for both males and females: a cluster of low‐scorers and a cluster of high‐scorers. Results show that while siblings as a group have intermediate levels of autistic traits compared to control individuals and participants with ASC, when examined on a cluster level, the low‐scoring sibling group is more similar to typical controls while the high‐scoring group is more similar to the ASC clinical group. Further investigation into the underlying genetic and epigenetic characteristics of these two subgroups will be informative in understanding autistic traits, both within the general population and in relation to those with a clinical diagnosis. Autism Res 2016, 9: 658–665. © 2015 The Authors Autism Research published by Wiley Periodicals, Inc. on behalf of International Society for Autism Research PMID:26332889

  9. Ranibizumab in Myopic Choroidal Neovascularization: A Subgroup Analysis by Ethnicity, Age, and Ocular Characteristics in RADIANCE.

    Science.gov (United States)

    Holz, Frank G; Tufail, Adnan; Leveziel, Nicolas; Lai, Timothy Y Y; Lanzetta, Paolo; Wong, Tien Y; Yu, Hyeong Gon; Chen, You Xin; Heinrichs, Nikol; Pilz, Stefan; Ohno-Matsui, Kyoko

    2016-01-01

    To assess the impact of ethnicity, age, and ocular characteristics on ranibizumab efficacy in myopic choroidal neovascularization (CNV). In this post hoc subgroup analysis from the phase III RADIANCE study, best-corrected visual acuity (BCVA) outcomes and treatment exposure were analyzed in 105 patients treated with ranibizumab 0.5 mg. Baseline categories included ethnicity, age, baseline BCVA, lesion area, CNV lesion area, refraction sphere, axial length, subretinal fluid, and location of CNV. At month 12, the mean change in BCVA was numerically higher in East-Asians than in Caucasians (17.0 vs. 14.1 letters). The median number of injections varied with ethnicity (East-Asians vs. Caucasians: 2 vs. 3), baseline BCVA (highest vs. lowest: 1 vs. 4), CNV lesion area and lesion area (largest vs. smallest: 5 vs. 1 and 5 vs. 2). East-Asians showed numerically higher BCVA gains than Caucasians. The number of injections varied across subgroups, emphasizing the need for individualized treatment. © 2016 S. Karger AG, Basel.

  10. Understanding Causal Distributional and Subgroup Effects with the Instrumental Propensity Score.

    Science.gov (United States)

    Cheng, Jing; Lin, Winston

    2017-08-17

    To address issues with measured and unmeasured confounding in observational studies, this paper develops a unified approach to using an instrumental variable in more flexible ways to evaluate treatment effects. The approach is based on an instrumental propensity score conditional on baseline variables, which can then be incorporated in matching, regression, subclassification or weighting along with various parametric, semiparametric or nonparametric methods for the assessment of treatment effects. Therefore, the application of the instrumental propensity score allows different methods for outcome effect evaluations in addition to standard two-stage least square models while controlling for unmeasured confounders. Several properties of the instrumental propensity score are discussed in the paper. The approach is then illustrated using subclassification along with a semiparametric density ratio model and empirical likelihood. This method allows us to evaluate distributional and subgroup treatment effects in addition to the overall average treatment effect. Simulation studies show that the method works well. We apply our method to a study of the effects of attending a Catholic school versus a public school and find that attending a Catholic school had significant beneficial effects on subsequent wages among a subgroup of subjects. © The Author(s) 2017. Published by Oxford University Press on behalf of the Johns Hopkins Bloomberg School of Public Health. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.

  11. Bayesian additive decision trees of biomarker by treatment interactions for predictive biomarker detection and subgroup identification.

    Science.gov (United States)

    Zhao, Yang; Zheng, Wei; Zhuo, Daisy Y; Lu, Yuefeng; Ma, Xiwen; Liu, Hengchang; Zeng, Zhen; Laird, Glen

    2017-10-11

    Personalized medicine, or tailored therapy, has been an active and important topic in recent medical research. Many methods have been proposed in the literature for predictive biomarker detection and subgroup identification. In this article, we propose a novel decision tree-based approach applicable in randomized clinical trials. We model the prognostic effects of the biomarkers using additive regression trees and the biomarker-by-treatment effect using a single regression tree. Bayesian approach is utilized to periodically revise the split variables and the split rules of the decision trees, which provides a better overall fitting. Gibbs sampler is implemented in the MCMC procedure, which updates the prognostic trees and the interaction tree separately. We use the posterior distribution of the interaction tree to construct the predictive scores of the biomarkers and to identify the subgroup where the treatment is superior to the control. Numerical simulations show that our proposed method performs well under various settings comparing to existing methods. We also demonstrate an application of our method in a real clinical trial.

  12. An observation on inappropriate probiotic subgroup classifications in the meta-analysis by Lau and Chamberlain

    Directory of Open Access Journals (Sweden)

    McFarl

    2016-09-01

    Full Text Available Lynne V McFarland Department of Medicinal Chemistry, University of Washington, Seattle, WA, USA I read with great interest the systematic review of meta-analysis assessing probiotics for the prevention of Clostridium difficile-associated diarrhea (CDAD published in the International Journal of General Medicine. These authors pooled 26 randomized controlled trials (RCTs and concluded that Lactobacilli, mixtures, and Saccharomyces probiotics were effective in preventing CDAD. However, the meta-analysis by Lau and Chamberlain is flawed due to improper classification by the types of probiotics. It is important to recognize that the efficacy of probiotics for various diseases has been shown to be strain specific for each probiotic product, and thus the data should only be pooled for probiotics that are of the identical type. In their analysis of probiotic subgroups by various species, the authors have inappropriately merged different types of Lactobacilli into one subgroup “Lactobacilli” and different types of mixtures into one group classified as “Mix”.View the original paper by Lau and Chamberlain. 

  13. Sinaloa Tomato Leaf Curl Geminivirus: Biological and Molecular Evidence for a New Subgroup III Virus.

    Science.gov (United States)

    Idris, A M; Brown, J K

    1998-07-01

    ABSTRACT The biological and molecular properties of Sinaloa tomato leaf curl virus (STLCV) were investigated in line with the hypothesis that STLCV is a previously uncharacterized, whitefly-transmitted geminivirus from North America. STLCV causes yellow leaf curl symptoms in tomato and yellow-green foliar mottle in pepper. Five species belonging to two plant families were STLCV experimental hosts. STLCV had a persistent relationship with its whitefly vector, Bemisia tabaci. Polymerase chain reaction fragments of STLCV common region (CR) sequences of the A or B genomic components and the viral coat protein gene (AV1) were molecularly cloned and sequenced. The STLCV A- and B-component CR sequences (174 nucleotides each) shared 97.9% identity and contained identical cis elements putatively involved in transcriptional regulation and an origin of replication (the AC cleavage site within the loop of the hairpin structure and two direct repeat sequences thought to constitute the Rep binding motif), which collectively are diagnostic for subgroup III geminiviruses. The STLCV CR sequence shared 23.1 to 77.6% identity with CR sequences of representative geminiviridae, indicating the STLCV CR sequence is unique. Molecular phylogenetic analysis of CR or AV1 sequences of STLCV and the respective sequences of 31 familial members supported the placement of STLCV as a unique bipartite, subgroup III virus most closely related to other viruses from the Western Hemisphere. STLCV is provisionally described as a new species within the genus Begomovirus, family Geminiviridae.

  14. Different outcomes in subgroups of patients with long-term musculoskeletal pain

    Directory of Open Access Journals (Sweden)

    Jan Sture Skouen

    2009-10-01

    Full Text Available Former studies have questioned the effectiveness of multidisciplinary rehabilitation for working-age adults with musculoskeletal pain problems. The lack of analysis within subgroups may explain why an effect of treatment of long-term musculoskeletal pain was not documented in former studies. In this article three later studies on long-term musculoskeletal pain patients are presented. The challenge of these studies was to identify subgroups of patients who benefit from different types of treatments. This article present the main findings of a large RCT with up till 54 months of follow-up among 664 persons sicklisted for musculoskeletal pain. It was hypothesised that different categories of patients need different treatment programs in order to get back to work. Patients with different prognoses for return to work were identified by means of a screening instrument, and it was tested whether those with poor prognosis need more extensive multidisciplinary treatment, compared to patients with less psychosocial and physical problems. Also, the effect of different treatment programs among patients with different diagnoses (ICD-9, low back pain and chronic widespread pain and among men and women was examined. The results of the three studies support the authors’ hypothesis that different categories of patients need different treatment programs. A higher percentage of return to work was demonstrated when the right treatment was given to the right patient, and considerable cost effectiveness was demonstrated

  15. Depressed serum IgM levels in SLE are restricted to defined subgroups.

    Science.gov (United States)

    Grönwall, Caroline; Hardt, Uta; Gustafsson, Johanna T; Elvin, Kerstin; Jensen-Urstad, Kerstin; Kvarnström, Marika; Grosso, Giorgia; Rönnelid, Johan; Padykov, Leonid; Gunnarsson, Iva; Silverman, Gregg J; Svenungsson, Elisabet

    2017-09-15

    Natural IgM autoantibodies have been proposed to convey protection from autoimmune pathogenesis. Herein, we investigated the IgM responses in 396 systemic lupus erythematosus (SLE) patients, divided into subgroups based on distinct autoantibody profiles. Depressed IgM levels were more common in SLE than in matched population controls. Strikingly, an autoreactivity profile defined by IgG anti-Ro/La was associated with reduced levels of specific natural IgM targeting phosphorylcholine (PC) antigens and malondialdehyde (MDA) modified-protein, as well as total IgM, while no differences were detected in SLE patients with an autoreactivity profile defined by anti-cardiolipin/β2glycoprotein-I. We also observed an association of reduced IgM levels with the HLA-DRB1*03 allelic variant among SLE patients and controls. Associations of low IgM anti-PC with cardiovascular disease were primarily found in patients without antiphospholipid antibodies. These studies further highlight the clinical relevance of depressed IgM. Our results suggest that low IgM levels in SLE patients reflect immunological and genetic differences between SLE subgroups. Copyright © 2017 Elsevier Inc. All rights reserved.

  16. {sup 1}H MR spectroscopy in histopathological subgroups of mesial temporal lobe epilepsy

    Energy Technology Data Exchange (ETDEWEB)

    Hajek, Milan; Dezortova, Monika [Institute for Clinical and Experimental Medicine, MR Unit, Department of Diagnostic and Interventional Radiology, Prague (Czech Republic); Krsek, Pavel; Komarek, Vladimir [Charles University, Department of Pediatric Neurology, Prague 5 (Czech Republic); Marusic, Petr; Tomasek, Martin; Krijtova, Hana [Charles University, Department of Neurology, Prague (Czech Republic); Zamecnik, Josef [Charles University, Department of Pathology and Molecular Medicine, Prague (Czech Republic); Kyncl, Martin [Charles University, Department of Radiology, Prague (Czech Republic)

    2009-02-15

    The aim of the study was to analyze the lateralizing value of proton magnetic resonance spectroscopy ({sup 1}H MRS) in histopathologically different subgroups of mesial temporal lobe epilepsies (MTLE) and to correlate results with clinical, MRI and seizure outcome data. A group of 35 patients who underwent resective epilepsy surgery was retrospectively studied. Hippocampal {sup 1}H MR spectra were evaluated. Metabolite concentrations were obtained using LCModel and NAA/Cr, NAA/Cho, NAA/(Cr+Cho), Cho/Cr ratios and coefficients of asymmetry were calculated. MRI correctly lateralized 89% of subjects and {sup 1}H MRS 83%. MRI together with {sup 1}H MRS correctly lateralized 100% of patients. Nineteen subjects had 'classical' hippocampal sclerosis (HS), whereas the remaining 16 patients had 'mild' HS. Nineteen patients had histopathologically proven malformation of cortical development (MCD) in the temporal pole; 16 subjects had only HS. No difference in {sup 1}H MRS findings was found between patients in different histopathological subgroups of MTLE. Our results support the hypothesis that {sup 1}H MRS abnormalities do not directly reflect histopathological changes in MTLE patients. Subjects with non-lateralized {sup 1}H MRS abnormalities did not have a worse postoperative seizure outcome. We found no significant impact of contralateral {sup 1}H MRS abnormality on post-surgical seizure outcome. (orig.)

  17. Subgroups of Paediatric Acute Lymphoblastic Leukaemia Might Differ Significantly in Genetic Predisposition to Asparaginase Hypersensitivity.

    Directory of Open Access Journals (Sweden)

    Nóra Kutszegi

    Full Text Available L-asparaginase (ASP is a key element in the treatment of paediatric acute lymphoblastic leukaemia (ALL. However, hypersensitivity reactions (HSRs to ASP are major challenges in paediatric patients. Our aim was to investigate genetic variants that may influence the risk to Escherichia coli-derived ASP hypersensitivity. Sample and clinical data collection was carried out from 576 paediatric ALL patients who were treated according to protocols from the Berlin-Frankfurt-Münster Study Group. A total of 20 single nucleotide polymorphisms (SNPs in GRIA1 and GALNT10 genes were genotyped. Patients with GRIA1 rs4958351 AA/AG genotype showed significantly reduced risk to ASP hypersensitivity compared to patients with GG genotype in the T-cell ALL subgroup (OR = 0.05 (0.01-0.26; p = 4.70E-04, while no such association was found in pre-B-cell ALL. In the medium risk group two SNPs of GRIA1 (rs2055083 and rs707176 were associated significantly with the occurrence of ASP hypersensitivity (OR = 0.21 (0.09-0.53; p = 8.48E-04 and OR = 3.02 (1.36-6.73; p = 6.76E-03, respectively. Evaluating the genders separately, however, the association of rs707176 with ASP HSRs was confined only to females. Our results suggest that genetic variants of GRIA1 might influence the risk to ASP hypersensitivity, but subgroups of patients can differ significantly in this respect.

  18. The Effect of Parkinson's Disease Subgroups on Verbal and Nonverbal Fluency

    Science.gov (United States)

    Jaywant, Abhishek; Musto, Giovanni; Neargarder, Sandy; Gilbert, Karina Stavitsky; Cronin-Golomb, Alice

    2014-01-01

    Background Parkinson's disease (PD) leads to deficits in executive function, including verbal and nonverbal fluency, as a result of compromised fronto-striatal circuits. It is unknown whether deficits in verbal and nonverbal fluency in PD are driven by certain subgroups of patients, or how strategy use may facilitate performance. Participants Sixty-five non-demented individuals with PD, including 36 with right-body onset (RPD; 20 with tremor as their initial symptom, 16 non-tremor) and 29 with left-body onset (LPD; 14 with tremor as their initial symptom, 15 non-tremor), and 52 normal control participants (NC). Measurements Verbal fluency was assessed using the FAS and Animals tests. Nonverbal fluency was assessed using the Ruff Figural Fluency Test. Results Both RPD and LPD were impaired in generating words and in using clustering and switching strategies on phonemic verbal fluency, whereas different patterns of impairment were found on nonverbal fluency depending on the interaction of side of onset and initial motor symptom (tremor vs. non-tremor). Strategy use correlated with number of correct responses on verbal fluency in LPD, RPD, and NC. By contrast, on nonverbal fluency, strategy use correlated with correct responses for RPD and LPD, but not for NC. Conclusion Our findings demonstrate the importance of considering subgroups in PD and analyzing subcomponents of verbal and nonverbal fluency (correct responses, errors, and strategies), which may depend differently on the integrity of dorsolateral prefrontal cortex, inferior frontal cortex, and anterior cingulate cortex. PMID:24533593

  19. Distinct neuropsychological subgroups in typically developing youth inform heterogeneity in children with ADHD.

    Science.gov (United States)

    Fair, Damien A; Bathula, Deepti; Nikolas, Molly A; Nigg, Joel T

    2012-04-24

    Research and clinical investigations in psychiatry largely rely on the de facto assumption that the diagnostic categories identified in the Diagnostic and Statistical Manual (DSM) represent homogeneous syndromes. However, the mechanistic heterogeneity that potentially underlies the existing classification scheme might limit discovery of etiology for most developmental psychiatric disorders. Another, perhaps less palpable, reality may also be interfering with progress-heterogeneity in typically developing populations. In this report we attempt to clarify neuropsychological heterogeneity in a large dataset of typically developing youth and youth with attention deficit/hyperactivity disorder (ADHD), using graph theory and community detection. We sought to determine whether data-driven neuropsychological subtypes could be discerned in children with and without the disorder. Because individual classification is the sine qua non for eventual clinical translation, we also apply support vector machine-based multivariate pattern analysis to identify how well ADHD status in individual children can be identified as defined by the community detection delineated subtypes. The analysis yielded several unique, but similar subtypes across both populations. Just as importantly, comparing typically developing children with ADHD children within each of these distinct subgroups increased diagnostic accuracy. Two important principles were identified that have the potential to advance our understanding of typical development and developmental neuropsychiatric disorders. The first tenet suggests that typically developing children can be classified into distinct neuropsychological subgroups with high precision. The second tenet proposes that some of the heterogeneity in individuals with ADHD might be "nested" in this normal variation.

  20. Tailoring the implementation of new biomarkers based on their added predictive value in subgroups of individuals.

    Science.gov (United States)

    van Giessen, A; Moons, K G M; de Wit, G A; Verschuren, W M M; Boer, J M A; Koffijberg, H

    2015-01-01

    The value of new biomarkers or imaging tests, when added to a prediction model, is currently evaluated using reclassification measures, such as the net reclassification improvement (NRI). However, these measures only provide an estimate of improved reclassification at population level. We present a straightforward approach to characterize subgroups of reclassified individuals in order to tailor implementation of a new prediction model to individuals expected to benefit from it. In a large Dutch population cohort (n = 21,992) we classified individuals to low (improved the NRI to 5.32% (95% CI [-0.13%; 12.06%]) within the events, 0.24% (95% CI [0.10%; 0.36%]) within the nonevents, and a total NRI of 0.055 (95% CI [0.001; 0.123]). Overall, the risk levels for individuals reclassified by tailored implementation of SCORE were more accurate. In our empirical example the presented approach successfully characterized subgroups of reclassified individuals that could be used to improve reclassification and reduce implementation burden. In particular when newly added biomarkers or imaging tests are costly or burdensome such a tailored implementation strategy may save resources and improve (cost-)effectiveness.

  1. The Colony meteorite and the possible existence of a new chemical subgroup of CO3 chondrites

    Science.gov (United States)

    Rubin, A. E.; James, J. A.; Keck, B. D.; Weeks, K. S.; Sears, D. W. G.

    1984-01-01

    The Colony meteorite, found in Oklahoma around 1975, has an unrecrystallized texture and contains heterogeneous olivine and low Ca pyroxene, kamacite with low Ni and Co and high Cr, amoeboid inclusions with low FeO and MnO, and numerous small chondrules with clear pink glass. These characteristics are shared by members of the least metamorphosed subgroup of CO3 chondrites. Colony contains a fine grained matrix that has higher FeO and K2O and lower MgO and Na2O than normal CO3 matrices. Allan Hills A77307 is another unmetamorphosed meteorite that has many petrologic similarities to normal CO chondrites, including matrix abundance, mineral compositions and chondrule size. However, it differs from them in its abundance of magnetite and presence of iron carbides. The olivine and low Ca pyroxene compositional distributions of Colony and A77307 are very similar. The shapes of the thermoluminescence glow curves of Colony and A77307 are very similar, but differ significantly from those of normal CO chondrites. It is suggested that Colony and A77307 represent a distinct chemical subgroup of CO3 chondrites, characterized by low Ni, Co, S, Ca, Mg, Mn and, possibly, high Cd.

  2. Blocking and binding folate receptor alpha autoantibodies identify novel autism spectrum disorder subgroups

    Directory of Open Access Journals (Sweden)

    Richard Eugene Frye

    2016-03-01

    Full Text Available Folate receptor α (FRα autoantibodies (FRAAs are prevalent in autism spectrum disorder (ASD. They disrupt the transportation of folate across the blood-brain barrier by binding to the FRα. Children with ASD with FRAAs have been reported to respond well to treatment with a form of folate known as folinic acid, suggesting that they may be an important ASD subgroup to identify and treat. There has been no investigation of whether they manifest unique behavioral and physiological characteristics. Thus, in this study we measured both blocking and binding FRAAs, physiological measurements including indices of redox and methylation metabolism and inflammation as well as serum folate and B12 concentrations and measurements of development and behavior in 94 children with ASD. Children positive for the binding FRAA were found to have higher serum B12 levels as compared to those negative for binding FRAAs while children positive for the blocking FRAA were found to have relatively better redox metabolism and inflammation markers as compared to those negative for blocking FRAAs. In addition, ASD children positive for the blocking FRAA demonstrated better communication on the Vineland Adaptive Behavior Scale, stereotyped behavior on the Aberrant Behavioral Checklist and Mannerisms on the Social Responsiveness Scale. This study suggests that FRAAs are associated with specific physiological and behavioral characteristics in children with ASD and provides support for the notion that these biomarkers may be useful for subgrouping children with ASD, especially with respect to targeted treatments.

  3. Dynamic expression of the TRPM subgroup of ion channels in developing mouse sensory neurons.

    Science.gov (United States)

    Staaf, Susanne; Franck, Marina C M; Marmigère, Frédéric; Mattsson, Jan P; Ernfors, Patrik

    2010-01-01

    Despite the significance of transient receptor potential (TRP) channels in sensory physiology, little is known of the expression and developmental regulation of the TRPM (melastatin) subgroup in sensory neurons. In order to find out if the eight TRPM subgroup members (TRPM1-TRPM8) have a possible role in the sensory nervous system, we characterized the developmental regulation of their expression in mouse dorsal root ganglion (DRG) from embryonic (E) day 12 to adulthood. Transcripts for all channels except for TRPM1 were detected in lumbar and thoracic DRG and in nodose ganglion (NG) with distinguishable expression patterns from E12 until adult. For most channels, the expression increased from E14 to adult with the exception of TRPM5, which displayed transient high levels during embryonic and early postnatal stages. Cellular localization of TRPM8 mRNA was found only in a limited subset of very small diameter neurons distinct in size from other populations. These neurons did not bind isolectin B4 (IB4) and expressed neither the neuropeptide calcitonin gene-related peptide (CGRP) nor neurofilament (NF)200. This suggests that TRPM8(+) thermoreceptive sensory neurons fall into a separate group of very small sized neurons distinct from peptidergic and IB4(+) subtypes of sensory neurons. Our results, showing the expression and dynamic regulation of TRPM channels during development, indicate that many TRPM subfamily members could participate during nervous system development and in the adult by determining distinct physiological properties of sensory neurons.

  4. CKM and PMNS Mixing Matrices from Discrete Subgroups of SU(2

    Directory of Open Access Journals (Sweden)

    Potter F.

    2014-07-01

    Full Text Available One of the greatest challenges in particle physics is to determine the first principles origin of the quark and lepton mixing matrices CKM and PMNS that relate the flavor states to the mass states. This first principles derivation of both the PMNS and CKM matrices utilizes quaternion generators of the three discrete (i.e., finite binary rotational subgroups of SU(2 called [3,3,2], [4,3,2], and [5,3,2] for three lepton families in R 3 and four related discrete binary rotational subgroups [3,3,3], [4,3,3], [3,4,3], and [5,3,3] represented by four quark families in R 4 . The traditional 3 3 CKM matrix is extracted as a submatrix of the 4 4 CKM4 matrix. The predicted fourth family of quarks has not been discovered yet. If these two additional quarks exist, there is the possibility that the Standard Model lagrangian may apply all the way down to the Planck scale.

  5. Differential Associations of Religious Involvement with the Mental Health of Asian-American Subgroups: A Cultural Perspective.

    Science.gov (United States)

    Ai, Amy L; Appel, Hoa B; Nicdao, Ethel G

    2016-12-01

    In the USA, Asian-Americans (AA) constitute the fastest growing ethnic minority group, in which heterogeneous religious patterns and acculturation experiences can impose significant impacts on their mental health. Using national data, the present study examined the contributions of religious involvement and social support to self-rated mental health (SRMH) of Chinese, Vietnamese, and Filipinos. Findings demonstrated cross-group variations, with Filipinos reporting the highest levels of SRMH, acculturation, and discrimination. However, religious involvement was associated with better SRMH in the least religious Chinese subgroup but not in the most religious Filipino subgroup. Social support predicted SRMH for both Chinese and Vietnamese subgroups. The differential religious patterns in the more acculturated generations between the two AA subgroups suggest religious assimilation as part of their acculturation in the context of divergent immigration experiences.

  6. MORS Workshop - Chem-Bio WMD: Understanding the Problem, Operations Analysis Working Group, Low Spectrum Conflict Subgroup

    National Research Council Canada - National Science Library

    Andreozzi, Gregory

    2001-01-01

    This report documents the insights developed by the Low Spectrum Conflict Subgroup of the Operations Analysis Working Group at the 30 January - 1 February 2001 Military Operations Research Society (MORS...

  7. Mixture model analysis identifies irritable bowel syndrome subgroups characterised by specific profiles of gastrointestinal, extraintestinal somatic and psychological symptoms.

    Science.gov (United States)

    Polster, A; Van Oudenhove, L; Jones, M; Öhman, L; Törnblom, H; Simrén, M

    2017-09-01

    Current subgrouping of Irritable Bowel Syndrome (IBS) is exclusively based on stool consistency without considering other relevant gastrointestinal (GI), extraintestinal somatic or psychological features. To identify subgroups based on a comprehensive set of IBS-related parameters. Mixture model analysis was used, with the following input variables: 13 single-item scores from the IBS-specific Gastrointestinal Symptom Rating Scale, average stool consistency and frequency from a 7-day Bristol Stool Form diary, 12 single-item extraintestinal symptom scores from the Patient Health Questionnaire-12, and anxiety and depression subscale scores from the Hospital Anxiety and Depression scale. The resulting latent subgroups were compared regarding symptom profiles using analysis of variance followed by pair-wise comparisons. One hundred and seventy-two IBS patients (Rome III; 69% female; mean age 33.7 [range 18-60] years) were included. The optimal subgrouping showed six latent groups, characterised by: (I) constipation with low comorbidities, (II) constipation with high comorbidities, (III) diarrhoea with low comorbidities, (IV) diarrhoea and pain with high comorbidities, (V) mixed GI symptoms with high comorbidities, (VI) a mix of symptoms with overall mild severity. The subgroups showed differences in the distribution of Rome III-subtypes, IBS severity, presence of anxiety and depression, and gender, but not regarding age, IBS duration or reported post-infectious onset of IBS. This model-based subgrouping of IBS partly supports the distinction of subgroups based on bowel habits, but additionally distinguishes subgroups with or without co-morbid extraintestinal somatic and psychological symptoms. The resulting groups show specific profiles of symptom combinations. © 2017 John Wiley & Sons Ltd.

  8. The effect of active video games by ethnicity, sex and fitness: subgroup analysis from a randomised controlled trial

    OpenAIRE

    Foley, Louise; Jiang, Yannan; Ni Mhurchu, Cliona; Jull, Andrew; Prapavessis, Harry; Rodgers,Anthony; Maddison, Ralph

    2014-01-01

    Background The prevention and treatment of childhood obesity is a key public health challenge. However, certain groups within populations have markedly different risk profiles for obesity and related health behaviours. Well-designed subgroup analysis can identify potential differential effects of obesity interventions, which may be important for reducing health inequalities. The study aim was to evaluate the consistency of the effects of active video games across important subgroups in a rand...

  9. Origins and biogeography of the Anolis crassulus subgroup (Squamata: Dactyloidae) in the highlands of Nuclear Central America.

    Science.gov (United States)

    Hofmann, Erich P; Townsend, Josiah H

    2017-12-21

    Recent studies have begun to reveal the complex evolutionary and biogeographic histories of mainland anoles in Central America, but the origins and relationships of many taxa remain poorly understood. One such group is the Anolis (Norops) crassulus species subgroup, which contains ten morphologically similar highland taxa, the majority of which have restricted distributions. The nominal taxon A. crassulus has a disjunct distribution from Chiapas, Mexico, through Guatemala, in the highlands of El Salvador, and in the Chortís Highlands of Honduras. We test the relationships of these species using multiple mitochondrial and nuclear loci in concatenated and multispecies coalescent frameworks, in an effort to both resolve long-standing taxonomic confusion and present new insights into the evolution and biogeography of these taxa. Sequences of multiple mitochondrial and nuclear loci were generated for eight of the ten species of the Anolis crassulus species subgroup. We analyzed phylogenetic relationships and estimated divergence times and ancestral ranges of the subgroup, recovering a monophyletic subgroup within Anolis. Within the nominal taxon Anolis crassulus, we recovered multiple genetically distinct lineages corresponding to allopatric populations, and show that the Chortís Highland lineage split from the others over 13 MYA. Additionally, distinct mitochondrial lineages are present within the taxa A. heteropholidotus and A. morazani, and importantly, samples of A. crassulus and A. sminthus previously used in major anole phylogenetic analyses are not recovered as conspecific with those taxa. We infer a Chortís Highland origin for the ancestor of this subgroup, and estimate cladogenesis of this subgroup began approximately 22 MYA. Our results provide new insights into the evolution, biogeography, and timing of diversification of the Anolis crassulus species subgroup. The disjunctly distributed Anolis crassulus sensu lato represents several morphologically

  10. Specific autoantibody profiles and disease subgroups correlate with circulating micro-RNA in systemic sclerosis.

    Science.gov (United States)

    Wuttge, Dirk M; Carlsen, Anting Liu; Teku, Gabriel; Steen, Samantha O; Wildt, Marie; Vihinen, Mauno; Hesselstrand, Roger; Heegaard, Niels H H

    2015-11-01

    To evaluate the expression profiles of cell-free plasma miRNAs in SSc and to characterize their correlation with disease subgroups (lcSSc and dcSSc) and with autoantibody profiles. Using quantitative RT-PCR, the abundance of 45 mature miRNAs in plasma was determined in 95 patients (lcSSc = 63; dcSSc = 32), representing the following autoantibody subgroups: ACA, anti-DNA topoisomerase I, anti-RNA polymerase III and anti-U1-ribonucleoprotein. MiRNA data were correlated with clinical and paraclinical data. Multiple regression was used to model membership of the lcSSc, dcSSc and autoantibody subgroups, based on miRNA expression profiles. Thirty-six miRNAs were measurable in all samples. Four (miRNA-223, -181b, -342-3p and -184) were differently expressed in lcSSc and dcSSc (false discovery rate < 0.05). Ten miRNAs exhibited statistically significantly different levels in one or more autoantibody groups, and five (miRNA-409, -184, -92a, -29a and -101) remained significant after correction for multiple comparisons. Multiple regression models accurately predicted ACA and anti-DNA topoisomerase I antibody-positive patients (area under the curve (AUC) = 0.97 and 0.93, respectively) as well as membership of the dcSSc and lcSSc groups (AUC = 0.88). Circulating miRNA profiles differ between lcSSc and dcSSc patients and between patients with different autoantibodies. This is the first time autoantibody profiles, disease phenotypes and plasma miRNA profiles have been shown to correlate in an autoimmune disease. The data support a pathobiological role of miRNAs because specific miRNAs associate with autoantibody profiles of known diagnostic and prognostic value. © The Author 2015. Published by Oxford University Press on behalf of the British Society for Rheumatology. All rights reserved. For Permissions, please email: journals.permissions@oup.com.

  11. Sequence and analysis of a whole genome from Kuwaiti population subgroup of Persian ancestry.

    Science.gov (United States)

    Thareja, Gaurav; John, Sumi Elsa; Hebbar, Prashantha; Behbehani, Kazem; Thanaraj, Thangavel Alphonse; Alsmadi, Osama

    2015-02-18

    The 1000 Genome project paved the way for sequencing diverse human populations. New genome projects are being established to sequence underrepresented populations helping in understanding human genetic diversity. The Kuwait Genome Project an initiative to sequence individual genomes from the three subgroups of Kuwaiti population namely, Saudi Arabian tribe; "tent-dwelling" Bedouin; and Persian, attributing their ancestry to different regions in Arabian Peninsula and to modern-day Iran (West Asia). These subgroups were in line with settlement history and are confirmed by genetic studies. In this work, we report whole genome sequence of a Kuwaiti native from Persian subgroup at >37X coverage. We document 3,573,824 SNPs, 404,090 insertions/deletions, and 11,138 structural variations. Out of the reported SNPs and indels, 85,939 are novel. We identify 295 'loss-of-function' and 2,314 'deleterious' coding variants, some of which carry homozygous genotypes in the sequenced genome; the associated phenotypes include pharmacogenomic traits such as greater triglyceride lowering ability with fenofibrate treatment, and requirement of high warfarin dosage to elicit anticoagulation response. 6,328 non-coding SNPs associate with 811 phenotype traits: in congruence with medical history of the participant for Type 2 diabetes and β-Thalassemia, and of participant's family for migraine, 72 (of 159 known) Type 2 diabetes, 3 (of 4) β-Thalassemia, and 76 (of 169) migraine variants are seen in the genome. Intergenome comparisons based on shared disease-causing variants, positions the sequenced genome between Asian and European genomes in congruence with geographical location of the region. On comparison, bead arrays perform better than sequencing platforms in correctly calling genotypes in low-coverage sequenced genome regions however in the event of novel SNP or indel near genotype calling position can lead to false calls using bead arrays. We report, for the first time, reference

  12. Prevalence and distribution of Gardnerella vaginalis subgroups in women with and without bacterial vaginosis.

    Science.gov (United States)

    Janulaitiene, Migle; Paliulyte, Virginija; Grinceviciene, Svitrigaile; Zakareviciene, Jolita; Vladisauskiene, Alma; Marcinkute, Agne; Pleckaityte, Milda

    2017-06-05

    Bacterial vaginosis (BV) is one of the leading causes of vaginal complaints among women of childbearing age. The role of Gardnerella vaginalis remains controversial due to its presence in healthy and BV-type vaginal microflora. The phenotypic and genotypic heterogeneity of G. vaginalis suggested the existence of strain variants linked with different health conditions. We sought to analyze prevalence and distribution of G. vaginalis subgroups (clades) in BV-positive (n = 29), partial BV (n = 27), and BV-negative (n = 53) vaginal samples from Lithuanian women. Vaginal samples were characterized by Amsel criteria and the Nugent method. Bacterial signatures characteristic of BV and concomitant infections were identified by culture and PCR. Using singleplex PCR assays, G. vaginalis subgroups were identified in 109 noncultured vaginal specimens by targeting clade-specific genes. Isolated G. vaginalis clinical strains were subtyped and the presence of the sialidase coding gene was detected by PCR. Data analysis was performed using GraphPad Prism statistical software. G. vaginalis was found in 87% of women without BV. Clade 4 was most frequently detected (79.4%), followed by clade 1 (63.7%), clade 2 (42.2%), and clade 3 (15.7%). Multi-clade G. vaginalis communities showed a positive association with Nugent score (NS) ≥ 4 (OR 3.64; 95% CI 1.48-8.91; p = 0.005). Clade 1 and clade 2 were statistically significantly more common in samples with NS 7-10 (OR 4.69; 95% CI 1.38-15.88; p = 0.01 and OR 6.26; 95% CI 2.20-17.81; p ≤ 0.001, respectively). Clade 3 and clade 4 showed no association with high NS (OR 0.88; 95% CI 0.26-3.04; p = 1.00 and OR 1.31; 95% CI 0.39-4.41; p = 0.767, respectively). The gene coding for sialidase was detected in all isolates of clade 1 and clade 2, but not in clade 4 isolates. We showed an association between the microbial state of vaginal microflora and specific subgroups of G. vaginalis, the distribution of which may determine the clinical

  13. Number of patients needed to discriminate between subgroups in patient reported outcome measures

    DEFF Research Database (Denmark)

    Paulsen, Aksel

    2011-01-01

    Background: Patient reported outcome-measures (PROs) are increasingly used in orthopedics. Information on number of patients needed in different settings is warranted. Aim: To assess the number of patients needed for different PROs to discriminate between subgroups of age, gender, and diagnosis...... with sample size calculations or by power calculations and simulated ANOVA F tests, depending on the number of groups. Results: To discriminate between gender, the least number needed to find a statistically significant difference in mean sum score in each group was 298 (OHS) while HOOS QoL required the most....... Methods: 5777 primary THA patients, operated 1‐2, 5‐6, and 10‐11 years ago. SF‐12 Health Survey (SF-12), EQ-5D, Oxford 12‐item Hip Score (OHS), and Hip dysfunction and Osteoarthritis Outcome Score (HOOS) were included. The different PRO subscales abilities to discriminate between groups were studied using...

  14. Identification of a CpG Island Methylator Phenotype that Defines a Distinct Subgroup of Glioma

    Science.gov (United States)

    Noushmehr, Houtan; Weisenberger, Daniel J.; Diefes, Kristin; Phillips, Heidi S.; Pujara, Kanan; Berman, Benjamin P.; Pan, Fei; Pelloski, Christopher E.; Sulman, Erik P.; Bhat, Krishna P.; Verhaak, Roel G.W.; Hoadley, Katherine A.; Hayes, D. Neil; Perou, Charles M.; Schmidt, Heather K.; Ding, Li; Wilson, Richard K.; Van Den Berg, David; Shen, Hui; Bengtsson, Henrik; Neuvial, Pierre; Cope, Leslie M.; Buckley, Jonathan; Herman, James G.; Baylin, Stephen B.; Laird, Peter W.; Aldape, Kenneth

    2010-01-01

    Summary We have profiled promoter DNA methylation alterations in 272 glioblastoma tumors in the context of The Cancer Genome Atlas (TCGA). We found that a distinct subset of samples displays concerted hypermethylation at a large number of loci, indicating the existence of a glioma-CpG Island Methylator Phenotype (G-CIMP). We validated G-CIMP in a set of non-TCGA glioblastomas and low-grade gliomas. G-CIMP tumors belong to the Proneural subgroup, are more prevalent among low-grade gliomas, display distinct copy-number alterations and are tightly associated with IDH1 somatic mutations. Patients with G-CIMP tumors are younger at the time of diagnosis and experience significantly improved outcome. These findings identify G-CIMP as a distinct subset of human gliomas on molecular and clinical grounds. PMID:20399149

  15. IQ subgroups in relation to neurocognitive profiles, psychopathology and brain volume in first-episode schizophrenia

    DEFF Research Database (Denmark)

    Jensen, Maria Høj; Glenthøj, Birte Yding; Rostrup, Egill

    Background and Aim: Approximately half of patients with schizophrenia experience a deterioration in IQ before or around illness onset and recent studies have found apositive association between IQ and brain volume in first episode schizophrenia. The aim of this study was to examine the combined...... impact of estimated IQ trajectory and IQ level at illness onset on psychopathology, neurocognitive profiles and brain volume. Materials and methods: The design is a cross-sectional, case-control study of 60 first-episode antipsychotic-naïve schizophrenia patients and 60 matched healthy controls....... Promorbid IQ was estimated using the Danish Adult Reading Test and current IQ using 4 subtests from Wechsler's Adult Intelligence Scale III. Patients were divided into 4 subgroups based on a combination of both IQ trajectory from premorbid levels (stable vs. deteriorating) and IQ at illness onset (high vs...

  16. Drinfeld Doubles for Finite Subgroups of SU(2 and SU(3 Lie Groups

    Directory of Open Access Journals (Sweden)

    Robert Coquereaux

    2013-05-01

    Full Text Available Drinfeld doubles of finite subgroups of SU(2 and SU(3 are investigated in detail. Their modular data – S, T and fusion matrices – are computed explicitly, and illustrated by means of fusion graphs. This allows us to reexamine certain identities on these tensor product or fusion multiplicities under conjugation of representations that had been discussed in our recent paper [J. Phys. A: Math. Theor. 44 (2011, 295208, 26 pages], proved to hold for simple and affine Lie algebras, and found to be generally wrong for finite groups. It is shown here that these identities fail also in general for Drinfeld doubles, indicating that modularity of the fusion category is not the decisive feature. Along the way, we collect many data on these Drinfeld doubles which are interesting for their own sake and maybe also in a relation with the theory of orbifolds in conformal field theory.

  17. When subgroups secede: extending and refining the social psychological model of schism in groups.

    Science.gov (United States)

    Sani, Fabio

    2005-08-01

    This article is about a field study (N=1,080) concerning the secession of a subgroup from the Church of England, and it is aimed at extending and refining the existing social psychological model of schisms in groups. It was found that the first step toward a schism is the belief that the group identity has been subverted. This belief will prompt negative emotions (i.e., dejection and agitation) and decrease both group identification and perceived group entitativity (i.e., cohesion, oneness). In turn, low group entitativity will reduce the level of group identification. Finally, low group identification and high negative emotions will increase schismatic intentions. It is also demonstrated that the negative impact of group identification, and the positive impact of negative emotions, on schismatic intentions is moderated by the perceived ability to voice dissent (i.e., the greater the perceived voice, the weaker the impact).

  18. Subgroup analysis of telehealthcare for patients with chronic obstructive pulmonary disease

    DEFF Research Database (Denmark)

    Witt Udsen, Flemming; Lilholt, Pernille H.; Hejlesen, Ole K.

    2017-01-01

    -to-pay threshold values. The purpose of this article was to assess potential sources of variation across subgroups, which could explain overall cost-effectiveness results or be utilized in future economic studies in telehealthcare research. METHODS: First, the cost-structures and cost-effectiveness across COPD...... investigated post hoc. In analyzing cost-effectiveness, two separate linear mixed-effects models with treatment-by-covariate interactions were applied: one for quality-adjusted life-year (QALY) gain and one for total healthcare and social sector costs. Probabilistic sensitivity analysis was used for each......PURPOSE: Results from the Danish cluster-randomized trial of telehealthcare to 1,225 patients with chronic obstructive pulmonary disease (COPD), the Danish Telecare North Trial, concluded that the telehealthcare solution was unlikely to be cost-effective, by applying international willingness...

  19. Distribution of cytokine gene polymorphisms in six Orang Asli subgroups in Peninsular Malaysia.

    Science.gov (United States)

    Norhalifah, Hanim K; Syafawati, Wan U Wan; Che Mat, Nor F; Chambers, Geoffrey K; Edinur, Hisham A

    2016-04-01

    Cytokines are involved in immune responses and the pathogenesis of various diseases. Allelic variations within the genes coding for various ∼30 kDa cytokine protein/glycoproteins have been reported for many populations and have been the subjects of many ancestry and health analyses. In this study, we typed 22 single nucleotide polymorphisms (SNPs) in 13 cytokine genes of 165 Orang Asli individuals by using sequence specific primer-polymerase chain reaction (SSP-PCR) assay. The volunteers came from all across the Peninsular of Malaysia and belong to six Orang Asli subgroups; Batek, Kensiu, Lanoh, Che Wong, Semai and Orang Kanaq. Here we report our general findings and original genotype data and their associated analyses (Hardy-Weinberg proportions, estimation of allele and haplotype frequencies) can be found in the supplementary files and will be held at Allele Frequency Net Database (AFND). Copyright © 2016 American Society for Histocompatibility and Immunogenetics. Published by Elsevier Inc. All rights reserved.

  20. Pain modulatory phenotypes differentiate subgroups with different clinical and experimental pain sensitivity

    DEFF Research Database (Denmark)

    Vaegter, Henrik Bjarke; Graven-Nielsen, Thomas

    2016-01-01

    between subgroups. Cuff algometry was performed on lower legs in 400 chronic pain patients to assess pressure pain threshold (cPPT), pressure pain tolerance (cPTT), temporal summation of pain (TSP: increase in pain scores to ten repeated stimulations), and conditioned pain modulation (CPM: increase in c......PPT during cuff pain conditioning on the contralateral leg). Heat detection (HDT) and heat pain thresholds (HPT) at clinical painful and non-painful body areas were assessed. Based on TSP and CPM four distinct groups were formed: Group 1 (n=85) had impaired CPM and facilitated TSP. Group 2 (n=148) had...... impaired CPM and normal TSP. Group 3 (n=45) had normal CPM and facilitated TSP. Group 4 (n=122) had normal CPM and normal TSP. Group 1 showed more pain regions compared with the other three groups (PTSP plays an important role in widespread pain. Group 1...

  1. A Data-Driven Approach to Responder Subgroup Identification after Paired Continuous Theta Burst Stimulation

    Directory of Open Access Journals (Sweden)

    Tonio Heidegger

    2017-08-01

    Full Text Available Background: Modulation of cortical excitability by transcranial magnetic stimulation (TMS is used for investigating human brain functions. A common observation is the high variability of long-term depression (LTD-like changes in human (motor cortex excitability. This study aimed at analyzing the response subgroup distribution after paired continuous theta burst stimulation (cTBS as a basis for subject selection.Methods: The effects of paired cTBS using 80% active motor threshold (AMT in 31 healthy volunteers were assessed at the primary motor cortex (M1 corresponding to the representation of the first dorsal interosseous (FDI muscle of the left hand, before and up to 50 min after plasticity induction. The changes in motor evoked potentials (MEPs were analyzed using machine-learning derived methods implemented as Gaussian mixture modeling (GMM and computed ABC analysis.Results: The probability density distribution of the MEP changes from baseline was tri-modal, showing a clear separation at 80.9%. Subjects displaying at least this degree of LTD-like changes were n = 6 responders. By contrast, n = 7 subjects displayed a paradox response with increase in MEP. Reassessment using ABC analysis as alternative approach led to the same n = 6 subjects as a distinct category.Conclusion: Depressive effects of paired cTBS using 80% AMT endure at least 50 min, however, only in a small subgroup of healthy subjects. Hence, plasticity induction by paired cTBS might not reflect a general mechanism in human motor cortex excitability. A mathematically supported criterion is proposed to select responders for enrolment in assessments of human brain functional networks using virtual brain lesions.

  2. Sub-grouping and sub-functionalization of the RIFIN multi-copy protein family

    Directory of Open Access Journals (Sweden)

    Sonnhammer Erik L

    2008-01-01

    Full Text Available Abstract Background Parasitic protozoans possess many multicopy gene families which have central roles in parasite survival and virulence. The number and variability of members of these gene families often make it difficult to predict possible functions of the encoded proteins. The families of extra-cellular proteins that are exposed to a host immune response have been driven via immune selection to become antigenically variant, and thereby avoid immune recognition while maintaining protein function to establish a chronic infection. Results We have combined phylogenetic and function shift analyses to study the evolution of the RIFIN proteins, which are antigenically variant and are encoded by the largest multicopy gene family in Plasmodium falciparum. We show that this family can be subdivided into two major groups that we named A- and B-RIFIN proteins. This suggested sub-grouping is supported by a recently published study that showed that, despite the presence of the Plasmodium export (PEXEL motif in all RIFIN variants, proteins from each group have different cellular localizations during the intraerythrocytic life cycle of the parasite. In the present study we show that function shift analysis, a novel technique to predict functional divergence between sub-groups of a protein family, indicates that RIFINs have undergone neo- or sub-functionalization. Conclusion These results question the general trend of clustering large antigenically variant protein groups into homogenous families. Assigning functions to protein families requires their subdivision into meaningful groups such as we have shown for the RIFIN protein family. Using phylogenetic and function shift analysis methods, we identify new directions for the investigation of this broad and complex group of proteins.

  3. Religious subgroups influencing vaccination coverage in the Dutch Bible belt: an ecological study

    Directory of Open Access Journals (Sweden)

    Knippenberg Hans

    2011-02-01

    Full Text Available Abstract Background The Netherlands has experienced epidemics of vaccine preventable diseases largely confined to the Bible belt, an area where -among others- orthodox protestant groups are living. Lacking information on the vaccination coverage in this minority, and its various subgroups, control of vaccine preventable diseases is focused on the geographical area of the Bible belt. However, the adequacy of this strategy is questionable. This study assesses the influence of presence of various orthodox protestant subgroups (orthodox protestant denominations, OPDs on municipal vaccination coverage in the Bible belt. Methods We performed an ecological study at municipality level. Data on number of inhabitants, urbanization level, socio-economical status, immigration and vaccination coverage were obtained from national databases. As religion is not registered in the Netherlands, membership numbers of the OPDs had to be obtained from church year books and via church offices. For all municipalities in the Netherlands, the effect of presence or absence of OPDs on vaccination coverage was assessed by comparing mean vaccination coverage. For municipalities where OPDs were present, the effect of each of them (measured as membership ratio, the number of members proportional to total number of inhabitants on vaccination coverage was assessed by bivariate correlation and multiple regression analysis in a model containing the determinants immigration, socio-economical status and urbanization as well. Results Mean vaccination coverage (93.5% ± 4.7 in municipalities with OPDs (n = 135 was significantly lower (p Conclusion As variance in municipal vaccination coverage in the Bible belt is largely explained by membership ratios of the various OPDs, control of vaccine preventable diseases should be focused on these specific risk groups. In current policy part of the orthodox protestant risk group is missed.

  4. The role of anger in psychosocial subgrouping for patients with low back pain.

    Science.gov (United States)

    Nisenzon, Anne N; George, Steven Z; Beneciuk, Jason M; Wandner, Laura D; Torres, Calia; Robinson, Michael E

    2014-06-01

    Low back pain (LBP) is a common and costly condition that often becomes chronic if not properly addressed. Recent research has shown that psychosocial symptoms can complicate LBP, necessitating more comprehensive screening measures. The present study investigated the role of psychosocial factors, including anger regulation, in pain and disability using a screening measure designed for LBP treated with physical therapy. One hundred three LBP patients initiating physical therapy completed an established screening measure to assess risk for developing chronic pain, and psychosocial measures assessing anger, depression, anxiety, fear-avoidance, and pain-catastrophizing before and after 4 weeks of treatment. Dependent variables were pain intensity, physical impairment, and patient-reported disability. Risk subgrouping based on anger and other psychosocial measures was examined using established screening methods and through using an empirical statistical approach. Analyses revealed that risk subgroups differed according to corresponding levels of negative affect, as opposed to anger alone. General psychosocial distress also predicted disability posttreatment, but, interestingly, did not have a strong relationship to pain. Subsequent hierarchical agglomerative clustering procedures divided patients into overall high-distress and low-distress groups, with follow-up analyses revealing that the high-distress group had higher baseline measures of pain, disability, and impairment. Findings suggest that anger may be part of a generalized negative affect rather than a unique predictor when assessing risk for pain and disability in LBP treatment. Continued research in the area of screening for psychosocial prognostic indicators in LBP may ultimately guide treatment protocols in physical therapy for more comprehensive patient care.

  5. Evolutionary Dynamics of Male Reproductive Genes in the Drosophila virilis Subgroup

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    Yasir H. Ahmed-Braimah

    2017-09-01

    Full Text Available Postcopulatory sexual selection (PCSS is a potent evolutionary force that can drive rapid changes of reproductive genes within species, and thus has the potential to generate reproductive incompatibilities between species. Male seminal fluid proteins (SFPs are major players in postmating interactions, and are important targets of PCSS in males. The virilis subgroup of Drosophila exhibits strong interspecific gametic incompatibilities, and can serve as a model to study the genetic basis of PCSS and gametic isolation. However, reproductive genes in this group have not been characterized. Here we utilize short-read RNA sequencing of male reproductive organs to examine the evolutionary dynamics of reproductive genes in members of the virilis subgroup: D. americana, D. lummei, D. novamexicana, and D. virilis. We find that the majority of male reproductive transcripts are testes-biased, accounting for ∼15% of all annotated genes. Ejaculatory bulb (EB-biased transcripts largely code for lipid metabolic enzymes, and contain orthologs of the D. melanogaster EB protein, Peb-me, which is involved in mating-plug formation. In addition, we identify 71 candidate SFPs, and show that this gene set has the highest rate of nonsynonymous codon substitution relative to testes- and EB-biased genes. Furthermore, we identify orthologs of 35 D. melanogaster SFPs that have conserved accessory gland expression in the virilis group. Finally, we show that several of the SFPs that have the highest rate of nonsynonymous codon substitution reside on chromosomal regions, which contributes to paternal gametic incompatibility between species. Our results show that SFPs rapidly diversify in the virilis group, and suggest that they likely play a role in PCSS and/or gametic isolation.

  6. Evolutionary Dynamics of Male Reproductive Genes in the Drosophila virilis Subgroup.

    Science.gov (United States)

    Ahmed-Braimah, Yasir H; Unckless, Robert L; Clark, Andrew G

    2017-09-07

    Postcopulatory sexual selection (PCSS) is a potent evolutionary force that can drive rapid changes of reproductive genes within species, and thus has the potential to generate reproductive incompatibilities between species. Male seminal fluid proteins (SFPs) are major players in postmating interactions, and are important targets of PCSS in males. The virilis subgroup of Drosophila exhibits strong interspecific gametic incompatibilities, and can serve as a model to study the genetic basis of PCSS and gametic isolation. However, reproductive genes in this group have not been characterized. Here we utilize short-read RNA sequencing of male reproductive organs to examine the evolutionary dynamics of reproductive genes in members of the virilis subgroup: D. americana, D. lummei, D. novamexicana, and D. virilis We find that the majority of male reproductive transcripts are testes-biased, accounting for ∼15% of all annotated genes. Ejaculatory bulb (EB)-biased transcripts largely code for lipid metabolic enzymes, and contain orthologs of the D. melanogaster EB protein, Peb-me, which is involved in mating-plug formation. In addition, we identify 71 candidate SFPs, and show that this gene set has the highest rate of nonsynonymous codon substitution relative to testes- and EB-biased genes. Furthermore, we identify orthologs of 35 D. melanogaster SFPs that have conserved accessory gland expression in the virilis group. Finally, we show that several of the SFPs that have the highest rate of nonsynonymous codon substitution reside on chromosomal regions, which contributes to paternal gametic incompatibility between species. Our results show that SFPs rapidly diversify in the virilis group, and suggest that they likely play a role in PCSS and/or gametic isolation. Copyright © 2017 Ahmed-Braimah et al.

  7. The Role of Anger in Psychosocial Subgrouping for Patients with Low Back Pain

    Science.gov (United States)

    Nisenzon, Anne N.; George, Steven Z.; Beneciuk, Jason M.; Wandner, Laura D.; Torres, Calia; Robinson, Michael E.

    2014-01-01

    Low back pain (LBP) is a common and costly condition that often becomes chronic if not properly addressed. Recent research has shown that psychosocial symptoms can complicate LBP, necessitating more comprehensive screening measures. The present study investigated the role of psychosocial factors, including anger regulation, in pain and disability using a screening measure designed for LBP treated with physical therapy. One-hundred and three LBP patients initiating physical therapy completed an established screening measure to assess risk for developing chronic pain, as well as psychosocial measures assessing anger, depression, anxiety, fear-avoidance, and pain-catastrophizing before and after four weeks of treatment. Dependent variables were pain intensity, physical impairment, and patient-reported disability. Risk subgrouping based on anger and other psychosocial measures was examined using established screening methods and through employing an empirical statistical approach. Analyses revealed that risk subgroups differed according to corresponding levels of negative affect, as opposed to anger alone. General psychosocial distress also predicted disability post-treatment, but, interestingly, did not have a strong relationship to pain. Subsequent hierarchical agglomerative clustering procedures divided patients into overall High and Low Distress groups, with follow-up analyses revealing that the High Distress group had higher baseline measures of pain, disability, and impairment. Findings suggest that anger may be part of generalized negative affect rather than a unique predictor when assessing risk for pain and disability in LBP treatment. Continued research in the area of screening for psychosocial prognostic indicators in LBP may ultimately guide treatment protocols in physical therapy for more comprehensive patient care. PMID:24281272

  8. Stratigraphy of the uppermost Old Red Sandstone of Svalbard (Mimerdalen Subgroup

    Directory of Open Access Journals (Sweden)

    Karsten Piepjohn

    2014-10-01

    Full Text Available Between the fjords Dicksonfjorden and Billefjorden in central Spitsbergen, Svalbard's youngest deposits (Early Givetian to Famennian in age of the Old Red Sandstone—the Mimerdalen Subgroup—are exposed. They form a narrow outcrop area parallel to the Billefjorden Fault Zone and overlie unconformably the multicoloured sandstones of the Lower Devonian Wood Bay Formation. Stratigraphic rank and subdivision of the succession were changed repeatedly since its first mention in 1910. Based on student work in 1996, as well as regional mapping by the authors in 1993 and 2003, the present work formalizes the stratigraphic framework of the succession. This framework has already been applied in recent geological maps. At the same time it is a continuation of the lithostratigraphic standardization carried out by the Committee on the Stratigraphy of Svalbard (1999, where only post-Devonian rocks were considered. Except for some small-pebble conglomerate layers in the Wood Bay Formation, the upper part of the Mimerdalen Subgroup contains the first coarse-grained deposits in Svalbard's Old Red since the lowermost Devonian Red Bay Group. Faulting between its formations as well as conglomerate pebbles derived from the Lower Devonian Wood Bay Formation indicate the onset of the Svalbardian Event after the tectonic stability during the deposition of the Wood Bay Formation. The Mimerdalen Subgroup is probably the detrital fill of a small foreland basin derived from erosion during the uplift of the Ny-Friesland Block to the east of the Billefjorden Fault Zone. It was later affected by compressional tectonic movements during the Svalbardian Event.

  9. Differences in MRI findings between subgroups of recent-onset childhood arthritis

    Energy Technology Data Exchange (ETDEWEB)

    Kirkhus, Eva [Oslo University Hospital, Rikshospitalet, Department of Radiology, Oslo (Norway); Flatoe, Berit; Smith, Hans-Joergen [Oslo University Hospital, Rikshospitalet and University of Oslo, Faculty of Medicine, Department of Radiology, Oslo (Norway); Riise, Oeystein [Oslo University Hospital, Rikshospitalet, Department of Pediatrics, Oslo (Norway); Reiseter, Tor [Oslo University Hospital, Ullevaal, Department of Radiology, Oslo (Norway)

    2011-04-15

    MRI is sensitive for joint inflammation, but its ability to separate subgroups of arthritis in children has been questioned. Infectious arthritis (IA), postinfectious arthritis (PA), transient arthritis (TA) and juvenile idiopathic arthritis (JIA) are subgroups that may need early, different treatment. To determine whether MRI findings differ in IA, PA/TA and JIA in recent-onset childhood arthritis. Fifty-nine children from a prospective study of incidence of arthritis (n = 216) were, based on clinical and biochemical criteria, examined by MRI. Joint fluid, synovium, bone marrow, soft tissue and cartilage were scored retrospectively and analysed by Pearson chi-square test and logistic regression analysis. Fifty-nine children had MRI of one station. IA was suggested by bone marrow oedema (OR 7.46, P = 0.011) and absence of T1-weighted and T2-weighted low signal intensity synovial tissue (OR 0.06, P = 0.015). Furthermore, soft-tissue oedema and reduced contrast enhancement in the epiphyses were more frequent in children with IA. JIA correlated positively with low signal intensity synovial tissue (OR 13.30, P < 0.001) and negatively with soft-tissue oedema (OR 0.20, P = 0.018). No significant positive determinants were found for PA/TA, but bone marrow oedema, soft-tissue oedema, irregular thickened synovium and low signal intensity synovial tissue was less frequent than in IA/JIA. In children with high clinical suspicion of recent onset arthritis, there was a significant difference in the distribution of specific MRI features among the diagnostic groups. (orig.)

  10. A Data-Driven Approach to Responder Subgroup Identification after Paired Continuous Theta Burst Stimulation.

    Science.gov (United States)

    Heidegger, Tonio; Hansen-Goos, Onno; Batlaeva, Olga; Annak, Onur; Ziemann, Ulf; Lötsch, Jörn

    2017-01-01

    Background: Modulation of cortical excitability by transcranial magnetic stimulation (TMS) is used for investigating human brain functions. A common observation is the high variability of long-term depression (LTD)-like changes in human (motor) cortex excitability. This study aimed at analyzing the response subgroup distribution after paired continuous theta burst stimulation (cTBS) as a basis for subject selection. Methods: The effects of paired cTBS using 80% active motor threshold (AMT) in 31 healthy volunteers were assessed at the primary motor cortex (M1) corresponding to the representation of the first dorsal interosseous (FDI) muscle of the left hand, before and up to 50 min after plasticity induction. The changes in motor evoked potentials (MEPs) were analyzed using machine-learning derived methods implemented as Gaussian mixture modeling (GMM) and computed ABC analysis. Results: The probability density distribution of the MEP changes from baseline was tri-modal, showing a clear separation at 80.9%. Subjects displaying at least this degree of LTD-like changes were n = 6 responders. By contrast, n = 7 subjects displayed a paradox response with increase in MEP. Reassessment using ABC analysis as alternative approach led to the same n = 6 subjects as a distinct category. Conclusion: Depressive effects of paired cTBS using 80% AMT endure at least 50 min, however, only in a small subgroup of healthy subjects. Hence, plasticity induction by paired cTBS might not reflect a general mechanism in human motor cortex excitability. A mathematically supported criterion is proposed to select responders for enrolment in assessments of human brain functional networks using virtual brain lesions.

  11. Whole-breast irradiation: a subgroup analysis of criteria to stratify for prone position treatment

    Energy Technology Data Exchange (ETDEWEB)

    Ramella, Sara, E-mail: s.ramella@unicampus.it [Radiation Oncology, Campus Bio-Medico University, Rome (Italy); Trodella, Lucio; Ippolito, Edy; Fiore, Michele; Cellini, Francesco; Stimato, Gerardina; Gaudino, Diego; Greco, Carlo [Radiation Oncology, Campus Bio-Medico University, Rome (Italy); Ramponi, Sara; Cammilluzzi, Eugenio; Cesarini, Claudio [Breast Unit, S. Pertini Hospital, Rome (Italy); Piermattei, Angelo [Department of Physics, Catholic University, Rome (Italy); Cesario, Alfredo [CdC San Raffaele Velletri (Italy); Department of Thoracic Surgery, Catholic University, Rome (Italy); D' Angelillo, Rolando Maria [Radiation Oncology, Campus Bio-Medico University, Rome (Italy)

    2012-07-01

    To select among breast cancer patients and according to breast volume size those who may benefit from 3D conformal radiotherapy after conservative surgery applied with prone-position technique. Thirty-eight patients with early-stage breast cancer were grouped according to the target volume (TV) measured in the supine position: small ({<=}400 mL), medium (400-700 mL), and large ({>=}700 ml). An ad-hoc designed and built device was used for prone set-up to displace the contralateral breast away from the tangential field borders. All patients underwent treatment planning computed tomography in both the supine and prone positions. Dosimetric data to explore dose distribution and volume of normal tissue irradiated were calculated for each patient in both positions. Homogeneity index, hot spot areas, the maximum dose, and the lung constraints were significantly reduced in the prone position (p < 0.05). The maximum heart distance and the V{sub 5Gy} did not vary consistently in the 2 positions (p = 0.06 and p = 0.7, respectively). The number of necessary monitor units was significantly higher in the supine position (312 vs. 232, p < 0.0001). The subgroups analysis pointed out the advantage in lung sparing in all TV groups (small, medium and large) for all the evaluated dosimetric constraints (central lung distance, maximum lung distance, and V{sub 5Gy}, p < 0.0001). In the small TV group, a dose reduction in nontarget areas of 22% in the prone position was detected (p = 0.056); in the medium and high TV groups, the difference was of about -10% (p = NS). The decrease in hot spot areas in nontarget tissues was 73%, 47%, and 80% for small, medium, and large TVs in the prone position, respectively. Although prone breast radiotherapy is normally proposed in patients with breasts of large dimensions, this study gives evidence of dosimetric benefit in all patient subgroups irrespective of breast volume size.

  12. Identification of subgroups of inflammatory and degenerative MRI findings in the spine and sacroiliac joints: a latent class analysis of 1037 patients with persistent low back pain

    DEFF Research Database (Denmark)

    Arnbak, Bodil; Jensen, Rikke Krüger; Manniche, Claus

    2016-01-01

    findings' (n = 84). The two SIJ subgroups (Subgroups 4 and 5) had a higher median activity limitation score (Roland Morris Disability Questionnaire calculated as a proportional score: 65 (IQR 48-78)/65 (48-78)) compared with Subgroups 1-3 (48 (35-74)/57 (39-74)/57 (39-74)), a higher prevalence of women (68...

  13. Plateau Iris Distribution Across Anterior Segment Optical Coherence Tomography Defined Subgroups of Subjects With Primary Angle Closure Glaucoma.

    Science.gov (United States)

    Verma, Sushma; Nongpiur, Monisha E; Oo, Hnin H; Atalay, Eray; Goh, David; Wong, Tina T; Perera, Shamira A; Aung, Tin

    2017-10-01

    We previously identified three distinct subgroups of patients with primary angle closure glaucoma (PACG) based on anterior segment optical coherence tomography (ASOCT) imaging. Group 1 was characterized by a large iris area with deepest anterior chambers, group 2 by a large lens vault (LV) and shallow anterior chamber depth (ACD), and group 3 displayed intermediate values across iris area, LV, and ACD. The purpose of the present study was to determine the distribution of plateau iris in these subgroups using ultrasound biomicroscopy (UBM) features. UBM images of the 210 subjects who were previously enrolled for the ASOCT subgrouping analysis and had undergone laser peripheral iridotomy were assessed and graded by a single glaucoma fellowship trained clinician. Plateau iris was defined as the presence of all the following UBM criteria in at least two quadrants: anteriorly directed ciliary body, absent ciliary sulcus, iris angulation, flat iris plane, and iridoangle touch. Of 210 subjects, 23 were excluded due to poor-quality images. Based on standardized UBM criteria, the overall prevalence of plateau iris was 36.9% (n = 187). The proportion of plateau iris was similar across the three groups (subgroup 1:35.4% (n = 29); subgroup 2:39.0% (n = 32); subgroup 3:34.8% (n = 8), P = 0.87). On multiple logistic regression analysis, iris thickness at 750 μm from the scleral spur (IT750) was the only variable associated with plateau iris (odds ratio: 1.5/100 μm increase in iris thickness [IT], P = 0.04). The proportion of plateau iris was similar across the three ASOCT-based PACG subgroups and more than one-third of subjects with PACG were diagnosed with plateau iris based on standardized UBM criteria. In addition, we noted that eyes with increased peripheral IT have an increased likelihood of plateau iris.

  14. The effect of active video games by ethnicity, sex and fitness: subgroup analysis from a randomised controlled trial.

    Science.gov (United States)

    Foley, Louise; Jiang, Yannan; Ni Mhurchu, Cliona; Jull, Andrew; Prapavessis, Harry; Rodgers, Anthony; Maddison, Ralph

    2014-04-03

    The prevention and treatment of childhood obesity is a key public health challenge. However, certain groups within populations have markedly different risk profiles for obesity and related health behaviours. Well-designed subgroup analysis can identify potential differential effects of obesity interventions, which may be important for reducing health inequalities. The study aim was to evaluate the consistency of the effects of active video games across important subgroups in a randomised controlled trial (RCT). A two-arm, parallel RCT was conducted in overweight or obese children (n=322; aged 10-14 years) to determine the effect of active video games on body composition. Statistically significant overall treatment effects favouring the intervention group were found for body mass index, body mass index z-score and percentage body fat at 24 weeks. For these outcomes, pre-specified subgroup analyses were conducted among important baseline demographic (ethnicity, sex) and prognostic (cardiovascular fitness) groups. No statistically significant interaction effects were found between the treatment and subgroup terms in the main regression model (p=0.36 to 0.93), indicating a consistent treatment effect across these groups. Preliminary evidence suggests an active video games intervention had a consistent positive effect on body composition among important subgroups. This may support the use of these games as a pragmatic public health intervention to displace sedentary behaviour with physical activity in young people.

  15. An overview of statistical and regulatory issues in the planning, analysis, and interpretation of subgroup analyses in confirmatory clinical trials.

    Science.gov (United States)

    Hemmings, Robert

    2014-01-01

    Whether confirmatory or exploratory in nature, the investigation of subgroups poses statistical and interpretational challenges, yet these investigations can have important consequences for product licensing, labeling, reimbursement, and prescribing decisions. This article provides a high-level, nontechnical summary of key statistical issues in the analysis of subgroups, with a focus on the regulatory context in which drug development and licensing decisions are made. References to specific aspects of regulatory processes are based on the system in Europe, though it is hoped that the principles outlined can be generally applied to other regulatory regions. This article challenges the common assumption that a clinical trial population should be assumed to be homogeneous, with homogeneous response to treatment, and asks whether commonly employed strategies for handling and identifying potential heterogeneity are sufficient. Investigations into subgroups are unavoidable, yet subgroup analyses suffer from fundamental complications and limitations of which those planning and interpreting clinical trials must be aware. Some areas for further methodological work and an improved methodological framework for the conduct of exploratory subgroup analyses are discussed. Above all, the need for an integrated scientific approach is highlighted.

  16. Mood, Disability, and Quality of Life among a Subgroup of Rheumatoid Arthritis Individuals with Experiential Avoidance and Anxiety Sensitivity

    Directory of Open Access Journals (Sweden)

    S. Mehta

    2016-01-01

    Full Text Available Objective. The current study aimed to identify and characterize distinct RA subgroups based on their level of EA and AS and compares the difference among the subgroups in mood, disability, and quality of life. Methods. Individuals with chronic pain for at least 3 months were recruited from an academic rheumatoid clinic. Participants were assessed for demographic, psychosocial, and personality measures. A two-step cluster analysis was conducted to identify distinct subgroups of patients. Differences in clinical outcomes were compared using the Multivariate ANOVA based on cluster membership. Results. From a total of 223 participants, three distinct subgroups were formed based on cluster analysis. Cluster 1 (N=78 included those with low levels of both EA and AS. Cluster 2 (N=81 consisted of individuals with moderate levels of EA and low levels AS. Cluster 3 (N=64 included those with moderate levels of EA and high AS. Compared to those in Cluster 1, those in Cluster 3 had significantly higher levels of mood impairment and disability and lower quality of life (p<0.05. Significantly lower levels of mood impairment were seen in Cluster 1 compared to Cluster 2 (p<0.05. However, no significant difference in disability or quality of life was seen between the two groups. Conclusions. The three subgroups differed significantly in levels of impairment in mood, disability, and quality of life. However, levels of EA had a greater impact on disability and quality of life than AS.

  17. Multiple invasions of Gypsy and Micropia retroelements in genus Zaprionus and melanogaster subgroup of the genus Drosophila

    Directory of Open Access Journals (Sweden)

    Carareto Claudia MA

    2009-12-01

    Full Text Available Abstract Background The Zaprionus genus shares evolutionary features with the melanogaster subgroup, such as space and time of origin. Although little information about the transposable element content in the Zaprionus genus had been accumulated, some of their elements appear to be more closely related with those of the melanogaster subgroup, indicating that these two groups of species were involved in horizontal transfer events during their evolution. Among these elements, the Gypsy and the Micropia retroelements were chosen for screening in seven species of the two Zaprionus subgenera, Anaprionus and Zaprionus. Results Screening allowed the identification of diverse Gypsy and Micropia retroelements only in species of the Zaprionus subgenus, showing that they are transcriptionally active in the sampled species. The sequences of each retroelement were closely related to those of the melanogaster species subgroup, and the most parsimonious hypothesis would be that 15 horizontal transfer events shaped their evolution. The Gypsy retroelement of the melanogaster subgroup probably invaded the Zaprionus genomes about 11 MYA. In contrast, the Micropia retroelement may have been introduced into the Zaprionus subgenus and the melanogaster subgroup from an unknown donor more recently (~3 MYA. Conclusion Gypsy and Micropia of Zaprionus and melanogaster species share similar evolutionary patterns. The sharing of evolutionary, ecological and ethological features probably allowed these species to pass through a permissive period of transposable element invasion, explaining the proposed waves of horizontal transfers.

  18. Mood, Disability, and Quality of Life among a Subgroup of Rheumatoid Arthritis Individuals with Experiential Avoidance and Anxiety Sensitivity.

    Science.gov (United States)

    Mehta, S; Rice, D; Janzen, S; Pope, J E; Harth, M; Shapiro, A P; Teasell, R W

    2016-01-01

    Objective. The current study aimed to identify and characterize distinct RA subgroups based on their level of EA and AS and compares the difference among the subgroups in mood, disability, and quality of life. Methods. Individuals with chronic pain for at least 3 months were recruited from an academic rheumatoid clinic. Participants were assessed for demographic, psychosocial, and personality measures. A two-step cluster analysis was conducted to identify distinct subgroups of patients. Differences in clinical outcomes were compared using the Multivariate ANOVA based on cluster membership. Results. From a total of 223 participants, three distinct subgroups were formed based on cluster analysis. Cluster 1 (N = 78) included those with low levels of both EA and AS. Cluster 2 (N = 81) consisted of individuals with moderate levels of EA and low levels AS. Cluster 3 (N = 64) included those with moderate levels of EA and high AS. Compared to those in Cluster 1, those in Cluster 3 had significantly higher levels of mood impairment and disability and lower quality of life (p impairment were seen in Cluster 1 compared to Cluster 2 (p disability or quality of life was seen between the two groups. Conclusions. The three subgroups differed significantly in levels of impairment in mood, disability, and quality of life. However, levels of EA had a greater impact on disability and quality of life than AS.

  19. Subgrouping of risky behaviors among Iranian college students: a latent class analysis

    Directory of Open Access Journals (Sweden)

    Safiri S

    2016-07-01

    Full Text Available Saeid Safiri,1,2 Afarin Rahimi-Movaghar,3 Masud Yunesian,4,5 Homayoun Sadeghi-Bazargani,6 Mansour Shamsipour,5 Mohammad Ali Mansournia,1 Akbar Fotouhi1 1Department of Epidemiology and Biostatistics, School of Public Health, Tehran University of Medical Sciences, Tehran, 2Department of Public Health, School of Nursing and Midwifery, Maragheh University of Medical Sciences, Maragheh, 3Iranian National Center for Addiction Studies (INCAS, Iranian Institute for Reduction of High-Risk Behaviors, Tehran University of Medical Sciences, Tehran, 4Department of Environmental Health Engineering, School of Public Health, 5Department of Research Methodology and Data Analysis, Institute for Environmental Research, Tehran University of Medical Sciences, Tehran, 6Road Traffic Injury Research Center, Department of Statistics & Epidemiology, Tabriz University of Medical Sciences, Tabriz, Iran Background: Risky behaviors may interrupt development or cause considerable morbidity or mortality. This study’s purpose was to determine subgroups of students based on risky behaviors and assess the prevalence of risky behaviors in each of the subgroups.Participants and methods: This anonymous cross-sectional study was carried out in October 2015 and November 2015, with 1,777 students from Tabriz University of Medical Sciences, through multistage random sampling method. The data were analyzed by latent class analysis.Results: The prevalence rates of cigarette smoking (more than or equal to ten cigarettes, hookah use (≥1 time/month, and alcohol consumption (≥1 time/month during the last year were 12.4% (95% confidence interval [CI]: 10.9–14.0, 11.6% (95% CI: 10.0–13.1, and 4.9% (95% CI: 3.8–5.9, respectively. The prevalence rates of illicit opioids (1.8%, 95% CI: 1.2–2.5, cannabis (1.2%, 95% CI: 0.7–1.7, methamphetamine (1.1%, 95% CI: 0.6–1.6, methylphenidate (2.5%, 95% CI: 1.7–3.2, and extramarital sex (5.5%, 95% CI: 4.5–6.6 over the last year were

  20. Recovery of motor deficit accompanying sciatica--subgroup analysis of a randomized controlled trial.

    Science.gov (United States)

    Overdevest, Gijsbert M; Vleggeert-Lankamp, Carmen L A M; Jacobs, Wilco C H; Brand, Ronald; Koes, Bart W; Peul, Wilco C

    2014-09-01

    In patients with sciatica due to a lumbar disc herniation, it is generally recommended to reserve surgical treatment for those who suffer from intolerable pain or those who demonstrate persistent symptoms after conservative management. Controversy exists about the necessity of early surgical intervention for those patients that have an additional motor deficit. The aim of this study was to compare the recovery of motor deficit among patients receiving early surgery to those receiving prolonged conservative treatment. Subgroup analysis of a randomized controlled trial. This subgroup analysis focuses on 150 (53%) of 283 patients with sciatica due to a lumbar disc herniation and whose symptoms at baseline (before randomization) were accompanied by a motor deficit. Motor deficit was assessed through manual muscle testing and graded according to the Medical Research Council (MRC) scale. In total, 150 patients with 6 to 12 weeks of sciatica due to a lumbar disc herniation and whose symptoms were accompanied by a moderate (MRC Grade 4) or severe (MRC Grade 3) motor deficit were randomly allocated to early surgery or prolonged conservative treatment. Repeated standardized neurologic examinations were performed at baseline and at 8, 26, and 52 weeks after randomization. This study was supported by a grant from the Netherlands Organization for Health Research and Development (ZonMW) and the Hoelen Foundation The Hague. Sciatica recovered among seven (10%) of the 70 patients assigned to early surgery before surgery could be performed, and of the 80 patients assigned to conservative treatment, 32 patients (40%) were treated surgically because of intolerable pain. Baseline severity of motor deficit was graded moderate in 84% of patients and severe in 16% of patients. Motor deficit recovered significantly faster among patients allocated to early surgery (p=.01), but the difference was no longer significant at 26 (p=.21) or 52 weeks (p=.92). At 1 year, complete recovery of motor

  1. How does unemployment affect self-assessed health? A systematic review focusing on subgroup effects.

    Science.gov (United States)

    Norström, Fredrik; Virtanen, Pekka; Hammarström, Anne; Gustafsson, Per E; Janlert, Urban

    2014-12-22

    Almost all studies on the effect on health from unemployment have concluded that unemployment is bad for your health. However, only a few review articles have dealt with this relation in recent years, and none of them have focused on the analysis of subgroups such as age, gender, and marital status. The objective of our article is to review how unemployment relates to self-assessed health with a focus on its effect on subgroups. A search was performed in Web of Science to find articles that measured the effect on health from unemployment. The selection of articles was limited to those written in English, consisting of original data, and published in 2003 or later. Our definition of health was restricted to self-assessed health. Mortality- and morbidity-related measurements were therefore not included in our analysis. For the 41 articles included, information about health measurements, employment status definitions, other factors included in the statistical analysis, study design (including study population), and statistical method were collected with the aim of analysing the results on both the population and factor level. Most of the studies in our review showed a negative effect on health from unemployment on a population basis. Results at the factor levels were most common for gender (25 articles), age (11 articles), geographic location (8 articles), and education level (5 articles). The analysis showed that there was a health effect for gender, age, education level, household income, and geographic location. However, this effect differed between studies and no clear pattern on who benefits or suffers more among these groups could be determined. The result instead seemed to depend on the study context. The only clear patterns of association found were for socioeconomic status (manual workers suffer more), reason for unemployment (being unemployed due to health reasons is worse), and social network (a strong network is beneficial). Unemployment affects groups of

  2. Cluster analysis for identifying sub-groups and selecting potential discriminatory variables in human encephalitis

    Directory of Open Access Journals (Sweden)

    Crowcroft Natasha S

    2010-12-01

    Full Text Available Abstract Background Encephalitis is an acute clinical syndrome of the central nervous system (CNS, often associated with fatal outcome or permanent damage, including cognitive and behavioural impairment, affective disorders and epileptic seizures. Infection of the central nervous system is considered to be a major cause of encephalitis and more than 100 different pathogens have been recognized as causative agents. However, a large proportion of cases have unknown disease etiology. Methods We perform hierarchical cluster analysis on a multicenter England encephalitis data set with the aim of identifying sub-groups in human encephalitis. We use the simple matching similarity measure which is appropriate for binary data sets and performed variable selection using cluster heatmaps. We also use heatmaps to visually assess underlying patterns in the data, identify the main clinical and laboratory features and identify potential risk factors associated with encephalitis. Results Our results identified fever, personality and behavioural change, headache and lethargy as the main characteristics of encephalitis. Diagnostic variables such as brain scan and measurements from cerebrospinal fluids are also identified as main indicators of encephalitis. Our analysis revealed six major clusters in the England encephalitis data set. However, marked within-cluster heterogeneity is observed in some of the big clusters indicating possible sub-groups. Overall, the results show that patients are clustered according to symptom and diagnostic variables rather than causal agents. Exposure variables such as recent infection, sick person contact and animal contact have been identified as potential risk factors. Conclusions It is in general assumed and is a common practice to group encephalitis cases according to disease etiology. However, our results indicate that patients are clustered with respect to mainly symptom and diagnostic variables rather than causal agents

  3. Religious subgroups influencing vaccination coverage in the Dutch Bible belt: an ecological study

    Science.gov (United States)

    2011-01-01

    Background The Netherlands has experienced epidemics of vaccine preventable diseases largely confined to the Bible belt, an area where -among others- orthodox protestant groups are living. Lacking information on the vaccination coverage in this minority, and its various subgroups, control of vaccine preventable diseases is focused on the geographical area of the Bible belt. However, the adequacy of this strategy is questionable. This study assesses the influence of presence of various orthodox protestant subgroups (orthodox protestant denominations, OPDs) on municipal vaccination coverage in the Bible belt. Methods We performed an ecological study at municipality level. Data on number of inhabitants, urbanization level, socio-economical status, immigration and vaccination coverage were obtained from national databases. As religion is not registered in the Netherlands, membership numbers of the OPDs had to be obtained from church year books and via church offices. For all municipalities in the Netherlands, the effect of presence or absence of OPDs on vaccination coverage was assessed by comparing mean vaccination coverage. For municipalities where OPDs were present, the effect of each of them (measured as membership ratio, the number of members proportional to total number of inhabitants) on vaccination coverage was assessed by bivariate correlation and multiple regression analysis in a model containing the determinants immigration, socio-economical status and urbanization as well. Results Mean vaccination coverage (93.5% ± 4.7) in municipalities with OPDs (n = 135) was significantly lower (p municipalities without OPDs (96.9% ± 2.1). Multiple regression analyses showed that in municipalities with OPDs 84% of the variance in vaccination coverage was explained by the presence of these OPDs. Immigration had a significant, but small explanatory effect as well. Membership ratios of all OPDs were negatively related to vaccination coverage; this relationship was

  4. “Real-life” inhaled corticosteroid withdrawal in COPD: a subgroup analysis of DACCORD

    Directory of Open Access Journals (Sweden)

    Vogelmeier C

    2017-02-01

    Full Text Available Claus Vogelmeier,1 Heinrich Worth,2 Roland Buhl,3 Carl-Peter Criée,4 Nadine S Lossi,5 Claudia Mailänder,5 Peter Kardos6 1Department of Medicine, Pulmonary and Critical Care Medicine, University Medical Center Giessen and Marburg, Philipps-University Marburg, Member of the German Center for Lung Research (DZL, Marburg, 2Facharzt Forum Fürth, Fürth, 3Pulmonary Department, Mainz University Hospital, Mainz, 4Department of Sleep and Respiratory Medicine, Evangelical Hospital Göttingen-Weende, Bovenden, 5Clinical Research, Respiratory, Novartis Pharma GmbH, Nürnberg, 6Group Practice and Centre for Allergy, Respiratory and Sleep Medicine, Red Cross Maingau Hospital, Frankfurt am Main, Germany Abstract: Many patients with chronic obstructive pulmonary disease (COPD receive inhaled corticosteroids (ICSs without a clear indication, and thus, the impact of ICS withdrawal on disease control is of great interest. DACCORD is a prospective, noninterventional 2-year study in the primary and secondary care throughout Germany. A subgroup of patients were taking ICS prior to entry – 1,022 patients continued to receive ICS for 2 years; physicians withdrew ICS on entry in 236 patients. Data from these two subgroups were analyzed to evaluate the impact of ICS withdrawal. Patients aged ≥40 years with COPD, initiating or changing COPD maintenance medication were recruited, excluding patients with asthma. Demographic and disease characteristics, prescribed COPD medication, COPD Assessment Test, exacerbations, and lung function were recorded. There were few differences in baseline characteristics; ICS withdrawn patients had shorter disease duration and better lung function, with 74.2% of ICS withdrawn patients not exacerbating, compared with 70.7% ICS-continued patients. During Year 1, exacerbation rates were 0.414 in the withdrawn group and 0.433 in the continued group. COPD Assessment Test total score improved from baseline in both groups. These data suggest

  5. Transfer of radiocaesium to the Swedish population and subgroups of special interest

    Energy Technology Data Exchange (ETDEWEB)

    Aagren, G. [Swedish Univ. of Agricultural Sciences, Uppsala (Sweden). Dept. of Radioecology

    1998-12-01

    As a result of the fallout from atmospheric nuclear weapon tests, whole body measurements of radiocesium in the population of Sweden were started in the late 1950`s. In the 1960`s the Saami population was recognised as a subgroup of the Swedish population with a greater risk than the general population of receiving high doses caused by their larger intake of reindeer meat. In 1986, a new deposition of radiocesium from the Chernobyl nuclear power plant accident occurred. The deposition from Chernobyl was, unlike the deposition from the atmospheric nuclear weapon tests, inhomogeneous with a higher deposition in areas where population groups depending on food products from semi-natural ecosystems can be found. Since 1986, whole body measurements have been used to monitor the effects from the Chernobyl accident on several different subgroups of the Swedish population. The group with the highest whole body contents of radiocesium has been the Saamis. Studies of {sup 137}Cs in different ecosystems have shown that population groups living on food products from the forest ecosystem could receive significant committed doses since the effective ecological half times here have been found to be close to the physical half life of {sup 137}Cs (30 years). However, whole body measurements of hunters, which is one such group, have still not confirmed these long half times. In all studied populations the transfer of radiocesium to man was found to decrease with increasing ground deposition and men were found to have about twice as high whole body content of radiocaesium as women. For adults, the whole body content increases slightly with age with a maximum around the age 50-70 years. The committed collective 50-year internal dose to the total Swedish population after Chernobyl will be 1100 personSv of which about half (500 personSv) will be to hunter families and originate in the forest ecosystem. The committed 50-year collective dose to the Saami population will be less (25 person

  6. Patient characteristics in low back pain subgroups based on an existing classification system. A descriptive cohort study in chiropractic practice

    DEFF Research Database (Denmark)

    Eirikstoft, Heidi; Kongsted, Alice

    2014-01-01

    Sub-grouping of low back pain (LBP) is believed to improve prediction of prognosis and treatment effects. The objectives of this study were: (1) to examine whether chiropractic patients could be sub-grouped according to an existing pathoanatomically-based classification system, (2) to describe...... reducible disc syndromes followed by facet joint pain, dysfunction and sacroiliac (SI)-joint pain. Classification was inconclusive in 5% of the patients. Differences in pain, activity limitation, and psychological factors were small across subgroups. Within 10 days, 82% were reported to belong to the same...... relevance of the classification system should be investigated by testing its value as a prognostic factor or a treatment effect modifier. It is recommended that this classification system be combined with psychological and social factors if it is to be useful....

  7. The Effectiveness of Mechanical Traction Among Subgroups of Patients With Low Back Pain and Leg Pain: A Randomized Trial.

    Science.gov (United States)

    Thackeray, Anne; Fritz, Julie M; Childs, John D; Brennan, Gerard P

    2016-03-01

    Randomized clinical trial. Background The recommended initial management strategy for patients with low back pain and signs of nerve root compression is conservative treatment, but there is little evidence to guide the most appropriate management strategy. Preliminary research suggests that a treatment protocol of mechanical traction and extension-oriented exercises may be effective, particularly in a specific subgroup of patients. To examine the effectiveness of mechanical traction in patients with lumbar nerve root compression and within a predefined subgroup. One hundred twenty patients with low back pain with nerve root compression were recruited from physical therapy clinics. Using predefined subgrouping criteria, patients were stratified at baseline and randomized to receive an extension-oriented treatment approach with or without the addition of mechanical traction. During a 6-week period, patients received up to 12 treatment visits. Primary outcomes of pain and disability were collected at 6 weeks, 6 months, and 1 year by assessors blinded to group allocation. Outcomes were examined using linear mixed-model analyses examining change over time by treatment and the interaction between treatment and subgrouping status. The mean ± SD age of participants was 41.1 ± 11.3 years, median duration of symptoms was 62 days, and 57% were male. No significant differences in disability or pain outcomes were noted between treatment groups at any time point, nor was any interaction found between subgroup status and treatment. Patients with lumbar nerve root compression presenting for physical therapy can expect significant changes in disability and pain over a 6-week treatment period. There is no evidence that mechanical lumbar traction in combination with an extension-oriented treatment is superior to extension-oriented exercises alone in the management of these patients or within a predefined subgroup of patients. The study protocol was registered with Clinical

  8. Prognostic subgroups for remission and response in the Coordinated Anxiety Learning and Management (CALM) trial.

    Science.gov (United States)

    Kelly, J MacLaren; Jakubovski, Ewgeni; Bloch, Michael H

    2015-03-01

    Most patients with anxiety disorders receive treatment in primary care settings. Limited moderator data are available to inform clinicians of likely prognostic outcomes for individual patients. We identify baseline characteristics associated with outcome in adults seeking treatment for anxiety disorders. We conducted an exploratory moderator analysis from the Coordinated Anxiety Learning and Management (CALM) trial. In the CALM trial, 1,004 adults who met DSM-IV criteria for generalized anxiety disorder (GAD), panic disorder, social anxiety disorder, and/or posttraumatic stress disorder (PTSD) were randomized to usual care (UC) or a collaborative care intervention (ITV) of cognitive-behavioral therapy and/or pharmacotherapy between June 2006 and April 2008. Logistic regression was used to examine baseline characteristics associated with remission and response overall and by treatment condition. Receiver operating curve (ROC) analyses identified subgroups associated with similar likelihood of response and remission of global anxiety symptoms. Remission was defined as score CALM in community treatment centers where patients typically are of low socioeconomic status and may particularly benefit from ITV. ClinicalTrials.gov identifier: NCT00347269. © Copyright 2015 Physicians Postgraduate Press, Inc.

  9. Polymerase chain reaction detection of circulating tumour cells. EORTC Melanoma Cooperative Group, Immunotherapy Subgroup.

    Science.gov (United States)

    Keilholz, U; Willhauck, M; Scheibenbogen, C; de Vries, T J; Burchill, S

    1997-08-01

    Reverse transcriptase polymerase chain reaction (RT-PCR)-based assays to detect occult neoplastic cells offer the highest sensitivity for the study of tumour dissemination and minimal residual disease. The detection of small numbers of tumour cells in a clinical sample may result in a redefinition of what constitutes residual disease and relapse, affecting future patient management. However, there remains disparity in the published data on the clinical value of RT-PCR for the detection of circulating tumour cells. This most likely reflects differences in the methods for sample preparation, RNA extraction, and cDNA synthesis among laboratories. Consequently the need for implementation of standard quality control measures is pressing in order to facilitate meaningful assessment of the methodology and it's clinical value. A 2-day workshop organized by the immunotherapy subgroup of the EORTC Melanoma Cooperative Group was held on this topic at the Ludwig Institute in Epalinges-sur-Lausanne, Switzerland in January 1996, with Stefan Carrel as the local host. Many pertinent issues were discussed in great detail, covering every step from sample handling to quality control. This workshop resulted in a concerted action leading to the preparation of laboratory guidelines, which are summarized in this review.

  10. VEGFR-1 Overexpression Identifies a Small Subgroup of Aggressive Prostate Cancers in Patients Treated by Prostatectomy

    Directory of Open Access Journals (Sweden)

    Maria Christina Tsourlakis

    2015-04-01

    Full Text Available The VEGFR-1 is suggested to promote tumor progression. In the current study we analyzed prevalence and prognostic impact of the VEGFR-1 by immunohistochemistry on a tissue microarray containing more than 3000 prostate cancer specimens. Results were compared to tumor phenotype, ETS-related gene (ERG status, and biochemical recurrence. Membranous VEGFR-1 expression was detectable in 32.6% of 2669 interpretable cancers and considered strong in 1.7%, moderate in 6.7% and weak in 24.2% of cases. Strong VEGFR-1 expression was associated with TMPRSS2:ERG fusion status as determined by fluorescence in situ hybridization (FISH and immunohistochemistry (p < 0.0001 each. Elevated VEGFR-1 expression was linked to high Gleason grade and advanced pT stage in TMPRSS2:ERG negative cancers (p = 0.0008 and p = 0.001, while these associations were absent in TMPRSS2:ERG positive cancers. VEGFR-1 expression was also linked to phosphatase and tensin homolog (PTEN deletions. A comparison with prostate specific antigen (PSA recurrence revealed that the 1.7% of prostate cancers with the highest VEGFR-1 levels had a strikingly unfavorable prognosis. This could be seen in all cancers, in the subsets of TMPRSS2:ERG positive or negative, PTEN deleted or undeleted carcinomas (p < 0.0001 each. High level VEGFR-1 expression is infrequent in prostate cancer, but identifies a subgroup of aggressive cancers, which may be candidates for anti-VEGFR-1 targeted therapy.

  11. Substitutions between dairy product subgroups and risk of type 2 diabetes

    DEFF Research Database (Denmark)

    Ibsen, Daniel B; Laursen, Anne Sofie D; Lauritzen, Lotte

    2017-01-01

    The aim of this study was to investigate the associations for specified substitutions between different subgroups of dairy products and the risk of type 2 diabetes. We used data from the Danish Diet, Cancer and Health cohort including 54 277 men and women aged 50-64 years at baseline. Information...... regarding intake of dairy products was obtained from a validated FFQ, and cases of type 2 diabetes were identified through the Danish National Diabetes Register. Cox proportional hazards regressions were used to estimate associations. During a median follow-up of 15·3 years, 7137 cases were identified. Low......-fat yogurt products in place of whole-fat yogurt products were associated with a higher rate of type 2 diabetes (hazard ratio (HR) 1·17; 95 % CI 1·06, 1·29) per serving/d substituted. Whole-fat yogurt products in place of low-fat milk, whole-fat milk or buttermilk were associated with a lower rate of type 2...

  12. Persistent Super-Utilization of Acute Care Services Among Subgroups of Veterans Experiencing Homelessness.

    Science.gov (United States)

    Szymkowiak, Dorota; Montgomery, Ann Elizabeth; Johnson, Erin E; Manning, Todd; O'Toole, Thomas P

    2017-10-01

    Acute health care utilization often occurs among persons experiencing homelessness. However, knowing which individuals will be persistent super-utilizers of acute care is less well understood. The objective of the study was to identify those more likely to be persistent super-utilizers of acute care services. We conducted a latent class analysis of secondary data from the Veterans Health Administration Corporate Data Warehouse, and Homeless Operations Management and Evaluation System. The study sample included 16,912 veterans who experienced homelessness and met super-utilizer criteria in any quarter between July 1, 2014 and December 31, 2015. The latent class analysis included veterans' diagnoses and acute care utilization. Medical, mental health, and substance use morbidity rates were high. More than half of the sample utilized Veterans Health Administration Homeless Programs concurrently with their super-utilization of acute care. There were 7 subgroups of super-utilizers, which varied considerably on the degree to which their super-utilization persisted over time. Approximately a third of the sample met super-utilizer criteria for ≥3 quarters; this group was older and disproportionately male, non-Hispanic white, and unmarried, with lower rates of post-9/11 service and higher rates of rural residence and service-connected disability. They were much more likely to be currently homeless with more medical, mental health, and substance use morbidity. Only a subset of homeless veterans were persistent super-utilizers, suggesting the need for more targeted interventions.

  13. Base excision repair dysfunction in a subgroup of patients with myelodysplastic syndrome.

    Science.gov (United States)

    Jankowska, A M; Gondek, L P; Szpurka, H; Nearman, Z P; Tiu, R V; Maciejewski, J P

    2008-03-01

    In myelodysplastic syndromes (MDS) increased chromosomal breaks point toward defects in DNA repair machinery including base excision repair (BER) pathway involved in handling of oxidative DNA damage. We investigated whether defects in this pathway can be found in MDS. Elevated levels of 8-oxoguanine (8-OG) were found in a significant proportion of MDS patients, indicating increased oxidative DNA damage or defective handling of oxidative load. In a distinct subgroup of patients, increased 8-OG content was associated with increased hOGG1 mRNA expression and activity. In some patients, increased numbers of abasic sites (AP sites) correlated with low levels of POLbeta. To further investigate the nature of this defect, we examined genetic lesions potentially explaining accumulation of 8-OG and AP sites. We genotyped a large cohort of MDS patients and found a correlation between increased oxidative damage and the presence of the hOGG1-Cys326 allele suggesting inadequate compensatory feedback. Overall, this hOGG1 variant was more frequent in MDS, particularly in advanced forms, as compared to controls. In summary, we demonstrated that BER dysfunction in some MDS patients may be responsible for the increased 8-OG incorporation and explains one aspect of the propensity to chromosomal breaks in MDS but other mechanisms may also be involved.

  14. Local inflammation increases vanilloid receptor 1 expression within distinct subgroups of DRG neurons.

    Science.gov (United States)

    Amaya, Fumimasa; Oh-hashi, Kentaro; Naruse, Yoshihisa; Iijima, Norio; Ueda, Masashi; Shimosato, Goshun; Tominaga, Makoto; Tanaka, Yoshifumi; Tanaka, Masaki

    2003-02-14

    Vanilloid receptor 1 (VR1) is essential to the development of inflammatory hyperalgesia. We investigated whether inflammation can increase in VR1 positive neuronal profiles in rat DRG neurons using histochemical methods. We also used size frequency analysis and double staining with several neuronal markers to investigate whether or not inflammation alters VR1 expression. Inflammation induced a 1.5-fold increase in percentage of VR1-like immunoreactivity (LI) positive profiles per total neuronal profiles, suggesting that the number of heat and pH sensitive neurons increase during inflammation. Area frequency histograms showed that VR1 expression increased in small and medium-sized neurons after inflammation. Double labeling of VR1 with NF200 showed that VR1 positive neurons with NF200 positive profiles significantly increased, indicating that the medium-sized VR1 positive neurons were neurons with myelinated A-fibers. Local inflammation thus increases in VR1 protein level within distinct subgroups of DRG neurons that may participate in the development and maintenance of inflammatory hyperalgesia.

  15. Mindfulness and Emotional Outcomes: Identifying Subgroups of College Students using Latent Profile Analysis.

    Science.gov (United States)

    Pearson, Matthew R; Lawless, Adrienne K; Brown, David B; Bravo, Adrian J

    2015-04-01

    In non-meditating samples, distinct facets of mindfulness are found to be negatively correlated, preventing the meaningful creation of a total mindfulness score. The present study used person-centered analyses to distinguish subgroups of college students based on their mindfulness scores, which allows the examination of individuals who are high (or low) on all facets of mindfulness. Using the Lo-Mendell-Rubin Adjusted LRT test, we settled on a 4-class solution that included a high mindfulness group (high on all 5 facets, N = 245), low mindfulness group (moderately low on all 5 facets, N = 563), judgmentally observing group (high on observing, but low on non-judging and acting with awareness, N =63), and non-judgmentally aware group (low on observing, but high on non-judging and acting with awareness, N =70). Consistent across all emotional outcomes including depressive symptoms, anxiety symptoms (i.e., worry), affective instability, and distress intolerance, we found that the judgmentally observing group had the most maladaptive emotional outcomes followed by the low mindfulness group. Both the high mindfulness group and the non-judgmentally aware group had the most adaptive emotional outcomes. We discuss the implications of person-centered analyses to exploring mindfulness as it relates to important psychological health outcomes.

  16. Avian metapneumovirus subgroup C induces autophagy through the ATF6 UPR pathway.

    Science.gov (United States)

    Hou, Lei; Wei, Li; Zhu, Shanshan; Wang, Jing; Quan, Rong; Li, Zixuan; Liu, Jue

    2017-10-03

    An increasing number of studies have demonstrated that macroautophagy/autophagy plays an important role in the infectious processes of diverse pathogens. However, it remains unknown whether autophagy is induced in avian metapneumovirus (aMPV)-infected host cells, and, if so, how this occurs. Here, we report that aMPV subgroup C (aMPV/C) induces autophagy in cultured cells. We demonstrated this relationship by detecting classical autophagic features, including the formation of autophagsomes, the presence of GFP-LC3 puncta and the conversation of LC3-I into LC3-II. Also, we used pharmacological regulators and siRNAs targeting ATG7 or LC3 to examine the role of autophagy in aMPV/C replication. The results showed that autophagy is required for efficient replication of aMPV/C. Moreover, infection with aMPV/C promotes autophagosome maturation and induces a complete autophagic process. Finally, the ATF6 pathway, of which one component is the unfolded protein response (UPR), becomes activated in aMPV/C-infected cells. Knockdown of ATF6 inhibited aMPV/C-induced autophagy and viral replication. Collectively, these results not only show that autophagy promotes aMPV/C replication in the cultured cells, but also reveal that the molecular mechanisms underlying aMPV/C-induced autophagy depends on regulation of the ER stress-related UPR pathway.

  17. Bovicin HJ50-like lantibiotics, a novel subgroup of lantibiotics featured by an indispensable disulfide bridge.

    Directory of Open Access Journals (Sweden)

    Jian Wang

    Full Text Available Lantibiotics are ribosomally-synthesized and posttranslationally modified peptides with potent antimicrobial activities. Discovery of novel lantibiotics has been greatly accelerated with the soaring release of genomic information of microorganisms. As a unique class II lantibiotic, bovicin HJ50 is produced by Streptococcus bovis HJ50 and contains one rare disulfide bridge. By using its precursor BovA as a drive sequence, 16 BovA-like peptides were revealed in a wide variety of species. From them, three representative novel lan loci from Clostridium perfringens D str. JGS1721, Bacillus cereus As 1.348 and B. thuringiensis As 1.013 were identified by PCR screening. The corresponding mature lantibiotics designated perecin, cerecin and thuricin were obtained and structurally elucidated to be bovicin HJ50-like lantibiotics especially by containing a conserved disulfide bridge. The disulfide bridge was substantiated to be essential for the function of bovicin HJ50-like lantibiotics as its disruption eliminated their antimicrobial activities. Further analysis indicated that the disulfide bridge played a crucial role in maintaining the hydrophobicity of bovicin HJ50, which might facilitate it to exert antimicrobial function. This study unveiled a novel subgroup of disulfide-containing lantibiotics from bacteria of different niches and further demonstrated the indispensable role of disulfide bridge in these novel bovicin HJ50-like lantibiotics.

  18. Subgrouping High School Students for Substance Abuse-Related Behaviors: A Latent Class Analysis.

    Science.gov (United States)

    Khayyati, Fariba; Mohammadpoorasl, Asghar; Allahverdipour, Hamid; AsghariJafarabadi, Mohammad; Kouzekanani, Kamiar

    2017-07-01

    The aim of the current study was to characterize the prevalence of latent groups in terms of smoking, hookah, and alcohol in a sample of Iranian high school students. In this cross-sectional study, 4,422 high school students were assessed in East Azerbaijan Province, Iran. Latent class analysis was applied to determine the subgroups and prevalence of each class using the procLCA in SAS 9.2 software. The prevalence of hookah smoking was the highest among the other substances and had the greatest abuse among males than females. Nearly 86%, 9.5%, and 4.6% of the participants were low risk, tobacco experimenter, and high risk, respectively. The odds ratio indices of membership in each class, compared with the first class, associated with the independent variables. A fair number of students, males in particular, were identified as high risk-takers. Considering the simultaneous incidence of multiple high-risk behaviors, interventions must cover multiple aspects of the issue at the same time.

  19. Genetic Sequencing Analysis of A307 Subgroup of ABO Blood Group.

    Science.gov (United States)

    Huang, Ying; Lin, Jiajin; Zhu, Suiyong

    2015-09-18

    BACKGROUND The aim of this study was to investigate the serology and gene sequence characteristics of the A307 subgroup of the ABO blood group. MATERIAL AND METHODS Monoclonal anti-A and anti-B antibodies were used to detect the ABO antigens of a proband whose positive blood type was not consistent with the negative blood type of the ABO blood group. Standard A-, B-, and O-negative typing cells were used to test for ABO antibodies in the serum. Additionally, polymerase chain reaction with sequence-specific primer (PCR-SSP) was used to confirm the genotype, and subsequently, exons 6 and 7 of the ABO gene were detected by gene sequencing. Samples from the wife and daughters of the proband were also used for serological and genetic testing. RESULTS Red blood cells of the proband showed weak agglutination reaction with anti-A antibody, while anti-B antibody was detected in the serum. Moreover, PCR-SSP detected A307 and O02 alleles, while gene sequencing revealed mutation of c.745C>T in exon 7, which produced a polypeptide chain p.R249W. The A307 gene of the proband was not inherited by his daughters. CONCLUSIONS A mutation (c.745 C>T) in exon 7 of the ABO blood group gene resulted in low activity of a-1,3-N-acetyl-galactosaminyl transferase, producing A3 phenotype.

  20. Widespread Positive Selection Drives Differentiation of Centromeric Proteins in the Drosophila melanogaster subgroup.

    Science.gov (United States)

    Beck, Emily A; Llopart, Ana

    2015-11-25

    Rapid evolution of centromeric satellite repeats is thought to cause compensatory amino acid evolution in interacting centromere-associated kinetochore proteins. Cid, a protein that mediates kinetochore/centromere interactions, displays particularly high amino acid turnover. Rapid evolution of both Cid and centromeric satellite repeats led us to hypothesize that the apparent compensatory evolution may extend to interacting partners in the Condensin I complex (i.e., SMC2, SMC4, Cap-H, Cap-D2, and Cap-G) and HP1s. Missense mutations in these proteins often result in improper centromere formation and aberrant chromosome segregation, thus selection for maintained function and coevolution among proteins of the complex is likely strong. Here, we report evidence of rapid evolution and recurrent positive selection in seven centromere-associated proteins in species of the Drosophila melanogaster subgroup, and further postulate that positive selection on these proteins could be a result of centromere drive and compensatory changes, with kinetochore proteins competing for optimal spindle attachment.