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Sample records for repetitive sequences implications

  1. Roles of repetitive sequences

    Energy Technology Data Exchange (ETDEWEB)

    Bell, G.I.

    1991-12-31

    The DNA of higher eukaryotes contains many repetitive sequences. The study of repetitive sequences is important, not only because many have important biological function, but also because they provide information on genome organization, evolution and dynamics. In this paper, I will first discuss some generic effects that repetitive sequences will have upon genome dynamics and evolution. In particular, it will be shown that repetitive sequences foster recombination among, and turnover of, the elements of a genome. I will then consider some examples of repetitive sequences, notably minisatellite sequences and telomere sequences as examples of tandem repeats, without and with respectively known function, and Alu sequences as an example of interspersed repeats. Some other examples will also be considered in less detail.

  2. Chromosome Mapping of Repetitive Sequences in Rachycentron canadum (Perciformes: Rachycentridae: Implications for Karyotypic Evolution and Perspectives for Biotechnological Uses

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    Uedson Pereira Jacobina

    2011-01-01

    Full Text Available The cobia, Rachycentron canadum, a species of marine fish, has been increasingly used in aquaculture worldwide. It is the only member of the family Rachycentridae (Perciformes showing wide geographic distribution and phylogenetic patterns still not fully understood. In this study, the species was cytogenetically analyzed by different methodologies, including Ag-NOR and chromomycin A3 (CMA3/DAPI staining, C-banding, early replication banding (RGB, and in situ fluorescent hybridization with probes for 18S and 5S ribosomal genes and for telomeric sequences (TTAGGGn. The results obtained allow a detailed chromosomal characterization of the Atlantic population. The chromosome diversification found in the karyotype of the cobia is apparently related to pericentric inversions, the main mechanism associated to the karyotypic evolution of Perciformes. The differential heterochromatin replication patterns found were in part associated to functional genes. Despite maintaining conservative chromosomal characteristics in relation to the basal pattern established for Perciformes, some chromosome pairs in the analyzed population exhibit markers that may be important for cytotaxonomic, population, and biodiversity studies as well as for monitoring the species in question.

  3. Directed PCR-free engineering of highly repetitive DNA sequences

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    Preissler Steffen

    2011-09-01

    Full Text Available Abstract Background Highly repetitive nucleotide sequences are commonly found in nature e.g. in telomeres, microsatellite DNA, polyadenine (poly(A tails of eukaryotic messenger RNA as well as in several inherited human disorders linked to trinucleotide repeat expansions in the genome. Therefore, studying repetitive sequences is of biological, biotechnological and medical relevance. However, cloning of such repetitive DNA sequences is challenging because specific PCR-based amplification is hampered by the lack of unique primer binding sites resulting in unspecific products. Results For the PCR-free generation of repetitive DNA sequences we used antiparallel oligonucleotides flanked by restriction sites of Type IIS endonucleases. The arrangement of recognition sites allowed for stepwise and seamless elongation of repetitive sequences. This facilitated the assembly of repetitive DNA segments and open reading frames encoding polypeptides with periodic amino acid sequences of any desired length. By this strategy we cloned a series of polyglutamine encoding sequences as well as highly repetitive polyadenine tracts. Such repetitive sequences can be used for diverse biotechnological applications. As an example, the polyglutamine sequences were expressed as His6-SUMO fusion proteins in Escherichia coli cells to study their aggregation behavior in vitro. The His6-SUMO moiety enabled affinity purification of the polyglutamine proteins, increased their solubility, and allowed controlled induction of the aggregation process. We successfully purified the fusions proteins and provide an example for their applicability in filter retardation assays. Conclusion Our seamless cloning strategy is PCR-free and allows the directed and efficient generation of highly repetitive DNA sequences of defined lengths by simple standard cloning procedures.

  4. Phylogenetic analysis of the genus Hordeum using repetitive DNA sequences

    DEFF Research Database (Denmark)

    Svitashev, S.; Bryngelsson, T.; Vershinin, A.

    1994-01-01

    A set of six cloned barley (Hordeum vulgare) repetitive DNA sequences was used for the analysis of phylogenetic relationships among 31 species (46 taxa) of the genus Hordeum, using molecular hybridization techniques. In situ hybridization experiments showed dispersed organization of the sequences...

  5. Repetitive sequences: the hidden diversity of heterochromatin in prochilodontid fish

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    Maria L. Terencio

    2015-08-01

    Full Text Available The structure and organization of repetitive elements in fish genomes are still relatively poorly understood, although most of these elements are believed to be located in heterochromatic regions. Repetitive elements are considered essential in evolutionary processes as hotspots for mutations and chromosomal rearrangements, among other functions – thus providing new genomic alternatives and regulatory sites for gene expression. The present study sought to characterize repetitive DNA sequences in the genomes of Semaprochilodus insignis (Jardine & Schomburgk, 1841 and Semaprochilodus taeniurus (Valenciennes, 1817 and identify regions of conserved syntenic blocks in this genome fraction of three species of Prochilodontidae (S. insignis, S. taeniurus, and Prochilodus lineatus (Valenciennes, 1836 by cross-FISH using Cot-1 DNA (renaturation kinetics probes. We found that the repetitive fractions of the genomes of S. insignis and S. taeniurus have significant amounts of conserved syntenic blocks in hybridization sites, but with low degrees of similarity between them and the genome of P. lineatus, especially in relation to B chromosomes. The cloning and sequencing of the repetitive genomic elements of S. insignis and S. taeniurus using Cot-1 DNA identified 48 fragments that displayed high similarity with repetitive sequences deposited in public DNA databases and classified as microsatellites, transposons, and retrotransposons. The repetitive fractions of the S. insignis and S. taeniurus genomes exhibited high degrees of conserved syntenic blocks in terms of both the structures and locations of hybridization sites, but a low degree of similarity with the syntenic blocks of the P. lineatus genome. Future comparative analyses of other prochilodontidae species will be needed to advance our understanding of the organization and evolution of the genomes in this group of fish.

  6. Involvement of Disperse Repetitive Sequences in Wheat/Rye Genome Adjustment

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    Manuela Silva

    2012-07-01

    Full Text Available The union of different genomes in the same nucleus frequently results in hybrid genotypes with improved genome plasticity related to both genome remodeling events and changes in gene expression. Most modern cereal crops are polyploid species. Triticale, synthesized by the cross between wheat and rye, constitutes an excellent model to study polyploidization functional implications. We intend to attain a deeper knowledge of dispersed repetitive sequence involvement in parental genome reshuffle in triticale and in wheat-rye addition lines that have the entire wheat genome plus each rye chromosome pair. Through Random Amplified Polymorphic DNA (RAPD analysis with OPH20 10-mer primer we unraveled clear alterations corresponding to the loss of specific bands from both parental genomes. Moreover, the sequential nature of those events was revealed by the increased absence of rye-origin bands in wheat-rye addition lines in comparison with triticale. Remodeled band sequencing revealed that both repetitive and coding genome domains are affected in wheat-rye hybrid genotypes. Additionally, the amplification and sequencing of pSc20H internal segments showed that the disappearance of parental bands may result from restricted sequence alterations and unraveled the involvement of wheat/rye related repetitive sequences in genome adjustment needed for hybrid plant stabilization.

  7. ReRep: Computational detection of repetitive sequences in genome survey sequences (GSS

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    Alves-Ferreira Marcelo

    2008-09-01

    Full Text Available Abstract Background Genome survey sequences (GSS offer a preliminary global view of a genome since, unlike ESTs, they cover coding as well as non-coding DNA and include repetitive regions of the genome. A more precise estimation of the nature, quantity and variability of repetitive sequences very early in a genome sequencing project is of considerable importance, as such data strongly influence the estimation of genome coverage, library quality and progress in scaffold construction. Also, the elimination of repetitive sequences from the initial assembly process is important to avoid errors and unnecessary complexity. Repetitive sequences are also of interest in a variety of other studies, for instance as molecular markers. Results We designed and implemented a straightforward pipeline called ReRep, which combines bioinformatics tools for identifying repetitive structures in a GSS dataset. In a case study, we first applied the pipeline to a set of 970 GSSs, sequenced in our laboratory from the human pathogen Leishmania braziliensis, the causative agent of leishmaniosis, an important public health problem in Brazil. We also verified the applicability of ReRep to new sequencing technologies using a set of 454-reads of an Escheria coli. The behaviour of several parameters in the algorithm is evaluated and suggestions are made for tuning of the analysis. Conclusion The ReRep approach for identification of repetitive elements in GSS datasets proved to be straightforward and efficient. Several potential repetitive sequences were found in a L. braziliensis GSS dataset generated in our laboratory, and further validated by the analysis of a more complete genomic dataset from the EMBL and Sanger Centre databases. ReRep also identified most of the E. coli K12 repeats prior to assembly in an example dataset obtained by automated sequencing using 454 technology. The parameters controlling the algorithm behaved consistently and may be tuned to the properties

  8. Graph-based clustering and characterization of repetitive sequences in next-generation sequencing data

    Czech Academy of Sciences Publication Activity Database

    Novák, Petr; Neumann, Pavel; Macas, Jiří

    2010-01-01

    Roč. 11, č. 1 (2010), s. 378-389 ISSN 1471-2105 R&D Projects: GA MŠk(CZ) OC10037; GA MŠk(CZ) LC06004 Institutional research plan: CEZ:AV0Z50510513 Keywords : repetitive DNA * plant genome * next generation sequencing Subject RIV: EB - Genetics ; Molecular Biology Impact factor: 3.028, year: 2010

  9. Methylation patterns of repetitive DNA sequences in germ cells of Mus musculus.

    OpenAIRE

    Sanford, J; Forrester, L; Chapman, V; Chandley, A; Hastie, N

    1984-01-01

    The major and the minor satellite sequences of Mus musculus were undermethylated in both sperm and oocyte DNAs relative to the amount of undermethylation observed in adult somatic tissue DNA. This hypomethylation was specific for satellite sequences in sperm DNA. Dispersed repetitive and low copy sequences show a high degree of methylation in sperm DNA; however, a dispersed repetitive sequence was undermethylated in oocyte DNA. This finding suggests a difference in the amount of total genomic...

  10. Methylation patterns of repetitive DNA sequences in germ cells of Mus musculus.

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    Sanford, J; Forrester, L; Chapman, V; Chandley, A; Hastie, N

    1984-03-26

    The major and the minor satellite sequences of Mus musculus were undermethylated in both sperm and oocyte DNAs relative to the amount of undermethylation observed in adult somatic tissue DNA. This hypomethylation was specific for satellite sequences in sperm DNA. Dispersed repetitive and low copy sequences show a high degree of methylation in sperm DNA; however, a dispersed repetitive sequence was undermethylated in oocyte DNA. This finding suggests a difference in the amount of total genomic DNA methylation between sperm and oocyte DNA. The methylation levels of the minor satellite sequences did not change during spermiogenesis, and were not associated with the onset of meiosis or a specific stage in sperm development.

  11. PCR amplification of repetitive sequences as a possible approach in relative species quantification

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    Ballin, Nicolai Zederkopff; Vogensen, Finn Kvist; Karlsson, Anders H

    2012-01-01

    Abstract Both relative and absolute quantifications are possible in species quantification when single copy genomic DNA is used. However, amplification of single copy genomic DNA does not allow a limit of detection as low as one obtained from amplification of repetitive sequences. Amplification...... of repetitive sequences is therefore frequently used in absolute quantification but problems occur in relative quantification as the number of repetitive sequences is unknown. A promising approach was developed where data from amplification of repetitive sequences were used in relative quantification of species...... to relatively quantify the amount of chicken DNA in a binary mixture of chicken DNA and pig DNA. However, the designed PCR primers lack the specificity required for regulatory species control....

  12. A dispersion-balanced Discrete Fourier Transform of repetitive pulse sequences using temporal Talbot effect

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    Fernández-Pousa, Carlos R.

    2017-11-01

    We propose a processor based on the concatenation of two fractional temporal Talbot dispersive lines with balanced dispersion to perform the DFT of a repetitive electrical sequence, for its use as a controlled source of optical pulse sequences. The electrical sequence is used to impart the amplitude and phase of a coherent train of optical pulses by use of a modulator placed between the two Talbot lines. The proposal has been built on a representation of the action of fractional Talbot effect on repetitive pulse sequences and a comparison with related results and proposals. It is shown that the proposed system is reconfigurable within a few repetition periods, has the same processing rate as the input optical pulse train, and requires the same technical complexity in terms of dispersion and pulse width as the standard, passive pulse-repetition rate multipliers based on fractional Talbot effect.

  13. The Effects of Delayed Reinforcement on Variability and Repetition of Response Sequences

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    Odum, Amy L.; Ward, Ryan D.; Burke, K. Anne; Barnes, Christopher A.

    2006-01-01

    Four experiments examined the effects of delays to reinforcement on key peck sequences of pigeons maintained under multiple schedules of contingencies that produced variable or repetitive behavior. In Experiments 1, 2, and 4, in the repeat component only the sequence right-right-left-left earned food, and in the vary component four-response…

  14. Functional role of a highly repetitive DNA sequence in anchorage of the mouse genome.

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    Neuer-Nitsche, B; Lu, X N; Werner, D

    1988-09-12

    The major portion of the eukaryotic genome consists of various categories of repetitive DNA sequences which have been studied with respect to their base compositions, organizations, copy numbers, transcription and species specificities; their biological roles, however, are still unclear. A novel quality of a highly repetitive mouse DNA sequence is described which points to a functional role: All copies (approximately 50,000 per haploid genome) of this DNA sequence reside on genomic Alu I DNA fragments each associated with nuclear polypeptides that are not released from DNA by proteinase K, SDS and phenol extraction. By this quality the repetitive DNA sequence is classified as a member of the sub-set of DNA sequences involved in tight DNA-polypeptide complexes which have been previously shown to be components of the subnuclear structure termed 'nuclear matrix'. From these results it has to be concluded that the repetitive DNA sequence characterized in this report represents or comprises a signal for a large number of site specific attachment points of the mouse genome in the nuclear matrix.

  15. Identification of two new repetitive elements and chromosomal mapping of repetitive DNA sequences in the fish Gymnothorax unicolor (Anguilliformes: Muraenidae

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    E. Coluccia

    2011-05-01

    Full Text Available Muraenidae is a species-rich family, with relationships among genera and species and taxonomy that have not been completely clarified. Few cytogenetic studies have been conducted on this family, and all of them showed the same diploid chromosome number (2n=42 but with conspicuous karyotypic variation among species. The Mediterranean moray eel Gymnothorax unicolor was previously cytogenetically studied using classical techniques that allowed the characterization of its karyotype structure and the constitutive heterochromatin and argyrophilic nucleolar organizer regions (Ag-NORs distribution pattern. In the present study, we describe two new repetitive elements (called GuMboI and GuDdeI obtained from restricted genomic DNA of G. unicolor that were characterized by Southern blot and physically localized by in situ hybridization on metaphase chromosomes. As they are highly repetitive DNA sequences, they map in heterochromatic regions. However, while GuDdeI was localized in the centromeric regions, the GuMboI fraction was distributed on some centromeres and was co-localized with the nucleolus organizer region (NOR. Comparative analysis with other Mediterranean species such as Muraena helena pointed out that these DNA fractions are species-specific and could potentially be used for species discrimination. As a new contribution to the karyotype of this species, we found that the major ribosomal genes are localized on acrocentric chromosome 9 and that the telomeres of each chromosome are composed of a tandem repeat derived from a poly-TTAGGG DNA sequence, as it occurs in most vertebrate species. The results obtained add new information useful in comparative genomics at the chromosomal level and contribute to the cytogenetic knowledge regarding this fish family, which has not been extensively studied.

  16. The Pinus taeda genome is characterized by diverse and highly diverged repetitive sequences

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    Yandell Mark

    2010-07-01

    Full Text Available Abstract Background In today's age of genomic discovery, no attempt has been made to comprehensively sequence a gymnosperm genome. The largest genus in the coniferous family Pinaceae is Pinus, whose 110-120 species have extremely large genomes (c. 20-40 Gb, 2N = 24. The size and complexity of these genomes have prompted much speculation as to the feasibility of completing a conifer genome sequence. Conifer genomes are reputed to be highly repetitive, but there is little information available on the nature and identity of repetitive units in gymnosperms. The pines have extensive genetic resources, with approximately 329000 ESTs from eleven species and genetic maps in eight species, including a dense genetic map of the twelve linkage groups in Pinus taeda. Results We present here the Sanger sequence and annotation of ten P. taeda BAC clones and Genome Analyzer II whole genome shotgun (WGS sequences representing 7.5% of the genome. Computational annotation of ten BACs predicts three putative protein-coding genes and at least fifteen likely pseudogenes in nearly one megabase of sequence. We found three conifer-specific LTR retroelements in the BACs, and tentatively identified at least 15 others based on evidence from the distantly related angiosperms. Alignment of WGS sequences to the BACs indicates that 80% of BAC sequences have similar copies (≥ 75% nucleotide identity elsewhere in the genome, but only 23% have identical copies (99% identity. The three most common repetitive elements in the genome were identified and, when combined, represent less than 5% of the genome. Conclusions This study indicates that the majority of repeats in the P. taeda genome are 'novel' and will therefore require additional BAC or genomic sequencing for accurate characterization. The pine genome contains a very large number of diverged and probably defunct repetitive elements. This study also provides new evidence that sequencing a pine genome using a WGS approach is

  17. Chromosome mapping of repetitive sequences in four Serrasalmidae species (Characiformes

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    Leila Braga Ribeiro

    2014-01-01

    Full Text Available The Serrasalmidae family is composed of a number of commercially interesting species, mainly in the Amazon region where most of these fishes occur. In the present study, we investigated the genomic organization of the 18S and 5S rDNA and telomeric sequences in mitotic chromosomes of four species from the basal clade of the Serrasalmidae family: Colossoma macropomum, Mylossoma aureum, M. duriventre, and Piaractus mesopotamicus, in order to understand the chromosomal evolution in the family. All the species studied had diploid numbers 2n = 54 and exclusively biarmed chromosomes, but variations of the karyotypic formulas were observed. C-banding resulted in similar patterns among the analyzed species, with heterochromatic blocks mainly present in centromeric regions. The 18S rDNA mapping of C. macropomum and P. mesopotamicus revealed multiple sites of this gene; 5S rDNA sites were detected in two chromosome pairs in all species, although not all of them were homeologs. Hybridization with a telomeric probe revealed signals in the terminal portions of chromosomes in all the species and an interstitial signal was observed in one pair of C. macropomum.

  18. New tool to assemble repetitive regions using next-generation sequencing data

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    Kuśmirek, Wiktor; Nowak, Robert M.; Neumann, Łukasz

    2017-08-01

    The next generation sequencing techniques produce a large amount of sequencing data. Some part of the genome are composed of repetitive DNA sequences, which are very problematic for the existing genome assemblers. We propose a modification of the algorithm for a DNA assembly, which uses the relative frequency of reads to properly reconstruct repetitive sequences. The new approach was implemented and tested, as a demonstration of the capability of our software we present some results for model organisms. The new implementation, using a three-layer software architecture was selected, where the presentation layer, data processing layer, and data storage layer were kept separate. Source code as well as demo application with web interface and the additional data are available at project web-page: http://dnaasm.sourceforge.net.

  19. [Identification of a repetitive sequence element for DNA fingerprinting in Phytophthora sojae].

    Science.gov (United States)

    Yin, Lihua; Wang, Qinhu; Ning, Feng; Zhu, Xiaoying; Zuo, Yuhu; Shan, Weixing

    2010-04-01

    Establishment of DNA fingerprinting in Phytophthora sojae and an analysis of genetic relationship of Heilongjiang and Xinjiang populations. Bioinformatics tools were used to search repetitive sequences in P. sojae and Southern blot analysis was employed for DNA fingerprinting analysis of P. sojae populations from Heilongjiang and Xinjiang using the identified repetitive sequence. A moderately repetitive sequence was identified and designated as PS1227. Southern blot analysis indicated 34 distinct bands ranging in size from 1.5 kb-23 kb, of which 21 were polymorphic among 49 isolates examined. Analysis of single-zoospore progenies showed that the PS1227 fingerprint pattern was mitotically stable. DNA fingerprinting showed that the P. sojae isolates HP4002, SY6 and GJ0105 of Heilongjiang are genetically identical to DW303, 71228 and 71222 of Xinjiang, respectively. A moderately repetitive sequence designated PS1227 which will be useful for epidemiology and population biology studies of P. sojae was obtained, and a PS1227-based DNA fingerprinting analysis provided molecular evidence that P. sojae in Xinjiang was likely introduced from Heilongjiang.

  20. Human CST Facilitates Genome-wide RAD51 Recruitment to GC-Rich Repetitive Sequences in Response to Replication Stress.

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    Chastain, Megan; Zhou, Qing; Shiva, Olga; Fadri-Moskwik, Maria; Whitmore, Leanne; Jia, Pingping; Dai, Xueyu; Huang, Chenhui; Ye, Ping; Chai, Weihang

    2016-08-02

    The telomeric CTC1/STN1/TEN1 (CST) complex has been implicated in promoting replication recovery under replication stress at genomic regions, yet its precise role is unclear. Here, we report that STN1 is enriched at GC-rich repetitive sequences genome-wide in response to hydroxyurea (HU)-induced replication stress. STN1 deficiency exacerbates the fragility of these sequences under replication stress, resulting in chromosome fragmentation. We find that upon fork stalling, CST proteins form distinct nuclear foci that colocalize with RAD51. Furthermore, replication stress induces physical association of CST with RAD51 in an ATR-dependent manner. Strikingly, CST deficiency diminishes HU-induced RAD51 foci formation and reduces RAD51 recruitment to telomeres and non-telomeric GC-rich fragile sequences. Collectively, our findings establish that CST promotes RAD51 recruitment to GC-rich repetitive sequences in response to replication stress to facilitate replication restart, thereby providing insights into the mechanism underlying genome stability maintenance. Copyright © 2016 The Author(s). Published by Elsevier Inc. All rights reserved.

  1. Comparative molecular cytogenetics of major repetitive sequence families of three Dendrobium species (Orchidaceae) from Bangladesh

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    Begum, Rabeya; Alam, Sheikh Shamimul; Menzel, Gerhard; Schmidt, Thomas

    2009-01-01

    Background and Aims Dendrobium species show tremendous morphological diversity and have broad geographical distribution. As repetitive sequence analysis is a useful tool to investigate the evolution of chromosomes and genomes, the aim of the present study was the characterization of repetitive sequences from Dendrobium moschatum for comparative molecular and cytogenetic studies in the related species Dendrobium aphyllum, Dendrobium aggregatum and representatives from other orchid genera. Methods In order to isolate highly repetitive sequences, a c0t-1 DNA plasmid library was established. Repeats were sequenced and used as probes for Southern hybridization. Sequence divergence was analysed using bioinformatic tools. Repetitive sequences were localized along orchid chromosomes by fluorescence in situ hybridization (FISH). Key Results Characterization of the c0t-1 library resulted in the detection of repetitive sequences including the (GA)n dinucleotide DmoO11, numerous Arabidopsis-like telomeric repeats and the highly amplified dispersed repeat DmoF14. The DmoF14 repeat is conserved in six Dendrobium species but diversified in representative species of three other orchid genera. FISH analyses showed the genome-wide distribution of DmoF14 in D. moschatum, D. aphyllum and D. aggregatum. Hybridization with the telomeric repeats demonstrated Arabidopsis-like telomeres at the chromosome ends of Dendrobium species. However, FISH using the telomeric probe revealed two pairs of chromosomes with strong intercalary signals in D. aphyllum. FISH showed the terminal position of 5S and 18S–5·8S–25S rRNA genes and a characteristic number of rDNA sites in the three Dendrobium species. Conclusions The repeated sequences isolated from D. moschatum c0t-1 DNA constitute major DNA families of the D. moschatum, D. aphyllum and D. aggregatum genomes with DmoF14 representing an ancient component of orchid genomes. Large intercalary telomere-like arrays suggest chromosomal

  2. Diversity in non-repetitive human sequences not found in the reference genome.

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    Kehr, Birte; Helgadottir, Anna; Melsted, Pall; Jonsson, Hakon; Helgason, Hannes; Jonasdottir, Adalbjörg; Jonasdottir, Aslaug; Sigurdsson, Asgeir; Gylfason, Arnaldur; Halldorsson, Gisli H; Kristmundsdottir, Snaedis; Thorgeirsson, Gudmundur; Olafsson, Isleifur; Holm, Hilma; Thorsteinsdottir, Unnur; Sulem, Patrick; Helgason, Agnar; Gudbjartsson, Daniel F; Halldorsson, Bjarni V; Stefansson, Kari

    2017-04-01

    Genomes usually contain some non-repetitive sequences that are missing from the reference genome and occur only in a population subset. Such non-repetitive, non-reference (NRNR) sequences have remained largely unexplored in terms of their characterization and downstream analyses. Here we describe 3,791 breakpoint-resolved NRNR sequence variants called using PopIns from whole-genome sequence data of 15,219 Icelanders. We found that over 95% of the 244 NRNR sequences that are 200 bp or longer are present in chimpanzees, indicating that they are ancestral. Furthermore, 149 variant loci are in linkage disequilibrium (r 2 > 0.8) with a genome-wide association study (GWAS) catalog marker, suggesting disease relevance. Additionally, we report an association (P = 3.8 × 10 -8 , odds ratio (OR) = 0.92) with myocardial infarction (23,360 cases, 300,771 controls) for a 766-bp NRNR sequence variant. Our results underline the importance of including variation of all complexity levels when searching for variants that associate with disease.

  3. Chromosomal localization of two novel repetitive sequences isolated from the Chenopodium quinoa Willd. genome.

    Science.gov (United States)

    Kolano, B; Gardunia, B W; Michalska, M; Bonifacio, A; Fairbanks, D; Maughan, P J; Coleman, C E; Stevens, M R; Jellen, E N; Maluszynska, J

    2011-09-01

    The chromosomal organization of two novel repetitive DNA sequences isolated from the Chenopodium quinoa Willd. genome was analyzed across the genomes of selected Chenopodium species. Fluorescence in situ hybridization (FISH) analysis with the repetitive DNA clone 18-24J in the closely related allotetraploids C. quinoa and Chenopodium berlandieri Moq. (2n = 4x = 36) evidenced hybridization signals that were mainly present on 18 chromosomes; however, in the allohexaploid Chenopodium album L. (2n = 6x = 54), cross-hybridization was observed on all of the chromosomes. In situ hybridization with rRNA gene probes indicated that during the evolution of polyploidy, the chenopods lost some of their rDNA loci. Reprobing with rDNA indicated that in the subgenome labeled with 18-24J, one 35S rRNA locus and at least half of the 5S rDNA loci were present. A second analyzed sequence, 12-13P, localized exclusively in pericentromeric regions of each chromosome of C. quinoa and related species. The intensity of the FISH signals differed considerably among chromosomes. The pattern observed on C. quinoa chromosomes after FISH with 12-13P was very similar to GISH results, suggesting that the 12-13P sequence constitutes a major part of the repetitive DNA of C. quinoa.

  4. Interactions of rat repetitive sequence MspI8 with nuclear matrix proteins during spermatogenesis

    International Nuclear Information System (INIS)

    Rogolinski, J.; Widlak, P.; Rzeszowska-Wolny, J.

    1996-01-01

    Using the Southwestern blot analysis we have studied the interactions between rat repetitive sequence MspI8 and the nuclear matrix proteins of rats testis cells. Starting from 2 weeks the young to adult animal showed differences in type of testis nuclear matrix proteins recognizing the MspI8 sequence. The same sets of nuclear matrix proteins were detected in some enriched in spermatocytes and spermatids and obtained after fractionation of cells of adult animal by the velocity sedimentation technique. (author). 21 refs, 5 figs

  5. Stored word sequences in language learning: the effect of familiarity on children's repetition of four-word combinations.

    Science.gov (United States)

    Bannard, Colin; Matthews, Danielle

    2008-03-01

    Recent accounts of the development of grammar propose that children remember utterances they hear and draw generalizations over these stored exemplars. This study tested these accounts' assumption that children store utterances as wholes by testing memory for familiar sequences of words. Using a newly available, dense corpus of child-directed speech, we identified frequently occurring chunks in the input (e.g., sit in your chair) and matched them to infrequent sequences (e.g., sit in your truck). We tested young children's ability to produce these sequences in a sentence-repetition test. Three-year-olds (n= 21) and 2-year-olds (n= 17) were significantly more likely to repeat frequent sequences correctly than to repeat infrequent sequences correctly. Moreover, the 3-year-olds were significantly faster to repeat the first three words of an item if they formed part of a chunk (e.g., they were quicker to say sit in your when the following word was chair than when it was truck). We discuss the implications of these results for theories of language development and processing.

  6. Dispersed repetitive sequences in eukaryotic genomes and their possible biological significance

    International Nuclear Information System (INIS)

    Georgiev, G.P.; Kramerov, D.A.; Ryskov, A.P.; Skryabin, K.G.; Lukanidin, E.M.

    1983-01-01

    In this paper is described the properties of a novel mouse mdg-like element, the A2 sequence, which is the most abundant repetitive sequence. We also characterized an ubiquitous B2 sequence that represents, after B1, the dominant family among the short interspersed repeats of the mouse genome. The existence of some putative transposition intermediates was shown for repeats of both A and B types of the mouse genome. These are closed circular DNA of the A type and small polyadenylated B + RNAs. The fundamental question that arises is whether these sequences are simply selfish DNA capable of transpositions or do they fulfill some useful biological functions within the genome. 66 references, 11 figures, 1 table

  7. Next Generation Sequencing-Based Analysis of Repetitive DNA in the Model Dioceous Plant Silene latifolia

    Czech Academy of Sciences Publication Activity Database

    Macas, Jiří; Kejnovský, Eduard; Neumann, Pavel; Novák, Petr; Koblížková, Andrea; Vyskot, Boris

    2011-01-01

    Roč. 6, č. 11 (2011), e27335 E-ISSN 1932-6203 R&D Projects: GA MŠk(CZ) OC10037; GA MŠk(CZ) LC06004; GA MŠk(CZ) LH11058; GA ČR(CZ) GAP501/10/0102; GA ČR(CZ) GAP305/10/0930 Institutional research plan: CEZ:AV0Z50510513; CEZ:AV0Z50040702 Keywords : Plant genome * Sequencing-Based Analyses * Repetitive DNA * Silene latifolia Subject RIV: EB - Genetics ; Molecular Biology Impact factor: 4.092, year: 2011

  8. Refined repetitive sequence searches utilizing a fast hash function and cross species information retrievals

    Directory of Open Access Journals (Sweden)

    Reneker Jeff

    2005-05-01

    Full Text Available Abstract Background Searching for small tandem/disperse repetitive DNA sequences streamlines many biomedical research processes. For instance, whole genomic array analysis in yeast has revealed 22 PHO-regulated genes. The promoter regions of all but one of them contain at least one of the two core Pho4p binding sites, CACGTG and CACGTT. In humans, microsatellites play a role in a number of rare neurodegenerative diseases such as spinocerebellar ataxia type 1 (SCA1. SCA1 is a hereditary neurodegenerative disease caused by an expanded CAG repeat in the coding sequence of the gene. In bacterial pathogens, microsatellites are proposed to regulate expression of some virulence factors. For example, bacteria commonly generate intra-strain diversity through phase variation which is strongly associated with virulence determinants. A recent analysis of the complete sequences of the Helicobacter pylori strains 26695 and J99 has identified 46 putative phase-variable genes among the two genomes through their association with homopolymeric tracts and dinucleotide repeats. Life scientists are increasingly interested in studying the function of small sequences of DNA. However, current search algorithms often generate thousands of matches – most of which are irrelevant to the researcher. Results We present our hash function as well as our search algorithm to locate small sequences of DNA within multiple genomes. Our system applies information retrieval algorithms to discover knowledge of cross-species conservation of repeat sequences. We discuss our incorporation of the Gene Ontology (GO database into these algorithms. We conduct an exhaustive time analysis of our system for various repetitive sequence lengths. For instance, a search for eight bases of sequence within 3.224 GBases on 49 different chromosomes takes 1.147 seconds on average. To illustrate the relevance of the search results, we conduct a search with and without added annotation terms for the

  9. Chromosomal structures and repetitive sequences divergence in Cucumis species revealed by comparative cytogenetic mapping.

    Science.gov (United States)

    Zhang, Yunxia; Cheng, Chunyan; Li, Ji; Yang, Shuqiong; Wang, Yunzhu; Li, Ziang; Chen, Jinfeng; Lou, Qunfeng

    2015-09-25

    Differentiation and copy number of repetitive sequences affect directly chromosome structure which contributes to reproductive isolation and speciation. Comparative cytogenetic mapping has been verified an efficient tool to elucidate the differentiation and distribution of repetitive sequences in genome. In present study, the distinct chromosomal structures of five Cucumis species were revealed through genomic in situ hybridization (GISH) technique and comparative cytogenetic mapping of major satellite repeats. Chromosome structures of five Cucumis species were investigated using GISH and comparative mapping of specific satellites. Southern hybridization was employed to study the proliferation of satellites, whose structural characteristics were helpful for analyzing chromosome evolution. Preferential distribution of repetitive DNAs at the subtelomeric regions was found in C. sativus, C hystrix and C. metuliferus, while majority was positioned at the pericentromeric heterochromatin regions in C. melo and C. anguria. Further, comparative GISH (cGISH) through using genomic DNA of other species as probes revealed high homology of repeats between C. sativus and C. hystrix. Specific satellites including 45S rDNA, Type I/II, Type III, Type IV, CentM and telomeric repeat were then comparatively mapped in these species. Type I/II and Type IV produced bright signals at the subtelomeric regions of C. sativus and C. hystrix simultaneously, which might explain the significance of their amplification in the divergence of Cucumis subgenus from the ancient ancestor. Unique positioning of Type III and CentM only at the centromeric domains of C. sativus and C. melo, respectively, combining with unique southern bands, revealed rapid evolutionary patterns of centromeric DNA in Cucumis. Obvious interstitial telomeric repeats were observed in chromosomes 1 and 2 of C. sativus, which might provide evidence of the fusion hypothesis of chromosome evolution from x = 12 to x = 7 in

  10. Repetitive part of the banana (Musa acuminata) genome investigated by low-depth 454 sequencing.

    Science.gov (United States)

    Hribová, Eva; Neumann, Pavel; Matsumoto, Takashi; Roux, Nicolas; Macas, Jirí; Dolezel, Jaroslav

    2010-09-16

    Bananas and plantains (Musa spp.) are grown in more than a hundred tropical and subtropical countries and provide staple food for hundreds of millions of people. They are seed-sterile crops propagated clonally and this makes them vulnerable to a rapid spread of devastating diseases and at the same time hampers breeding improved cultivars. Although the socio-economic importance of bananas and plantains cannot be overestimated, they remain outside the focus of major research programs. This slows down the study of nuclear genome and the development of molecular tools to facilitate banana improvement. In this work, we report on the first thorough characterization of the repeat component of the banana (M. acuminata cv. 'Calcutta 4') genome. Analysis of almost 100 Mb of sequence data (0.15× genome coverage) permitted partial sequence reconstruction and characterization of repetitive DNA, making up about 30% of the genome. The results showed that the banana repeats are predominantly made of various types of Ty1/copia and Ty3/gypsy retroelements representing 16 and 7% of the genome respectively. On the other hand, DNA transposons were found to be rare. In addition to new families of transposable elements, two new satellite repeats were discovered and found useful as cytogenetic markers. To help in banana sequence annotation, a specific Musa repeat database was created, and its utility was demonstrated by analyzing the repeat composition of 62 genomic BAC clones. A low-depth 454 sequencing of banana nuclear genome provided the largest amount of DNA sequence data available until now for Musa and permitted reconstruction of most of the major types of DNA repeats. The information obtained in this study improves the knowledge of the long-range organization of banana chromosomes, and provides sequence resources needed for repeat masking and annotation during the Musa genome sequencing project. It also provides sequence data for isolation of DNA markers to be used in genetic

  11. The peculiar landscape of repetitive sequences in the olive (Olea europaea L.) genome.

    Science.gov (United States)

    Barghini, Elena; Natali, Lucia; Cossu, Rosa Maria; Giordani, Tommaso; Pindo, Massimo; Cattonaro, Federica; Scalabrin, Simone; Velasco, Riccardo; Morgante, Michele; Cavallini, Andrea

    2014-04-01

    Analyzing genome structure in different species allows to gain an insight into the evolution of plant genome size. Olive (Olea europaea L.) has a medium-sized haploid genome of 1.4 Gb, whose structure is largely uncharacterized, despite the growing importance of this tree as oil crop. Next-generation sequencing technologies and different computational procedures have been used to study the composition of the olive genome and its repetitive fraction. A total of 2.03 and 2.3 genome equivalents of Illumina and 454 reads from genomic DNA, respectively, were assembled following different procedures, which produced more than 200,000 differently redundant contigs, with mean length higher than 1,000 nt. Mapping Illumina reads onto the assembled sequences was used to estimate their redundancy. The genome data set was subdivided into highly and medium redundant and nonredundant contigs. By combining identification and mapping of repeated sequences, it was established that tandem repeats represent a very large portion of the olive genome (∼31% of the whole genome), consisting of six main families of different length, two of which were first discovered in these experiments. The other large redundant class in the olive genome is represented by transposable elements (especially long terminal repeat-retrotransposons). On the whole, the results of our analyses show the peculiar landscape of the olive genome, related to the massive amplification of tandem repeats, more than that reported for any other sequenced plant genome.

  12. Repetitive sequences and epigenetic modification: inseparable partners play important roles in the evolution of plant sex chromosomes.

    Science.gov (United States)

    Li, Shu-Fen; Zhang, Guo-Jun; Yuan, Jin-Hong; Deng, Chuan-Liang; Gao, Wu-Jun

    2016-05-01

    The present review discusses the roles of repetitive sequences played in plant sex chromosome evolution, and highlights epigenetic modification as potential mechanism of repetitive sequences involved in sex chromosome evolution. Sex determination in plants is mostly based on sex chromosomes. Classic theory proposes that sex chromosomes evolve from a specific pair of autosomes with emergence of a sex-determining gene(s). Subsequently, the newly formed sex chromosomes stop recombination in a small region around the sex-determining locus, and over time, the non-recombining region expands to almost all parts of the sex chromosomes. Accumulation of repetitive sequences, mostly transposable elements and tandem repeats, is a conspicuous feature of the non-recombining region of the Y chromosome, even in primitive one. Repetitive sequences may play multiple roles in sex chromosome evolution, such as triggering heterochromatization and causing recombination suppression, leading to structural and morphological differentiation of sex chromosomes, and promoting Y chromosome degeneration and X chromosome dosage compensation. In this article, we review the current status of this field, and based on preliminary evidence, we posit that repetitive sequences are involved in sex chromosome evolution probably via epigenetic modification, such as DNA and histone methylation, with small interfering RNAs as the mediator.

  13. B chromosome in the beetle Coprophanaeus cyanescens (Scarabaeidae: emphasis in the organization of repetitive DNA sequences

    Directory of Open Access Journals (Sweden)

    Gomes de Oliveira Sarah

    2012-11-01

    Full Text Available Abstract Background To contribute to the knowledge of coleopteran cytogenetics, especially with respect to the genomic content of B chromosomes, we analyzed the composition and organization of repetitive DNA sequences in the Coprophanaeus cyanescens karyotype. We used conventional staining and the application of fluorescence in situ hybridization (FISH mapping using as probes C0t-1 DNA fraction, the 18S and 5S rRNA genes, and the LOA-like non-LTR transposable element (TE. Results The conventional analysis detected 3 individuals (among 50 analyzed carrying one small metacentric and mitotically unstable B chromosome. The FISH analysis revealed a pericentromeric block of C0t-1 DNA in the B chromosome but no 18S or 5S rDNA clusters in this extra element. Using the LOA-like TE probe, the FISH analysis revealed large pericentromeric blocks in eight autosomal bivalents and in the B chromosome, and a pericentromeric block extending to the short arm in one autosomal pair. No positive hybridization signal was observed for the LOA-like element in the sex chromosomes. Conclusions The results indicate that the origin of the B chromosome is associated with the autosomal elements, as demonstrated by the hybridization with C0t-1 DNA and the LOA-like TE. The present study is the first report on the cytogenetic mapping of a TE in coleopteran chromosomes. These TEs could have been involved in the origin and evolution of the B chromosome in C. cyanescens.

  14. The use of mycobacterial interspersed repetitive unit typing and whole genome sequencing to inform tuberculosis prevention and control activities.

    Science.gov (United States)

    Gilbert, Gwendolyn L; Sintchenko, Vitali

    2013-07-01

    Molecular strain typing of Mycobacterium tuberculosis has been possible for only about 20 years; it has significantly improved our understanding of the evolution and epidemiology of Mycobacterium tuberculosis and tuberculosis disease. Mycobacterial interspersed repetitive unit typing, based on 24 variable number tandem repeat unit loci, is highly discriminatory, relatively easy to perform and interpret and is currently the most widely used molecular typing system for tuberculosis surveillance. Nevertheless, clusters identified by mycobacterial interspersed repetitive unit typing sometimes cannot be confirmed or adequately defined by contact tracing and additional methods are needed. Recently, whole genome sequencing has been used to identify single nucleotide polymorphisms and other mutations, between genotypically indistinguishable isolates from the same cluster, to more accurately trace transmission pathways. Rapidly increasing speed and quality and reduced costs will soon make large scale whole genome sequencing feasible, combined with the use of sophisticated bioinformatics tools, for epidemiological surveillance of tuberculosis.

  15. Genomic Variability of Haemophilus influenzae Isolated from Mexican Children Determined by Using Enterobacterial Repetitive Intergenic Consensus Sequences and PCR

    OpenAIRE

    Gomez-De-Leon, Patricia; Santos, Jose I.; Caballero, Javier; Gomez, Demostenes; Espinosa, Luz E.; Moreno, Isabel; Piñero, Daniel; Cravioto, Alejandro

    2000-01-01

    Genomic fingerprints from 92 capsulated and noncapsulated strains of Haemophilus influenzae from Mexican children with different diseases and healthy carriers were generated by PCR using the enterobacterial repetitive intergenic consensus (ERIC) sequences. A cluster analysis by the unweighted pair-group method with arithmetic averages based on the overall similarity as estimated from the characteristics of the genomic fingerprints, was conducted to group the strains. A total of 69 fingerprint...

  16. Next-generation sequencing detects repetitive elements expansion in giant genomes of annual killifish genus Austrolebias (Cyprinodontiformes, Rivulidae).

    Science.gov (United States)

    García, G; Ríos, N; Gutiérrez, V

    2015-06-01

    Among Neotropical fish fauna, the South American killifish genus Austrolebias (Cyprinodontiformes: Rivulidae) constitutes an excellent model to study the genomic evolutionary processes underlying speciation events. Recently, unusually large genome size has been described in 16 species of this genus, with an average DNA content of about 5.95 ± 0.45 pg per diploid cell (mean C-value of about 2.98 pg). In the present paper we explore the possible origin of this unparallel genomic increase by means of comparative analysis of the repetitive components using NGS (454-Roche) technology in the lowest and highest Rivulidae genomes. Here, we provide the first annotated Rivulidae-repeated sequences composition and their relative repetitive fraction in both genomes. Remarkably, the genomic proportion of the moderately repetitive DNA in Austrolebias charrua genome represents approximately twice (45%) of the repetitive components of the highly related rivulinae taxon Cynopoecilus melanotaenia (25%). Present work provides evidence about the impact of the repeat families that could be distinctly proliferated among sublineages within Rivulidae fish group, explaining the great genome size differences encompassing the differentiation and speciation events in this family.

  17. Whole-genome in-silico subtractive hybridization (WISH - using massive sequencing for the identification of unique and repetitive sex-specific sequences: the example of Schistosoma mansoni

    Directory of Open Access Journals (Sweden)

    Parrinello Hugues

    2010-06-01

    Full Text Available Abstract Background Emerging methods of massive sequencing that allow for rapid re-sequencing of entire genomes at comparably low cost are changing the way biological questions are addressed in many domains. Here we propose a novel method to compare two genomes (genome-to-genome comparison. We used this method to identify sex-specific sequences of the human blood fluke Schistosoma mansoni. Results Genomic DNA was extracted from male and female (heterogametic S. mansoni adults and sequenced with a Genome Analyzer (Illumina. Sequences are available at the NCBI sequence read archive http://www.ncbi.nlm.nih.gov/Traces/sra/ under study accession number SRA012151.6. Sequencing reads were aligned to the genome, and a pseudogenome composed of known repeats. Straightforward comparative bioinformatics analysis was performed to compare male and female schistosome genomes and identify female-specific sequences. We found that the S. mansoni female W chromosome contains only few specific unique sequences (950 Kb i.e. about 0.2% of the genome. The majority of W-specific sequences are repeats (10.5 Mb i.e. about 2.5% of the genome. Arbitrarily selected W-specific sequences were confirmed by PCR. Primers designed for unique and repetitive sequences allowed to reliably identify the sex of both larval and adult stages of the parasite. Conclusion Our genome-to-genome comparison method that we call "whole-genome in-silico subtractive hybridization" (WISH allows for rapid identification of sequences that are specific for a certain genotype (e.g. the heterogametic sex. It can in principle be used for the detection of any sequence differences between isolates (e.g. strains, pathovars or even closely related species.

  18. [Short interspersed repetitive sequences (SINEs) and their use as a phylogenetic tool].

    Science.gov (United States)

    Kramerov, D A; Vasetskiĭ, N S

    2009-01-01

    The data on one of the most common repetitive elements of eukaryotic genomes, short interspersed elements (SINEs), are reviewed. Their structure, origin, and functioning in the genome are discussed. The variation and abundance of these neutral genomic markers makes them a convenient and reliable tool for phylogenetic analysis. The main methods of such analysis are presented, and the potential and limitations of this approach are discussed using specific examples.

  19. Next-Generation Sequencing Reveals the Impact of Repetitive DNA Across Phylogenetically Closely Related Genomes of Orobanchaceae

    Science.gov (United States)

    Piednoël, Mathieu; Aberer, Andre J.; Schneeweiss, Gerald M.; Macas, Jiri; Novak, Petr; Gundlach, Heidrun; Temsch, Eva M.; Renner, Susanne S.

    2013-01-01

    We used next-generation sequencing to characterize the genomes of nine species of Orobanchaceae of known phylogenetic relationships, different life forms, and including a polyploid species. The study species are the autotrophic, nonparasitic Lindenbergia philippensis, the hemiparasitic Schwalbea americana, and seven nonphotosynthetic parasitic species of Orobanche (Orobanche crenata, Orobanche cumana, Orobanche gracilis (tetraploid), and Orobanche pancicii) and Phelipanche (Phelipanche lavandulacea, Phelipanche purpurea, and Phelipanche ramosa). Ty3/Gypsy elements comprise 1.93%–28.34% of the nine genomes and Ty1/Copia elements comprise 8.09%–22.83%. When compared with L. philippensis and S. americana, the nonphotosynthetic species contain higher proportions of repetitive DNA sequences, perhaps reflecting relaxed selection on genome size in parasitic organisms. Among the parasitic species, those in the genus Orobanche have smaller genomes but higher proportions of repetitive DNA than those in Phelipanche, mostly due to a diversification of repeats and an accumulation of Ty3/Gypsy elements. Genome downsizing in the tetraploid O. gracilis probably led to sequence loss across most repeat types. PMID:22723303

  20. The effect of exercise repetition on the frequency characteristics of motor output force: implications for Achilles tendinopathy rehabilitation.

    Science.gov (United States)

    Grigg, Nicole L; Wearing, Scott C; O'Toole, John M; Smeathers, James E

    2014-01-01

    To investigate the frequency characteristics of the ground reaction force (GRF) recorded throughout the eccentric Achilles tendon rehabilitation programme described by Alfredson. Controlled laboratory study, longitudinal. Nine healthy adult males performed six sets (15 repetitions per set) of eccentric ankle exercise. Ground reaction force was recorded throughout the exercise protocol. For each exercise repetition the frequency power spectrum of the resultant ground reaction force was calculated and normalised to total power. The magnitude of peak relative power within the 8-12 Hz bandwidth and the frequency at which this peak occurred was determined. The magnitude of peak relative power within the 8-12 Hz bandwidth increased with each successive exercise set and following the 4th set (60 repetitions) of exercise the frequency at which peak relative power occurred shifted from 9 to 10 Hz. The increase in magnitude and frequency of ground reaction force vibrations with an increasing number of exercise repetitions is likely connected to changes in muscle activation with fatigue and tendon conditioning. This research illustrates the potential for the number of exercise repetitions performed to influence the tendons' mechanical environment, with implications for tendon remodelling and the clinical efficacy of eccentric rehabilitation programmes for Achilles tendinopathy. Copyright © 2013 Sports Medicine Australia. Published by Elsevier Ltd. All rights reserved.

  1. Strategy for complete NMR assignment of disordered proteins with highly repetitive sequences based on resolution-enhanced 5D experiments

    Energy Technology Data Exchange (ETDEWEB)

    Motackova, Veronika; Novacek, Jiri [Masaryk University, Faculty of Science, National Centre for Biomolecular Research (Czech Republic); Zawadzka-Kazimierczuk, Anna; Kazimierczuk, Krzysztof [University of Warsaw, Faculty of Chemistry (Poland); Zidek, Lukas, E-mail: lzidek@chemi.muni.c [Masaryk University, Faculty of Science, National Centre for Biomolecular Research (Czech Republic); Sanderova, Hana; Krasny, Libor [Academy of Sciences of the Czech Republic, Laboratory of Molecular Genetics of Bacteria and Department of Bacteriology, Institute of Microbiology (Czech Republic); Kozminski, Wiktor [University of Warsaw, Faculty of Chemistry (Poland); Sklenar, Vladimir [Masaryk University, Faculty of Science, National Centre for Biomolecular Research (Czech Republic)

    2010-11-15

    A strategy for complete backbone and side-chain resonance assignment of disordered proteins with highly repetitive sequence is presented. The protocol is based on three resolution-enhanced NMR experiments: 5D HN(CA)CONH provides sequential connectivity, 5D HabCabCONH is utilized to identify amino acid types, and 5D HC(CC-TOCSY)CONH is used to assign the side-chain resonances. The improved resolution was achieved by a combination of high dimensionality and long evolution times, allowed by non-uniform sampling in the indirect dimensions. Random distribution of the data points and Sparse Multidimensional Fourier Transform processing were used. Successful application of the assignment procedure to a particularly difficult protein, {delta} subunit of RNA polymerase from Bacillus subtilis, is shown to prove the efficiency of the strategy. The studied protein contains a disordered C-terminal region of 81 amino acids with a highly repetitive sequence. While the conventional assignment methods completely failed due to a very small differences in chemical shifts, the presented strategy provided a complete backbone and side-chain assignment.

  2. Genomic organization and dynamics of repetitive DNA sequences in representatives of three Fagaceae genera.

    Science.gov (United States)

    Alves, Sofia; Ribeiro, Teresa; Inácio, Vera; Rocheta, Margarida; Morais-Cecílio, Leonor

    2012-05-01

    Oaks, chestnuts, and beeches are economically important species of the Fagaceae. To understand the relationship between these members of this family, a deep knowledge of their genome composition and organization is needed. In this work, we have isolated and characterized several AFLP fragments obtained from Quercus rotundifolia Lam. through homology searches in available databases. Genomic polymorphisms involving some of these sequences were evaluated in two species of Quercus, one of Castanea, and one of Fagus with specific primers. Comparative FISH analysis with generated sequences was performed in interphase nuclei of the four species, and the co-immunolocalization of 5-methylcytosine was also studied. Some of the sequences isolated proved to be genus-specific, while others were present in all the genera. Retroelements, either gypsy-like of the Tat/Athila clade or copia-like, are well represented, and most are dispersed in euchromatic regions of these species with no DNA methylation associated, pointing to an interspersed arrangement of these retroelements with potential gene-rich regions. A particular gypsy-sequence is dispersed in oaks and chestnut nuclei, but its confinement to chromocenters in beech evidences genome restructuring events during evolution of Fagaceae. Several sequences generated in this study proved to be good tools to comparatively study Fagaceae genome organization.

  3. The impact of targeting repetitive BamHI-W sequences on the sensitivity and precision of EBV DNA quantification.

    Directory of Open Access Journals (Sweden)

    Armen Sanosyan

    Full Text Available Viral load monitoring and early Epstein-Barr virus (EBV DNA detection are essential in routine laboratory testing, especially in preemptive management of Post-transplant Lymphoproliferative Disorder. Targeting the repetitive BamHI-W sequence was shown to increase the sensitivity of EBV DNA quantification, but the variability of BamHI-W reiterations was suggested to be a source of quantification bias. We aimed to assess the extent of variability associated with BamHI-W PCR and its impact on the sensitivity of EBV DNA quantification using the 1st WHO international standard, EBV strains and clinical samples.Repetitive BamHI-W- and LMP2 single- sequences were amplified by in-house qPCRs and BXLF-1 sequence by a commercial assay (EBV R-gene™, BioMerieux. Linearity and limits of detection of in-house methods were assessed. The impact of repeated versus single target sequences on EBV DNA quantification precision was tested on B95.8 and Raji cell lines, possessing 11 and 7 copies of the BamHI-W sequence, respectively, and on clinical samples.BamHI-W qPCR demonstrated a lower limit of detection compared to LMP2 qPCR (2.33 log10 versus 3.08 log10 IU/mL; P = 0.0002. BamHI-W qPCR underestimated the EBV DNA load on Raji strain which contained fewer BamHI-W copies than the WHO standard derived from the B95.8 EBV strain (mean bias: - 0.21 log10; 95% CI, -0.54 to 0.12. Comparison of BamHI-W qPCR versus LMP2 and BXLF-1 qPCR showed an acceptable variability between EBV DNA levels in clinical samples with the mean bias being within 0.5 log10 IU/mL EBV DNA, whereas a better quantitative concordance was observed between LMP2 and BXLF-1 assays.Targeting BamHI-W resulted to a higher sensitivity compared to LMP2 but the variable reiterations of BamHI-W segment are associated with higher quantification variability. BamHI-W can be considered for clinical and therapeutic monitoring to detect an early EBV DNA and a dynamic change in viral load.

  4. The impact of targeting repetitive BamHI-W sequences on the sensitivity and precision of EBV DNA quantification.

    Science.gov (United States)

    Sanosyan, Armen; Fayd'herbe de Maudave, Alexis; Bollore, Karine; Zimmermann, Valérie; Foulongne, Vincent; Van de Perre, Philippe; Tuaillon, Edouard

    2017-01-01

    Viral load monitoring and early Epstein-Barr virus (EBV) DNA detection are essential in routine laboratory testing, especially in preemptive management of Post-transplant Lymphoproliferative Disorder. Targeting the repetitive BamHI-W sequence was shown to increase the sensitivity of EBV DNA quantification, but the variability of BamHI-W reiterations was suggested to be a source of quantification bias. We aimed to assess the extent of variability associated with BamHI-W PCR and its impact on the sensitivity of EBV DNA quantification using the 1st WHO international standard, EBV strains and clinical samples. Repetitive BamHI-W- and LMP2 single- sequences were amplified by in-house qPCRs and BXLF-1 sequence by a commercial assay (EBV R-gene™, BioMerieux). Linearity and limits of detection of in-house methods were assessed. The impact of repeated versus single target sequences on EBV DNA quantification precision was tested on B95.8 and Raji cell lines, possessing 11 and 7 copies of the BamHI-W sequence, respectively, and on clinical samples. BamHI-W qPCR demonstrated a lower limit of detection compared to LMP2 qPCR (2.33 log10 versus 3.08 log10 IU/mL; P = 0.0002). BamHI-W qPCR underestimated the EBV DNA load on Raji strain which contained fewer BamHI-W copies than the WHO standard derived from the B95.8 EBV strain (mean bias: - 0.21 log10; 95% CI, -0.54 to 0.12). Comparison of BamHI-W qPCR versus LMP2 and BXLF-1 qPCR showed an acceptable variability between EBV DNA levels in clinical samples with the mean bias being within 0.5 log10 IU/mL EBV DNA, whereas a better quantitative concordance was observed between LMP2 and BXLF-1 assays. Targeting BamHI-W resulted to a higher sensitivity compared to LMP2 but the variable reiterations of BamHI-W segment are associated with higher quantification variability. BamHI-W can be considered for clinical and therapeutic monitoring to detect an early EBV DNA and a dynamic change in viral load.

  5. MRI of bone marrow: opposed-phase gradient-echo sequences with long repetition time

    International Nuclear Information System (INIS)

    Seiderer, M.; Staebler, A.; Wagner, H.

    1999-01-01

    Signal intensity for opposed-phase gradient-echo (GE) sequences of tissues composed of fat- and water-equivalent cells such as red bone marrow is extremely sensitive to variation of the ratio of both cell populations (fat-to-water ratio Q F/W ). Because most bone marrow pathology results in variation of Q F/W , GE sequences are characterized by high-contrast imaging of pathology. The aim of this study was to evaluate the influence of TR, TE, FA, Q F/W and histology on signal intensity. Signal intensity of opposed-phase GE sequences as a function of TR, TE, FA, and Q F/W was measured for a fat-water phantom and cadaver specimens of normal bone marrow (red and yellow) and pathological bone marrow (tumors). All specimens were correlated to histology. Opposed-phase GE imaging of red bone marrow pathology results in low-signal-intensity imaging of intact red bone marrow and high-signal-intensity positive contrast imaging of pathology associated with a change in Q F/W . In first-order approximation the signal intensity of pathology is linearly correlated to the change in Q F/W . Opposed-phase GE imaging is a sensitive imaging technique for red bone marrow pathology. Relative contrast of red bone marrow pathology is similar to fat-suppressed imaging techniques. Acquisition time is identical to T1-weighted SE sequences. (orig.)

  6. Structural analysis of a repetitive protein sequence motif in strepsirrhine primate amelogenin.

    Directory of Open Access Journals (Sweden)

    Rodrigo S Lacruz

    2011-03-01

    Full Text Available Strepsirrhines are members of a primate suborder that has a distinctive set of features associated with the development of the dentition. Amelogenin (AMEL, the better known of the enamel matrix proteins, forms 90% of the secreted organic matrix during amelogenesis. Although AMEL has been sequenced in numerous mammalian lineages, the only reported strepsirrhine AMEL sequences are those of the ring-tailed lemur and galago, which contain a set of additional proline-rich tandem repeats absent in all other primates species analyzed to date, but present in some non-primate mammals. Here, we first determined that these repeats are present in AMEL from three additional lemur species and thus are likely to be widespread throughout this group. To evaluate the functional relevance of these repeats in strepsirrhines, we engineered a mutated murine amelogenin sequence containing a similar proline-rich sequence to that of Lemur catta. In the monomeric form, the MQP insertions had no influence on the secondary structure or refolding properties, whereas in the assembled form, the insertions increased the hydrodynamic radii. We speculate that increased AMEL nanosphere size may influence enamel formation in strepsirrhine primates.

  7. Analysis of 90 Mb of the potato genome reveals conservation of gene structures and order with tomato but divergence in repetitive sequence composition

    Directory of Open Access Journals (Sweden)

    O'Brien Kimberly

    2008-06-01

    Full Text Available Abstract Background The Solanaceae family contains a number of important crop species including potato (Solanum tuberosum which is grown for its underground storage organ known as a tuber. Albeit the 4th most important food crop in the world, other than a collection of ~220,000 Expressed Sequence Tags, limited genomic sequence information is currently available for potato and advances in potato yield and nutrition content would be greatly assisted through access to a complete genome sequence. While morphologically diverse, Solanaceae species such as potato, tomato, pepper, and eggplant share not only genes but also gene order thereby permitting highly informative comparative genomic analyses. Results In this study, we report on analysis 89.9 Mb of potato genomic sequence representing 10.2% of the genome generated through end sequencing of a potato bacterial artificial chromosome (BAC clone library (87 Mb and sequencing of 22 potato BAC clones (2.9 Mb. The GC content of potato is very similar to Solanum lycopersicon (tomato and other dicotyledonous species yet distinct from the monocotyledonous grass species, Oryza sativa. Parallel analyses of repetitive sequences in potato and tomato revealed substantial differences in their abundance, 34.2% in potato versus 46.3% in tomato, which is consistent with the increased genome size per haploid genome of these two Solanum species. Specific classes and types of repetitive sequences were also differentially represented between these two species including a telomeric-related repetitive sequence, ribosomal DNA, and a number of unclassified repetitive sequences. Comparative analyses between tomato and potato at the gene level revealed a high level of conservation of gene content, genic feature, and gene order although discordances in synteny were observed. Conclusion Genomic level analyses of potato and tomato confirm that gene sequence and gene order are conserved between these solanaceous species and that

  8. Repetitive part of the banana (Musa acuminata) genome investigated by low-depth 454 sequencing

    Czech Academy of Sciences Publication Activity Database

    Hřibová, Eva; Neumann, Pavel; Matsumoto, T.; Roux, N.; Macas, Jiří; Doležel, Jaroslav

    2010-01-01

    Roč. 10, č. 204 (2010), s. 1-10 ISSN 1471-2229 R&D Projects: GA AV ČR KJB500380901; GA AV ČR IAA600380703; GA MŠk(CZ) LC06004 Institutional research plan: CEZ:AV0Z50380511; CEZ:AV0Z50510513 Keywords : IN-SITU HYBRIDIZATION * RIBOSOMAL-RNA GENES * DNA-SEQUENCES Subject RIV: EB - Genetics ; Molecular Biology Impact factor: 4.085, year: 2010

  9. Comparative genomics and repetitive sequence divergence in the species of diploid Nicotiana section Alatae.

    Science.gov (United States)

    Lim, K Yoong; Kovarik, Ales; Matyasek, Roman; Chase, Mark W; Knapp, Sandra; McCarthy, Elizabeth; Clarkson, James J; Leitch, Andrew R

    2006-12-01

    Combining phylogenetic reconstructions of species relationships with comparative genomic approaches is a powerful way to decipher evolutionary events associated with genome divergence. Here, we reconstruct the history of karyotype and tandem repeat evolution in species of diploid Nicotiana section Alatae. By analysis of plastid DNA, we resolved two clades with high bootstrap support, one containing N. alata, N. langsdorffii, N. forgetiana and N. bonariensis (called the n = 9 group) and another containing N. plumbaginifolia and N. longiflora (called the n = 10 group). Despite little plastid DNA sequence divergence, we observed, via fluorescent in situ hybridization, substantial chromosomal repatterning, including altered chromosome numbers, structure and distribution of repeats. Effort was focussed on 35S and 5S nuclear ribosomal DNA (rDNA) and the HRS60 satellite family of tandem repeats comprising the elements HRS60, NP3R and NP4R. We compared divergence of these repeats in diploids and polyploids of Nicotiana. There are dramatic shifts in the distribution of the satellite repeats and complete replacement of intergenic spacers (IGSs) of 35S rDNA associated with divergence of the species in section Alatae. We suggest that sequence homogenization has replaced HRS60 family repeats at sub-telomeric regions, but that this process may not occur, or occurs more slowly, when the repeats are found at intercalary locations. Sequence homogenization acts more rapidly (at least two orders of magnitude) on 35S rDNA than 5S rDNA and sub-telomeric satellite sequences. This rapid rate of divergence is analogous to that found in polyploid species, and is therefore, in plants, not only associated with polyploidy.

  10. Formulaic Sequences and the Implications for Second Language Learning

    Science.gov (United States)

    Xu, Qi

    2016-01-01

    The present paper is a review of literature in relation to formulaic sequences and the implications for second language learning. The formulaic sequence is a significant part of our language, and plays an essential role in both first and second language learning. The paper first introduces the definition, classifications, and major features of…

  11. Billions of basepairs of recently expanded, repetitive sequences are eliminated from the somatic genome during copepod development.

    Science.gov (United States)

    Sun, Cheng; Wyngaard, Grace; Walton, D Brian; Wichman, Holly A; Mueller, Rachel Lockridge

    2014-03-11

    Chromatin diminution is the programmed deletion of DNA from presomatic cell or nuclear lineages during development, producing single organisms that contain two different nuclear genomes. Phylogenetically diverse taxa undergo chromatin diminution--some ciliates, nematodes, copepods, and vertebrates. In cyclopoid copepods, chromatin diminution occurs in taxa with massively expanded germline genomes; depending on species, germline genome sizes range from 15 - 75 Gb, 12-74 Gb of which are lost from pre-somatic cell lineages at germline--soma differentiation. This is more than an order of magnitude more sequence than is lost from other taxa. To date, the sequences excised from copepods have not been analyzed using large-scale genomic datasets, and the processes underlying germline genomic gigantism in this clade, as well as the functional significance of chromatin diminution, have remained unknown. Here, we used high-throughput genomic sequencing and qPCR to characterize the germline and somatic genomes of Mesocyclops edax, a freshwater cyclopoid copepod with a germline genome of ~15 Gb and a somatic genome of ~3 Gb. We show that most of the excised DNA consists of repetitive sequences that are either 1) verifiable transposable elements (TEs), or 2) non-simple repeats of likely TE origin. Repeat elements in both genomes are skewed towards younger (i.e. less divergent) elements. Excised DNA is a non-random sample of the germline repeat element landscape; younger elements, and high frequency DNA transposons and LINEs, are disproportionately eliminated from the somatic genome. Our results suggest that germline genome expansion in M. edax reflects explosive repeat element proliferation, and that billions of base pairs of such repeats are deleted from the somatic genome every generation. Thus, we hypothesize that chromatin diminution is a mechanism that controls repeat element load, and that this load can evolve to be divergent between tissue types within single organisms.

  12. Human β satellite DNA: Genomic organization and sequence definition of a class of highly repetitive tandem DNA

    International Nuclear Information System (INIS)

    Waye, J.S.; Willard, H.F.

    1989-01-01

    The authors describe a class of human repetitive DNA, called β satellite, that, at a most fundamental level, exists as tandem arrays of diverged ∼68-base-pair monomer repeat units. The monomer units are organized as distinct subsets, each characterized by a multimeric higher-order repeat unit that is tandemly reiterated and represents a recent unit of amplification. They have cloned, characterized, and determined the sequence of two β satellite higher-order repeat units: one located on chromosome 9, the other on the acrocentric chromosomes (13, 14, 15, 21, and 22) and perhaps other sites in the genome. Analysis by pulsed-field gel electrophoresis reveals that these tandem arrays are localized in large domains that are marked by restriction fragment length polymorphisms. In total, β-satellite sequences comprise several million base pairs of DNA in the human genome. Analysis of this DNA family should permit insights into the nature of chromosome-specific and nonspecific modes of satellite DNA evolution and provide useful tools for probing the molecular organization and concerted evolution of the acrocentric chromosomes

  13. Implicity Defined Neural Networks for Sequence Labeling

    Science.gov (United States)

    2017-02-13

    assumption - that a hid- den variable changes its state based only on its current state and observables. In finding maximum likelihood state sequences...this setup, we have the following variables : data X labels Y parameters θ and functions: implicit hidden layer definition H = F (θ, ξ,H) loss function L...tagging task. In future work, we intend to consider implicit varia - tions of other archetectures, such as the LSTM, as well as additional, more challenging

  14. Location analysis for the estrogen receptor-α reveals binding to diverse ERE sequences and widespread binding within repetitive DNA elements

    Science.gov (United States)

    Mason, Christopher E.; Shu, Feng-Jue; Wang, Cheng; Session, Ryan M.; Kallen, Roland G.; Sidell, Neil; Yu, Tianwei; Liu, Mei Hui; Cheung, Edwin; Kallen, Caleb B.

    2010-01-01

    Location analysis for estrogen receptor-α (ERα)-bound cis-regulatory elements was determined in MCF7 cells using chromatin immunoprecipitation (ChIP)-on-chip. Here, we present the estrogen response element (ERE) sequences that were identified at ERα-bound loci and quantify the incidence of ERE sequences under two stringencies of detection: ERE sequence. We demonstrate that ∼50% of all ERα-bound loci do not have a discernable ERE and show that most ERα-bound EREs are not perfect consensus EREs. Approximately one-third of all ERα-bound ERE sequences reside within repetitive DNA sequences, most commonly of the AluS family. In addition, the 3-bp spacer between the inverted ERE half-sites, rather than being random nucleotides, is C(A/T)G-enriched at bona fide receptor targets. Diverse ERα-bound loci were validated using electrophoretic mobility shift assay and ChIP-polymerase chain reaction (PCR). The functional significance of receptor-bound loci was demonstrated using luciferase reporter assays which proved that repetitive element ERE sequences contribute to enhancer function. ChIP-PCR demonstrated estrogen-dependent recruitment of the coactivator SRC3 to these loci in vivo. Our data demonstrate that ERα binds to widely variant EREs with less sequence specificity than had previously been suspected and that binding at repetitive and nonrepetitive genomic targets is favored by specific trinucleotide spacers. PMID:20047966

  15. Location analysis for the estrogen receptor-alpha reveals binding to diverse ERE sequences and widespread binding within repetitive DNA elements.

    Science.gov (United States)

    Mason, Christopher E; Shu, Feng-Jue; Wang, Cheng; Session, Ryan M; Kallen, Roland G; Sidell, Neil; Yu, Tianwei; Liu, Mei Hui; Cheung, Edwin; Kallen, Caleb B

    2010-04-01

    Location analysis for estrogen receptor-alpha (ERalpha)-bound cis-regulatory elements was determined in MCF7 cells using chromatin immunoprecipitation (ChIP)-on-chip. Here, we present the estrogen response element (ERE) sequences that were identified at ERalpha-bound loci and quantify the incidence of ERE sequences under two stringencies of detection: ERE sequence. We demonstrate that approximately 50% of all ERalpha-bound loci do not have a discernable ERE and show that most ERalpha-bound EREs are not perfect consensus EREs. Approximately one-third of all ERalpha-bound ERE sequences reside within repetitive DNA sequences, most commonly of the AluS family. In addition, the 3-bp spacer between the inverted ERE half-sites, rather than being random nucleotides, is C(A/T)G-enriched at bona fide receptor targets. Diverse ERalpha-bound loci were validated using electrophoretic mobility shift assay and ChIP-polymerase chain reaction (PCR). The functional significance of receptor-bound loci was demonstrated using luciferase reporter assays which proved that repetitive element ERE sequences contribute to enhancer function. ChIP-PCR demonstrated estrogen-dependent recruitment of the coactivator SRC3 to these loci in vivo. Our data demonstrate that ERalpha binds to widely variant EREs with less sequence specificity than had previously been suspected and that binding at repetitive and nonrepetitive genomic targets is favored by specific trinucleotide spacers.

  16. RepeatExplorer: a Galaxy-based web server for genome-wide characterization of eukaryotic repetitive elements from next-generation sequence reads

    Czech Academy of Sciences Publication Activity Database

    Novák, Petr; Neumann, Pavel; Pech, Jiří; Steinhaisl, J.; Macas, Jiří

    2013-01-01

    Roč. 29, č. 6 (2013), s. 792-793 ISSN 1367-4803 R&D Projects: GA ČR GBP501/12/G090; GA MŠk(CZ) OC10037 Institutional support: RVO:60077344 Keywords : repetitiveDNA * computational analysis * next generation sequencing Subject RIV: EB - Genetics ; Molecular Biology Impact factor: 4.621, year: 2013

  17. Evaluation of short repetition time, partial flip angle, gradient recalled echo pulse sequences in cervical spine imaging

    International Nuclear Information System (INIS)

    Enzmann, D.; Rubin, J.B.

    1987-01-01

    A short repetition time (TR), partial flip angle, gradient recalled echo pulse sequence (GRASS) was prospectively studied to optimize it for the diagnosis of cervical disk and cord disease in 98 patients. Changes in signal-to-noise ratio (SNR) and contrast were measured as the following parameters were varied: flip angle (3 0 to 18 0 ), TR (22-60 msec), and echo time (TE) (12.5-25 msec). Flip angle was the single most important parameter. For disk disease, cerebrospinal fluid (CSF) SNR peaked at an 8 0 flip angle in the axial view but at a 4 0 flip angle in the sagittal view. In the sagittal view, disk-CSF contrast decreased progressively from a flip angle of 3 0 , while in the axial view it peaked at 10 0 . For cord lesions the findings were similar except that lesion-cord contrast could be increased by lengthening both TR and TE. No one combination of parameters proved greatly superior for either disk disease or cord disease. The selection of parameters required balancing of several factors that often had opposing effects

  18. Transference, counter-transference and repetition: some implications for nursing practice.

    Science.gov (United States)

    Jones, Alun C

    2005-11-01

    This discussion paper offers an introductory text for nurses and explores the psychoanalytic ideas of transference, counter-transference and repetition compulsion. Disguised case vignettes provide illustrations of the ideas as they might apply to nursing, including professional practice and occupational choice. The literature suggests that transference can be a source of creativity as well as destructiveness and influence important communications with oneself and others including the choice of nursing and other health professions as an occupation. Recognizing possibilities of transference, counter-transference along with repetitive patterns of behaviours, can help nurses of all specialities to address situations constructively by responding thoughtfully and appropriately. This discussion concludes with the suggestions that we know little about the motivational factors underlying nursing as an occupational preference; moreover, nursing does not have a culture of personal therapy. As such nurses are denied opportunities to understand the possible reasons underlying their occupational choice or gain experiential knowledge of interpersonal dynamics occurring between patients and colleagues. Transference and counter-transference are thought to have some bearing on all relationships. Forming a natural part of the way human beings relate to each other, transference and counter-transference can bring about sincere human interest, caring and concern. However, there is also potential for disagreements. Recognizing the possible origins of relational difficulties can offer opportunities for professional development to nurses along with the benefits for health service users.

  19. Repetitive tactile stimulation changes resting-state functional connectivity – implications for treatment of sensorimotor decline

    Directory of Open Access Journals (Sweden)

    Frank eFreyer

    2012-05-01

    Full Text Available Neurological disorders and physiological aging can lead to a decline of perceptual abilities. In contrast to the conventional therapeutic approach that comprises intensive training and practicing, passive repetitive sensory stimulation (RSS has recently gained increasing attention as an alternative to countervail the sensory decline by improving perceptual abilities without the need of active participation. A particularly effective type of high-frequency RSS, utilizing Hebbian learning principles, improves perceptual acuity as well as sensorimotor functions and has been successfully applied to treat chronic stroke patients and elderly subjects. High-frequency RSS has been shown to induce plastic changes of somatosensory cortex such as representational map reorganization, but its impact on the brain’s ongoing network activity and resting-state functional connectivity has not been investigated so far. Here, we applied high-frequency RSS in healthy human subjects and analyzed resting state Electroencephalography (EEG functional connectivity patterns before and after RSS by means of imaginary coherency (ImCoh, a frequency-specific connectivity measure which is known to reduce overestimation biases due to volume conduction and common reference. Thirty minutes of passive high-frequency RSS lead to significant ImCoh-changes of the resting state mu-rhythm in the individual upper alpha frequency band within distributed sensory and motor cortical areas. These stimulation induced distributed functional connectivity changes likely underlie the previously observed improvement in sensorimotor integration.

  20. Enterobacterial repetitive intergenic consensus sequences and the PCR to generate fingerprints of genomic DNAs from Vibrio cholerae O1, O139, and non-O1 strains.

    OpenAIRE

    Rivera, I G; Chowdhury, M A; Huq, A; Jacobs, D; Martins, M T; Colwell, R R

    1995-01-01

    Enterobacterial repetitive intergenic consensus (ERIC) sequence polymorphism was studied in Vibrio Cholerae strains isolated before and after the cholera epidemic in Brazil (in 1991), along with epidemic strains from Peru, Mexico, and India, by PCR. A total of 17 fingerprint patterns (FPs) were detected in the V. cholerae strains examined; 96.7% of the toxigenic V. cholerae O1 strains and 100% of the O139 serogroup strains were found to belong to the same FP group comprising four fragments (F...

  1. DNA Fingerprinting of Lactobacillus crispatus Strain CTV-05 by Repetitive Element Sequence-Based PCR Analysis in a Pilot Study of Vaginal Colonization

    OpenAIRE

    Antonio, May A. D.; Hillier, Sharon L.

    2003-01-01

    Lactobacillus crispatus is one of the predominant hydrogen peroxide (H2O2)-producing species found in the vagina and is under development as a probiotic for the treatment of bacterial vaginosis. In this study, we assessed whether DNA fingerprinting by repetitive element sequence-based PCR (rep-PCR) can be used to distinguish the capsule strain of L. crispatus (CTV-05) from other endogenous strains as well as other species of vaginal lactobacilli. Vaginal and rectal lactobacilli were identifie...

  2. Work-related musculoskeletal disorders in the automotive industry due to repetitive work - implications for rehabilitation

    Directory of Open Access Journals (Sweden)

    Quarcoo David

    2010-04-01

    Full Text Available Abstract Background Musculoskeletal disorders (MSDs due to repetitive work are common in manufacturing industries, such as the automotive industry. However, it's still unclear which MSDs of the upper limb are to be expected in the automotive industry in a first aid unit as well as in occupational precaution examinations. It is also unclear which examination method could be performed effectively for practical reasons and under rehabilitation aspects. Additionally, it was to discuss whether the conception of unspecific description for MSDs has advantages or disadvantages in contrast to a precise medical diagnosis. Methods We investigated the health status of two study populations working at two automotive plants in Germany. The first part included 67 consecutive patients who were seen for acute or chronic MSDs at the forearm over a 4-month period at the plants' medical services. Information about patients' working conditions and musculoskeletal symptoms was obtained during a standardized interview, which was followed by a standardized orthopedic-chiropractic physical examination. In the second part, 209 workers with daily exposure to video display terminals (VDT completed a standardized questionnaire and were examined with function-oriented muscular tests on the occasion of their routine occupational precaution medical check-up. Results The majority of the 67 patients seen by the company's medical services were blue-collar works from the assembly lines and trainees rather than white-collar workers from offices. Rates of musculoskeletal complaints were disproportionately higher among experienced people performing new tasks and younger trainees. The most common MSD in this group were disorders of flexor tendons of the forearm. By contrast, among the 209 employees working at VDT disorders of the neck and shoulders were more common than discomfort in the forearm. A positive tendency between restricted rotation of the cervical vertebrae and years

  3. Work-related musculoskeletal disorders in the automotive industry due to repetitive work - implications for rehabilitation.

    Science.gov (United States)

    Spallek, Michael; Kuhn, Walter; Uibel, Stefanie; van Mark, Anke; Quarcoo, David

    2010-04-07

    Musculoskeletal disorders (MSDs) due to repetitive work are common in manufacturing industries, such as the automotive industry. However, it's still unclear which MSDs of the upper limb are to be expected in the automotive industry in a first aid unit as well as in occupational precaution examinations. It is also unclear which examination method could be performed effectively for practical reasons and under rehabilitation aspects. Additionally, it was to discuss whether the conception of unspecific description for MSDs has advantages or disadvantages in contrast to a precise medical diagnosis. We investigated the health status of two study populations working at two automotive plants in Germany. The first part included 67 consecutive patients who were seen for acute or chronic MSDs at the forearm over a 4-month period at the plants' medical services. Information about patients' working conditions and musculoskeletal symptoms was obtained during a standardized interview, which was followed by a standardized orthopedic-chiropractic physical examination. In the second part, 209 workers with daily exposure to video display terminals (VDT) completed a standardized questionnaire and were examined with function-oriented muscular tests on the occasion of their routine occupational precaution medical check-up. The majority of the 67 patients seen by the company's medical services were blue-collar works from the assembly lines and trainees rather than white-collar workers from offices. Rates of musculoskeletal complaints were disproportionately higher among experienced people performing new tasks and younger trainees. The most common MSD in this group were disorders of flexor tendons of the forearm. By contrast, among the 209 employees working at VDT disorders of the neck and shoulders were more common than discomfort in the forearm. A positive tendency between restricted rotation of the cervical vertebrae and years worked at VDT was observed. In addition, only less than 8

  4. Karyotypic evolution and organization of the highly repetitive DNA sequences in the Japanese shrew-moles, Dymecodon pilirostris and Urotrichus talpoides.

    Science.gov (United States)

    Nakata, A; Yoshimura, A; Kuro-o, M; Obara, Y

    2005-01-01

    The karyological relationship and organization of highly repetitive DNA sequences in Japanese shrew-moles were studied by zoo-blot hybridization and fluorescence in situ hybridization (FISH). When the genomic DNA of the eastern race of Urotrichus talpoides was digested with PstI, three fragments of highly repetitive DNA sequences, approximately 0.7, 0.9, and 1.4 kb in length, were observed as distinct bands. The results of FISH in the eastern race of U. talpoides using these three fragments separately as probes showed that the 0.7-kb PstI fragment was distributed in the centromeric regions of most chromosomes, and that the 0.9- and 1.4-kb fragments were predominantly located in the C-heterochromatin region of chromosome 13p. Although the western race of U. talpoides also had three PstI fragments, 0.9- and 1.4-kb PstI fragments were more ambiguous than those of the eastern race. The PstI- digested genomic DNA in Dymecodonpilirostris produced only a faint 0.9-kb band, and its signal patterns obtained by zoo-blot hybridization were clearly different from those of U. talpoides. The 0.7-kb fragment of U. talpoides hybridized strongly with the 0.9-kb fragment of D. pilirostris. In a FISH analysis, the 0.9-kb fragment of D. pilirostris hybridized with highly repetitive DNA in the centromeric regions of most chromosomes from both D. pilirostris and U. talpoides. Zoo-blot hybridization and FISH analyses suggest that the 0.9- and 1.4-kb PstI fragments were generated specifically in the genome of U. talpoides after the common ancestor differentiated into two extant shrew-mole species. A difference in the length of the centromeric elements between U. talpoides and D. pilirostris might be observed due to certain modifications of the repeating unit.

  5. Variation in extragenic repetitive DNA sequences in Pseudomonas syringae and potential use of modified REP primers in the identification of closely related isolates

    Directory of Open Access Journals (Sweden)

    Elif Çepni

    2012-01-01

    Full Text Available In this study, Pseudomonas syringe pathovars isolated from olive, tomato and bean were identified by species-specific PCR and their genetic diversity was assessed by repetitive extragenic palindromic (REP-PCR. Reverse universal primers for REP-PCR were designed by using the bases of A, T, G or C at the positions of 1, 4 and 11 to identify additional polymorphism in the banding patterns. Binding of the primers to different annealing sites in the genome revealed additional fingerprint patterns in eight isolates of P. savastanoi pv. savastanoi and two isolates of P. syringae pv. tomato. The use of four different bases in the primer sequences did not affect the PCR reproducibility and was very efficient in revealing intra-pathovar diversity, particularly in P. savastanoi pv. savastanoi. At the pathovar level, the primer BOX1AR yielded shared fragments, in addition to five bands that discriminated among the pathovars P. syringae pv. phaseolicola, P. savastanoi pv. savastanoi and P. syringae pv. tomato. REP-PCR with a modified primer containing C produced identical bands among the isolates in a pathovar but separated three pathovars more distinctly than four other primers. Although REP-and BOX-PCRs have been successfully used in the molecular identification of Pseudomonas isolates from Turkish flora, a PCR based on inter-enterobacterial repetitive intergenic concensus (ERIC sequences failed to produce clear banding patterns in this study.

  6. The soybean-Phytophthora resistance locus Rps1-k encompasses coiled coil-nucleotide binding-leucine rich repeat-like genes and repetitive sequences

    Directory of Open Access Journals (Sweden)

    Bhattacharyya Madan K

    2008-03-01

    Full Text Available Abstract Background A series of Rps (resistance to Pytophthora sojae genes have been protecting soybean from the root and stem rot disease caused by the Oomycete pathogen, Phytophthora sojae. Five Rps genes were mapped to the Rps1 locus located near the 28 cM map position on molecular linkage group N of the composite genetic soybean map. Among these five genes, Rps1-k was introgressed from the cultivar, Kingwa. Rps1-k has been providing stable and broad-spectrum Phytophthora resistance in the major soybean-producing regions of the United States. Rps1-k has been mapped and isolated. More than one functional Rps1-k gene was identified from the Rps1-k locus. The clustering feature at the Rps1-k locus might have facilitated the expansion of Rps1-k gene numbers and the generation of new recognition specificities. The Rps1-k region was sequenced to understand the possible evolutionary steps that shaped the generation of Phytophthora resistance genes in soybean. Results Here the analyses of sequences of three overlapping BAC clones containing the 184,111 bp Rps1-k region are reported. A shotgun sequencing strategy was applied in sequencing the BAC contig. Sequence analysis predicted a few full-length genes including two Rps1-k genes, Rps1-k-1 and Rps1-k-2. Previously reported Rps1-k-3 from this genomic region 1 was evolved through intramolecular recombination between Rps1-k-1 and Rps1-k-2 in Escherichia coli. The majority of the predicted genes are truncated and therefore most likely they are nonfunctional. A member of a highly abundant retroelement, SIRE1, was identified from the Rps1-k region. The Rps1-k region is primarily composed of repetitive sequences. Sixteen simple repeat and 63 tandem repeat sequences were identified from the locus. Conclusion These data indicate that the Rps1 locus is located in a gene-poor region. The abundance of repetitive sequences in the Rps1-k region suggested that the location of this locus is in or near a

  7. Repetitive DNA in the pea (Pisum sativum L. genome: comprehensive characterization using 454 sequencing and comparison to soybean and Medicago truncatula

    Directory of Open Access Journals (Sweden)

    Navrátilová Alice

    2007-11-01

    Full Text Available Abstract Background Extraordinary size variation of higher plant nuclear genomes is in large part caused by differences in accumulation of repetitive DNA. This makes repetitive DNA of great interest for studying the molecular mechanisms shaping architecture and function of complex plant genomes. However, due to methodological constraints of conventional cloning and sequencing, a global description of repeat composition is available for only a very limited number of higher plants. In order to provide further data required for investigating evolutionary patterns of repeated DNA within and between species, we used a novel approach based on massive parallel sequencing which allowed a comprehensive repeat characterization in our model species, garden pea (Pisum sativum. Results Analysis of 33.3 Mb sequence data resulted in quantification and partial sequence reconstruction of major repeat families occurring in the pea genome with at least thousands of copies. Our results showed that the pea genome is dominated by LTR-retrotransposons, estimated at 140,000 copies/1C. Ty3/gypsy elements are less diverse and accumulated to higher copy numbers than Ty1/copia. This is in part due to a large population of Ogre-like retrotransposons which alone make up over 20% of the genome. In addition to numerous types of mobile elements, we have discovered a set of novel satellite repeats and two additional variants of telomeric sequences. Comparative genome analysis revealed that there are only a few repeat sequences conserved between pea and soybean genomes. On the other hand, all major families of pea mobile elements are well represented in M. truncatula. Conclusion We have demonstrated that even in a species with a relatively large genome like pea, where a single 454-sequencing run provided only 0.77% coverage, the generated sequences were sufficient to reconstruct and analyze major repeat families corresponding to a total of 35–48% of the genome. These data

  8. Location analysis for the estrogen receptor-? reveals binding to diverse ERE sequences and widespread binding within repetitive DNA elements

    OpenAIRE

    Mason, Christopher E.; Shu, Feng-Jue; Wang, Cheng; Session, Ryan M.; Kallen, Roland G.; Sidell, Neil; Yu, Tianwei; Liu, Mei Hui; Cheung, Edwin; Kallen, Caleb B.

    2010-01-01

    Location analysis for estrogen receptor-? (ER?)-bound cis-regulatory elements was determined in MCF7 cells using chromatin immunoprecipitation (ChIP)-on-chip. Here, we present the estrogen response element (ERE) sequences that were identified at ER?-bound loci and quantify the incidence of ERE sequences under two stringencies of detection:

  9. Translocation and gross deletion breakpoints in human inherited disease and cancer II: Potential involvement of repetitive sequence elements in secondary structure formation between DNA ends.

    Science.gov (United States)

    Chuzhanova, Nadia; Abeysinghe, Shaun S; Krawczak, Michael; Cooper, David N

    2003-09-01

    Translocations and gross deletions are responsible for a significant proportion of both cancer and inherited disease. Although such gene rearrangements are nonuniformly distributed in the human genome, the underlying mutational mechanisms remain unclear. We have studied the potential involvement of various types of repetitive sequence elements in the formation of secondary structure intermediates between the single-stranded DNA ends that recombine during rearrangements. Complexity analysis was used to assess the potential of these ends to form secondary structures, the maximum decrease in complexity consequent to a gross rearrangement being used as an indicator of the type of repeat and the specific DNA ends involved. A total of 175 pairs of deletion/translocation breakpoint junction sequences available from the Gross Rearrangement Breakpoint Database [GRaBD; www.uwcm.ac.uk/uwcm/mg/grabd/grabd.html] were analyzed. Potential secondary structure was noted between the 5' flanking sequence of the first breakpoint and the 3' flanking sequence of the second breakpoint in 49% of rearrangements and between the 5' flanking sequence of the second breakpoint and the 3' flanking sequence of the first breakpoint in 36% of rearrangements. Inverted repeats, inversions of inverted repeats, and symmetric elements were found in association with gross rearrangements at approximately the same frequency. However, inverted repeats and inversions of inverted repeats accounted for the vast majority (83%) of deletions plus small insertions, symmetric elements for one-half of all antigen receptor-mediated translocations, while direct repeats appear only to be involved in mediating simple deletions. These findings extend our understanding of illegitimate recombination by highlighting the importance of secondary structure formation between single-stranded DNA ends at breakpoint junctions. Copyright 2003 Wiley-Liss, Inc.

  10. Survey Sequencing Reveals Elevated DNA Transposon Activity, Novel Elements, and Variation in Repetitive Landscapes among Vesper Bats

    Czech Academy of Sciences Publication Activity Database

    Pagán, H.J.T.; Macas, Jiří; Novák, Petr; McCulloch, E.S.; Stevens, R.D.; Ray, D.A.

    2012-01-01

    Roč. 4, č. 4 (2012), s. 575-585 ISSN 1759-6653 Institutional research plan: CEZ:AV0Z50510513 Keywords : HORIZONTAL TRANSFER * AUTOMATED CLASSIFICATION * GENOME SEQUENCE Subject RIV: EB - Genetics ; Molecular Biology Impact factor: 4.759, year: 2012

  11. Next-Generation Sequencing Reveals the Impact of Repetitive DNA Across Phylogenetically Closely Related Genomes of Orobanchaceae

    Czech Academy of Sciences Publication Activity Database

    Piednoël, M.; Aberer, A.J.; Schneeweiss, G. M.; Macas, Jiří; Novák, Petr; Gundlach, H.; Temsch, E.M.; Renner, S.S.

    2012-01-01

    Roč. 29, č. 11 (2012), s. 3601-3611 ISSN 0737-4038 Institutional research plan: CEZ:AV0Z50510513 Institutional support: RVO:60077344 Keywords : next-generation sequencing * polyploidy * genome size * Ty3/Gypsy * transposable elements Subject RIV: EB - Genetics ; Molecular Biology Impact factor: 10.353, year: 2012

  12. Efficacy of Pulsed-Field Gel Electrophoresis and Repetitive Element Sequence-Based PCR in Typing of Salmonella Isolates from Assam, India.

    Science.gov (United States)

    Gogoi, Purnima; Borah, Probodh; Hussain, Iftikar; Das, Leena; Hazarika, Girin; Tamuly, Shantanu; Barkalita, Luit Moni

    2018-05-01

    A total of 12 Salmonella isolates belonging to different serovars, viz , Salmonella enterica serovar Enteritidis ( n = 4), Salmonella enterica serovar Weltevreden ( n = 4), Salmonella enterica serovar Newport ( n = 1), Salmonella enterica serovar Litchifield ( n = 1), and untypeable strains ( n = 2) were isolated from 332 diarrheic fecal samples collected from animals, birds, and humans. Of the two molecular typing methods applied, viz , repetitive element sequence-based PCR (REP-PCR) and pulsed-field gel electrophoresis (PFGE), PFGE could clearly differentiate the strains belonging to different serovars as well as differentiate between strains of the same serovar with respect to their source of isolation, whereas REP-PCR could not differentiate between strains of the same serovar. Thus, it can be suggested that PFGE is more useful and appropriate for molecular typing of Salmonella isolates during epidemiological investigations than REP-PCR. Copyright © 2018 American Society for Microbiology.

  13. Contrasting Evolutionary Paths Among Indo-Pacific Pomacentrus Species Promoted by Extensive Pericentric Inversions and Genome Organization of Repetitive Sequences.

    Science.gov (United States)

    Getlekha, Nuntaporn; Cioffi, Marcelo de Bello; Maneechot, Nuntiya; Bertollo, Luiz Antônio Carlos; Supiwong, Weerayuth; Tanomtong, Alongklod; Molina, Wagner Franco

    2018-02-01

    Pomacentrus (damselfishes) is one of the most characteristic groups of fishes in the Indo-Pacific coral reef. Its 77 described species exhibit a complex taxonomy with cryptic lineages across their extensive distribution. Periods of evolutionary divergences between them are very variable, and the cytogenetic events that followed their evolutionary diversification are largely unknown. In this respect, analyses of chromosomal divergence, within a phylogenetic perspective, are particularly informative regarding karyoevolutionary trends. As such, we conducted conventional cytogenetic and cytogenomic analyses in four Pomacentrus species (Pomacentrus similis, Pomacentrus auriventris, Pomacentrus moluccensis, and Pomacentrus cuneatus), through the mapping of repetitive DNA classes and transposable elements, including 18S rDNA, 5S rDNA, (CA) 15 , (GA) 15 , (CAA) 10 , Rex6, and U2 snDNA as markers. P. auriventris and P. similis, belonging to the Pomacentrus coelestis complex, have indistinguishable karyotypes (2n = 48; NF = 48), with a peculiar syntenic organization of ribosomal genes. On the other hand, P. moluccensis and P. cuneatus, belonging to another clade, exhibit very different karyotypes (2n = 48, NF = 86 and 92, respectively), with a large number of bi-armed chromosomes, where multiple pericentric inversions played a significant role in their karyotype organization. In this sense, different chromosomal pathways followed the phyletic diversification in the Pomacentrus genus, making possible the characterization of two well-contrasting species groups regarding their karyotype features. Despite this, pericentric inversions act as an effective postzygotic barrier in many organisms, which appear to be also the case for P. moluccensis and P. cuneatus; the extensive chromosomal similarities in the two species of P. coelestis complex suggest minor participation of chromosomal postzygotic barriers in the phyletic diversification of these species.

  14. Repetitive flood victims and acceptance of FEMA mitigation offers: an analysis with community-system policy implications.

    Science.gov (United States)

    Kick, Edward L; Fraser, James C; Fulkerson, Gregory M; McKinney, Laura A; De Vries, Daniel H

    2011-07-01

    Of all natural disasters, flooding causes the greatest amount of economic and social damage. The United States' Federal Emergency Management Agency (FEMA) uses a number of hazard mitigation grant programmes for flood victims, including mitigation offers to relocate permanently repetitive flood loss victims. This study examines factors that help to explain the degree of difficulty repetitive flood loss victims experience when they make decisions about relocating permanently after multiple flood losses. Data are drawn from interviews with FEMA officials and a survey of flood victims from eight repetitive flooding sites. The qualitative and quantitative results show the importance of rational choices by flood victims in their mitigation decisions, as they relate to financial variables, perceptions of future risk, attachments to home and community, and the relationships between repetitive flood loss victims and the local flood management officials who help them. The results offer evidence to suggest the value of a more community-system approach to FEMA relocation practices. © 2011 The Author(s). Disasters © Overseas Development Institute, 2011.

  15. Repetitive transpositions of mitochondrial DNA sequences to the nucleus during the radiation of horseshoe bats (Rhinolophus, Chiroptera).

    Science.gov (United States)

    Shi, Huizhen; Dong, Ji; Irwin, David M; Zhang, Shuyi; Mao, Xiuguang

    2016-05-01

    Transposition of mitochondrial DNA into the nucleus, which gives rise to nuclear mitochondrial DNAs (NUMTs), has been well documented in eukaryotes. However, very few studies have assessed the frequency of these transpositions during the evolutionary history of a specific taxonomic group. Here we used the horseshoe bats (Rhinolophus) as a case study to determine the frequency and relative timing of nuclear transfers of mitochondrial control region sequences. For this, phylogenetic and coalescent analyzes were performed on NUMTs and authentic mtDNA sequences generated from eight horseshoe bat species. Our results suggest at least three independent transpositions, including two ancient and one more recent, during the evolutionary history of Rhinolophus. The two ancient transpositions are represented by the NUMT-1 and -2 clades, with each clade consisting of NUMTs from almost all studied species but originating from different portions of the mtDNA genome. Furthermore, estimates of the most recent common ancestor for each clade corresponded to the time of the initial diversification of this genus. The recent transposition is represented by NUMT-3, which was discovered only in a specific subgroup of Rhinolophus and exhibited a close relationship to its mitochondrial counterpart. Our similarity searches of mtDNA in the R. ferrumequinum genome confirmed the presence of NUMT-1 and NUMT-2 clade sequences and, for the first time, assessed the extent of NUMTs in a bat genome. To our knowledge, this is the first study to report on the frequency of transpositions of mtDNA occurring before the common ancestry of a genus. Copyright © 2016 Elsevier B.V. All rights reserved.

  16. Differential chromosomal organization between Saguinus midas and Saguinus bicolor with accumulation of differences the repetitive sequence DNA.

    Science.gov (United States)

    Serfaty, Dayane Martins Barbosa; Carvalho, Natália Dayane Moura; Gross, Maria Claudia; Gordo, Marcelo; Schneider, Carlos Henrique

    2017-10-01

    Saguinus is the largest and most complex genus of the subfamily Callitrichinae, with 23 species distributed from the south of Central America to the north of South America with Saguinus midas having the largest geographical distribution while Saguinus bicolor has a very restricted one, affected by the population expansion in the state of Amazonas. Considering the phylogenetic proximity of the two species along with evidence on the existence of hybrids between them, as well as cytogenetic studies on Saguinus describing a conserved karyotypic macrostructure, we carried out a physical mapping of DNA repeated sequences in the mitotic chromosome of both species, since these sequences are less susceptible to evolutionary pressure and possibly perform an important function in speciation. Both species presented 2n = 46 chromosomes; in S. midas, chromosome Y is the smallest. Multiple ribosomal sites occur in both species, but chromosome pairs three and four may be regarded as markers that differ the species when subjected to G banding and distribution of retroelement LINE 1, suggesting that it may be cytogenetic marker in which it can contribute to identification of first generation hybrids in contact zone. Saguinus bicolor also presented differences in the LINE 1 distribution pattern for sexual chromosome X in individuals from different urban fragments, probably due to geographical isolation. In this context, cytogenetic analyses reveal a differential genomic organization pattern between species S. midas and S. bicolor, in addition to indicating that individuals from different urban fragments have been accumulating differences because of the isolation between them.

  17. IS1111 insertion sequences of Coxiella burnetii: characterization and use for repetitive element PCR-based differentiation of Coxiella burnetii isolates

    Directory of Open Access Journals (Sweden)

    Massung Robert F

    2007-10-01

    Full Text Available Abstract Background Coxiella burnetii contains the IS1111 transposase which is present 20 times in the Nine Mile phase I (9Mi/I genome. A single PCR primer that binds to each IS element, and primers specific to a region ~500-bp upstream of each of the 20 IS1111 elements were designed. The amplified products were characterized and used to develop a repetitive element PCR genotyping method. Results Isolates Nine Mile phase II, Nine Mile RSA 514, Nine Mile Baca, Scottish, Ohio, Australian QD, Henzerling phase I, Henzerling phase II, M44, KAV, PAV, Q238, Q195 and WAV were tested by PCR and compared to 9Mi/I. Sequencing was used to determine the exact differences in isolates which lacked specific IS elements or produced PCR products of differing size. From this data, an algorithm was created utilizing four primer pairs that allows for differentiation of unknown isolates into five genomic groups. Additional isolates (Priscilla Q177, Idaho Q, Qiyi, Poker Cat, Q229 and Q172 and nine veterinary samples were characterized using the algorithm which resulted in their placement into three distinct genomic groups. Conclusion Through this study significant differences, including missing elements and sequence alterations within and near IS element coding regions, were found between the isolates tested. Further, a method for differentiation of C. burnetii isolates into one of five genomic groups was created. This algorithm may ultimately help to determine the relatedness between known and unknown isolates of C. burnetii.

  18. Reconstruction of putative DNA virus from endogenous rice tungro bacilliform virus-like sequences in the rice genome: implications for integration and evolution

    Directory of Open Access Journals (Sweden)

    Kishima Yuji

    2004-10-01

    Full Text Available Abstract Background Plant genomes contain various kinds of repetitive sequences such as transposable elements, microsatellites, tandem repeats and virus-like sequences. Most of them, with the exception of virus-like sequences, do not allow us to trace their origins nor to follow the process of their integration into the host genome. Recent discoveries of virus-like sequences in plant genomes led us to set the objective of elucidating the origin of the repetitive sequences. Endogenous rice tungro bacilliform virus (RTBV-like sequences (ERTBVs have been found throughout the rice genome. Here, we reconstructed putative virus structures from RTBV-like sequences in the rice genome and characterized to understand evolutionary implication, integration manner and involvements of endogenous virus segments in the corresponding disease response. Results We have collected ERTBVs from the rice genomes. They contain rearranged structures and no intact ORFs. The identified ERTBV segments were shown to be phylogenetically divided into three clusters. For each phylogenetic cluster, we were able to make a consensus alignment for a circular virus-like structure carrying two complete ORFs. Comparisons of DNA and amino acid sequences suggested the closely relationship between ERTBV and RTBV. The Oryza AA-genome species vary in the ERTBV copy number. The species carrying low-copy-number of ERTBV segments have been reported to be extremely susceptible to RTBV. The DNA methylation state of the ERTBV sequences was correlated with their copy number in the genome. Conclusions These ERTBV segments are unlikely to have functional potential as a virus. However, these sequences facilitate to establish putative virus that provided information underlying virus integration and evolutionary relationship with existing virus. Comparison of ERTBV among the Oryza AA-genome species allowed us to speculate a possible role of endogenous virus segments against its related disease.

  19. Conformational Diversity of Single-Stranded DNA from Bacterial Repetitive Extragenic Palindromes: Implications for the DNA Recognition Elements of Transposases

    Czech Academy of Sciences Publication Activity Database

    Charnavets, Tatsiana; Nunvář, Jaroslav; Nečasová, Iva; Voelker, J.; Breslauer, K.J.; Schneider, Bohdan

    2015-01-01

    Roč. 103, č. 10 (2015), s. 585-596 ISSN 0006-3525 R&D Projects: GA MŠk(CZ) ED1.1.00/02.0109; GA ČR GAP305/12/1801; GA MŠk(CZ) EE2.3.30.0020 Institutional support: RVO:86652036 Keywords : bacterial repetitive extragenic palindromes (REP) * circular dichroism spectroscopy * REP associated tyrosine transposases (RAYTs) Subject RIV: EB - Genetics ; Molecular Biology Impact factor: 2.248, year: 2015

  20. Characterization of Erwinia amylovora strains from different host plants using repetitive-sequences PCR analysis, and restriction fragment length polymorphism and short-sequence DNA repeats of plasmid pEA29.

    Science.gov (United States)

    Barionovi, D; Giorgi, S; Stoeger, A R; Ruppitsch, W; Scortichini, M

    2006-05-01

    The three main aims of the study were the assessment of the genetic relationship between a deviating Erwinia amylovora strain isolated from Amelanchier sp. (Maloideae) grown in Canada and other strains from Maloideae and Rosoideae, the investigation of the variability of the PstI fragment of the pEA29 plasmid using restriction fragment length polymorphism (RFLP) analysis and the determination of the number of short-sequence DNA repeats (SSR) by DNA sequence analysis in representative strains. Ninety-three strains obtained from 12 plant genera and different geographical locations were examined by repetitive-sequences PCR using Enterobacterial Repetitive Intergenic Consensus, BOX and Repetitive Extragenic Palindromic primer sets. Upon the unweighted pair group method with arithmetic mean analysis, a deviating strain from Amelanchier sp. was analysed using amplified ribosomal DNA restriction analysis (ARDRA) analysis and the sequencing of the 16S rDNA gene. This strain showed 99% similarity to other E. amylovora strains in the 16S gene and the same banding pattern with ARDRA. The RFLP analysis of pEA29 plasmid using MspI and Sau3A restriction enzymes showed a higher variability than that previously observed and no clear-cut grouping of the strains was possible. The number of SSR units reiterated two to 12 times. The strains obtained from pear orchards showing for the first time symptoms of fire blight had a low number of SSR units. The strains from Maloideae exhibit a wider genetic variability than previously thought. The RFLP analysis of a fragment of the pEA29 plasmid would not seem a reliable method for typing E. amylovora strains. A low number of SSR units was observed with first epidemics of fire blight. The current detection techniques are mainly based on the genetic similarities observed within the strains from the cultivated tree-fruit crops. For a more reliable detection of the fire blight pathogen also in wild and ornamentals Rosaceous plants the genetic

  1. Optimization of analytical parameters for inferring relationships among Escherichia coli isolates from repetitive-element PCR by maximizing correspondence with multilocus sequence typing data.

    Science.gov (United States)

    Goldberg, Tony L; Gillespie, Thomas R; Singer, Randall S

    2006-09-01

    Repetitive-element PCR (rep-PCR) is a method for genotyping bacteria based on the selective amplification of repetitive genetic elements dispersed throughout bacterial chromosomes. The method has great potential for large-scale epidemiological studies because of its speed and simplicity; however, objective guidelines for inferring relationships among bacterial isolates from rep-PCR data are lacking. We used multilocus sequence typing (MLST) as a "gold standard" to optimize the analytical parameters for inferring relationships among Escherichia coli isolates from rep-PCR data. We chose 12 isolates from a large database to represent a wide range of pairwise genetic distances, based on the initial evaluation of their rep-PCR fingerprints. We conducted MLST with these same isolates and systematically varied the analytical parameters to maximize the correspondence between the relationships inferred from rep-PCR and those inferred from MLST. Methods that compared the shapes of densitometric profiles ("curve-based" methods) yielded consistently higher correspondence values between data types than did methods that calculated indices of similarity based on shared and different bands (maximum correspondences of 84.5% and 80.3%, respectively). Curve-based methods were also markedly more robust in accommodating variations in user-specified analytical parameter values than were "band-sharing coefficient" methods, and they enhanced the reproducibility of rep-PCR. Phylogenetic analyses of rep-PCR data yielded trees with high topological correspondence to trees based on MLST and high statistical support for major clades. These results indicate that rep-PCR yields accurate information for inferring relationships among E. coli isolates and that accuracy can be enhanced with the use of analytical methods that consider the shapes of densitometric profiles.

  2. Trends of reactive hyperaemia responses to repetitive loading on skin tissue of rats - Implications for pressure ulcer prevention.

    Science.gov (United States)

    Yapp, Jong-Heng; Kamil, Raja; Rozi, M; Mohtarrudin, Norhafizah; Loqman, M Y; Ezamin, A R; Ahmad, Siti Anom; Abu Bakar, Zuki

    2017-08-01

    Tissue recovery is important in preventing tissue deterioration, which is induced by pressure and may lead to pressure ulcers (PU). Reactive hyperaemia (RH) is an indicator used to identify people at risk of PU. In this study, the effect of different recovery times on RH trend is investigated during repetitive loading. Twenty-one male Sprague-Dawley rats (seven per group), with body weight of 385-485 g, were categorised into three groups and subjected to different recovery times with three repetitive loading cycles. The first, second, and third groups were subjected to short (3 min), moderate (10 min), and prolonged (40 min) recovery, respectively, while fixed loading time and pressure (10 min and 50 mmHg, respectively). Peak hyperaemia was measured in the three cycles to determine trends associated with different recovery times. Three RH trends (increasing, decreasing, and inconsistent) were observed. As the recovery time is increased (3 min vs. 10 min vs. 40 min), the number of samples with increasing RH trend decreases (57% vs. 29% vs. 14%) and the number of samples with inconsistent RH trend increases (29% vs. 57% vs. 72%). All groups consists of one sample with decreasing RH trend (14%). Results confirm that different recovery times affect the RH trend during repetitive loading. The RH trend may be used to determine the sufficient recovery time of an individual to avoid PU development. Copyright © 2017 Tissue Viability Society. Published by Elsevier Ltd. All rights reserved.

  3. Identification and molecular epidemiology of dermatophyte isolates by repetitive-sequence-PCR-based DNA fingerprinting using the DiversiLab system in Turkey.

    Science.gov (United States)

    Koc, A Nedret; Atalay, Mustafa A; Inci, Melek; Sariguzel, Fatma M; Sav, Hafize

    2017-05-01

    Dermatophyte species, isolation and identification in clinical samples are still difficult and take a long time. The identification and molecular epidemiology of dermatophytes commonly isolated in a clinical laboratory in Turkey by repetitive sequence-based PCR (rep-PCR) were assessed by comparing the results with those of reference identification. A total of 44 dermatophytes isolated from various clinical specimens of 20 patients with superficial mycoses in Kayseri and 24 patients in Hatay were studied. The identification of dermatophyte isolates was based on the reference identification and rep-PCR using the DiversiLab System (BioMerieux). The genotyping of dermatophyte isolates from different patients was determined by rep-PCR. In the identification of dermatophyte isolates, agreement between rep-PCR and conventional methods was 87.8 % ( 36 of 41). The dermatophyte strains belonged to four clones (A -D) which were determined by the use of rep-PCR. The dermatophyte strains in Clone B, D showed identical patterns with respect to the region. In conclusion, rep-PCR appears to be useful for evaluation of the identification and clonal relationships between Trichophyton rubrum species complex and Trichophyton mentagrophytes species complex isolates. The similarity and diversity of these isolates may be assessed according to different regions by rep-PCR. © 2017 Blackwell Verlag GmbH.

  4. DNA Methylation Status of the Interspersed Repetitive Sequences for LINE-1, Alu, HERV-E, and HERV-K in Trabeculectomy Specimens from Glaucoma Eyes

    Directory of Open Access Journals (Sweden)

    Sunee Chansangpetch

    2018-01-01

    Full Text Available Background/Aims. Epigenetic mechanisms via DNA methylation may be related to glaucoma pathogenesis. This study aimed to determine the global DNA methylation level of the trabeculectomy specimens among patients with different types of glaucoma and normal subjects. Methods. Trabeculectomy sections from 16 primary open-angle glaucoma (POAG, 12 primary angle-closure glaucoma (PACG, 16 secondary glaucoma patients, and 10 normal controls were assessed for DNA methylation using combined-bisulfite restriction analysis. The percentage of global methylation level of the interspersed repetitive sequences for LINE-1, Alu, HERV-E, and HERV-K were compared between the 4 groups. Results. There were no significant differences in the methylation for LINE-1 and HERV-E between patients and normal controls. For the Alu marker, the methylation was significantly lower in all types of glaucoma patients compared to controls (POAG 52.19% versus control 52.83%, p=0.021; PACG 51.50% versus control, p=0.005; secondary glaucoma 51.95% versus control, p=0.014, whereas the methylation level of HERV-K was statistically higher in POAG patients compared to controls (POAG 49.22% versus control 48.09%, p=0.017. Conclusions. The trabeculectomy sections had relative DNA hypomethylation of Alu in all glaucoma subtypes and relative DNA hypermethylation of HERV-K in POAG patients. These methylation changes may lead to the fibrotic phenotype in the trabecular meshwork.

  5. The Role of Memory Processes in Repetition Blindness

    Science.gov (United States)

    Johnston, James C.; Hochhaus, Larry; Null, Cynthia H. (Technical Monitor)

    1995-01-01

    We investigated whether Repetition Blindness (RB) in processing RSVP strings depends critically on memory demands. When all items in the sequence had to be reported, strong RB was found. When only the 2 critical items (cued by color) had to be reported, no RB was found. Preliminary results show that imposing a separate memory load, while reporting only the critical items, also produces little RB. Implications for the processing locus of RB will be discussed.

  6. Novel porcine repetitive elements

    Directory of Open Access Journals (Sweden)

    Nonneman Dan J

    2006-12-01

    Full Text Available Abstract Background Repetitive elements comprise ~45% of mammalian genomes and are increasingly known to impact genomic function by contributing to the genomic architecture, by direct regulation of gene expression and by affecting genomic size, diversity and evolution. The ubiquity and increasingly understood importance of repetitive elements contribute to the need to identify and annotate them. We set out to identify previously uncharacterized repetitive DNA in the porcine genome. Once found, we characterized the prevalence of these repeats in other mammals. Results We discovered 27 repetitive elements in 220 BACs covering 1% of the porcine genome (Comparative Vertebrate Sequencing Initiative; CVSI. These repeats varied in length from 55 to 1059 nucleotides. To estimate copy numbers, we went to an independent source of data, the BAC-end sequences (Wellcome Trust Sanger Institute, covering approximately 15% of the porcine genome. Copy numbers in BAC-ends were less than one hundred for 6 repeat elements, between 100 and 1000 for 16 and between 1,000 and 10,000 for 5. Several of the repeat elements were found in the bovine genome and we have identified two with orthologous sites, indicating that these elements were present in their common ancestor. None of the repeat elements were found in primate, rodent or dog genomes. We were unable to identify any of the replication machinery common to active transposable elements in these newly identified repeats. Conclusion The presence of both orthologous and non-orthologous sites indicates that some sites existed prior to speciation and some were generated later. The identification of low to moderate copy number repetitive DNA that is specific to artiodactyls will be critical in the assembly of livestock genomes and studies of comparative genomics.

  7. Repetitive Stress Injuries

    Science.gov (United States)

    ... Safe Videos for Educators Search English Español Repetitive Stress Injuries KidsHealth / For Teens / Repetitive Stress Injuries What's ... t had any problems since. What Are Repetitive Stress Injuries? Repetitive stress injuries (RSIs) are injuries that ...

  8. Enterobacterial repetitive intergenic consensus sequences and the PCR to generate fingerprints of genomic DNAs from Vibrio cholerae O1, O139, and non-O1 strains.

    Science.gov (United States)

    Rivera, I G; Chowdhury, M A; Huq, A; Jacobs, D; Martins, M T; Colwell, R R

    1995-08-01

    Enterobacterial repetitive intergenic consensus (ERIC) sequence polymorphism was studied in Vibrio Cholerae strains isolated before and after the cholera epidemic in Brazil (in 1991), along with epidemic strains from Peru, Mexico, and India, by PCR. A total of 17 fingerprint patterns (FPs) were detected in the V. cholerae strains examined; 96.7% of the toxigenic V. cholerae O1 strains and 100% of the O139 serogroup strains were found to belong to the same FP group comprising four fragments (FP1). The nontoxigenic V. cholerae O1 also yielded four fragments but constituted a different FP group (FP2). A total of 15 different patterns were observed among the V. cholerae non-O1 strains. Two patterns were observed most frequently for V. cholerae non-01 strains, 25% of which have FP3, with five fragments, and 16.7% of which have FP4, with two fragments. Three fragments, 1.75, 0.79, and 0.5 kb, were found to be common to both toxigenic and nontoxigenic V. cholerae O1 strains as well as to group FP3, containing V. cholerae non-O1 strains. Two fragments of group FP3, 1.3 and 1.0 kb, were present in FP1 and FP2 respectively. The 0.5-kb fragment was common to all strains and serogroups of V. cholerae analyzed. It is concluded from the results of this study, based on DNA FPs of environmental isolates, that it is possible to detect an emerging virulent strain in a cholera-endemic region. ERIC-PCR constitutes a powerful tool for determination of the virulence potential of V. cholerae O1 strains isolated in surveillance programs and for molecular epidemiological investigations.

  9. Repetitive box lifting performance is impaired in a hot environment: implications for altered work-rest cycles.

    Science.gov (United States)

    Maresh, Carl M; Sökmen, Bulent; Armstrong, Lawrence E; Dias, Joao C; Pryor, J Luke; Creighton, Brent C; Muñoz, Colleen X; Apicella, Jenna M; Casa, Douglas J; Lee, Elaine C; Anderson, Jeffery M; Kraemer, William J

    2014-01-01

    This study investigated the effects of environmental temperature on repetitive box lifting (RBL) performance, associated stress hormone and creatine kinase (CK) responses. Ten healthy males performed two experimental trials in a random crossover design. The trials consisted of three 40 min (10 min sitting, 20 min standing, and 10 min RBL) circuits performed in either 23 °C or 38 °C followed by a 180 min seated recovery period in 23 °C. RBL performance (i.e., number of boxes lifted) was reduced (p ≤ 0.05) in 38 °C compared to the 23 °C trial. Physiological Strain Index was significantly different between trials (38 °C: 8.5 ± 1.1 versus 23 °C: 7.2 ± 0.7; p ≤ 0.01). Plasma testosterone was elevated (p ≤ 0.05) across both trials and then decreased at 60 min recovery, compared to pre-exercise (PRE) measures, but was higher (p ≤ 0.05) during the 38 °C trial. Plasma cortisol increased (p ≤ 0.05) at 60 min during both trials and remained elevated until 120 min in 23 °C, and until 60 min recovery in 38 °C. Serum CK was greater through 48 hr post compared to PRE values in both trials. Thus, 10 min RBL performance was reduced in 38 °C despite the 30-min rest periods between RBL intervals. Plasma testosterone and cortisol were generally higher during the 38 °C trial, suggesting a greater stress response. Additional research is needed to determine optimal work:rest cycles for maximizing work performance in thermally oppressive environments.

  10. Long Aftershock Sequences within Continents and Implications for Earthquake Hazard Assessment

    Science.gov (United States)

    Stein, S. A.; Liu, M.

    2014-12-01

    Recent seismicity in the Tangshan region in North China has prompted concern about a repetition of the 1976 M7.8 earthquake that destroyed the city, killing more than 242,000 people. However, the decay of seismicity there implies that the recent earthquakes are probably aftershocks of the 1976 event. This 37-year sequence is an example of the phenomenon that aftershock sequences within continents are often significantly longer than the typical 10 years at plate boundaries. The long sequence of aftershocks in continents is consistent with a simple friction-based model predicting that the length of aftershock sequences varies inversely with the rate at which faults are loaded. Hence the slowly-deforming continents tend to have aftershock sequences significantly longer than at rapidly-loaded plate boundaries. This effect has two consequences for hazard assessment. First, within the heavily populated continents that are typically within plate interiors, assessments of earthquake hazards rely significantly on the assumption that the locations of small earthquakes shown by the short historical record reflect continuing deformation that will cause future large earthquakes. This assumption would lead to overestimation of the hazard in presently active areas and underestimation elsewhere, if some of these small events are aftershocks. Second, successful attempts to remove aftershocks from catalogs used for hazard assessment would underestimate the hazard, because much of the hazard is due to the aftershocks, and the declustering algorithms implicitly assume short aftershock sequences and thus do not remove long-duration ones.

  11. Whole Exome Sequencing in Pediatric Neurology Patients: Clinical Implications and Estimated Cost Analysis.

    Science.gov (United States)

    Nolan, Danielle; Carlson, Martha

    2016-06-01

    Genetic heterogeneity in neurologic disorders has been an obstacle to phenotype-based diagnostic testing. The authors hypothesized that information compiled via whole exome sequencing will improve clinical diagnosis and management of pediatric neurology patients. The authors performed a retrospective chart review of patients evaluated in the University of Michigan Pediatric Neurology clinic between 6/2011 and 6/2015. The authors recorded previous diagnostic testing, indications for whole exome sequencing, and whole exome sequencing results. Whole exome sequencing was recommended for 135 patients and obtained in 53 patients. Insurance barriers often precluded whole exome sequencing. The most common indication for whole exome sequencing was neurodevelopmental disorders. Whole exome sequencing improved the presumptive diagnostic rate in the patient cohort from 25% to 48%. Clinical implications included family planning, medication selection, and systemic investigation. Compared to current second tier testing, whole exome sequencing can result in lower long-term charges and more timely diagnosis. Overcoming barriers related to whole exome sequencing insurance authorization could allow for more efficient and fruitful diagnostic neurological evaluations. © The Author(s) 2016.

  12. Chromosomal distribution of pTa-535, pTa-86, pTa-713, 35S rDNA repetitive sequences in interspecific hexaploid hybrids of common wheat (Triticum aestivum L.) and spelt (Triticum spelta L.).

    Science.gov (United States)

    Goriewa-Duba, Klaudia; Duba, Adrian; Kwiatek, Michał; Wiśniewska, Halina; Wachowska, Urszula; Wiwart, Marian

    2018-01-01

    Fluorescent in situ hybridization (FISH) relies on fluorescent-labeled probes to detect specific DNA sequences in the genome, and it is widely used in cytogenetic analyses. The aim of this study was to determine the karyotype of T. aestivum and T. spelta hybrids and their parental components (three common wheat cultivars and five spelt breeding lines), to identify chromosomal aberrations in the evaluated wheat lines, and to analyze the distribution of polymorphisms of repetitive sequences in the examined hybrids. The FISH procedure was carried out with four DNA clones, pTa-86, pTa-535, pTa-713 and 35S rDNA used as probes. The observed polymorphisms between the investigated lines of common wheat, spelt and their hybrids was relatively low. However, differences were observed in the distribution of repetitive sequences on chromosomes 4A, 6A, 1B and 6B in selected hybrid genomes. The polymorphisms observed in common wheat and spelt hybrids carry valuable information for wheat breeders. The results of our study are also a valuable source of knowledge about genome organization and diversification in common wheat, spelt and their hybrids. The relevant information is essential for common wheat breeders, and it can contribute to breeding programs aimed at biodiversity preservation.

  13. Chromosomal distribution of pTa-535, pTa-86, pTa-713, 35S rDNA repetitive sequences in interspecific hexaploid hybrids of common wheat (Triticum aestivum L. and spelt (Triticum spelta L..

    Directory of Open Access Journals (Sweden)

    Klaudia Goriewa-Duba

    Full Text Available Fluorescent in situ hybridization (FISH relies on fluorescent-labeled probes to detect specific DNA sequences in the genome, and it is widely used in cytogenetic analyses. The aim of this study was to determine the karyotype of T. aestivum and T. spelta hybrids and their parental components (three common wheat cultivars and five spelt breeding lines, to identify chromosomal aberrations in the evaluated wheat lines, and to analyze the distribution of polymorphisms of repetitive sequences in the examined hybrids. The FISH procedure was carried out with four DNA clones, pTa-86, pTa-535, pTa-713 and 35S rDNA used as probes. The observed polymorphisms between the investigated lines of common wheat, spelt and their hybrids was relatively low. However, differences were observed in the distribution of repetitive sequences on chromosomes 4A, 6A, 1B and 6B in selected hybrid genomes. The polymorphisms observed in common wheat and spelt hybrids carry valuable information for wheat breeders. The results of our study are also a valuable source of knowledge about genome organization and diversification in common wheat, spelt and their hybrids. The relevant information is essential for common wheat breeders, and it can contribute to breeding programs aimed at biodiversity preservation.

  14. Genomic sequencing: assessing the health care system, policy, and big-data implications.

    Science.gov (United States)

    Phillips, Kathryn A; Trosman, Julia R; Kelley, Robin K; Pletcher, Mark J; Douglas, Michael P; Weldon, Christine B

    2014-07-01

    New genomic sequencing technologies enable the high-speed analysis of multiple genes simultaneously, including all of those in a person's genome. Sequencing is a prominent example of a "big data" technology because of the massive amount of information it produces and its complexity, diversity, and timeliness. Our objective in this article is to provide a policy primer on sequencing and illustrate how it can affect health care system and policy issues. Toward this end, we developed an easily applied classification of sequencing based on inputs, methods, and outputs. We used it to examine the implications of sequencing for three health care system and policy issues: making care more patient-centered, developing coverage and reimbursement policies, and assessing economic value. We conclude that sequencing has great promise but that policy challenges include how to optimize patient engagement as well as privacy, develop coverage policies that distinguish research from clinical uses and account for bioinformatics costs, and determine the economic value of sequencing through complex economic models that take into account multiple findings and downstream costs. Project HOPE—The People-to-People Health Foundation, Inc.

  15. Repetition and the Concept of Repetition

    Directory of Open Access Journals (Sweden)

    Arne Grøn

    2013-11-01

    Full Text Available This paper offers a description of the meaning of the category of repetition. Firstly, it is pointed out that Constantin uses repetition as a concept that means the creation of epochs; the passing from Greece to Modernity is accomplished distinguishing between recollection, a concept that looks back to the past, and repetition, a concept that looks forward to future. Secondly, it is showed that the category of repetition, as a religious category, relates with what Climacus calls “ethic despair” and with what Vigilius calls “second ethics”; it is through repetition that it can be understood that sin finds its place in ethics and these shows the tension between it and dogmatics. And thirdly, it is showed that the descovery of the new category of repetition is a rediscovery of what Kierkegaard calls category of spirit; repetition has for its object the individuality, and coming to be oneself is what Kierkegaard undertands as liberty. At the end of the paper it is questioned if the category of repetition is inconsistent with the book Repetition.

  16. Karyological characterization and identification of four repetitive element groups (the 18S – 28S rRNA gene, telomeric sequences, microsatellite repeat motifs, Rex retroelements) of the Asian swamp eel (Monopterus albus)

    Science.gov (United States)

    Suntronpong, Aorarat; Thapana, Watcharaporn; Twilprawat, Panupon; Prakhongcheep, Ornjira; Somyong, Suthasinee; Muangmai, Narongrit; Surin Peyachoknagul; Srikulnath, Kornsorn

    2017-01-01

    Abstract Among teleost fishes, Asian swamp eel (Monopterus albus Zuiew, 1793) possesses the lowest chromosome number, 2n = 24. To characterize the chromosome constitution and investigate the genome organization of repetitive sequences in M. albus, karyotyping and chromosome mapping were performed with the 18S – 28S rRNA gene, telomeric repeats, microsatellite repeat motifs, and Rex retroelements. The 18S – 28S rRNA genes were observed to the pericentromeric region of chromosome 4 at the same position with large propidium iodide and C-positive bands, suggesting that the molecular structure of the pericentromeric regions of chromosome 4 has evolved in a concerted manner with amplification of the 18S – 28S rRNA genes. (TTAGGG)n sequences were found at the telomeric ends of all chromosomes. Eight of 19 microsatellite repeat motifs were dispersedly mapped on different chromosomes suggesting the independent amplification of microsatellite repeat motifs in M. albus. Monopterus albus Rex1 (MALRex1) was observed at interstitial sites of all chromosomes and in the pericentromeric regions of most chromosomes whereas MALRex3 was scattered and localized to all chromosomes and MALRex6 to several chromosomes. This suggests that these retroelements were independently amplified or lost in M. albus. Among MALRexs (MALRex1, MALRex3, and MALRex6), MALRex6 showed higher interspecific sequence divergences from other teleost species in comparison. This suggests that the divergence of Rex6 sequences of M. albus might have occurred a relatively long time ago. PMID:29093797

  17. Avian endogenous provirus (ev-3) env gene sequencing: implication for pathogenic retrovirus origination.

    Science.gov (United States)

    Tikhonenko, A T; Lomovskaya, O L

    1990-02-01

    The avian endogenous env gene product blocks the surface receptor and, as a result, cells become immune to related exogenous retroviruses. On the other hand, the same sequence can be included in the pathogenic retrovirus genome, as shown by oligonucleotide mapping. However, since the complete env gene sequence was not known, the comparison of genomic nucleotide sequences was not possible. Therefore an avian endogenous provirus with an intact env gene was cloned from a chicken gene bank and the regions coding for the C terminus of the gp85 and gp37 proteins were sequenced. Comparison of this sequence with those of other retroviruses proved that one of the pathogenic viruses associated with osteopetrosis is a cross between avian endogenous virus and Rous sarcoma virus. Retroviruses and, especially, endogenous retroviruses are traditionally of the most developed models of viral carcinogenesis. Many endogenous retroviruses are implicated in neoplastic transformation of the cell. For instance, endogenous mouse mammary tumor virus of some inbred lines appears to be the only causative agent in these mammary cancers. Other even nonpathogenic murine endogenous retroviruses are involved in the origination of MCF-type recombinant acute leukosis viruses. Some endogenous retroviruses are implicated in the transduction or activation of cellular protooncogenes. Our interest in endogenous viruses is based on their ability to make cells resistant to exogenous retroviruses. Expression of their major envelope glycoprotein leads to cellular surface receptor blockage and imparts immunity to infection by the related leukemia retroviruses. This problem is quite elaborated for chicken endogenous virus RAV-O (7-9).(ABSTRACT TRUNCATED AT 250 WORDS)

  18. Complete chloroplast DNA sequence from a Korean endemic genus, Megaleranthis saniculifolia, and its evolutionary implications.

    Science.gov (United States)

    Kim, Young-Kyu; Park, Chong-wook; Kim, Ki-Joong

    2009-03-31

    The chloroplast DNA sequences of Megaleranthis saniculifolia, an endemic and monotypic endangered plant species, were completed in this study (GenBank FJ597983). The genome is 159,924 bp in length. It harbors a pair of IR regions consisting of 26,608 bp each. The lengths of the LSC and SSC regions are 88,326 bp and 18,382 bp, respectively. The structural organizations, gene and intron contents, gene orders, AT contents, codon usages, and transcription units of the Megaleranthis chloroplast genome are similar to those of typical land plant cp DNAs. However, the detailed features of Megaleranthis chloroplast genomes are substantially different from that of Ranunculus, which belongs to the same family, the Ranunculaceae. First, the Megaleranthis cp DNA was 4,797 bp longer than that of Ranunculus due to an expanded IR region into the SSC region and duplicated sequence elements in several spacer regions of the Megaleranthis cp genome. Second, the chloroplast genomes of Megaleranthis and Ranunculus evidence 5.6% sequence divergence in the coding regions, 8.9% sequence divergence in the intron regions, and 18.7% sequence divergence in the intergenic spacer regions, respectively. In both the coding and noncoding regions, average nucleotide substitution rates differed markedly, depending on the genome position. Our data strongly implicate the positional effects of the evolutionary modes of chloroplast genes. The genes evidencing higher levels of base substitutions also have higher incidences of indel mutations and low Ka/Ks ratios. A total of 54 simple sequence repeat loci were identified from the Megaleranthis cp genome. The existence of rich cp SSR loci in the Megaleranthis cp genome provides a rare opportunity to study the population genetic structures of this endangered species. Our phylogenetic trees based on the two independent markers, the nuclear ITS and chloroplast matK sequences, strongly support the inclusion of the Megaleranthis to the Trollius. Therefore, our

  19. Exome sequencing identifies three novel candidate genes implicated in intellectual disability.

    Directory of Open Access Journals (Sweden)

    Zehra Agha

    Full Text Available Intellectual disability (ID is a major health problem mostly with an unknown etiology. Recently exome sequencing of individuals with ID identified novel genes implicated in the disease. Therefore the purpose of the present study was to identify the genetic cause of ID in one syndromic and two non-syndromic Pakistani families. Whole exome of three ID probands was sequenced. Missense variations in two plausible novel genes implicated in autosomal recessive ID were identified: lysine (K-specific methyltransferase 2B (KMT2B, zinc finger protein 589 (ZNF589, as well as hedgehog acyltransferase (HHAT with a de novo mutation with autosomal dominant mode of inheritance. The KMT2B recessive variant is the first report of recessive Kleefstra syndrome-like phenotype. Identification of plausible causative mutations for two recessive and a dominant type of ID, in genes not previously implicated in disease, underscores the large genetic heterogeneity of ID. These results also support the viewpoint that large number of ID genes converge on limited number of common networks i.e. ZNF589 belongs to KRAB-domain zinc-finger proteins previously implicated in ID, HHAT is predicted to affect sonic hedgehog, which is involved in several disorders with ID, KMT2B associated with syndromic ID fits the epigenetic module underlying the Kleefstra syndromic spectrum. The association of these novel genes in three different Pakistani ID families highlights the importance of screening these genes in more families with similar phenotypes from different populations to confirm the involvement of these genes in pathogenesis of ID.

  20. Discovery of rare variants via sequencing: implications for the design of complex trait association studies.

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    Bingshan Li

    2009-05-01

    Full Text Available There is strong evidence that rare variants are involved in complex disease etiology. The first step in implicating rare variants in disease etiology is their identification through sequencing in both randomly ascertained samples (e.g., the 1,000 Genomes Project and samples ascertained according to disease status. We investigated to what extent rare variants will be observed across the genome and in candidate genes in randomly ascertained samples, the magnitude of variant enrichment in diseased individuals, and biases that can occur due to how variants are discovered. Although sequencing cases can enrich for casual variants, when a gene or genes are not involved in disease etiology, limiting variant discovery to cases can lead to association studies with dramatically inflated false positive rates.

  1. The Genomic Architecture of Novel Simulium damnosum Wolbachia Prophage Sequence Elements and Implications for Onchocerciasis Epidemiology

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    James L. Crainey

    2017-05-01

    WO phage sequences was also detected. These findings provide insights into how Wolbachia could affect a medically important vector of onchocerciasis, with potential implications for future control methods, as well as supporting the hypothesis that Wolbachia phages do not follow the standard model of phage evolution.

  2. RNA sequencing atopic dermatitis transcriptome profiling provides insights into novel disease mechanisms with potential therapeutic implications

    DEFF Research Database (Denmark)

    Suárez-Fariñas, Mayte; Ungar, Benjamin; Correa da Rosa, Joel

    2015-01-01

    . These limitations might be lessened with next-generation RNA sequencing (RNA-seq). Objective: We sought to define the lesional AD transcriptome using RNA-seq and compare it using microarrays performed on the same cohort. Methods: RNA-seq and microarrays were performed to identify differentially expressed genes...... RNA-seq showed somewhat better agreement with RT-PCR (intraclass correlation coefficient, 0.57 and 0.70 for microarrays and RNA-seq vs RT-PCR, respectively), bias was not eliminated. Among genes uniquely identified by using RNA-seq were triggering receptor expressed on myeloid cells 1 (TREM-1......) signaling (eg, CCL2, CCL3, and single immunoglobulin domain IL1R1 related [SIGIRR]) and IL-36 isoform genes. TREM-1 is a surface receptor implicated in innate and adaptive immunity that amplifies infection-related inflammation. Conclusions: This is the first report of a lesional AD phenotype using RNA...

  3. The Hydrologic Implications Of Unique Urban Soil Horizon Sequencing On The Functions Of Passive Green Infrastructure

    Science.gov (United States)

    Shuster, W.; Schifman, L. A.; Herrmann, D.

    2017-12-01

    Green infrastructure represents a broad set of site- to landscape-scale practices that can be flexibly implemented to increase sewershed retention capacity, and can thereby improve on the management of water quantity and quality. Although much green infrastructure presents as formal engineered designs, urbanized landscapes with highly-interspersed pervious surfaces (e.g., right-of-way, parks, lawns, vacant land) may offer ecosystem services as passive, infiltrative green infrastructure. Yet, infiltration and drainage processes are regulated by soil surface conditions, and then the layering of subsoil horizons, respectively. Drawing on a unique urban soil taxonomic and hydrologic dataset collected in 12 cities (each city representing a major soil order), we determined how urbanization processes altered the sequence of soil horizons (compared to pre-urbanized reference soil pedons) and modeled the hydrologic implications of these shifts in layering with an unsaturated zone code (HYDRUS2D). We found that the different layering sequences in urbanized soils render different types and extents of supporting (plant-available soil water), provisioning (productive vegetation), and regulating (runoff mitigation) ecosystem services.

  4. Chronology of Eocene-Miocene sequences on the New Jersey shallow shelf: implications for regional, interregional, and global correlations

    Science.gov (United States)

    Browning, James V.; Miller, Kenneth G.; Sugarman, Peter J.; Barron, John; McCarthy, Francine M.G.; Kulhanek, Denise K.; Katz, Miriam E.; Feigenson, Mark D.

    2013-01-01

    Integrated Ocean Drilling Program Expedition 313 continuously cored and logged latest Eocene to early-middle Miocene sequences at three sites (M27, M28, and M29) on the inner-middle continental shelf offshore New Jersey, providing an opportunity to evaluate the ages, global correlations, and significance of sequence boundaries. We provide a chronology for these sequences using integrated strontium isotopic stratigraphy and biostratigraphy (primarily calcareous nannoplankton, diatoms, and dinocysts [dinoflagellate cysts]). Despite challenges posed by shallow-water sediments, age resolution is typically ±0.5 m.y. and in many sequences is as good as ±0.25 m.y. Three Oligocene sequences were sampled at Site M27 on sequence bottomsets. Fifteen early to early-middle Miocene sequences were dated at Sites M27, M28, and M29 across clinothems in topsets, foresets (where the sequences are thickest), and bottomsets. A few sequences have coarse (∼1 m.y.) or little age constraint due to barren zones; we constrain the age estimates of these less well dated sequences by applying the principle of superposition, i.e., sediments above sequence boundaries in any site are younger than the sediments below the sequence boundaries at other sites. Our age control provides constraints on the timing of deposition in the clinothem; sequences on the topsets are generally the youngest in the clinothem, whereas the bottomsets generally are the oldest. The greatest amount of time is represented on foresets, although we have no evidence for a correlative conformity. Our chronology provides a baseline for regional and interregional correlations and sea-level reconstructions: (1) we correlate a major increase in sedimentation rate precisely with the timing of the middle Miocene climate changes associated with the development of a permanent East Antarctic Ice Sheet; and (2) the timing of sequence boundaries matches the deep-sea oxygen isotopic record, implicating glacioeustasy as a major driver

  5. Repetition and Translation Shifts

    Directory of Open Access Journals (Sweden)

    Simon Zupan

    2006-06-01

    Full Text Available Repetition manifests itself in different ways and at different levels of the text. The first basic type of repetition involves complete recurrences; in which a particular textual feature repeats in its entirety. The second type involves partial recurrences; in which the second repetition of the same textual feature includes certain modifications to the first occurrence. In the article; repetitive patterns in Edgar Allan Poe’s short story “The Fall of the House of Usher” and its Slovene translation; “Konec Usherjeve hiše”; are compared. The author examines different kinds of repetitive patterns. Repetitions are compared at both the micro- and macrostructural levels. As detailed analyses have shown; considerable microstructural translation shifts occur in certain types of repetitive patterns. Since these are not only occasional; sporadic phenomena; but are of a relatively high frequency; they reduce the translated text’s potential for achieving some of the gothic effects. The macrostructural textual property particularly affected by these shifts is the narrator’s experience as described by the narrative; which suffers a reduction in intensity.

  6. Repetitive Questioning Exasperates Caregivers

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    R. C. Hamdy MD

    2018-01-01

    Full Text Available Repetitive questioning is due to an impaired episodic memory and is a frequent, often presenting, problem in patients with Alzheimer’s disease (amnestic type. It is due to the patients’ difficulties learning new information, retaining it, and recalling it, and is often aggravated by a poor attention span and easy distractibility. A number of factors may trigger and maintain repetitive questioning. Caregivers should try to identify and address these triggers. In the case discussion presented, it is due to the patient’s concerns about her and her family’s safety triggered by watching a particularly violent movie aired on TV. What went wrong in the patient/caregiver interaction and how it could have been avoided or averted are explored. Also reviewed are the impact of repetitive questioning, the challenges it raises for caregivers, and some effective intervention strategies that may be useful to diffuse the angst that caregivers experience with repetitive questioning.

  7. Exome sequences of multiplex, multigenerational families reveal schizophrenia risk loci with potential implications for neurocognitive performance.

    Science.gov (United States)

    Kos, Mark Z; Carless, Melanie A; Peralta, Juan; Curran, Joanne E; Quillen, Ellen E; Almeida, Marcio; Blackburn, August; Blondell, Lucy; Roalf, David R; Pogue-Geile, Michael F; Gur, Ruben C; Göring, Harald H H; Nimgaonkar, Vishwajit L; Gur, Raquel E; Almasy, Laura

    2017-12-01

    Schizophrenia is a serious mental illness, involving disruptions in thought and behavior, with a worldwide prevalence of about one percent. Although highly heritable, much of the genetic liability of schizophrenia is yet to be explained. We searched for susceptibility loci in multiplex, multigenerational families affected by schizophrenia, targeting protein-altering variation with in silico predicted functional effects. Exome sequencing was performed on 136 samples from eight European-American families, including 23 individuals diagnosed with schizophrenia or schizoaffective disorder. In total, 11,878 non-synonymous variants from 6,396 genes were tested for their association with schizophrenia spectrum disorders. Pathway enrichment analyses were conducted on gene-based test results, protein-protein interaction (PPI) networks, and epistatic effects. Using a significance threshold of FDR < 0.1, association was detected for rs10941112 (p = 2.1 × 10 -5 ; q-value = 0.073) in AMACR, a gene involved in fatty acid metabolism and previously implicated in schizophrenia, with significant cis effects on gene expression (p = 5.5 × 10 -4 ), including brain tissue data from the Genotype-Tissue Expression project (minimum p = 6.0 × 10 -5 ). A second SNP, rs10378 located in TMEM176A, also shows risk effects in the exome data (p = 2.8 × 10 -5 ; q-value = 0.073). PPIs among our top gene-based association results (p < 0.05; n = 359 genes) reveal significant enrichment of genes involved in NCAM-mediated neurite outgrowth (p = 3.0 × 10 -5 ), while exome-wide SNP-SNP interaction effects for rs10941112 and rs10378 indicate a potential role for kinase-mediated signaling involved in memory and learning. In conclusion, these association results implicate AMACR and TMEM176A in schizophrenia risk, whose effects may be modulated by genes involved in synaptic plasticity and neurocognitive performance. © 2017 Wiley Periodicals, Inc.

  8. Nonlinear analysis of sequence repeats of multi-domain proteins

    Energy Technology Data Exchange (ETDEWEB)

    Huang Yanzhao [Biomolecular Physics and Modeling Group, Department of Physics, Huazhong University of Science and Technology, Wuhan 430074, Hubei (China); Li Mingfeng [Biomolecular Physics and Modeling Group, Department of Physics, Huazhong University of Science and Technology, Wuhan 430074, Hubei (China); Xiao Yi [Biomolecular Physics and Modeling Group, Department of Physics, Huazhong University of Science and Technology, Wuhan 430074, Hubei (China)]. E-mail: lmf_bill@sina.com

    2007-11-15

    Many multi-domain proteins have repetitive three-dimensional structures but nearly-random amino acid sequences. In the present paper, by using a modified recurrence plot proposed by us previously, we show that these amino acid sequences have hidden repetitions in fact. These results indicate that the repetitive domain structures are encoded by the repetitive sequences. This also gives a method to detect the repetitive domain structures directly from amino acid sequences.

  9. The role of short-term memory impairment in nonword repetition, real word repetition, and nonword decoding: A case study.

    Science.gov (United States)

    Peter, Beate

    2018-01-01

    In a companion study, adults with dyslexia and adults with a probable history of childhood apraxia of speech showed evidence of difficulty with processing sequential information during nonword repetition, multisyllabic real word repetition and nonword decoding. Results suggested that some errors arose in visual encoding during nonword reading, all levels of processing but especially short-term memory storage/retrieval during nonword repetition, and motor planning and programming during complex real word repetition. To further investigate the role of short-term memory, a participant with short-term memory impairment (MI) was recruited. MI was confirmed with poor performance during a sentence repetition and three nonword repetition tasks, all of which have a high short-term memory load, whereas typical performance was observed during tests of reading, spelling, and static verbal knowledge, all with low short-term memory loads. Experimental results show error-free performance during multisyllabic real word repetition but high counts of sequence errors, especially migrations and assimilations, during nonword repetition, supporting short-term memory as a locus of sequential processing deficit during nonword repetition. Results are also consistent with the hypothesis that during complex real word repetition, short-term memory is bypassed as the word is recognized and retrieved from long-term memory prior to producing the word.

  10. Repetitive Elements in Mycoplasma hyopneumoniae Transcriptional Regulation.

    Directory of Open Access Journals (Sweden)

    Amanda Malvessi Cattani

    Full Text Available Transcriptional regulation, a multiple-step process, is still poorly understood in the important pig pathogen Mycoplasma hyopneumoniae. Basic motifs like promoters and terminators have already been described, but no other cis-regulatory elements have been found. DNA repeat sequences have been shown to be an interesting potential source of cis-regulatory elements. In this work, a genome-wide search for tandem and palindromic repetitive elements was performed in the intergenic regions of all coding sequences from M. hyopneumoniae strain 7448. Computational analysis demonstrated the presence of 144 tandem repeats and 1,171 palindromic elements. The DNA repeat sequences were distributed within the 5' upstream regions of 86% of transcriptional units of M. hyopneumoniae strain 7448. Comparative analysis between distinct repetitive sequences found in related mycoplasma genomes demonstrated different percentages of conservation among pathogenic and nonpathogenic strains. qPCR assays revealed differential expression among genes showing variable numbers of repetitive elements. In addition, repeats found in 206 genes already described to be differentially regulated under different culture conditions of M. hyopneumoniae strain 232 showed almost 80% conservation in relation to M. hyopneumoniae strain 7448 repeats. Altogether, these findings suggest a potential regulatory role of tandem and palindromic DNA repeats in the M. hyopneumoniae transcriptional profile.

  11. Repetitive Elements in Mycoplasma hyopneumoniae Transcriptional Regulation.

    Science.gov (United States)

    Cattani, Amanda Malvessi; Siqueira, Franciele Maboni; Guedes, Rafael Lucas Muniz; Schrank, Irene Silveira

    2016-01-01

    Transcriptional regulation, a multiple-step process, is still poorly understood in the important pig pathogen Mycoplasma hyopneumoniae. Basic motifs like promoters and terminators have already been described, but no other cis-regulatory elements have been found. DNA repeat sequences have been shown to be an interesting potential source of cis-regulatory elements. In this work, a genome-wide search for tandem and palindromic repetitive elements was performed in the intergenic regions of all coding sequences from M. hyopneumoniae strain 7448. Computational analysis demonstrated the presence of 144 tandem repeats and 1,171 palindromic elements. The DNA repeat sequences were distributed within the 5' upstream regions of 86% of transcriptional units of M. hyopneumoniae strain 7448. Comparative analysis between distinct repetitive sequences found in related mycoplasma genomes demonstrated different percentages of conservation among pathogenic and nonpathogenic strains. qPCR assays revealed differential expression among genes showing variable numbers of repetitive elements. In addition, repeats found in 206 genes already described to be differentially regulated under different culture conditions of M. hyopneumoniae strain 232 showed almost 80% conservation in relation to M. hyopneumoniae strain 7448 repeats. Altogether, these findings suggest a potential regulatory role of tandem and palindromic DNA repeats in the M. hyopneumoniae transcriptional profile.

  12. If you negate, you may forget: negated repetitions impair memory compared with affirmative repetitions.

    Science.gov (United States)

    Mayo, Ruth; Schul, Yaacov; Rosenthal, Meytal

    2014-08-01

    One of the most robust laws of memory is that repeated activation improves memory. Our study shows that the nature of repetition matters. Specifically, although both negated repetition and affirmative repetition improve memory compared with no repetition, negated repetition hinders memory compared with affirmative repetition. After showing participants different entities, we asked them about features of these entities, leading to either "yes" or "no" responses. Our findings show that correctly negating an incorrect feature of an entity elicits an active forgetting effect compared with correctly affirming its true features. For example, after seeing someone drink a glass of white wine, answering "no" to "was it red wine?" may lead one to greater memory loss of the individual drinking wine at all compared with answering "yes" to "was it white wine?" We find this negation-induced forgetting effect in 4 experiments that differ in (a) the meaning given for the negation, (b) the type of stimuli (visual or verbal), and (c) the memory measure (recognition or free recall). We discuss possible underlying mechanisms and offer theoretical and applied implications of the negation-induced forgetting effect in relation to other known inhibition effects. PsycINFO Database Record (c) 2014 APA, all rights reserved.

  13. Repetitive Questioning II

    Directory of Open Access Journals (Sweden)

    R. C. Hamdy MD

    2018-02-01

    Full Text Available Repetitive questioning is a major problem for caregivers, particularly taxing if they are unable to recognize and understand the reasons why their loved one keeps asking the same question over and over again. Caregivers may be tempted to believe that the patient does not even try to remember the answer given or is just getting obnoxious. This is incorrect. Repetitive questioning is due to the underlying disease: The patient’s short term memory is impaired and he is unable to register, encode, retain and retrieve the answer. If he is concerned about a particular topic, he will keep asking the same question over and over again. To the patient each time she asks the question, it is as if she asked it for the first time. Just answering repetitive questioning by providing repeatedly the same answer is not sufficient. Caregivers should try to identify the underlying cause for this repetitive questioning. In an earlier case study, the patient was concerned about her and her family’s safety and kept asking whether the doors are locked. In this present case study, the patient does not know how to handle the awkward situation he finds himself in. He just does not know what to do. He is not able to adjust to the new unexpected situation. So he repeatedly wants to reassure himself that he is not intruding by asking the same question over and over again. We discuss how the patient’s son-in-law could have avoided this situation and averted the catastrophic ending.

  14. Epithelial topography for repetitive tooth formation

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    Marcia Gaete

    2015-12-01

    Full Text Available During the formation of repetitive ectodermally derived organs such as mammary glands, lateral line and teeth, the tissue primordium iteratively initiates new structures. In the case of successional molar development, new teeth appear sequentially in the posterior region of the jaw from Sox2+ cells in association with the posterior aspect of a pre-existing tooth. The sequence of molar development is well known, however, the epithelial topography involved in the formation of a new tooth is unclear. Here, we have examined the morphology of the molar dental epithelium and its development at different stages in the mouse in vivo and in molar explants. Using regional lineage tracing we show that within the posterior tail of the first molar the primordium for the second and third molar are organized in a row, with the tail remaining in connection with the surface, where a furrow is observed. The morphology and Sox2 expression of the tail retains characteristics reminiscent of the earlier stages of tooth development, such that position along the A-P axes of the tail correlates with different temporal stages. Sox9, a stem/progenitor cell marker in other organs, is expressed mainly in the suprabasal epithelium complementary with Sox2 expression. This Sox2 and Sox9 expressing molar tail contains actively proliferating cells with mitosis following an apico-basal direction. Snail2, a transcription factor implicated in cell migration, is expressed at high levels in the tip of the molar tail while E-cadherin and laminin are decreased. In conclusion, our studies propose a model in which the epithelium of the molar tail can grow by posterior movement of epithelial cells followed by infolding and stratification involving a population of Sox2+/Sox9+ cells.

  15. Substrate sequence selectivity of APOBEC3A implicates intra-DNA interactions.

    Science.gov (United States)

    Silvas, Tania V; Hou, Shurong; Myint, Wazo; Nalivaika, Ellen; Somasundaran, Mohan; Kelch, Brian A; Matsuo, Hiroshi; Kurt Yilmaz, Nese; Schiffer, Celia A

    2018-05-14

    The APOBEC3 (A3) family of human cytidine deaminases is renowned for providing a first line of defense against many exogenous and endogenous retroviruses. However, the ability of these proteins to deaminate deoxycytidines in ssDNA makes A3s a double-edged sword. When overexpressed, A3s can mutate endogenous genomic DNA resulting in a variety of cancers. Although the sequence context for mutating DNA varies among A3s, the mechanism for substrate sequence specificity is not well understood. To characterize substrate specificity of A3A, a systematic approach was used to quantify the affinity for substrate as a function of sequence context, length, secondary structure, and solution pH. We identified the A3A ssDNA binding motif as (T/C)TC(A/G), which correlated with enzymatic activity. We also validated that A3A binds RNA in a sequence specific manner. A3A bound tighter to substrate binding motif within a hairpin loop compared to linear oligonucleotide, suggesting A3A affinity is modulated by substrate structure. Based on these findings and previously published A3A-ssDNA co-crystal structures, we propose a new model with intra-DNA interactions for the molecular mechanism underlying A3A sequence preference. Overall, the sequence and structural preferences identified for A3A leads to a new paradigm for identifying A3A's involvement in mutation of endogenous or exogenous DNA.

  16. Repetition or Reconfiguration

    DEFF Research Database (Denmark)

    Andersen, Kristina Vaarst

    , the cognitive quality of knowledge held by individual professionals is the key microfoundation for project level performance. This paper empirically tests effects of project participants with and without knowledge diversity for project level performance for projects aiming for varying degrees of repetition...... and reconfiguration. The results indicate that project performance benefits form contributions from individuals holding diverse knowledge only when projects aim for high differentiation levels. This positive association is not just moderated, it may even be reversed in the case of professionals participating in low...

  17. MIMICRY, DIFFERENCE AND REPETITION

    Directory of Open Access Journals (Sweden)

    Marcelo Mendes de Souza

    2008-07-01

    Full Text Available This article addresses Homi K. Bhabha’s concept of mimicry in a broader context, other than that of cultural studies and post-colonial studies, bringing together other concepts, such as that of Gilles Deleuze in Difference and repetition, among other texts, and other names, such as Silviano Santiago, Jorge Luís Borges, Franz Kafka and Giorgio Agamben. As a partial conclusion, the article intends to oppose Bhabha’s freudian-marxist view to Five propositions on Psychoanalysis (1973, Gilles Deleuze’s text about Psychoanalysis published right after his book The Anti-Oedipus.

  18. Transcription of repetitive DNA in Neurospora crassa

    Energy Technology Data Exchange (ETDEWEB)

    Dutta, S K; Chaudhuri, R K

    1975-01-01

    Repeated DNA sequences of Neurospora crassa were isolated and characterized. Approximately 10 to 12 percent of N. crassa DNA sequence were repeated, of which 7.3 percent were found to be transcribed in mid-log phase of mycelial growth as measured by DNA:RNA hybridization. It is suggested that part of repetitive DNA transcripts in N. crassa were mitochondrial and part were nuclear DNA. Most of the nuclear repeated DNAs, however, code for rRNA and tRNA in N. crassa. (auth)

  19. Serine protease isoforms in Gloydius intermedius venom: Full sequences, molecular phylogeny and evolutionary implications.

    Science.gov (United States)

    Yang, Zhang-Min; Yu, Hui; Liu, Zhen-Zhen; Pei, Jian-Zhu; Yang, Yu-E; Yan, Su-Xian; Zhang, Cui; Zhao, Wen-Long; Wang, Zhe-Zhi; Wang, Ying-Ming; Tsai, Inn-Ho

    2017-07-05

    Nine distinct venom serine proteases (vSPs) of Gloydius intermedius were studied by transcriptomic, sub-proteomic and phylogenetic analyses. Their complete amino acid sequences were deduced after Expression Sequence Tag (EST) analyses followed by cDNA cloning and sequencing. These vSPs appear to be paralogs and contain the catalytic triads and 1-4 potential N-glycosylation sites. Their relative expression levels evaluated by qPCR were grossly consistent with their EST hit-numbers. The major vSPs were purified by HPLC and their N-terminal sequences matched well to the deduced sequences, while fragments of the minor vSPs were detected by LC-MS/MS identification. Specific amidolytic activities of the fractions from HPLC and anion exchange separation were assayed using four chromogenic substrates, respectively. Molecular phylogenetic tree based on the sequences of these vSPs and their orthologs revealed six major clusters, one of them covered four lineages of plasminogen activator like vSPs. N-glycosylation patterns and variations for the vSPs are discussed. The high sequence similarities between G. intermedius vSPs and their respective orthologs from American pitvipers suggest that most of the isoforms evolved before Asian pitvipers migrated to the New World. Our results also indicate that the neurotoxic venoms contain more kallikrein-like vSPs and hypotensive components than the hemorrhagic venoms. Full sequences and expression levels of nine paralogous serine proteases (designated as GiSPs) of Gloydius intermedius venom have been studied. A kallikrein-like enzyme is most abundant and four isoforms homologous to venom plasminogen-activators are also expressed in this venom. Taken together, the present and previous data demonstrate that the neurotoxic G. intermedius venoms contain more hypotensive vSPs relative to other hemorrhagic pitviper venoms and the pitviper vSPs are highly versatile and diverse. Their structure-function relationships remain to be explored and

  20. Detailed observations of California foreshock sequences: Implications for the earthquake initiation process

    Science.gov (United States)

    Dodge, D.A.; Beroza, G.C.; Ellsworth, W.L.

    1996-01-01

    We find that foreshocks provide clear evidence for an extended nucleation process before some earthquakes. In this study, we examine in detail the evolution of six California foreshock sequences, the 1986 Mount Lewis (ML, = 5.5), the 1986 Chalfant (ML = 6.4), the. 1986 Stone Canyon (ML = 4.7), the 1990 Upland (ML = 5.2), the 1992 Joshua Tree (MW= 6.1), and the 1992 Landers (MW = 7.3) sequence. Typically, uncertainties in hypocentral parameters are too large to establish the geometry of foreshock sequences and hence to understand their evolution. However, the similarity of location and focal mechanisms for the events in these sequences leads to similar foreshock waveforms that we cross correlate to obtain extremely accurate relative locations. We use these results to identify small-scale fault zone structures that could influence nucleation and to determine the stress evolution leading up to the mainshock. In general, these foreshock sequences are not compatible with a cascading failure nucleation model in which the foreshocks all occur on a single fault plane and trigger the mainshock by static stress transfer. Instead, the foreshocks seem to concentrate near structural discontinuities in the fault and may themselves be a product of an aseismic nucleation process. Fault zone heterogeneity may also be important in controlling the number of foreshocks, i.e., the stronger the heterogeneity, the greater the number of foreshocks. The size of the nucleation region, as measured by the extent of the foreshock sequence, appears to scale with mainshock moment in the same manner as determined independently by measurements of the seismic nucleation phase. We also find evidence for slip localization as predicted by some models of earthquake nucleation. Copyright 1996 by the American Geophysical Union.

  1. The First Complete Mitochondrial Genome Sequences for Stomatopod Crustaceans: Implications for Phylogeny

    Energy Technology Data Exchange (ETDEWEB)

    Swinstrom, Kirsten; Caldwell, Roy; Fourcade, H. Matthew; Boore, Jeffrey L.

    2005-09-07

    We report the first complete mitochondrial genome sequences of stomatopods and compare their features to each other and to those of other crustaceans. Phylogenetic analyses of the concatenated mitochondrial protein-coding sequences were used to explore relationships within the Stomatopoda, within the malacostracan crustaceans, and among crustaceans and insects. Although these analyses support the monophyly of both Malacostraca and, within it, Stomatopoda, it also confirms the view of a paraphyletic Crustacea, with Malacostraca being more closely related to insects than to the branchiopod crustaceans.

  2. Complete plastid genome sequence of Daucus carota: implications for biotechnology and phylogeny of angiosperms.

    Science.gov (United States)

    Ruhlman, Tracey; Lee, Seung-Bum; Jansen, Robert K; Hostetler, Jessica B; Tallon, Luke J; Town, Christopher D; Daniell, Henry

    2006-08-31

    Carrot (Daucus carota) is a major food crop in the US and worldwide. Its capacity for storage and its lifecycle as a biennial make it an attractive species for the introduction of foreign genes, especially for oral delivery of vaccines and other therapeutic proteins. Until recently efforts to express recombinant proteins in carrot have had limited success in terms of protein accumulation in the edible tap roots. Plastid genetic engineering offers the potential to overcome this limitation, as demonstrated by the accumulation of BADH in chromoplasts of carrot taproots to confer exceedingly high levels of salt resistance. The complete plastid genome of carrot provides essential information required for genetic engineering. Additionally, the sequence data add to the rapidly growing database of plastid genomes for assessing phylogenetic relationships among angiosperms. The complete carrot plastid genome is 155,911 bp in length, with 115 unique genes and 21 duplicated genes within the IR. There are four ribosomal RNAs, 30 distinct tRNA genes and 18 intron-containing genes. Repeat analysis reveals 12 direct and 2 inverted repeats > or = 30 bp with a sequence identity > or = 90%. Phylogenetic analysis of nucleotide sequences for 61 protein-coding genes using both maximum parsimony (MP) and maximum likelihood (ML) were performed for 29 angiosperms. Phylogenies from both methods provide strong support for the monophyly of several major angiosperm clades, including monocots, eudicots, rosids, asterids, eurosids II, euasterids I, and euasterids II. The carrot plastid genome contains a number of dispersed direct and inverted repeats scattered throughout coding and non-coding regions. This is the first sequenced plastid genome of the family Apiaceae and only the second published genome sequence of the species-rich euasterid II clade. Both MP and ML trees provide very strong support (100% bootstrap) for the sister relationship of Daucus with Panax in the euasterid II clade. These

  3. Complete plastid genome sequence of Daucus carota: Implications for biotechnology and phylogeny of angiosperms

    Directory of Open Access Journals (Sweden)

    Ruhlman Tracey

    2006-08-01

    Full Text Available Abstract Background Carrot (Daucus carota is a major food crop in the US and worldwide. Its capacity for storage and its lifecycle as a biennial make it an attractive species for the introduction of foreign genes, especially for oral delivery of vaccines and other therapeutic proteins. Until recently efforts to express recombinant proteins in carrot have had limited success in terms of protein accumulation in the edible tap roots. Plastid genetic engineering offers the potential to overcome this limitation, as demonstrated by the accumulation of BADH in chromoplasts of carrot taproots to confer exceedingly high levels of salt resistance. The complete plastid genome of carrot provides essential information required for genetic engineering. Additionally, the sequence data add to the rapidly growing database of plastid genomes for assessing phylogenetic relationships among angiosperms. Results The complete carrot plastid genome is 155,911 bp in length, with 115 unique genes and 21 duplicated genes within the IR. There are four ribosomal RNAs, 30 distinct tRNA genes and 18 intron-containing genes. Repeat analysis reveals 12 direct and 2 inverted repeats ≥ 30 bp with a sequence identity ≥ 90%. Phylogenetic analysis of nucleotide sequences for 61 protein-coding genes using both maximum parsimony (MP and maximum likelihood (ML were performed for 29 angiosperms. Phylogenies from both methods provide strong support for the monophyly of several major angiosperm clades, including monocots, eudicots, rosids, asterids, eurosids II, euasterids I, and euasterids II. Conclusion The carrot plastid genome contains a number of dispersed direct and inverted repeats scattered throughout coding and non-coding regions. This is the first sequenced plastid genome of the family Apiaceae and only the second published genome sequence of the species-rich euasterid II clade. Both MP and ML trees provide very strong support (100% bootstrap for the sister relationship of

  4. Modeling repetitive motions using structured light.

    Science.gov (United States)

    Xu, Yi; Aliaga, Daniel G

    2010-01-01

    Obtaining models of dynamic 3D objects is an important part of content generation for computer graphics. Numerous methods have been extended from static scenarios to model dynamic scenes. If the states or poses of the dynamic object repeat often during a sequence (but not necessarily periodically), we call such a repetitive motion. There are many objects, such as toys, machines, and humans, undergoing repetitive motions. Our key observation is that when a motion-state repeats, we can sample the scene under the same motion state again but using a different set of parameters; thus, providing more information of each motion state. This enables robustly acquiring dense 3D information difficult for objects with repetitive motions using only simple hardware. After the motion sequence, we group temporally disjoint observations of the same motion state together and produce a smooth space-time reconstruction of the scene. Effectively, the dynamic scene modeling problem is converted to a series of static scene reconstructions, which are easier to tackle. The varying sampling parameters can be, for example, structured-light patterns, illumination directions, and viewpoints resulting in different modeling techniques. Based on this observation, we present an image-based motion-state framework and demonstrate our paradigm using either a synchronized or an unsynchronized structured-light acquisition method.

  5. Spared behavioral repetition effects in Alzheimer's disease linked to an altered neural mechanism at posterior cortex.

    Science.gov (United States)

    Broster, Lucas S; Li, Juan; Wagner, Benjamin; Smith, Charles D; Jicha, Gregory A; Schmitt, Frederick A; Munro, Nancy; Haney, Ryan H; Jiang, Yang

    2018-02-20

    Individuals with dementia of the Alzheimer type (AD) classically show disproportionate impairment in measures of working memory, but repetition learning effects are relatively preserved. As AD affects brain regions implicated in both working memory and repetition effects, the neural basis of this discrepancy is poorly understood. We hypothesized that the posterior repetition effect could account for this discrepancy due to the milder effects of AD at visual cortex. Participants with early AD, amnestic mild cognitive impairment (MCI), and healthy controls performed a working memory task with superimposed repetition effects while electroencephalography was collected to identify possible neural mechanisms of preserved repetition effects. Participants with AD showed preserved behavioral repetition effects and a change in the posterior repetition effect. Visual cortex may play a role in maintained repetition effects in persons with early AD.

  6. Depositional sequence stratigraphy and architecture of the cretaceous ferron sandstone: Implications for coal and coalbed methane resources - A field excursion

    Science.gov (United States)

    Garrison, J.R.; Van Den, Bergh; Barker, C.E.; Tabet, D.E.

    1997-01-01

    This Field Excursion will visit outcrops of the fluvial-deltaic Upper Cretaceous (Turonian) Ferron Sandstone Member of the Mancos Shale, known as the Last Chance delta or Upper Ferron Sandstone. This field guide and the field stops will outline the architecture and depositional sequence stratigraphy of the Upper Ferron Sandstone clastic wedge and explore the stratigraphic positions and compositions of major coal zones. The implications of the architecture and stratigraphy of the Ferron fluvial-deltaic complex for coal and coalbed methane resources will be discussed. Early works suggested that the southwesterly derived deltaic deposits of the the upper Ferron Sandstone clastic wedge were a Type-2 third-order depositional sequence, informally called the Ferron Sequence. These works suggested that the Ferron Sequence is separated by a type-2 sequence boundary from the underlying 3rd-order Hyatti Sequence, which has its sediment source from the northwest. Within the 3rd-order depositional sequence, the deltaic events of the Ferron clastic wedge, recognized as parasequence sets, appear to be stacked into progradational, aggradational, and retrogradational patterns reflecting a generally decreasing sediment supply during an overall slow sea-level rise. The architecture of both near-marine facies and non-marine fluvial facies exhibit well defined trends in response to this decrease in available sediment. Recent studies have concluded that, unless coincident with a depositional sequence boundary, regionally extensive coal zones occur at the tops of the parasequence sets within the Ferron clastic wedge. These coal zones consist of coal seams and their laterally equivalent fissile carbonaceous shales, mudstones, and siltstones, paleosols, and flood plain mudstones. Although the compositions of coal zones vary along depositional dip, the presence of these laterally extensive stratigraphic horizons, above parasequence sets, provides a means of correlating and defining the tops

  7. Population genetic implications from sequence variation in four Y chromosome genes.

    Science.gov (United States)

    Shen, P; Wang, F; Underhill, P A; Franco, C; Yang, W H; Roxas, A; Sung, R; Lin, A A; Hyman, R W; Vollrath, D; Davis, R W; Cavalli-Sforza, L L; Oefner, P J

    2000-06-20

    Some insight into human evolution has been gained from the sequencing of four Y chromosome genes. Primary genomic sequencing determined gene SMCY to be composed of 27 exons that comprise 4,620 bp of coding sequence. The unfinished sequencing of the 5' portion of gene UTY1 was completed by primer walking, and a total of 20 exons were found. By using denaturing HPLC, these two genes, as well as DBY and DFFRY, were screened for polymorphic sites in 53-72 representatives of the five continents. A total of 98 variants were found, yielding nucleotide diversity estimates of 2.45 x 10(-5), 5. 07 x 10(-5), and 8.54 x 10(-5) for the coding regions of SMCY, DFFRY, and UTY1, respectively, with no variant having been observed in DBY. In agreement with most autosomal genes, diversity estimates for the noncoding regions were about 2- to 3-fold higher and ranged from 9. 16 x 10(-5) to 14.2 x 10(-5) for the four genes. Analysis of the frequencies of derived alleles for all four genes showed that they more closely fit the expectation of a Luria-Delbrück distribution than a distribution expected under a constant population size model, providing evidence for exponential population growth. Pairwise nucleotide mismatch distributions date the occurrence of population expansion to approximately 28,000 years ago. This estimate is in accord with the spread of Aurignacian technology and the disappearance of the Neanderthals.

  8. Complete Plastid Genome Sequencing of Four Tilia Species (Malvaceae: A Comparative Analysis and Phylogenetic Implications.

    Directory of Open Access Journals (Sweden)

    Jie Cai

    Full Text Available Tilia is an ecologically and economically important genus in the family Malvaceae. However, there is no complete plastid genome of Tilia sequenced to date, and the taxonomy of Tilia is difficult owing to frequent hybridization and polyploidization. A well-supported interspecific relationships of this genus is not available due to limited informative sites from the commonly used molecular markers. We report here the complete plastid genome sequences of four Tilia species determined by the Illumina technology. The Tilia plastid genome is 162,653 bp to 162,796 bp in length, encoding 113 unique genes and a total number of 130 genes. The gene order and organization of the Tilia plastid genome exhibits the general structure of angiosperms and is very similar to other published plastid genomes of Malvaceae. As other long-lived tree genera, the sequence divergence among the four Tilia plastid genomes is very low. And we analyzed the nucleotide substitution patterns and the evolution of insertions and deletions in the Tilia plastid genomes. Finally, we build a phylogeny of the four sampled Tilia species with high supports using plastid phylogenomics, suggesting that it is an efficient way to resolve the phylogenetic relationships of this genus.

  9. Whole Exome Sequencing in Females with Autism Implicates Novel and Candidate Genes

    Directory of Open Access Journals (Sweden)

    Merlin G. Butler

    2015-01-01

    Full Text Available Classical autism or autistic disorder belongs to a group of genetically heterogeneous conditions known as Autism Spectrum Disorders (ASD. Heritability is estimated as high as 90% for ASD with a recently reported compilation of 629 clinically relevant candidate and known genes. We chose to undertake a descriptive next generation whole exome sequencing case study of 30 well-characterized Caucasian females with autism (average age, 7.7 ± 2.6 years; age range, 5 to 16 years from multiplex families. Genomic DNA was used for whole exome sequencing via paired-end next generation sequencing approach and X chromosome inactivation status. The list of putative disease causing genes was developed from primary selection criteria using machine learning-derived classification score and other predictive parameters (GERP2, PolyPhen2, and SIFT. We narrowed the variant list to 10 to 20 genes and screened for biological significance including neural development, function and known neurological disorders. Seventy-eight genes identified met selection criteria ranging from 1 to 9 filtered variants per female. Five females presented with functional variants of X-linked genes (IL1RAPL1, PIR, GABRQ, GPRASP2, SYTL4 with cadherin, protocadherin and ankyrin repeat gene families most commonly altered (e.g., CDH6, FAT2, PCDH8, CTNNA3, ANKRD11. Other genes related to neurogenesis and neuronal migration (e.g., SEMA3F, MIDN, were also identified.

  10. Complete sequencing of five araliaceae chloroplast genomes and the phylogenetic implications.

    Directory of Open Access Journals (Sweden)

    Rong Li

    Full Text Available BACKGROUND: The ginseng family (Araliaceae includes a number of economically important plant species. Previously phylogenetic studies circumscribed three major clades within the core ginseng plant family, yet the internal relationships of each major group have been poorly resolved perhaps due to rapid radiation of these lineages. Recent studies have shown that phyogenomics based on chloroplast genomes provides a viable way to resolve complex relationships. METHODOLOGY/PRINCIPAL FINDINGS: We report the complete nucleotide sequences of five Araliaceae chloroplast genomes using next-generation sequencing technology. The five chloroplast genomes are 156,333-156,459 bp in length including a pair of inverted repeats (25,551-26,108 bp separated by the large single-copy (86,028-86,566 bp and small single-copy (18,021-19,117 bp regions. Each chloroplast genome contains the same 114 unique genes consisting of 30 transfer RNA genes, four ribosomal RNA genes, and 80 protein coding genes. Gene size, content, and order, AT content, and IR/SC boundary structure are similar among all Araliaceae chloroplast genomes. A total of 140 repeats were identified in the five chloroplast genomes with palindromic repeat as the most common type. Phylogenomic analyses using parsimony, likelihood, and Bayesian inference based on the complete chloroplast genomes strongly supported the monophyly of the Asian Palmate group and the Aralia-Panax group. Furthermore, the relationships among the sampled taxa within the Asian Palmate group were well resolved. Twenty-six DNA markers with the percentage of variable sites higher than 5% were identified, which may be useful for phylogenetic studies of Araliaceae. CONCLUSION: The chloroplast genomes of Araliaceae are highly conserved in all aspects of genome features. The large-scale phylogenomic data based on the complete chloroplast DNA sequences is shown to be effective for the phylogenetic reconstruction of Araliaceae.

  11. Structural and sequence analysis of imelysin-like proteins implicated in bacterial iron uptake.

    Directory of Open Access Journals (Sweden)

    Qingping Xu

    Full Text Available Imelysin-like proteins define a superfamily of bacterial proteins that are likely involved in iron uptake. Members of this superfamily were previously thought to be peptidases and were included in the MEROPS family M75. We determined the first crystal structures of two remotely related, imelysin-like proteins. The Psychrobacter arcticus structure was determined at 2.15 Å resolution and contains the canonical imelysin fold, while higher resolution structures from the gut bacteria Bacteroides ovatus, in two crystal forms (at 1.25 Å and 1.44 Å resolution, have a circularly permuted topology. Both structures are highly similar to each other despite low sequence similarity and circular permutation. The all-helical structure can be divided into two similar four-helix bundle domains. The overall structure and the GxHxxE motif region differ from known HxxE metallopeptidases, suggesting that imelysin-like proteins are not peptidases. A putative functional site is located at the domain interface. We have now organized the known homologous proteins into a superfamily, which can be separated into four families. These families share a similar functional site, but each has family-specific structural and sequence features. These results indicate that imelysin-like proteins have evolved from a common ancestor, and likely have a conserved function.

  12. Sedimentary petrography of the Early Proterozoic Pretoria Group, Transvaal Sequence, South Africa: implications for tectonic setting

    Science.gov (United States)

    Schreiber, U. M.; Eriksson, P. G.; van der Neut, M.; Snyman, C. P.

    1992-11-01

    Sandstone petrography, geochemistry and petrotectonic assemblages of the predominantly clastic sedimentary rocks of the Early Proterozoic Pretoria Group, Transvaal Sequence, point to relatively stable cratonic conditions at the beginning of sedimentation, interrupted by minor rifting events. Basement uplift and a second period of rifting occurred towards the end of Pretoria Group deposition, which was followed by the intrusion of mafic sill swarms and the emplacement of the Bushveld Complex in the Kaapvaal Craton at about 2050 Ma, the latter indicating increased extensional tectonism, and incipient continental rifting. An overall intracratonic lacustrine tectonic setting for the Pretoria Group is supported by periods of subaerial volcanic activity and palaeosol formation, rapid sedimentary facies changes, significant arkosic sandstones, the presence of non-glacial varves and a highly variable mudrock geochemistry.

  13. Ligation bias in illumina next-generation DNA libraries: implications for sequencing ancient genomes.

    Directory of Open Access Journals (Sweden)

    Andaine Seguin-Orlando

    Full Text Available Ancient DNA extracts consist of a mixture of endogenous molecules and contaminant DNA templates, often originating from environmental microbes. These two populations of templates exhibit different chemical characteristics, with the former showing depurination and cytosine deamination by-products, resulting from post-mortem DNA damage. Such chemical modifications can interfere with the molecular tools used for building second-generation DNA libraries, and limit our ability to fully characterize the true complexity of ancient DNA extracts. In this study, we first use fresh DNA extracts to demonstrate that library preparation based on adapter ligation at AT-overhangs are biased against DNA templates starting with thymine residues, contrarily to blunt-end adapter ligation. We observe the same bias on fresh DNA extracts sheared on Bioruptor, Covaris and nebulizers. This contradicts previous reports suggesting that this bias could originate from the methods used for shearing DNA. This also suggests that AT-overhang adapter ligation efficiency is affected in a sequence-dependent manner and results in an uneven representation of different genomic contexts. We then show how this bias could affect the base composition of ancient DNA libraries prepared following AT-overhang ligation, mainly by limiting the ability to ligate DNA templates starting with thymines and therefore deaminated cytosines. This results in particular nucleotide misincorporation damage patterns, deviating from the signature generally expected for authenticating ancient sequence data. Consequently, we show that models adequate for estimating post-mortem DNA damage levels must be robust to the molecular tools used for building ancient DNA libraries.

  14. Joint linkage and association analysis with exome sequence data implicates SLC25A40 in hypertriglyceridemia.

    Science.gov (United States)

    Rosenthal, Elisabeth A; Ranchalis, Jane; Crosslin, David R; Burt, Amber; Brunzell, John D; Motulsky, Arno G; Nickerson, Deborah A; Wijsman, Ellen M; Jarvik, Gail P

    2013-12-05

    Hypertriglyceridemia (HTG) is a heritable risk factor for cardiovascular disease. Investigating the genetics of HTG may identify new drug targets. There are ~35 known single-nucleotide variants (SNVs) that explain only ~10% of variation in triglyceride (TG) level. Because of the genetic heterogeneity of HTG, a family study design is optimal for identification of rare genetic variants with large effect size because the same mutation can be observed in many relatives and cosegregation with TG can be tested. We considered HTG in a five-generation family of European American descent (n = 121), ascertained for familial combined hyperlipidemia. By using Bayesian Markov chain Monte Carlo joint oligogenic linkage and association analysis, we detected linkage to chromosomes 7 and 17. Whole-exome sequence data revealed shared, highly conserved, private missense SNVs in both SLC25A40 on chr7 and PLD2 on chr17. Jointly, these SNVs explained 49% of the genetic variance in TG; however, only the SLC25A40 SNV was significantly associated with TG (p = 0.0001). This SNV, c.374A>G, causes a highly disruptive p.Tyr125Cys substitution just outside the second helical transmembrane region of the SLC25A40 inner mitochondrial membrane transport protein. Whole-gene testing in subjects from the Exome Sequencing Project confirmed the association between TG and SLC25A40 rare, highly conserved, coding variants (p = 0.03). These results suggest a previously undescribed pathway for HTG and illustrate the power of large pedigrees in the search for rare, causal variants. Copyright © 2013 The American Society of Human Genetics. Published by Elsevier Inc. All rights reserved.

  15. Exome sequence analysis and follow up genotyping implicates rare ULK1 variants to be involved in susceptibility to schizophrenia

    Science.gov (United States)

    Al Eissa, Mariam M.; Fiorentino, Alessia; Sharp, Sally I.; O'Brien, Niamh L.; Wolfe, Kate; Giaroli, Giovanni; Curtis, David; Bass, Nicholas J.

    2017-01-01

    Summary Schizophrenia (SCZ) is a severe, highly heritable psychiatric disorder. Elucidation of the genetic architecture of the disorder will facilitate greater understanding of the altered underlying neurobiological mechanisms. The aim of this study was to identify likely aetiological variants in subjects affected with SCZ. Exome sequence data from a SCZ cas–control sample from Sweden was analysed for likely aetiological variants using a weighted burden test. Suggestive evidence implicated the UNC‐51‐like kinase (ULK1) gene, and it was observed that four rare variants that were more common in the Swedish SCZ cases were also more common in UK10K SCZ cases, as compared to obesity cases. These three missense variants and one intronic variant were genotyped in the University College London cohort of 1304 SCZ cases and 1348 ethnically matched controls. All four variants were more common in the SCZ cases than controls and combining them produced a result significant at P = 0.02. The results presented here demonstrate the importance of following up exome sequencing studies using additional datasets. The roles of ULK1 in autophagy and mTOR signalling strengthen the case that these pathways may be important in the pathophysiology of SCZ. The findings reported here await independent replication. PMID:29148569

  16. Intrastrain heterogeneity of the mgpB gene in Mycoplasma genitalium is extensive in vitro and in vivo and suggests that variation is generated via recombination with repetitive chromosomal sequences.

    Science.gov (United States)

    Iverson-Cabral, Stefanie L; Astete, Sabina G; Cohen, Craig R; Rocha, Eduardo P C; Totten, Patricia A

    2006-07-01

    Mycoplasma genitalium is associated with reproductive tract disease in women and may persist in the lower genital tract for months, potentially increasing the risk of upper tract infection and transmission to uninfected partners. Despite its exceptionally small genome (580 kb), approximately 4% is composed of repeated elements known as MgPar sequences (MgPa repeats) based on their homology to the mgpB gene that encodes the immunodominant MgPa adhesin protein. The presence of these MgPar sequences, as well as mgpB variability between M. genitalium strains, suggests that mgpB and MgPar sequences recombine to produce variant MgPa proteins. To examine the extent and generation of diversity within single strains of the organism, we examined mgpB variation within M. genitalium strain G-37 and observed sequence heterogeneity that could be explained by recombination between the mgpB expression site and putative donor MgPar sequences. Similarly, we analyzed mgpB sequences from cervical specimens from a persistently infected woman (21 months) and identified 17 different mgpB variants within a single infecting M. genitalium strain, confirming that mgpB heterogeneity occurs over the course of a natural infection. These observations support the hypothesis that recombination occurs between the mgpB gene and MgPar sequences and that the resulting antigenically distinct MgPa variants may contribute to immune evasion and persistence of infection.

  17. Evaluation of the cranial base in amnion rupture sequence involving the anterior neural tube: implications regarding recurrence risk.

    Science.gov (United States)

    Jones, Kenneth Lyons; Robinson, Luther K; Benirschke, Kurt

    2006-09-01

    Amniotic bands can cause disruption of the cranial end of the developing fetus, leading in some cases to a neural tube closure defect. Although recurrence for unaffected parents of an affected child with a defect in which the neural tube closed normally but was subsequently disrupted by amniotic bands is negligible; for a primary defect in closure of the neural tube to which amnion has subsequently adhered, recurrence risk is 1.7%. In that primary defects of neural tube closure are characterized by typical abnormalities of the base of the skull, evaluation of the cranial base in such fetuses provides an approach for making a distinction between these 2 mechanisms. This distinction has implications regarding recurrence risk. The skull base of 2 fetuses with amnion rupture sequence involving the cranial end of the neural tube were compared to that of 1 fetus with anencephaly as well as that of a structurally normal fetus. The skulls were cleaned, fixed in 10% formalin, recleaned, and then exposed to 10% KOH solution. After washing and recleaning, the skulls were exposed to hydrogen peroxide for bleaching and photography. Despite involvement of the anterior neural tube in both fetuses with amnion rupture sequence, in Case 3 the cranial base was normal while in Case 4 the cranial base was similar to that seen in anencephaly. This technique provides a method for determining the developmental pathogenesis of anterior neural tube defects in cases of amnion rupture sequence. As such, it provides information that can be used to counsel parents of affected children with respect to recurrence risk.

  18. Crystallization sequence of the Upper Border Series of the Skaergaard Intrusion: Revised subdivision and implications for Chamber-Scale Magma Homogeneity

    DEFF Research Database (Denmark)

    Salmonsen, Lars Peter; Tegner, Christian

    2013-01-01

    from the roof of the magma chamber, differs from that in the Layered Series formed at the floor. The proposed deviation would require chemical stratification of the magma, and a reexamination of the crystallization sequence therefore has important implications for understanding the dynamics...... of the crystallization sequences and the anorthite contents of plagioclase cores in the three series imply that the Skaergaard magma chamber solidified by in situ crystallization along the floor, walls and roof from one, largely homogenous, convecting magma body....

  19. Estimating Rheological Parameters of Anhydrite from Folded Evaporite sequences: Implications for Internal Dynamics of Salt Structure

    Science.gov (United States)

    Adamuszek, Marta; Dabrowski, Marcin; Schmalholz, Stefan M.; Urai, Janos L.; Raith, Alexander

    2015-04-01

    Salt structures have been identified as a potential target for hydrocarbon, CO2, or radioactive waste storage. The most suitable locations for magazines are considered in the thick and relatively homogeneous rock salt layers. However, salt structures often consist of the evaporite sequence including rock salt intercalated with other rock types e.g.: anhydrite, gypsum, potassium and magnesium salt, calcite, dolomite, or shale. The presence of such heterogeneities causes a serious disturbance in the structure management. Detailed analysis of the internal architecture and internal dynamics of the salt structure are crucial for evaluating them as suitable repositories and also their long-term stability. The goal of this study is to analyse the influence of the presence of anhydrite layers on the internal dynamics of salt structures. Anhydrite is a common rock in evaporite sequences. Its physical and mechanical properties strongly differ from the properties of rock salt. The density of anhydrite is much higher than the density of salt, thus anhydrite is likely to sink in salt causing the disturbance of the surrounding structures. This suggestion was the starting point to the discussion about the long-term stability of the magazines in salt structures [1]. However, the other important parameter that has to be taken into account is the viscosity of anhydrite. The high viscosity ratio between salt and anhydrite can restrain the layer from sinking. The rheological behaviour of anhydrite has been studied in laboratory experiments [2], but the results only provide information about the short-term behaviour. The long-term behaviour can be best predicted using indirect methods e.g. based on the analysis of natural structures that developed over geological time scale. One of the most promising are fold structures, the shape of which is very sensitive to the rheological parameters of the deforming materials. Folds can develop in mechanically stratified materials during layer

  20. Assessing the geographic origin of the invasive grey squirrel using DNA sequencing: Implications for management strategies

    Directory of Open Access Journals (Sweden)

    Claire D. Stevenson-Holt

    2015-01-01

    Full Text Available The invasive grey squirrel Sciurus carolinensis has become a major pest species causing negative effects to forestry and biodiversity. This study aims to assess the origin of grey squirrel within Cumbria using phylogeographic analysis to aid in management and control. The work reported analysed mitochondrial DNA sequences in the D-Loop gene of 73 grey squirrel individuals from multiple locations in the UK. The results indicate that individuals in north Cumbria are derived from individuals from Scotland and North East England. Other individuals in north Cumbria share a unique haplotype with south Cumbria and Lancashire suggesting a southerly origin and movement around or over the Cumbrian Mountain range which is thought of as a barrier to movements. The assessment of invasive species geographical origin and the identification of potential wildlife transit corridors through natural barriers are becoming more important as species shift range in response to environmental and ecological changes. With the grey squirrel population expansion also occurring in Italy, the European red squirrel may become threatened across its entire range. It is crucial to understand the population origins of the invasive grey squirrel and landscape usage to successfully manage the incursion routes and control the population.

  1. THE QUADRUPLE PRE-MAIN-SEQUENCE SYSTEM LkCa 3: IMPLICATIONS FOR STELLAR EVOLUTION MODELS

    International Nuclear Information System (INIS)

    Torres, Guillermo; Latham, David W.; Ruíz-Rodríguez, Dary; Prato, L.; Wasserman, Lawrence H.; Badenas, Mariona; Schaefer, G. H.; Mathieu, Robert D.

    2013-01-01

    We report the discovery that the pre-main-sequence (PMS) object LkCa 3 in the Taurus-Auriga star-forming region is a hierarchical quadruple system of M stars. It was previously known to be a close (∼0.''5) visual pair, with one component being a moderately eccentric 12.94 day single-lined spectroscopic binary. A re-analysis of archival optical spectra complemented by new near-infrared (NIR) spectroscopy shows both visual components to be double lined; the second one has a period of 4.06 days and a circular orbit. In addition to the orbital elements, we determine optical and NIR flux ratios, effective temperatures, and projected rotational velocities for all four stars. Using existing photometric monitoring observations of the system that had previously revealed the rotational period of the primary in the longer-period binary, we also detect the rotational signal of the primary in the 4.06 day binary, which is synchronized with the orbital motion. With only the assumption of coevality, a comparison of all of these constraints with current stellar evolution models from the Dartmouth series points to an age of 1.4 Myr and a distance of 133 pc, consistent with previous estimates for the region and suggesting that the system is on the near side of the Taurus complex. Similar comparisons of the properties of LkCa 3 and the well-known quadruple PMS system GG Tau with the widely used models from the Lyon series for a mixing length parameter of α ML = 1.0 strongly favor the Dartmouth models

  2. Emotional response to musical repetition.

    Science.gov (United States)

    Livingstone, Steven R; Palmer, Caroline; Schubert, Emery

    2012-06-01

    Two experiments examined the effects of repetition on listeners' emotional response to music. Listeners heard recordings of orchestral music that contained a large section repeated twice. The music had a symmetric phrase structure (same-length phrases) in Experiment 1 and an asymmetric phrase structure (different-length phrases) in Experiment 2, hypothesized to alter the predictability of sensitivity to musical repetition. Continuous measures of arousal and valence were compared across music that contained identical repetition, variation (related), or contrasting (unrelated) structure. Listeners' emotional arousal ratings differed most for contrasting music, moderately for variations, and least for repeating musical segments. A computational model for the detection of repeated musical segments was applied to the listeners' emotional responses. The model detected the locations of phrase boundaries from the emotional responses better than from performed tempo or physical intensity in both experiments. These findings indicate the importance of repetition in listeners' emotional response to music and in the perceptual segmentation of musical structure.

  3. LANGUAGE REPETITION AND SHORT-TERM MEMORY: AN INTEGRATIVE FRAMEWORK

    Directory of Open Access Journals (Sweden)

    Steve eMajerus

    2013-07-01

    Full Text Available Short-term maintenance of verbal information is a core factor of language repetition, especially when reproducing multiple or unfamiliar stimuli. Many models of language processing locate the verbal short-term maintenance function in the left posterior superior temporo-parietal area and its connections with the inferior frontal gyrus. However, research in the field of short-term memory has implicated bilateral fronto-parietal networks, involved in attention and serial order processing, as being critical for the maintenance and reproduction of verbal sequences. We present here an integrative framework aimed at bridging research in the language processing and short-term memory fields. This framework considers verbal short-term maintenance as an emergent function resulting from synchronized and integrated activation in dorsal and ventral language processing networks as well as fronto-parietal attention and serial order processing networks. To-be-maintained item representations are temporarily activated in the dorsal and ventral language processing networks, novel phoneme and word serial order information is proposed to be maintained via a right fronto-parietal serial order processing network, and activation in these different networks is proposed to be coordinated and maintained via a left fronto-parietal attention processing network. This framework provides new perspectives for our understanding of information maintenance at the nonword-, word- and sentence-level as well as of verbal maintenance deficits in case of brain injury.

  4. Language repetition and short-term memory: an integrative framework.

    Science.gov (United States)

    Majerus, Steve

    2013-01-01

    Short-term maintenance of verbal information is a core factor of language repetition, especially when reproducing multiple or unfamiliar stimuli. Many models of language processing locate the verbal short-term maintenance function in the left posterior superior temporo-parietal area and its connections with the inferior frontal gyrus. However, research in the field of short-term memory has implicated bilateral fronto-parietal networks, involved in attention and serial order processing, as being critical for the maintenance and reproduction of verbal sequences. We present here an integrative framework aimed at bridging research in the language processing and short-term memory fields. This framework considers verbal short-term maintenance as an emergent function resulting from synchronized and integrated activation in dorsal and ventral language processing networks as well as fronto-parietal attention and serial order processing networks. To-be-maintained item representations are temporarily activated in the dorsal and ventral language processing networks, novel phoneme and word serial order information is proposed to be maintained via a right fronto-parietal serial order processing network, and activation in these different networks is proposed to be coordinated and maintained via a left fronto-parietal attention processing network. This framework provides new perspectives for our understanding of information maintenance at the non-word-, word- and sentence-level as well as of verbal maintenance deficits in case of brain injury.

  5. Implication of the cause of differences in 3D structures of proteins with high sequence identity based on analyses of amino acid sequences and 3D structures.

    Science.gov (United States)

    Matsuoka, Masanari; Sugita, Masatake; Kikuchi, Takeshi

    2014-09-18

    Proteins that share a high sequence homology while exhibiting drastically different 3D structures are investigated in this study. Recently, artificial proteins related to the sequences of the GA and IgG binding GB domains of human serum albumin have been designed. These artificial proteins, referred to as GA and GB, share 98% amino acid sequence identity but exhibit different 3D structures, namely, a 3α bundle versus a 4β + α structure. Discriminating between their 3D structures based on their amino acid sequences is a very difficult problem. In the present work, in addition to using bioinformatics techniques, an analysis based on inter-residue average distance statistics is used to address this problem. It was hard to distinguish which structure a given sequence would take only with the results of ordinary analyses like BLAST and conservation analyses. However, in addition to these analyses, with the analysis based on the inter-residue average distance statistics and our sequence tendency analysis, we could infer which part would play an important role in its structural formation. The results suggest possible determinants of the different 3D structures for sequences with high sequence identity. The possibility of discriminating between the 3D structures based on the given sequences is also discussed.

  6. Lesser Himalayan sequences in Eastern Himalaya and their deformation: Implications for Paleoproterozoic tectonic activity along the northern margin of India

    Directory of Open Access Journals (Sweden)

    Dilip Saha

    2013-05-01

    Full Text Available Substantial part of the northern margin of Indian plate is subducted beneath the Eurasian plate during the Caenozoic Himalayan orogeny, obscuring older tectonic events in the Lesser Himalaya known to host Proterozoic sedimentary successions and granitic bodies. Tectonostratigraphic units of the Proterozoic Lesser Himalayan sequence (LHS of Eastern Himalaya, namely the Daling Group in Sikkim and the Bomdila Group in Arunachal Pradesh, provide clues to the nature and extent of Proterozoic passive margin sedimentation, their involvement in pre-Himalayan orogeny and implications for supercontinent reconstruction. The Daling Group, consisting of flaggy quartzite, meta-greywacke and metapelite with minor mafic dyke and sill, and the overlying Buxa Formation with stromatolitic carbonate-quartzite-slate, represent shallow marine, passive margin platformal association. Similar lithostratigraphy and broad depositional framework, and available geochronological data from intrusive granites in Eastern Himalaya indicate strikewise continuity of a shallow marine Paleoproterozoic platformal sequence up to Arunachal Pradesh through Bhutan. Multiple fold sets and tectonic foliations in LHS formed during partial or complete closure of the sea/ocean along the northern margin of Paleoproterozoic India. Such deformation fabrics are absent in the upper Palaeozoic–Mesozoic Gondwana formations in the Lesser Himalaya of Darjeeling-Sikkim indicating influence of older orogeny. Kinematic analysis based on microstructure, and garnet composition suggest Paleoproterozoic deformation and metamorphism of LHS to be distinct from those associated with the foreland propagating thrust systems of the Caenozoic Himalayan collisional belt. Two possibilities are argued here: (1 the low greenschist facies domain in the LHS enveloped the amphibolite to granulite facies domains, which were later tectonically severed; (2 the older deformation and metamorphism relate to a Pacific type

  7. Analysis of repetitive DNA in chromosomes by flow cytometry

    NARCIS (Netherlands)

    Brind'Amour, Julie; Lansdorp, Peter M.

    We developed a flow cytometry method, chromosome flow fluorescence in situ hybridization (FISH), called CFF, to analyze repetitive DNA in chromosomes using FISH with directly labeled peptide nucleic acid (PNA) probes. We used CFF to measure the abundance of interstitial telomeric sequences in

  8. Impact of repetitive DNA on sex chromosome evolution in plants

    Czech Academy of Sciences Publication Activity Database

    Hobza, Roman; Kubát, Z.; Čegan, R.; Jesionek, W.; Vyskot, B.; Kejnovský, E.

    2015-01-01

    Roč. 23, č. 3 (2015), s. 561-570 ISSN 0967-3849 R&D Projects: GA ČR GBP501/12/G090; GA ČR GAP501/12/2220 Institutional support: RVO:61389030 Keywords : repetitive sequences * transposable elements * tandem repeats (satellites) Subject RIV: EB - Genetics ; Molecular Biology Impact factor: 2.590, year: 2015

  9. Reading Nature- experienced teachers’ reflections on a teaching sequence in ecology: implications for future teacher training

    Directory of Open Access Journals (Sweden)

    Ola Magntorn

    2012-10-01

    Full Text Available This article explores experienced primary teachers views on teaching for ‘reading nature’. The concept ‘reading nature’ has to do with an ability to recognise organisms and relate them to material cycling and energy flow in the specific habitat which is to be read. It has to do with the natural world that we face outside and the tools we have are our experiences from previous learning situations both in and out-of-doors. The teachers were asked to comment on the content of a CD-ROM with teaching sequences from a primary class studying a river ecosystem. Perceptions that teachers held were found to be supportive but complex and varied regarding the possibilities and advantages of implementing this type of teaching design in the everyday classroom. The paper finishes by identifying some implications for teacher training to support fieldwork and ecological literacy in primary schools in the future.

  10. Genome-wide survey of repetitive DNA elements in the button mushroom Agaricus bisporus

    NARCIS (Netherlands)

    Foulongne-Oriol, M.; Murat, C.; Castanera, R.; Ramírez, L.; Sonnenberg, A.S.M.

    2013-01-01

    Repetitive DNA elements are ubiquitous constituents of eukaryotic genomes. The biological roles of these repetitive elements, supposed to impact genome organization and evolution, are not completely elucidated yet. The availability of whole genome sequence offers the opportunity to draw a picture of

  11. Repetition and lag effects in movement recognition.

    Science.gov (United States)

    Hall, C R; Buckolz, E

    1982-03-01

    Whether repetition and lag improve the recognition of movement patterns was investigated. Recognition memory was tested for one repetition, two-repetitions massed, and two-repetitions distributed with movement patterns at lags of 3, 5, 7, and 13. Recognition performance was examined both immediately afterwards and following a 48 hour delay. Both repetition and lag effects failed to be demonstrated, providing some support for the claim that memory is unaffected by repetition at a constant level of processing (Craik & Lockhart, 1972). There was, as expected, a significant decrease in recognition memory following the retention interval, but this appeared unrelated to repetition or lag.

  12. Deep Sequencing of Three Loci Implicated in Large-Scale Genome-Wide Association Study Smoking Meta-Analyses.

    Science.gov (United States)

    Clark, Shaunna L; McClay, Joseph L; Adkins, Daniel E; Aberg, Karolina A; Kumar, Gaurav; Nerella, Sri; Xie, Linying; Collins, Ann L; Crowley, James J; Quakenbush, Corey R; Hillard, Christopher E; Gao, Guimin; Shabalin, Andrey A; Peterson, Roseann E; Copeland, William E; Silberg, Judy L; Maes, Hermine; Sullivan, Patrick F; Costello, Elizabeth J; van den Oord, Edwin J

    2016-05-01

    Genome-wide association study meta-analyses have robustly implicated three loci that affect susceptibility for smoking: CHRNA5\\CHRNA3\\CHRNB4, CHRNB3\\CHRNA6 and EGLN2\\CYP2A6. Functional follow-up studies of these loci are needed to provide insight into biological mechanisms. However, these efforts have been hampered by a lack of knowledge about the specific causal variant(s) involved. In this study, we prioritized variants in terms of the likelihood they account for the reported associations. We employed targeted capture of the CHRNA5\\CHRNA3\\CHRNB4, CHRNB3\\CHRNA6, and EGLN2\\CYP2A6 loci and flanking regions followed by next-generation deep sequencing (mean coverage 78×) to capture genomic variation in 363 individuals. We performed single locus tests to determine if any single variant accounts for the association, and examined if sets of (rare) variants that overlapped with biologically meaningful annotations account for the associations. In total, we investigated 963 variants, of which 71.1% were rare (minor allele frequency < 0.01), 6.02% were insertion/deletions, and 51.7% were catalogued in dbSNP141. The single variant results showed that no variant fully accounts for the association in any region. In the variant set results, CHRNB4 accounts for most of the signal with significant sets consisting of directly damaging variants. CHRNA6 explains most of the signal in the CHRNB3\\CHRNA6 locus with significant sets indicating a regulatory role for CHRNA6. Significant sets in CYP2A6 involved directly damaging variants while the significant variant sets suggested a regulatory role for EGLN2. We found that multiple variants implicating multiple processes explain the signal. Some variants can be prioritized for functional follow-up. © The Author 2015. Published by Oxford University Press on behalf of the Society for Research on Nicotine and Tobacco. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.

  13. Object color affects identification and repetition priming.

    Science.gov (United States)

    Uttl, Bob; Graf, Peter; Santacruz, Pilar

    2006-10-01

    We investigated the influence of color on the identification of both non-studied and studied objects. Participants studied black and white and color photos of common objects and memory was assessed with an identification test. Consistent with our meta-analysis of prior research, we found that objects were easier to identify from color than from black and white photos. We also found substantial priming in all conditions, and study-to-test changes in an object's color reduced the magnitude of priming. Color-specific priming effects were large for color-complex objects, but minimal for color-simple objects. The pattern and magnitude of priming effects was not influenced either by the extent to which an object always appears in the same color (i.e., whether a color is symptomatic of an object) or by the object's origin (natural versus fabricated). We discuss the implications of our findings for theoretical accounts of object perception and repetition priming.

  14. Global Repetition Influences Contextual Cueing

    Science.gov (United States)

    Zang, Xuelian; Zinchenko, Artyom; Jia, Lina; Li, Hong

    2018-01-01

    Our visual system has a striking ability to improve visual search based on the learning of repeated ambient regularities, an effect named contextual cueing. Whereas most of the previous studies investigated contextual cueing effect with the same number of repeated and non-repeated search displays per block, the current study focused on whether a global repetition frequency formed by different presentation ratios between the repeated and non-repeated configurations influence contextual cueing effect. Specifically, the number of repeated and non-repeated displays presented in each block was manipulated: 12:12, 20:4, 4:20, and 4:4 in Experiments 1–4, respectively. The results revealed a significant contextual cueing effect when the global repetition frequency is high (≥1:1 ratio) in Experiments 1, 2, and 4, given that processing of repeated displays was expedited relative to non-repeated displays. Nevertheless, the contextual cueing effect reduced to a non-significant level when the repetition frequency reduced to 4:20 in Experiment 3. These results suggested that the presentation frequency of repeated relative to the non-repeated displays could influence the strength of contextual cueing. In other words, global repetition statistics could be a crucial factor to mediate contextual cueing effect. PMID:29636716

  15. Repetitive elements in parasitic protozoa

    Directory of Open Access Journals (Sweden)

    Clayton Christine

    2010-05-01

    Full Text Available Abstract A recent paper published in BMC Genomics suggests that retrotransposition may be active in the human gut parasite Entamoeba histolytica. This adds to our knowledge of the various types of repetitive elements in parasitic protists and the potential influence of such elements on pathogenicity. See research article http://www.biomedcentral.com/1471-2164/11/321

  16. Extensive 16S rRNA gene sequence diversity in Campylobacter hyointestinalis strains: taxonomic and applied implications

    DEFF Research Database (Denmark)

    Harrington, C.S.; On, Stephen L.W.

    1999-01-01

    Phylogenetic relationships of Campylobacter hyointestinalis subspecies were examined by means of 16S rRNA gene sequencing. Sequence similarities among C. hyointestinalis subsp. lawsonii strains exceeded 99.0 %, but values among C. hyointestinalis subsp. hyointestinalis strains ranged from 96...... of the genus Campylobacter, emphasizing the need for multiple strain analysis when using 16S rRNA gene sequence comparisons for taxonomic investigations........4 to 100 %. Sequence similarites between strains representing the two different subspecies ranged from 95.7 to 99.0 %. An intervening sequence was identified in certain of the C. hyointestinalis subsp. lawsonii strains. C. hyointestinalis strains occupied two distinct branches in a phylogenetic analysis...

  17. Repetition code of 15 qubits

    Science.gov (United States)

    Wootton, James R.; Loss, Daniel

    2018-05-01

    The repetition code is an important primitive for the techniques of quantum error correction. Here we implement repetition codes of at most 15 qubits on the 16 qubit ibmqx3 device. Each experiment is run for a single round of syndrome measurements, achieved using the standard quantum technique of using ancilla qubits and controlled operations. The size of the final syndrome is small enough to allow for lookup table decoding using experimentally obtained data. The results show strong evidence that the logical error rate decays exponentially with code distance, as is expected and required for the development of fault-tolerant quantum computers. The results also give insight into the nature of noise in the device.

  18. Computer-Related Repetitive Stress Injuries

    Science.gov (United States)

    ... Staying Safe Videos for Educators Search English Español Computer-Related Repetitive Stress Injuries KidsHealth / For Parents / Computer-Related Repetitive Stress Injuries What's in this article? ...

  19. Repetitive learning control of continuous chaotic systems

    International Nuclear Information System (INIS)

    Chen Maoyin; Shang Yun; Zhou Donghua

    2004-01-01

    Combining a shift method and the repetitive learning strategy, a repetitive learning controller is proposed to stabilize unstable periodic orbits (UPOs) within chaotic attractors in the sense of least mean square. If nonlinear parts in chaotic systems satisfy Lipschitz condition, the proposed controller can be simplified into a simple proportional repetitive learning controller

  20. Fracture propagation through a layered shale and limestone sequence at Nash Point, South Wales: Implications on the development of fracture networks in layered sequences

    Science.gov (United States)

    Forbes Inskip, N.; Meredith, P. G.; Gudmundsson, A.

    2017-12-01

    While considerable effort has been expended on the study of fracture propagation in rocks in recent years, our understanding of how fractures propagate through sedimentary rocks composed of layers with different mechanical and elastic properties remains poor. Yet the mechanical layering is a key parameter controlling the propagation of fractures in sedimentary sequences. Here we report measurements of the contrasting properties of the Lower Lias at Nash Point, South Wales, which comprises a sequence of interbedded shale and limestone layers, and how those properties influence fracture propagation. The static Young's modulus (Estat) of both rock types has been measured parallel and normal to bedding. The shale is highly anisotropic, with Estat varying from 2.4 GPa, in the bedding-normal orientation, to 7.9 GPa, in the bedding-parallel orientation, yielding an anisotropy of 107%. By contrast the limestone has a very low anisotropy of 8%, with Estat values varying from 28.5 GPa, in the bedding-normal orientation, to 26.3 GPa in the bedding-parallel orientation. It follows that for a vertical fracture propagating in this sequence the modulus contrast is by a factor of about 12. This is important because the contrast in elastic properties is a key factor in controlling whether fractures arrest, deflect, or propagate across interfaces between layers in a sequence. Preliminary numerical modelling results (using a finite element modelling software) of induced fractures at Nash Point demonstrate a rotation of the maximum principal compressive stress across interfaces but also the concentration of tensile stress within the more competent (high Estat) limestone layers. The tensile strength (σT), using the Brazil-disk technique, and fracture toughness (KIc), using the semi-circular bend methodology, of both rock types have been measured. Measurements were made in the three principal orientations relative to bedding, Arrester, Divider, and Short-Transverse, and also at 15

  1. Hemispheric Asymmetries in Repetition Enhancement and Suppression Effects in the Newborn Brain.

    Science.gov (United States)

    Bouchon, Camillia; Nazzi, Thierry; Gervain, Judit

    2015-01-01

    The repeated presentation of stimuli typically attenuates neural responses (repetition suppression) or, less commonly, increases them (repetition enhancement) when stimuli are highly complex, degraded or presented under noisy conditions. In adult functional neuroimaging research, these repetition effects are considered as neural correlates of habituation. The development and respective functional significance of these effects in infancy remain largely unknown. This study investigates repetition effects in newborns using functional near-infrared spectroscopy, and specifically the role of stimulus complexity in evoking a repetition enhancement vs. a repetition suppression response, following up on Gervain et al. (2008). In that study, abstract rule-learning was found at birth in cortical areas specific to speech processing, as evidenced by a left-lateralized repetition enhancement of the hemodynamic response to highly variable speech sequences conforming to a repetition-based ABB artificial grammar, but not to a random ABC grammar. Here, the same paradigm was used to investigate how simpler stimuli (12 different sequences per condition as opposed to 140), and simpler presentation conditions (blocked rather than interleaved) would influence repetition effects at birth. Results revealed that the two grammars elicited different dynamics in the two hemispheres. In left fronto-temporal areas, we reproduce the early perceptual discrimination of the two grammars, with ABB giving rise to a greater response at the beginning of the experiment than ABC. In addition, the ABC grammar evoked a repetition enhancement effect over time, whereas a stable response was found for the ABB grammar. Right fronto-temporal areas showed neither initial discrimination, nor change over time to either pattern. Taken together with Gervain et al. (2008), this is the first evidence that manipulating methodological factors influences the presence or absence of neural repetition enhancement effects in

  2. Hemispheric Asymmetries in Repetition Enhancement and Suppression Effects in the Newborn Brain.

    Directory of Open Access Journals (Sweden)

    Camillia Bouchon

    Full Text Available The repeated presentation of stimuli typically attenuates neural responses (repetition suppression or, less commonly, increases them (repetition enhancement when stimuli are highly complex, degraded or presented under noisy conditions. In adult functional neuroimaging research, these repetition effects are considered as neural correlates of habituation. The development and respective functional significance of these effects in infancy remain largely unknown.This study investigates repetition effects in newborns using functional near-infrared spectroscopy, and specifically the role of stimulus complexity in evoking a repetition enhancement vs. a repetition suppression response, following up on Gervain et al. (2008. In that study, abstract rule-learning was found at birth in cortical areas specific to speech processing, as evidenced by a left-lateralized repetition enhancement of the hemodynamic response to highly variable speech sequences conforming to a repetition-based ABB artificial grammar, but not to a random ABC grammar.Here, the same paradigm was used to investigate how simpler stimuli (12 different sequences per condition as opposed to 140, and simpler presentation conditions (blocked rather than interleaved would influence repetition effects at birth.Results revealed that the two grammars elicited different dynamics in the two hemispheres. In left fronto-temporal areas, we reproduce the early perceptual discrimination of the two grammars, with ABB giving rise to a greater response at the beginning of the experiment than ABC. In addition, the ABC grammar evoked a repetition enhancement effect over time, whereas a stable response was found for the ABB grammar. Right fronto-temporal areas showed neither initial discrimination, nor change over time to either pattern.Taken together with Gervain et al. (2008, this is the first evidence that manipulating methodological factors influences the presence or absence of neural repetition enhancement

  3. A Repetition Test for Pseudo-Random Number Generators

    OpenAIRE

    Gil, Manuel; Gonnet, Gaston H.; Petersen, Wesley P.

    2017-01-01

    A new statistical test for uniform pseudo-random number generators (PRNGs) is presented. The idea is that a sequence of pseudo-random numbers should have numbers reappear with a certain probability. The expectation time that a repetition occurs provides the metric for the test. For linear congruential generators (LCGs) failure can be shown theoretically. Empirical test results for a number of commonly used PRNGs are reported, showing that some PRNGs considered to have good statistical propert...

  4. Genotypic Characterization of Bradyrhizobium Strains Nodulating Endemic Woody Legumes of the Canary Islands by PCR-Restriction Fragment Length Polymorphism Analysis of Genes Encoding 16S rRNA (16S rDNA) and 16S-23S rDNA Intergenic Spacers, Repetitive Extragenic Palindromic PCR Genomic Fingerprinting, and Partial 16S rDNA Sequencing

    Science.gov (United States)

    Vinuesa, Pablo; Rademaker, Jan L. W.; de Bruijn, Frans J.; Werner, Dietrich

    1998-01-01

    We present a phylogenetic analysis of nine strains of symbiotic nitrogen-fixing bacteria isolated from nodules of tagasaste (Chamaecytisus proliferus) and other endemic woody legumes of the Canary Islands, Spain. These and several reference strains were characterized genotypically at different levels of taxonomic resolution by computer-assisted analysis of 16S ribosomal DNA (rDNA) PCR-restriction fragment length polymorphisms (PCR-RFLPs), 16S-23S rDNA intergenic spacer (IGS) RFLPs, and repetitive extragenic palindromic PCR (rep-PCR) genomic fingerprints with BOX, ERIC, and REP primers. Cluster analysis of 16S rDNA restriction patterns with four tetrameric endonucleases grouped the Canarian isolates with the two reference strains, Bradyrhizobium japonicum USDA 110spc4 and Bradyrhizobium sp. strain (Centrosema) CIAT 3101, resolving three genotypes within these bradyrhizobia. In the analysis of IGS RFLPs with three enzymes, six groups were found, whereas rep-PCR fingerprinting revealed an even greater genotypic diversity, with only two of the Canarian strains having similar fingerprints. Furthermore, we show that IGS RFLPs and even very dissimilar rep-PCR fingerprints can be clustered into phylogenetically sound groupings by combining them with 16S rDNA RFLPs in computer-assisted cluster analysis of electrophoretic patterns. The DNA sequence analysis of a highly variable 264-bp segment of the 16S rRNA genes of these strains was found to be consistent with the fingerprint-based classification. Three different DNA sequences were obtained, one of which was not previously described, and all belonged to the B. japonicum/Rhodopseudomonas rDNA cluster. Nodulation assays revealed that none of the Canarian isolates nodulated Glycine max or Leucaena leucocephala, but all nodulated Acacia pendula, C. proliferus, Macroptilium atropurpureum, and Vigna unguiculata. PMID:9603820

  5. Haben repetitive DNA-Sequenzen biologische Funktionen?

    Science.gov (United States)

    John, Maliyakal E.; Knöchel, Walter

    1983-05-01

    By DNA reassociation kinetics it is known that the eucaryotic genome consists of non-repetitive DNA, middle-repetitive DNA and highly repetitive DNA. Whereas the majority of protein-coding genes is located on non-repetitive DNA, repetitive DNA forms a constitutive part of eucaryotic DNA and its amount in most cases equals or even substantially exceeds that of non-repetitive DNA. During the past years a large body of data on repetitive DNA has accumulated and these have prompted speculations ranging from specific roles in the regulation of gene expression to that of a selfish entity with inconsequential functions. The following article summarizes recent findings on structural, transcriptional and evolutionary aspects and, although by no means being proven, some possible biological functions are discussed.

  6. Identification of the bovine Arachnomelia mutation by massively parallel sequencing implicates sulfite oxidase (SUOX in bone development.

    Directory of Open Access Journals (Sweden)

    Cord Drögemüller

    2010-08-01

    Full Text Available Arachnomelia is a monogenic recessive defect of skeletal development in cattle. The causative mutation was previously mapped to a ∼7 Mb interval on chromosome 5. Here we show that array-based sequence capture and massively parallel sequencing technology, combined with the typical family structure in livestock populations, facilitates the identification of the causative mutation. We re-sequenced the entire critical interval in a healthy partially inbred cow carrying one copy of the critical chromosome segment in its ancestral state and one copy of the same segment with the arachnomelia mutation, and we detected a single heterozygous position. The genetic makeup of several partially inbred cattle provides extremely strong support for the causality of this mutation. The mutation represents a single base insertion leading to a premature stop codon in the coding sequence of the SUOX gene and is perfectly associated with the arachnomelia phenotype. Our findings suggest an important role for sulfite oxidase in bone development.

  7. Identification of the Bovine Arachnomelia Mutation by Massively Parallel Sequencing Implicates Sulfite Oxidase (SUOX) in Bone Development

    Science.gov (United States)

    Drögemüller, Cord; Tetens, Jens; Sigurdsson, Snaevar; Gentile, Arcangelo; Testoni, Stefania; Lindblad-Toh, Kerstin; Leeb, Tosso

    2010-01-01

    Arachnomelia is a monogenic recessive defect of skeletal development in cattle. The causative mutation was previously mapped to a ∼7 Mb interval on chromosome 5. Here we show that array-based sequence capture and massively parallel sequencing technology, combined with the typical family structure in livestock populations, facilitates the identification of the causative mutation. We re-sequenced the entire critical interval in a healthy partially inbred cow carrying one copy of the critical chromosome segment in its ancestral state and one copy of the same segment with the arachnomelia mutation, and we detected a single heterozygous position. The genetic makeup of several partially inbred cattle provides extremely strong support for the causality of this mutation. The mutation represents a single base insertion leading to a premature stop codon in the coding sequence of the SUOX gene and is perfectly associated with the arachnomelia phenotype. Our findings suggest an important role for sulfite oxidase in bone development. PMID:20865119

  8. Location of core diagnostic information across various sequences in brain MRI and implications for efficiency of MRI scanner utilization.

    Science.gov (United States)

    Sharma, Aseem; Chatterjee, Arindam; Goyal, Manu; Parsons, Matthew S; Bartel, Seth

    2015-04-01

    Targeting redundancy within MRI can improve its cost-effective utilization. We sought to quantify potential redundancy in our brain MRI protocols. In this retrospective review, we aggregated 207 consecutive adults who underwent brain MRI and reviewed their medical records to document clinical indication, core diagnostic information provided by MRI, and its clinical impact. Contributory imaging abnormalities constituted positive core diagnostic information whereas absence of imaging abnormalities constituted negative core diagnostic information. The senior author selected core sequences deemed sufficient for extraction of core diagnostic information. For validating core sequences selection, four readers assessed the relative ease of extracting core diagnostic information from the core sequences. Potential redundancy was calculated by comparing the average number of core sequences to the average number of sequences obtained. Scanning had been performed using 9.4±2.8 sequences over 37.3±12.3 minutes. Core diagnostic information was deemed extractable from 2.1±1.1 core sequences, with an assumed scanning time of 8.6±4.8 minutes, reflecting a potential redundancy of 74.5%±19.1%. Potential redundancy was least in scans obtained for treatment planning (14.9%±25.7%) and highest in scans obtained for follow-up of benign diseases (81.4%±12.6%). In 97.4% of cases, all four readers considered core diagnostic information to be either easily extractable from core sequences or the ease to be equivalent to that from the entire study. With only one MRI lacking clinical impact (0.48%), overutilization did not seem to contribute to potential redundancy. High potential redundancy that can be targeted for more efficient scanner utilization exists in brain MRI protocols.

  9. Repetitively pulsed material testing facility

    International Nuclear Information System (INIS)

    Zucker, O.; Bostick, W.; Gullickson, R; Long, J.; Luce, J.; Sahlin, H.

    1975-01-01

    A continuously operated, 1 pps, dense-plasma-focus device capable of delivering a minimum of 10 15 neutrons per pulse for material testing purposes is described. Moderate scaling from existing results is sufficient to provide 2 x 10 13 n/cm 2 .s to a suitable target. The average power consumption, which has become a major issue as a result of the energy crisis, is analyzed with respect to other plasma devices and is shown to be highly favorable. A novel approach to the capacitor bank and switch design allowing repetitive operation is discussed. (U.S.)

  10. Repetitively pulsed material testing facility

    International Nuclear Information System (INIS)

    Zucker, O.; Bostick, W.; Gullickson, R.; Long, J.; Luce, J.; Sahlin, H.

    1975-01-01

    A continuously operated, 1 pps, dense-plasma-focus device capable of delivering a minimum of 10 15 neutrons per pulse for material testing purposes is described. Moderate scaling from existing results is sufficient to provide 2 x 10 13 n/cm 2 . s to a suitable target. The average power consumption, which has become a major issue as a result of the energy crisis, is analyzed with respect to other plasma devices and is shown to be highly favorable. A novel approach to the capacitor bank and switch design allowing repetitive operation is discussed

  11. Exploiting repetitive sequences and BAC clones in Festuca pratensis karyotyping

    Czech Academy of Sciences Publication Activity Database

    Majka, J.; Ksiazczyk, T.; Kiełbowicz-Matuk, A.; Kopecký, David; Kosmala, A.

    2017-01-01

    Roč. 12, č. 6 (2017), č. článku e0179043. E-ISSN 1932-6203 Institutional support: RVO:61389030 Keywords : IN-SITU HYBRIDIZATION * RIBOSOMAL-RNA GENES * LOLIUM-MULTIFLORUM Subject RIV: EB - Genetics ; Molecular Biology OBOR OECD: Plant sciences, botany Impact factor: 2.806, year: 2016

  12. Repetitive trauma and nerve compression.

    Science.gov (United States)

    Carragee, E J; Hentz, V R

    1988-01-01

    Repetitive movement of the upper extremity, whether recreational or occupational, may result in various neuropathies, the prototype of which is the median nerve neuropathic in the carpal canal. The pathophysiology of this process is incompletely understood but likely involves both mechanical and ischemic features. Experimentally increased pressures within the carpal canal produced reproducible progressive neuropathy. Changes in vibratory (threshold-type) sensibility appears to be more sensitive than two-point (innervation density-type) sensibility. The specific occupational etiologies of carpal neuropathy are obscured by methodologic and sociological difficulties, but clearly some occupations have high incidences of CTS. History and physical examination are usually sufficient for the diagnosis, but diagnostic assistance when required is available through electrophysiological testing, CT scanning, and possibly MRI. Each of these tests has limitations in both sensitivity and specificity. Treatment by usual conservative means should be combined with rest from possible provocative activities. Surgical release of the carpal canal is helpful in patients failing conservative therapy. Occupational modifications are important in both treatment and prevention of median neuropathy due to repetitive trauma.

  13. Learning Correct Responses and Errors in the Hebb Repetition Effect: Two Faces of the Same Coin

    Science.gov (United States)

    Couture, Mathieu; Lafond, Daniel; Tremblay, Sebastien

    2008-01-01

    In a serial recall task, the "Hebb repetition effect" occurs when recall performance improves for a sequence repeated throughout the experimental session. This phenomenon has been replicated many times. Nevertheless, such cumulative learning seldom leads to perfect recall of the whole sequence, and errors persist. Here the authors report…

  14. Long aftershock sequences in North China and Central US: implications for hazard assessment in mid-continents

    Science.gov (United States)

    Liu, Mian; Luo, Gang; Wang, Hui; Stein, Seth

    2014-02-01

    Because seismic activity within mid-continents is usually much lower than that along plate boundary zones, even small earthquakes can cause widespread concerns, especially when these events occur in the source regions of previous large earthquakes. However, these small earthquakes may be just aftershocks that continue for decades or even longer. The recent seismicity in the Tangshan region in North China is likely aftershocks of the 1976 Great Tangshan earthquake. The current earthquake sequence in the New Madrid seismic zone in central United States, which includes a cluster of M ~ 7.0 events in 1811-1812 and a number of similar events in the past millennium, is believed to result from recent fault reactivation that releases pre-stored strain energy in the crust. If so, this earthquake sequence is similar to aftershocks in that the rates of energy release should decay with time and the sequence of earthquakes will eventually end. We use simple physical analysis and numerical simulations to show that the current sequence of large earthquakes in the New Madrid fault zone is likely ending or has ended. Recognizing that mid-continental earthquakes have long aftershock sequences and complex spatiotemporal occurrences are critical to improve hazard assessments.

  15. Electrophysiological Repetition Effects in Persons with Mild Cognitive Impairment depend upon Working Memory Demand.

    Science.gov (United States)

    Broster, Lucas S; Jenkins, Shonna L; Holmes, Sarah D; Edwards, Matthew G; Jicha, Gregory A; Jiang, Yang

    2018-05-07

    Forms of implicit memory, including repetition effects, are preserved relative to explicit memory in clinical Alzheimer's disease. Consequently, cognitive interventions for persons with Alzheimer's disease have been developed that leverage this fact. However, despite the clinical robustness of behavioral repetition effects, altered neural mechanisms of repetition effects are studied as biomarkers of both clinical Alzheimer's disease and pre-morbid Alzheimer's changes in the brain. We hypothesized that the clinical preservation of behavioral repetition effects results in part from concurrent operation of discrete memory systems. We developed two experiments that included probes of emotional repetition effects differing in that one included an embedded working memory task. We found that neural repetition effects manifested in patients with amnestic mild cognitive impairment, the earliest form of clinical Alzheimer's disease, during emotional working memory tasks, but they did not manifest during the task that lacked the embedded working memory manipulation. Specifically, the working memory task evoked neural repetition effects in the P600 time-window, but the same neural mechanism was only minimally implicated in the task without a working memory component. We also found that group differences in behavioral repetition effects were smaller in the experiment with a working memory task. We suggest that cross-domain cognitive challenge can expose "defunct" neural capabilities of individuals with amnestic mild cognitive impairment. Copyright © 2018. Published by Elsevier Ltd.

  16. Metre-scale cyclicity in Middle Eocene platform carbonates in northern Egypt: Implications for facies development and sequence stratigraphy

    Science.gov (United States)

    Tawfik, Mohamed; El-Sorogy, Abdelbaset; Moussa, Mahmoud

    2016-07-01

    The shallow-water carbonates of the Middle Eocene in northern Egypt represent a Tethyan reef-rimmed carbonate platform with bedded inner-platform facies. Based on extensive micro- and biofacies documentation, five lithofacies associations were defined and their respective depositional environments were interpreted. Investigated sections were subdivided into three third-order sequences, named S1, S2 and S3. Sequence S1 is interpreted to correspond to the Lutetian, S2 corresponds to the Late Lutetian and Early Bartonian, and S3 represents the Late Bartonian. Each of the three sequences was further subdivided into fourth-order cycle sets and fifth-order cycles. The complete hierarchy of cycles can be correlated along 190 km across the study area, and highlighting a general "layer-cake" stratigraphic architecture. The documentation of the studied outcrops may contribute to the better regional understanding of the Middle Eocene formations in northern Egypt and to Tethyan pericratonic carbonate models in general.

  17. Genetic variation within clonal lineages of Phytophthora infestans revealed through genotyping-by-sequencing, and implications for late blight epidemiology

    Science.gov (United States)

    Genotyping-by-sequencing (GBS) was performed on 257 Phytophthora infestans isolates belonging to four clonal lineages to study within-lineage diversity. The four lineages used in the study included US-8 (n=28), US-11 (n=27), US-23 (n=166), and US-24 (n=36), with isolates originating from 23 of the U...

  18. Magnetostratigraphic dating of the Xiashagou Fauna and implication for sequencing the mammalian faunas in the Nihewan Basin, North China

    NARCIS (Netherlands)

    Liu, Ping; Deng, Chenglong; Li, Shihu; Cai, Shuhui; Cheng, Hongjiang; Wei, Qi; Zhu, Rixiang

    2012-01-01

    The Nihewan Basin sedimentary sequences in northern China are rich in mammalian fossil and Paleolithic sites, thus providing insights into our understanding of Quaternary land mammal biochronology and early human settlements in East Asia. Here we present high-resolution magnetostratigraphic results

  19. Draft Genome Sequences of Four Salmonella enterica subsp. enterica Serovar Enteritidis Strains Implicated in Infections of Avian and Human Hosts

    KAUST Repository

    An, Ran; Lin, Pengpeng; Bougouffa, Salim; Essack, Magbubah; Boxrud, David; Bajic, Vladimir B.; Vidovic, Sinisa

    2018-01-01

    Salmonella enterica subsp. enterica serovar Enteritidis is a wide-host-range pathogen. Occasionally, it is involved in invasive infections, leading to a high mortality rate. Here, we present the draft genome sequences of four S Enteritidis strains obtained from human and avian hosts that had been involved in bacteremia, gastroenteritis, and primary infections.

  20. Integrated stratigraphy of the Jurassic-Cretaceous sequences of the Kurovice Quarry, Outer Western Carpathians: correlations and tectonic implications

    Czech Academy of Sciences Publication Activity Database

    Pruner, Petr; Schnabl, Petr; Čížková, Kristýna; Elbra, Tiiu; Kdýr, Šimon; Svobodová, Andrea; Reháková, D.

    2017-01-01

    Roč. 120 (2017), s. 216-216 ISSN 1017-8880. [International Symposium on the Cretaceous /10./. 21.08.2017-26.08.2017, Vienna] R&D Projects: GA ČR(CZ) GA16-09979S Institutional support: RVO:67985831 Keywords : stratigraphy * Jurassic-Cretaceous sequences * Western Carpathians Subject RIV: DB - Geology ; Mineralogy

  1. Draft Genome Sequences of Four Salmonella enterica subsp. enterica Serovar Enteritidis Strains Implicated in Infections of Avian and Human Hosts

    KAUST Repository

    An, Ran

    2018-01-24

    Salmonella enterica subsp. enterica serovar Enteritidis is a wide-host-range pathogen. Occasionally, it is involved in invasive infections, leading to a high mortality rate. Here, we present the draft genome sequences of four S Enteritidis strains obtained from human and avian hosts that had been involved in bacteremia, gastroenteritis, and primary infections.

  2. Whole-exome sequencing of individuals from an isolated population implicates rare risk variants in bipolar disorder

    DEFF Research Database (Denmark)

    Lescai, F; Als, T D; Li, Q

    2017-01-01

    Bipolar disorder affects about 1% of the world's population, and its estimated heritability is about 75%. Only few whole genome or whole-exome sequencing studies in bipolar disorder have been reported, and no rare coding variants have yet been robustly identified. The use of isolated populations...

  3. Stimulus repetition and the perception of time: the effects of prior exposure on temporal discrimination, judgment, and production.

    Directory of Open Access Journals (Sweden)

    William J Matthews

    Full Text Available It has been suggested that repeated stimuli have shorter subjective duration than novel items, perhaps because of a reduction in the neural response to repeated presentations of the same object. Five experiments investigated the effects of repetition on time perception and found further evidence that immediate repetition reduces apparent duration, consistent with the idea that subjective duration is partly based on neural coding efficiency. In addition, the experiments found (a no effect of repetition on the precision of temporal discrimination, (b that the effects of repetition disappeared when there was a modest lag between presentations, (c that, across participants, the size of the repetition effect correlated with temporal discrimination, and (d that the effects of repetition suggested by a temporal production task were the opposite of those suggested by temporal judgments. The theoretical and practical implications of these results are discussed.

  4. Paleomagnetism of Holocene lava flows from the Reykjanes Peninsula and the Tungnaá lava sequence (Iceland): implications for flow correlation and ages

    Science.gov (United States)

    Pinton, Annamaria; Giordano, Guido; Speranza, Fabio; Þórðarson, Þorvaldur

    2018-01-01

    The impact of Holocene eruptive events from hot spots like Iceland may have had significant global implications; thus, dating and knowledge of past eruptions chronology is important. However, at high-latitude volcanic islands, the paucity of soils severely limits 14C dating, while the poor K content of basalts strongly restricts the use of K/Ar and Ar/Ar methods. Even tephrochronology, based on 14C age determinations, refers to layers that rarely lie directly above lava flows to be dated. We report on the paleomagnetic dating of 25 sites from the Reykjanes Peninsula and the Tungnaá lava sequence of Iceland. The gathered paleomagnetic directions were compared with the available reference paleosecular variation curves of the Earth magnetic field to obtain the possible emplacement age intervals. To test the method's validity, we sampled the precisely dated Laki (1783-1784 AD) and Eldgjà (934-938 AD) lavas. The age windows obtained for these events encompass the true flow ages. For sites from the Reykjanes peninsula and the Tugnaá lava sequence, we derived multiple possible eruption events and ages. In the Reykjanes peninsula, we propose an older emplacement age (immediately following the 870 AD Iceland Settlement age) for Ogmundarhraun and Kapelluhraun lava fields. For pre-historical (older than the settlement age) Tugnaá eruptions, the method has a dating precision of 300-400 years which allows an increase of the detail in the chronostratigraphy and distribution of lavas in the Tugnaá sequence.

  5. Source modeling of the 2015 Mw 7.8 Nepal (Gorkha) earthquake sequence: Implications for geodynamics and earthquake hazards

    Science.gov (United States)

    McNamara, D. E.; Yeck, W. L.; Barnhart, W. D.; Schulte-Pelkum, V.; Bergman, E.; Adhikari, L. B.; Dixit, A.; Hough, S. E.; Benz, H. M.; Earle, P. S.

    2017-09-01

    The Gorkha earthquake on April 25th, 2015 was a long anticipated, low-angle thrust-faulting event on the shallow décollement between the India and Eurasia plates. We present a detailed multiple-event hypocenter relocation analysis of the Mw 7.8 Gorkha Nepal earthquake sequence, constrained by local seismic stations, and a geodetic rupture model based on InSAR and GPS data. We integrate these observations to place the Gorkha earthquake sequence into a seismotectonic context and evaluate potential earthquake hazard. Major results from this study include (1) a comprehensive catalog of calibrated hypocenters for the Gorkha earthquake sequence; (2) the Gorkha earthquake ruptured a 150 × 60 km patch of the Main Himalayan Thrust (MHT), the décollement defining the plate boundary at depth, over an area surrounding but predominantly north of the capital city of Kathmandu (3) the distribution of aftershock seismicity surrounds the mainshock maximum slip patch; (4) aftershocks occur at or below the mainshock rupture plane with depths generally increasing to the north beneath the higher Himalaya, possibly outlining a 10-15 km thick subduction channel between the overriding Eurasian and subducting Indian plates; (5) the largest Mw 7.3 aftershock and the highest concentration of aftershocks occurred to the southeast the mainshock rupture, on a segment of the MHT décollement that was positively stressed towards failure; (6) the near surface portion of the MHT south of Kathmandu shows no aftershocks or slip during the mainshock. Results from this study characterize the details of the Gorkha earthquake sequence and provide constraints on where earthquake hazard remains high, and thus where future, damaging earthquakes may occur in this densely populated region. Up-dip segments of the MHT should be considered to be high hazard for future damaging earthquakes.

  6. A Foxp2 mutation implicated in human speech deficits alters sequencing of ultrasonic vocalizations in adult male mice

    Directory of Open Access Journals (Sweden)

    Jonathan Chabout

    2016-10-01

    Full Text Available Development of proficient spoken language skills is disrupted by mutations of the FOXP2 transcription factor. A heterozygous missense mutation in the KE family causes speech apraxia, involving difficulty producing words with complex learned sequences of syllables. Manipulations in songbirds have helped to elucidate the role of this gene in vocal learning, but findings in non-human mammals have been limited or inconclusive. Here we performed a systematic study of ultrasonic vocalizations (USVs of adult male mice carrying the KE family mutation. Using novel statistical tools, we found that Foxp2 heterozygous mice did not have detectable changes in USV syllable acoustic structure, but produced shorter sequences and did not shift to more complex syntax in social contexts where wildtype animals did. Heterozygous mice also displayed a shift in the position of their rudimentary laryngeal motor cortex layer-5 neurons. Our findings indicate that although mouse USVs are mostly innate, the underlying contributions of FoxP2 to sequencing of vocalizations are conserved with humans.

  7. POST-MAIN SEQUENCE EVOLUTION OF ICY MINOR PLANETS: IMPLICATIONS FOR WATER RETENTION AND WHITE DWARF POLLUTION

    Energy Technology Data Exchange (ETDEWEB)

    Malamud, Uri; Perets, Hagai B., E-mail: uri.mal@tx.technion.ac.il, E-mail: hperets@physics.technion.ac.il [Department of Physics, Technion (Israel)

    2016-12-01

    Most observations of polluted white dwarf atmospheres are consistent with accretion of water-depleted planetary material. Among tens of known cases, merely two involve accretion of objects that contain a considerable mass fraction of water. The purpose of this study is to investigate the relative scarcity of these detections. Based on a new and highly detailed model, we evaluate the retention of water inside icy minor planets during the high-luminosity stellar evolution that follows the main sequence. Our model fully considers the thermal, physical, and chemical evolution of icy bodies, following their internal differentiation as well as water depletion, from the moment of their birth and through all stellar evolution phases preceding the formation of the white dwarf. We also account for different initial compositions and formation times. Our results differ from previous studies, which have either underestimated or overestimated water retention. We show that water can survive in a variety of circumstances and in great quantities, and therefore other possibilities are discussed in order to explain the infrequency of water detection. We predict that the sequence of accretion is such that water accretes earlier, and more rapidly, than the rest of the silicate disk, considerably reducing the chance of its detection in H-dominated atmospheres. In He-dominated atmospheres, the scarcity of water detections could be observationally biased. It implies that the accreted material is typically intrinsically dry, which may be the result of the inside-out depopulation sequence of minor planets.

  8. All 37 Mitochondrial Genes of Aphid Aphis craccivora Obtained from Transcriptome Sequencing: Implications for the Evolution of Aphids.

    Directory of Open Access Journals (Sweden)

    Nan Song

    Full Text Available The availability of mitochondrial genome data for Aphididae, one of the economically important insect pest families, in public databases is limited. The advent of next generation sequencing technology provides the potential to generate mitochondrial genome data for many species timely and cost-effectively. In this report, we used transcriptome sequencing technology to determine all the 37 mitochondrial genes of the cowpea aphid, Aphis craccivora. This method avoids the necessity of finding suitable primers for long PCRs or primer-walking amplicons, and is proved to be effective in obtaining the whole set of mitochondrial gene data for insects with difficulty in sequencing mitochondrial genome by PCR-based strategies. Phylogenetic analyses of aphid mitochondrial genome data show clustering based on tribe level, and strongly support the monophyly of the family Aphididae. Within the monophyletic Aphidini, three samples from Aphis grouped together. In another major clade of Aphididae, Pterocomma pilosum was recovered as a potential sister-group of Cavariella salicicola, as part of Macrosiphini.

  9. POST-MAIN SEQUENCE EVOLUTION OF ICY MINOR PLANETS: IMPLICATIONS FOR WATER RETENTION AND WHITE DWARF POLLUTION

    International Nuclear Information System (INIS)

    Malamud, Uri; Perets, Hagai B.

    2016-01-01

    Most observations of polluted white dwarf atmospheres are consistent with accretion of water-depleted planetary material. Among tens of known cases, merely two involve accretion of objects that contain a considerable mass fraction of water. The purpose of this study is to investigate the relative scarcity of these detections. Based on a new and highly detailed model, we evaluate the retention of water inside icy minor planets during the high-luminosity stellar evolution that follows the main sequence. Our model fully considers the thermal, physical, and chemical evolution of icy bodies, following their internal differentiation as well as water depletion, from the moment of their birth and through all stellar evolution phases preceding the formation of the white dwarf. We also account for different initial compositions and formation times. Our results differ from previous studies, which have either underestimated or overestimated water retention. We show that water can survive in a variety of circumstances and in great quantities, and therefore other possibilities are discussed in order to explain the infrequency of water detection. We predict that the sequence of accretion is such that water accretes earlier, and more rapidly, than the rest of the silicate disk, considerably reducing the chance of its detection in H-dominated atmospheres. In He-dominated atmospheres, the scarcity of water detections could be observationally biased. It implies that the accreted material is typically intrinsically dry, which may be the result of the inside-out depopulation sequence of minor planets.

  10. Bifunctional cis-Abienol Synthase from Abies balsamea Discovered by Transcriptome Sequencing and Its Implications for Diterpenoid Fragrance Production*

    Science.gov (United States)

    Zerbe, Philipp; Chiang, Angela; Yuen, Macaire; Hamberger, Björn; Hamberger, Britta; Draper, Jason A.; Britton, Robert; Bohlmann, Jörg

    2012-01-01

    The labdanoid diterpene alcohol cis-abienol is a major component of the aromatic oleoresin of balsam fir (Abies balsamea) and serves as a valuable bioproduct material for the fragrance industry. Using high-throughput 454 transcriptome sequencing and metabolite profiling of balsam fir bark tissue, we identified candidate diterpene synthase sequences for full-length cDNA cloning and functional characterization. We discovered a bifunctional class I/II cis-abienol synthase (AbCAS), along with the paralogous levopimaradiene/abietadiene synthase and isopimaradiene synthase, all of which are members of the gymnosperm-specific TPS-d subfamily. The AbCAS-catalyzed formation of cis-abienol proceeds via cyclization and hydroxylation at carbon C-8 of a postulated carbocation intermediate in the class II active site, followed by cleavage of the diphosphate group and termination of the reaction sequence without further cyclization in the class I active site. This reaction mechanism is distinct from that of synthases of the isopimaradiene- or levopimaradiene/abietadiene synthase type, which employ deprotonation reactions in the class II active site and secondary cyclizations in the class I active site, leading to tricyclic diterpenes. Comparative homology modeling suggested the active site residues Asp-348, Leu-617, Phe-696, and Gly-723 as potentially important for the specificity of AbCAS. As a class I/II bifunctional enzyme, AbCAS is a promising target for metabolic engineering of cis-abienol production. PMID:22337889

  11. Identification of somatic mutations in postmortem human brains by whole genome sequencing and their implications for psychiatric disorders.

    Science.gov (United States)

    Nishioka, Masaki; Bundo, Miki; Ueda, Junko; Katsuoka, Fumiki; Sato, Yukuto; Kuroki, Yoko; Ishii, Takao; Ukai, Wataru; Murayama, Shigeo; Hashimoto, Eri; Nagasaki, Masao; Yasuda, Jun; Kasai, Kiyoto; Kato, Tadafumi; Iwamoto, Kazuya

    2018-04-01

    Somatic mutations in the human brain are hypothesized to contribute to the functional diversity of brain cells as well as the pathophysiology of neuropsychiatric diseases. However, there are still few reports on somatic mutations in non-neoplastic human brain tissues. This study attempted to unveil the landscape of somatic mutations in the human brain. We explored the landscape of somatic mutations in human brain tissues derived from three individuals with no neuropsychiatric diseases by whole-genome deep sequencing at a depth of around 100. The candidate mutations underwent multi-layered filtering, and were validated by ultra-deep target amplicon sequencing at a depth of around 200 000. Thirty-one somatic mutations were identified in the human brain, demonstrating the utility of whole-genome sequencing of bulk brain tissue. The mutations were enriched in neuron-expressed genes, and two-thirds of the identified somatic single nucleotide variants in the brain tissues were cytosine-to-thymine transitions, half of which were in CpG dinucleotides. Our developed filtering and validation approaches will be useful to identify somatic mutations in the human brain. The vulnerability of neuron-expressed genes to mutational events suggests their potential relevance to neuropsychiatric diseases. © 2017 The Authors. Psychiatry and Clinical Neurosciences published by John Wiley & Sons Australia, Ltd on behalf of Japanese Society of Psychiatry and Neurology.

  12. Characterization and distribution of repetitive elements in association with genes in the human genome.

    Science.gov (United States)

    Liang, Kai-Chiang; Tseng, Joseph T; Tsai, Shaw-Jenq; Sun, H Sunny

    2015-08-01

    Repetitive elements constitute more than 50% of the human genome. Recent studies implied that the complexity of living organisms is not just a direct outcome of a number of coding sequences; the repetitive elements, which do not encode proteins, may also play a significant role. Though scattered studies showed that repetitive elements in the regulatory regions of a gene control gene expression, no systematic survey has been done to report the characterization and distribution of various types of these repetitive elements in the human genome. Sequences from 5' and 3' untranslated regions and upstream and downstream of a gene were downloaded from the Ensembl database. The repetitive elements in the neighboring of each gene were identified and classified using cross-matching implemented in the RepeatMasker. The annotation and distribution of distinct classes of repetitive elements associated with individual gene were collected to characterize genes in association with different types of repetitive elements using systems biology program. We identified a total of 1,068,400 repetitive elements which belong to 37-class families and 1235 subclasses that are associated with 33,761 genes and 57,365 transcripts. In addition, we found that the tandem repeats preferentially locate proximal to the transcription start site (TSS) of genes and the major function of these genes are involved in developmental processes. On the other hand, interspersed repetitive elements showed a tendency to be accumulated at distal region from the TSS and the function of interspersed repeat-containing genes took part in the catabolic/metabolic processes. Results from the distribution analysis were collected and used to construct a gene-based repetitive element database (GBRED; http://www.binfo.ncku.edu.tw/GBRED/index.html). A user-friendly web interface was designed to provide the information of repetitive elements associated with any particular gene(s). This is the first study focusing on the gene

  13. A Nonword Repetition Task for Speakers with Misarticulations: The Syllable Repetition Task (SRT)

    Science.gov (United States)

    Shriberg, Lawrence D.; Lohmeier, Heather L.; Campbell, Thomas F.; Dollaghan, Christine A.; Green, Jordan R.; Moore, Christopher A.

    2009-01-01

    Purpose: Conceptual and methodological confounds occur when non(sense) word repetition tasks are administered to speakers who do not have the target speech sounds in their phonetic inventories or who habitually misarticulate targeted speech sounds. In this article, the authors (a) describe a nonword repetition task, the Syllable Repetition Task…

  14. N-2 repetition leads to a cost within working memory and a benefit outside it.

    Science.gov (United States)

    Kessler, Yoav

    2018-03-15

    Removal has been suggested to play a key role in controlling the contents of working memory. The present study examined the aftereffects of removal in a working memory updating task. Participants performed the reference-back paradigm, a version of the n-back task that is composed of two trial types: reference trials that required working memory updating and comparison trials that did not require updating. N-2 repetition effects-the difference in performance between trials that presented the same stimulus as the one presented two trials before (ABA sequences) and trials in which the stimulus differed from the two previous stimuli (ABC sequences)-were examined. In two experiments, n-2 repetition costs were observed within sequences of reference trials, while n-2 repetition benefits were observed within sequences of comparison trials. This pattern suggests that removal takes place during working memory updating. Furthermore, automatic formation and updating of representation outside working memory, which takes place in comparison trials and gives rise to n-2 repetition benefits, does not involve removal. Removal, demonstrated by phenomena such as n-2 repetition costs, is therefore proposed to be a marker for the utilization of working memory within a given task. © 2018 New York Academy of Sciences.

  15. Genomic Organization and Physical Mapping of Tandemly Arranged Repetitive DNAs in Sterlet (Acipenser ruthenus).

    Science.gov (United States)

    Biltueva, Larisa S; Prokopov, Dimitry Y; Makunin, Alexey I; Komissarov, Alexey S; Kudryavtseva, Anna V; Lemskaya, Natalya A; Vorobieva, Nadezhda V; Serdyukova, Natalia A; Romanenko, Svetlana A; Gladkikh, Olga L; Graphodatsky, Alexander S; Trifonov, Vladimir A

    2017-01-01

    Acipenseriformes represent a phylogenetically basal clade of ray-finned fish characterized by unusual genomic traits, including paleopolyploid states of extant genomes with high chromosome numbers and slow rates of molecular evolution. Despite a high interest in this fish group, only a limited number of studies have been accomplished on the isolation and characterization of repetitive DNA, karyotype standardization is not yet complete, and sex chromosomes are still to be identified. Here, we applied next-generation sequencing and cluster analysis to characterize major fractions of sterlet (Acipenser ruthenus) repetitive DNA. Using FISH, we mapped 16 tandemly arranged sequences on sterlet chromosomes and found them to be unevenly distributed in the genome with a tendency to cluster in particular regions. Some of the satellite DNAs might be used as specific markers to identify individual chromosomes and their paralogs, resulting in the unequivocal identification of at least 18 chromosome pairs. Our results provide an insight into the characteristic genomic distribution of the most common sterlet repetitive sequences. Biased accumulation of repetitive DNAs in particular chromosomes makes them especially interesting for further search for cryptic sex chromosomes. Future studies of these sequences in other acipenserid species will provide new perspectives regarding the evolution of repetitive DNA within the genomes of this fish order. © 2017 S. Karger AG, Basel.

  16. The Developmental Trajectory of Nonword Repetition

    Science.gov (United States)

    Chiat, Shula

    2006-01-01

    In line with the original presentation of nonword repetition as a measure of phonological short-term memory (Gathercole & Baddeley, 1989), the theoretical account Gathercole (2006) puts forward in her Keynote Article focuses on phonological storage as the key capacity common to nonword repetition and vocabulary acquisition. However, evidence that…

  17. Grade Repetition in Queensland State Prep Classes

    Science.gov (United States)

    Anderson, Robyn

    2012-01-01

    The current study considers grade repetition rates in the early years of schooling in Queensland state schools with specific focus on the pre-schooling year, Prep. In particular, it provides empirical evidence of grade repetition in Queensland state schools along with groups of students who are more often repeated. At the same time, much of the…

  18. Relationship between mRNA secondary structure and sequence variability in Chloroplast genes: possible life history implications.

    Science.gov (United States)

    Krishnan, Neeraja M; Seligmann, Hervé; Rao, Basuthkar J

    2008-01-28

    Synonymous sites are freer to vary because of redundancy in genetic code. Messenger RNA secondary structure restricts this freedom, as revealed by previous findings in mitochondrial genes that mutations at third codon position nucleotides in helices are more selected against than those in loops. This motivated us to explore the constraints imposed by mRNA secondary structure on evolutionary variability at all codon positions in general, in chloroplast systems. We found that the evolutionary variability and intrinsic secondary structure stability of these sequences share an inverse relationship. Simulations of most likely single nucleotide evolution in Psilotum nudum and Nephroselmis olivacea mRNAs, indicate that helix-forming propensities of mutated mRNAs are greater than those of the natural mRNAs for short sequences and vice-versa for long sequences. Moreover, helix-forming propensity estimated by the percentage of total mRNA in helices increases gradually with mRNA length, saturating beyond 1000 nucleotides. Protection levels of functionally important sites vary across plants and proteins: r-strategists minimize mutation costs in large genes; K-strategists do the opposite. Mrna length presumably predisposes shorter mRNAs to evolve under different constraints than longer mRNAs. The positive correlation between secondary structure protection and functional importance of sites suggests that some sites might be conserved due to packing-protection constraints at the nucleic acid level in addition to protein level constraints. Consequently, nucleic acid secondary structure a priori biases mutations. The converse (exposure of conserved sites) apparently occurs in a smaller number of cases, indicating a different evolutionary adaptive strategy in these plants. The differences between the protection levels of functionally important sites for r- and K-strategists reflect their respective molecular adaptive strategies. These converge with increasing domestication levels of

  19. Structure-Based Sequence Alignment of the Transmembrane Domains of All Human GPCRs: Phylogenetic, Structural and Functional Implications

    Science.gov (United States)

    Cvicek, Vaclav; Goddard, William A.; Abrol, Ravinder

    2016-01-01

    The understanding of G-protein coupled receptors (GPCRs) is undergoing a revolution due to increased information about their signaling and the experimental determination of structures for more than 25 receptors. The availability of at least one receptor structure for each of the GPCR classes, well separated in sequence space, enables an integrated superfamily-wide analysis to identify signatures involving the role of conserved residues, conserved contacts, and downstream signaling in the context of receptor structures. In this study, we align the transmembrane (TM) domains of all experimental GPCR structures to maximize the conserved inter-helical contacts. The resulting superfamily-wide GpcR Sequence-Structure (GRoSS) alignment of the TM domains for all human GPCR sequences is sufficient to generate a phylogenetic tree that correctly distinguishes all different GPCR classes, suggesting that the class-level differences in the GPCR superfamily are encoded at least partly in the TM domains. The inter-helical contacts conserved across all GPCR classes describe the evolutionarily conserved GPCR structural fold. The corresponding structural alignment of the inactive and active conformations, available for a few GPCRs, identifies activation hot-spot residues in the TM domains that get rewired upon activation. Many GPCR mutations, known to alter receptor signaling and cause disease, are located at these conserved contact and activation hot-spot residue positions. The GRoSS alignment places the chemosensory receptor subfamilies for bitter taste (TAS2R) and pheromones (Vomeronasal, VN1R) in the rhodopsin family, known to contain the chemosensory olfactory receptor subfamily. The GRoSS alignment also enables the quantification of the structural variability in the TM regions of experimental structures, useful for homology modeling and structure prediction of receptors. Furthermore, this alignment identifies structurally and functionally important residues in all human GPCRs

  20. Petrogenesis of the NE Gondwanan uppermost Ediacaran-Lower Cretaceous siliciclastic sequence of Jordan: Provenance, tectonic, and climatic implications

    Science.gov (United States)

    Amireh, Belal S.

    2018-04-01

    Detrital framework modes of the NE Gondwanan uppermost Ediacaran-Lower Cretaceous siliciclastic sequence of Jordan are determined employing the routine polarized light microscope. The lower part of this sequence constitutes a segment of the vast lower Paleozoic siliciclastic sheet flanking the northern Gondwana margin that was deposited over a regional unconformity truncating the outskirts of the East African orogen in the aftermath of the Neoproterozoic amalgamation of Gondwana. The research aims to evaluate the factors governing the detrital light mineral composition of this sandstone. The provenance terranes of the Arabian craton controlled by plate tectonics appear to be the primary factor in most of the formations, which could be either directly inferred employing Dickinson's compositional triangles or implied utilizing the petrographic data achieved and the available tectonic and geological data. The Arabian-Nubian Shield constitutes invariably the craton interior or the transitional provenance terrane within the NE Gondwana continental block that consistently supplied sandy detritus through northward-flowing braided rivers to all the lower Paleozoic formations. On the other hand, the Lower Cretaceous Series received siliciclastic debris, through braided-meandering rivers having same northward dispersal direction, additionally from the lower Paleozoic and lower-middle Mesozoic platform strata in the Arabian Craton. The formations making about 50% of the siliciclastic sequence represent a success for Dickinson's plate tectonics-provenance approach in attributing the detrital framework components primarily to the plate tectonic setting of the provenance terranes. However, even under this success, the varying effects of the other secondary sedimentological and paleoclimatological factors are important and could be crucial. The inapplicability of this approach to infer the appropriate provenance terranes of the remaining formations could be ascribed either to the

  1. Comparative sequence and structural analyses of G-protein-coupled receptor crystal structures and implications for molecular models.

    Directory of Open Access Journals (Sweden)

    Catherine L Worth

    Full Text Available BACKGROUND: Up until recently the only available experimental (high resolution structure of a G-protein-coupled receptor (GPCR was that of bovine rhodopsin. In the past few years the determination of GPCR structures has accelerated with three new receptors, as well as squid rhodopsin, being successfully crystallized. All share a common molecular architecture of seven transmembrane helices and can therefore serve as templates for building molecular models of homologous GPCRs. However, despite the common general architecture of these structures key differences do exist between them. The choice of which experimental GPCR structure(s to use for building a comparative model of a particular GPCR is unclear and without detailed structural and sequence analyses, could be arbitrary. The aim of this study is therefore to perform a systematic and detailed analysis of sequence-structure relationships of known GPCR structures. METHODOLOGY: We analyzed in detail conserved and unique sequence motifs and structural features in experimentally-determined GPCR structures. Deeper insight into specific and important structural features of GPCRs as well as valuable information for template selection has been gained. Using key features a workflow has been formulated for identifying the most appropriate template(s for building homology models of GPCRs of unknown structure. This workflow was applied to a set of 14 human family A GPCRs suggesting for each the most appropriate template(s for building a comparative molecular model. CONCLUSIONS: The available crystal structures represent only a subset of all possible structural variation in family A GPCRs. Some GPCRs have structural features that are distributed over different crystal structures or which are not present in the templates suggesting that homology models should be built using multiple templates. This study provides a systematic analysis of GPCR crystal structures and a consistent method for identifying

  2. Comparative sequence and structural analyses of G-protein-coupled receptor crystal structures and implications for molecular models.

    Science.gov (United States)

    Worth, Catherine L; Kleinau, Gunnar; Krause, Gerd

    2009-09-16

    Up until recently the only available experimental (high resolution) structure of a G-protein-coupled receptor (GPCR) was that of bovine rhodopsin. In the past few years the determination of GPCR structures has accelerated with three new receptors, as well as squid rhodopsin, being successfully crystallized. All share a common molecular architecture of seven transmembrane helices and can therefore serve as templates for building molecular models of homologous GPCRs. However, despite the common general architecture of these structures key differences do exist between them. The choice of which experimental GPCR structure(s) to use for building a comparative model of a particular GPCR is unclear and without detailed structural and sequence analyses, could be arbitrary. The aim of this study is therefore to perform a systematic and detailed analysis of sequence-structure relationships of known GPCR structures. We analyzed in detail conserved and unique sequence motifs and structural features in experimentally-determined GPCR structures. Deeper insight into specific and important structural features of GPCRs as well as valuable information for template selection has been gained. Using key features a workflow has been formulated for identifying the most appropriate template(s) for building homology models of GPCRs of unknown structure. This workflow was applied to a set of 14 human family A GPCRs suggesting for each the most appropriate template(s) for building a comparative molecular model. The available crystal structures represent only a subset of all possible structural variation in family A GPCRs. Some GPCRs have structural features that are distributed over different crystal structures or which are not present in the templates suggesting that homology models should be built using multiple templates. This study provides a systematic analysis of GPCR crystal structures and a consistent method for identifying suitable templates for GPCR homology modelling that will

  3. REPETITIVE STRENGTH AMONG STUDENTS OF AGE 14

    Directory of Open Access Journals (Sweden)

    Besim Halilaj

    2014-06-01

    Full Text Available The study involved 82 male students of the primary school “Qamil Ilazi” in Kaçanik-Kosovo.Four movement tests, which test the repetitive strength, were conducted: 1. Pull-up, 2. Sit-Up, 3. Back extension, 4. Push-up.The main goal of this study was to verify the actual motor status, respectively the component of the repetitive strength among students of age 14 of masculine gender. In addition to verifying the actual motor status, another objective was to verify the relationship between the variables employed.Basic statistical parameters show a distribution which is not significantly different from the normal distribution, yielded highly correlative values among the repetitive strength tests. Space factorization resulted in extracting two latent squares defined as repetitive strength of arms factor, and repetitive strength of body factor.

  4. Discovery of J chain in African lungfish (Protopterus dolloi, Sarcopterygii using high throughput transcriptome sequencing: implications in mucosal immunity.

    Directory of Open Access Journals (Sweden)

    Luca Tacchi

    Full Text Available J chain is a small polypeptide responsible for immunoglobulin (Ig polymerization and transport of Igs across mucosal surfaces in higher vertebrates. We identified a J chain in dipnoid fish, the African lungfish (Protopterus dolloi by high throughput sequencing of the transcriptome. P. dolloi J chain is 161 aa long and contains six of the eight Cys residues present in mammalian J chain. Phylogenetic studies place the lungfish J chain closer to tetrapod J chain than to the coelacanth or nurse shark sequences. J chain expression occurs in all P. dolloi immune tissues examined and it increases in the gut and kidney in response to an experimental bacterial infection. Double fluorescent in-situ hybridization shows that 88.5% of IgM⁺ cells in the gut co-express J chain, a significantly higher percentage than in the pre-pyloric spleen. Importantly, J chain expression is not restricted to the B-cell compartment since gut epithelial cells also express J chain. These results improve our current view of J chain from a phylogenetic perspective.

  5. Egg laying sequence influences egg mercury concentrations and egg size in three bird species: Implications for contaminant monitoring programs

    Science.gov (United States)

    Ackerman, Joshua T.; Eagles-Smith, Collin A.; Herzog, Mark P.; Yee, Julie L.; Hartman, C. Alex

    2016-01-01

    Bird eggs are commonly used in contaminant monitoring programs and toxicological risk assessments, but intra-clutch variation and sampling methodology could influence interpretability. We examined the influence of egg laying sequence on egg mercury concentrations and burdens in American avocets, black-necked stilts, and Forster's terns. The average decline in mercury concentrations between the first and last egg laid was 33% for stilts, 22% for terns, and 11% for avocets, and most of this decline occurred between the first and second eggs laid (24% for stilts, 18% for terns, and 9% for avocets). Trends in egg size with egg laying order were inconsistent among species and overall differences in egg volume, mass, length, and width were mercury concentrations generally declined by 16% between the first and second eggs laid. Despite the strong effect of egg laying sequence, most of the variance in egg mercury concentrations still occurred among clutches (75%-91%) rather than within clutches (9%-25%). Using simulations, we determined that to accurately estimate a population's mean egg mercury concentration using only a single random egg from a subset of nests, it would require sampling >60 nests to represent a large population (10% accuracy) or ≥14 nests to represent a small colony that contained <100 nests (20% accuracy).

  6. Stratigraphy, Sequence, and Crater Populations of Lunar Impact Basins from Lunar Orbiter Laser Altimeter (LOLA) Data: Implications for the Late Heavy Bombardment

    Science.gov (United States)

    Fassett, C. I.; Head, J. W.; Kadish, S. J.; Mazarico, E.; Neumann, G. A.; Smith, D. E.; Zuber, M. T.

    2012-01-01

    New measurements of the topography of the Moon from the Lunar Orbiter Laser Altimeter (LOLA)[1] provide an excellent base-map for analyzing the large crater population (D.20 km)of the lunar surface [2, 3]. We have recently used this data to calculate crater size-frequency distributions (CSFD) for 30 lunar impact basins, which have implications for their stratigraphy and sequence. These data provide an avenue for assessing the timing of the transitions between distinct crater populations characteristic of ancient and young lunar terrains, which has been linked to the late heavy bombardment (LHB). We also use LOLA data to re-examine relative stratigraphic relationships between key lunar basins.

  7. Repetitive negative thinking and suicide: a burgeoning literature with need for further exploration.

    Science.gov (United States)

    Law, Keyne C; Tucker, Raymond P

    2017-08-24

    Extant research has found a significant overlap between various repetitive negative thinking (RNT) patterns, such as rumination and worry, across different affective disorders implicating that the process of repetitive negative thinking is likely trans-diagnostic. Furthermore, RNT patterns at the core of psychiatric disorders associated with suicide (e.g., rumination and worry) have been found to be associated with suicide even after accounting for the disorder. A synthesis of existing literature on repetitive negative thoughts suggest that following negative emotional experiences, RNTs may lead to a sense of entrapment and hopelessness that may contribute to the onset of suicidal ideation and then facilitate the transition from thinking about suicide to making a suicide attempt by increasing an individual's capability for suicide through repetitive exposure to violent thoughts and imagery associated with suicide. Copyright © 2017 Elsevier Ltd. All rights reserved.

  8. Transduction of Repetitive Mechanical Stimuli by Piezo1 and Piezo2 Ion Channels

    Directory of Open Access Journals (Sweden)

    Amanda H. Lewis

    2017-06-01

    Full Text Available Several cell types experience repetitive mechanical stimuli, including vein endothelial cells during pulsating blood flow, inner ear hair cells upon sound exposure, and skin cells and their innervating dorsal root ganglion (DRG neurons when sweeping across a textured surface or touching a vibrating object. While mechanosensitive Piezo ion channels have been clearly implicated in sensing static touch, their roles in transducing repetitive stimulations are less clear. Here, we perform electrophysiological recordings of heterologously expressed mouse Piezo1 and Piezo2 responding to repetitive mechanical stimulations. We find that both channels function as pronounced frequency filters whose transduction efficiencies vary with stimulus frequency, waveform, and duration. We then use numerical simulations and human disease-related point mutations to demonstrate that channel inactivation is the molecular mechanism underlying frequency filtering and further show that frequency filtering is conserved in rapidly adapting mouse DRG neurons. Our results give insight into the potential contributions of Piezos in transducing repetitive mechanical stimuli.

  9. A repetitive probe for FISH analysis of bovine interphase nuclei

    Directory of Open Access Journals (Sweden)

    Cribiu Edmond

    2000-03-01

    Full Text Available Abstract The purpose of this study was to generate repetitive DNA sequence probes for the analysis of interphase nuclei by fluorescent in situ hybridisation (FISH. Such probes are useful for the diagnosis of chromosomal abnormalities in bovine preimplanted embryos. Of the seven probes (E1A, E4A, Ba, H1A, W18, W22, W5 that were generated and partially sequenced, five corresponded to previously described Bos taurus repetitive DNA (E1A, E4A, Ba, W18, W5, one probe (W22 shared no homology with other DNA sequences and one (H1A displayed a significant homology with Rattus norvegicus mRNA for secretin receptor transmembrane domain 3. Fluorescent in situ hybridisation was performed on metaphase bovine fibroblast cells and showed that five of the seven probes hybridised most centromeres (E1A, E4A, Ba, W18, W22, one labelled the arms of all chromosomes (W5 and the H1A probe was specific to three chromosomes (ch14, ch20, and ch25. Moreover, FISH with H1A resulted in interpretable signals on interphase nuclei in 88% of the cases, while the other probes yielded only dispersed overlapping signals.

  10. Whole-exome sequencing implicates DGKH as a risk gene for panic disorder in the Faroese population

    DEFF Research Database (Denmark)

    Gregersen, Noomi; Lescai, Francesco; Liang, Jieqin

    2016-01-01

    attacks, and genetic factors have been estimated to explain around 40% of the risk. In this study the potential enrichment of PD risk variants was explored based on whole-exome sequencing of 54 patients with PD and 211 control individuals from the Faroese population. No genome-wide significant......The demographic history of the isolated population of the Faroe Islands may have induced enrichment of variants rarely seen in outbred European populations, including enrichment of risk variants for panic disorder (PD). PD is a common mental disorder, characterized by recurring and unprovoked panic...... mental disorders. Additionally, we found an enrichment of PD risk variants in the Faroese population; variants with otherwise low frequency in more outbreed European populations. © 2016 Wiley Periodicals, Inc....

  11. Whole-exome sequencing of individuals from an isolated population implicates rare risk variants in bipolar disorder

    DEFF Research Database (Denmark)

    Lescai, F; Als, T D; Li, Q

    2017-01-01

    Bipolar disorder affects about 1% of the world's population, and its estimated heritability is about 75%. Only few whole genome or whole-exome sequencing studies in bipolar disorder have been reported, and no rare coding variants have yet been robustly identified. The use of isolated populations...... PITPNM2 missense variant, which is located in a highly significant schizophrenia GWAS locus. Likewise, PIK3C2A identified in the gene-based analysis is located in a combined bipolar and schizophrenia GWAS locus. Our results show support both for existing findings in the literature, as well as for new...... risk genes, and identify rare variants that might provide additional information on the underlying biology of bipolar disorder....

  12. Obsidian from volcanic sequences and rent alluvial deposits, Erzurum district, north-eastern Anatolia: Chemical characterisation and archaeological implications

    International Nuclear Information System (INIS)

    Brennan, P.; Sagona, T.

    1997-01-01

    Full text: Recent geoarchaeological research in the Erzurum district, north-eastern Anatolia, has revealed an abundance of obsidian at numerous neolithic and Bronze Age sites. Geochemical characterisation using neutron activation analysis indicates that the obsidian was obtained from several sources that are chemically distinct from the major sources already known from Central Anatolia an the Lake Van area. Multiple sources are represented in the samples collected from at least two of the sites, namely the sites of Sos and Pulur. The primary source of some of the obsidian utilised at the site of Sos has been located in the volcanic sequence outcropping tot he north-west of Pasinler. Field survey however has shown that the alluvial deposits along the main rivers and some of their tributaries were the main sources of the obsidian utilised at the sites near Erzurum. Trade or exchange of obsidian with sites outside the Erzurum area seems to have been limited

  13. Egg-laying sequence influences egg mercury concentrations and egg size in three bird species: Implications for contaminant monitoring programs.

    Science.gov (United States)

    Ackerman, Joshua T; Eagles-Smith, Collin A; Herzog, Mark P; Yee, Julie L; Hartman, C Alex

    2016-06-01

    Bird eggs are commonly used in contaminant monitoring programs and toxicological risk assessments, but intraclutch variation and sampling methodology could influence interpretability. The authors examined the influence of egg-laying sequence on egg mercury concentrations and burdens in American avocets, black-necked stilts, and Forster's terns. The average decline in mercury concentrations between the first and last eggs laid was 33% for stilts, 22% for terns, and 11% for avocets, and most of this decline occurred between the first and second eggs laid (24% for stilts, 18% for terns, and 9% for avocets). Trends in egg size with egg-laying order were inconsistent among species, and overall differences in egg volume, mass, length, and width were eggs laid. Despite the strong effect of egg-laying sequence, most of the variance in egg mercury concentrations still occurred among clutches (75-91%) rather than within clutches (9%-25%). Using simulations, the authors determined that accurate estimation of a population's mean egg mercury concentration using only a single random egg from a subset of nests would require sampling >60 nests to represent a large population (10% accuracy) or ≥14 nests to represent a small colony that contained <100 nests (20% accuracy). Environ Toxicol Chem 2016;35:1458-1469. Published 2015 Wiley Periodicals Inc. on behalf of SETAC. This article is a US Government work and, as such, is in the public domain in the United States of America. Published 2015 Wiley Periodicals Inc. on behalf of SETAC. This article is a US Government work and, as such, is in the public domain in the United States of America.

  14. MASS LOSS IN PRE-MAIN-SEQUENCE STARS VIA CORONAL MASS EJECTIONS AND IMPLICATIONS FOR ANGULAR MOMENTUM LOSS

    Energy Technology Data Exchange (ETDEWEB)

    Aarnio, Alicia N. [Astronomy Department, University of Michigan, 830 Dennison Building, 500 Church Street, Ann Arbor, MI 48109 (United States); Matt, Sean P. [Laboratoire AIM Paris-Saclay, CEA/Irfu Universite Paris-Diderot CNRS/INSU, F-91191 Gif-sur-Yvette (France); Stassun, Keivan G., E-mail: aarnio@umich.edu [Department of Physics and Astronomy, Vanderbilt University, Nashville, TN 37235 (United States)

    2012-11-20

    We develop an empirical model to estimate mass-loss rates via coronal mass ejections (CMEs) for solar-type pre-main-sequence (PMS) stars. Our method estimates the CME mass-loss rate from the observed energies of PMS X-ray flares, using our empirically determined relationship between solar X-ray flare energy and CME mass: log (M {sub CME}[g]) = 0.63 Multiplication-Sign log (E {sub flare}[erg]) - 2.57. Using masses determined for the largest flaring magnetic structures observed on PMS stars, we suggest that this solar-calibrated relationship may hold over 10 orders of magnitude in flare energy and 7 orders of magnitude in CME mass. The total CME mass-loss rate we calculate for typical solar-type PMS stars is in the range 10{sup -12}-10{sup -9} M {sub Sun} yr{sup -1}. We then use these CME mass-loss rate estimates to infer the attendant angular momentum loss leading up to the main sequence. Assuming that the CME outflow rate for a typical {approx}1 M {sub Sun} T Tauri star is <10{sup -10} M {sub Sun} yr{sup -1}, the resulting spin-down torque is too small during the first {approx}1 Myr to counteract the stellar spin-up due to contraction and accretion. However, if the CME mass-loss rate is {approx}> 10{sup -10} M {sub Sun} yr{sup -1}, as permitted by our calculations, then the CME spin-down torque may influence the stellar spin evolution after an age of a few Myr.

  15. Single-Cell Genome and Group-Specific dsrAB Sequencing Implicate Marine Members of the Class Dehalococcoidia (Phylum Chloroflexi) in Sulfur Cycling

    DEFF Research Database (Denmark)

    Wasmund, Kenneth; Cooper, Myriel; Schreiber, Lars

    2016-01-01

    The marine subsurface sediment biosphere is widely inhabited by bacteria affiliated with the class Dehalococcoidia (DEH), phylum Chloroflexi, and yet little is known regarding their metabolisms. In this report, genomic content from a single DEH cell (DEH-C11) with a 16S rRNA gene that was affilia......The marine subsurface sediment biosphere is widely inhabited by bacteria affiliated with the class Dehalococcoidia (DEH), phylum Chloroflexi, and yet little is known regarding their metabolisms. In this report, genomic content from a single DEH cell (DEH-C11) with a 16S rRNA gene...... that was affiliated with a diverse cluster of 16S rRNA gene sequences prevalent in marine sediments was obtained from sediments of Aarhus Bay, Denmark. The distinctive gene content of this cell suggests metabolic characteristics that differ from those of known DEH and Chloroflexi. The presence of genes encoding...... dissimilatory sulfite reductase (Dsr) suggests that DEH could respire oxidized sulfur compounds, although Chloroflexi have never been implicated in this mode of sulfur cycling. Using long-range PCR assays targeting DEH dsr loci, dsrAB genes were amplified and sequenced from various marine sediments. Many...

  16. Subjective duration distortions mirror neural repetition suppression.

    Science.gov (United States)

    Pariyadath, Vani; Eagleman, David M

    2012-01-01

    Subjective duration is strongly influenced by repetition and novelty, such that an oddball stimulus in a stream of repeated stimuli appears to last longer in duration in comparison. We hypothesize that this duration illusion, called the temporal oddball effect, is a result of the difference in expectation between the oddball and the repeated stimuli. Specifically, we conjecture that the repeated stimuli contract in duration as a result of increased predictability; these duration contractions, we suggest, result from decreased neural response amplitude with repetition, known as repetition suppression. Participants viewed trials consisting of lines presented at a particular orientation (standard stimuli) followed by a line presented at a different orientation (oddball stimulus). We found that the size of the oddball effect correlates with the number of repetitions of the standard stimulus as well as the amount of deviance from the oddball stimulus; both of these results are consistent with a repetition suppression hypothesis. Further, we find that the temporal oddball effect is sensitive to experimental context--that is, the size of the oddball effect for a particular experimental trial is influenced by the range of duration distortions seen in preceding trials. Our data suggest that the repetition-related duration contractions causing the oddball effect are a result of neural repetition suppression. More generally, subjective duration may reflect the prediction error associated with a stimulus and, consequently, the efficiency of encoding that stimulus. Additionally, we emphasize that experimental context effects need to be taken into consideration when designing duration-related tasks.

  17. Understanding communicative actions: a repetitive TMS study.

    Science.gov (United States)

    Stolk, Arjen; Noordzij, Matthijs L; Volman, Inge; Verhagen, Lennart; Overeem, Sebastiaan; van Elswijk, Gijs; Bloem, Bas; Hagoort, Peter; Toni, Ivan

    2014-02-01

    Despite the ambiguity inherent in human communication, people are remarkably efficient in establishing mutual understanding. Studying how people communicate in novel settings provides a window into the mechanisms supporting the human competence to rapidly generate and understand novel shared symbols, a fundamental property of human communication. Previous work indicates that the right posterior superior temporal sulcus (pSTS) is involved when people understand the intended meaning of novel communicative actions. Here, we set out to test whether normal functioning of this cerebral structure is required for understanding novel communicative actions using inhibitory low-frequency repetitive transcranial magnetic stimulation (rTMS). A factorial experimental design contrasted two tightly matched stimulation sites (right pSTS vs left MT+, i.e., a contiguous homotopic task-relevant region) and tasks (a communicative task vs a visual tracking task that used the same sequences of stimuli). Overall task performance was not affected by rTMS, whereas changes in task performance over time were disrupted according to TMS site and task combinations. Namely, rTMS over pSTS led to a diminished ability to improve action understanding on the basis of recent communicative history, while rTMS over MT+ perturbed improvement in visual tracking over trials. These findings qualify the contributions of the right pSTS to human communicative abilities, showing that this region might be necessary for incorporating previous knowledge, accumulated during interactions with a communicative partner, to constrain the inferential process that leads to action understanding. Copyright © 2013 Elsevier Ltd. All rights reserved.

  18. Preschool speech articulation and nonword repetition abilities may help predict eventual recovery or persistence of stuttering.

    Science.gov (United States)

    Spencer, Caroline; Weber-Fox, Christine

    2014-09-01

    In preschool children, we investigated whether expressive and receptive language, phonological, articulatory, and/or verbal working memory proficiencies aid in predicting eventual recovery or persistence of stuttering. Participants included 65 children, including 25 children who do not stutter (CWNS) and 40 who stutter (CWS) recruited at age 3;9-5;8. At initial testing, participants were administered the Test of Auditory Comprehension of Language, 3rd edition (TACL-3), Structured Photographic Expressive Language Test, 3rd edition (SPELT-3), Bankson-Bernthal Test of Phonology-Consonant Inventory subtest (BBTOP-CI), Nonword Repetition Test (NRT; Dollaghan & Campbell, 1998), and Test of Auditory Perceptual Skills-Revised (TAPS-R) auditory number memory and auditory word memory subtests. Stuttering behaviors of CWS were assessed in subsequent years, forming groups whose stuttering eventually persisted (CWS-Per; n=19) or recovered (CWS-Rec; n=21). Proficiency scores in morphosyntactic skills, consonant production, verbal working memory for known words, and phonological working memory and speech production for novel nonwords obtained at the initial testing were analyzed for each group. CWS-Per were less proficient than CWNS and CWS-Rec in measures of consonant production (BBTOP-CI) and repetition of novel phonological sequences (NRT). In contrast, receptive language, expressive language, and verbal working memory abilities did not distinguish CWS-Rec from CWS-Per. Binary logistic regression analysis indicated that preschool BBTOP-CI scores and overall NRT proficiency significantly predicted future recovery status. Results suggest that phonological and speech articulation abilities in the preschool years should be considered with other predictive factors as part of a comprehensive risk assessment for the development of chronic stuttering. At the end of this activity the reader will be able to: (1) describe the current status of nonlinguistic and linguistic predictors for

  19. Tool Sequence Trends in Minimally Invasive Surgery: Statistical Analysis and Implications for Predictive Control of Multifunction Instruments

    Directory of Open Access Journals (Sweden)

    Carl A. Nelson

    2012-01-01

    Full Text Available This paper presents an analysis of 67 minimally invasive surgical procedures covering 11 different procedure types to determine patterns of tool use. A new graph-theoretic approach was taken to organize and analyze the data. Through grouping surgeries by type, trends of common tool changes were identified. Using the concept of signal/noise ratio, these trends were found to be statistically strong. The tool-use trends were used to generate tool placement patterns for modular (multi-tool, cartridge-type surgical tool systems, and the same 67 surgeries were numerically simulated to determine the optimality of these tool arrangements. The results indicate that aggregated tool-use data (by procedure type can be employed to predict tool-use sequences with good accuracy, and also indicate the potential for artificial intelligence as a means of preoperative and/or intraoperative planning. Furthermore, this suggests that the use of multifunction surgical tools can be optimized to streamline surgical workflow.

  20. Molecular phylogeny of north mediterranean freshwater barbs (genus Barbus: cyprinidae) inferred from cytochrome b sequences: biogeographic and systematic implications.

    Science.gov (United States)

    Tsigenopoulos, C S; Berrebi, P

    2000-02-01

    We investigated phylogenetic relationships among north Mediterranean species of the genus Barbus using sequences of the cytochrome b gene. Our results indicate that the species belong to two major clades that are consistent with those previously defined from morphological features. The first clade includes species ranging from France to the Black Sea. In this clade, there is a well-supported monophyletic group of large-sized fluvio-lacustrine barbs; however, the monophyly of the small-sized rheophilic species is not clear. The second clade comprises species found in Spain, Greece, and Asia Minor and probably represents the oldest group present in the north Mediterranean rivers. In general, there is good concordance between geography and phylogenetic relationships. These results are compared to those from previous morphological- and allozyme-based studies and demonstrate widespread discordance and polyphyly in the traditional taxonomy of the genus Barbus. This study is one of the first reporting the phylogenetic and biogeographic relationships of a genus that is widely distributed in European rivers and contains species that are a major component of the European ichthyofauna. Copyright 2000 Academic Press.

  1. 15N/14N variations in Cretaceous Atlantic sedimentary sequences: implication for past changes in marine nitrogen biogeochemistry

    Science.gov (United States)

    Rau, G.H.; Arthur, M.A.; Dean, W.E.

    1987-01-01

    At two locations in the Atlantic Ocean (DSDP Sites 367 and 530) early to middle Cretaceous organic-carbon-rich beds ("black shales") were found to have significantly lower ??15N values (lower 15N/14N ratios) than adjacent organic-carbon-poor beds (white limestones or green claystones). While these lithologies are of marine origin, the black strata in particular have ??15N values that are significantly lower than those previously found in the marine sediment record and most contemporary marine nitrogen pools. In contrast, black, organic-carbon-rich beds at a third site (DSDP Site 603) contain predominantly terrestrial organic matter and have C- and N-isotopic compositions similar to organic matter of modern terrestrial origin. The recurring 15N depletion in the marine-derived Cretaceous sequences prove that the nitrogen they contain is the end result of an episodic and atypical biogeochemistry. Existing isotopic and other data indicate that the low 15N relative abundance is the consequence of pelagic rather than post-depositional processes. Reduced ocean circulation, increased denitrification, and, hence, reduced euphotic zone nitrate availability may have led to Cretaceous phytoplankton assemblages that were periodically dominated by N2-fixing blue-green algae, a possible source of this sediment 15N-depletion. Lack of parallel isotopic shifts in Cretaceous terrestrially-derived nitrogen (Site 603) argues that the above change in nitrogen cycling during this period did not extend beyond the marine environment. ?? 1987.

  2. A phylogenetic hypothesis for passerine birds: taxonomic and biogeographic implications of an analysis of nuclear DNA sequence data.

    Science.gov (United States)

    Barker, F Keith; Barrowclough, George F; Groth, Jeff G

    2002-02-07

    Passerine birds comprise over half of avian diversity, but have proved difficult to classify. Despite a long history of work on this group, no comprehensive hypothesis of passerine family-level relationships was available until recent analyses of DNA-DNA hybridization data. Unfortunately, given the value of such a hypothesis in comparative studies of passerine ecology and behaviour, the DNA-hybridization results have not been well tested using independent data and analytical approaches. Therefore, we analysed nucleotide sequence variation at the nuclear RAG-1 and c-mos genes from 69 passerine taxa, including representatives of most currently recognized families. In contradiction to previous DNA-hybridization studies, our analyses suggest paraphyly of suboscine passerines because the suboscine New Zealand wren Acanthisitta was found to be sister to all other passerines. Additionally, we reconstructed the parvorder Corvida as a basal paraphyletic grade within the oscine passerines. Finally, we found strong evidence that several family-level taxa are misplaced in the hybridization results, including the Alaudidae, Irenidae, and Melanocharitidae. The hypothesis of relationships we present here suggests that the oscine passerines arose on the Australian continental plate while it was isolated by oceanic barriers and that a major northern radiation of oscines (i.e. the parvorder Passerida) originated subsequent to dispersal from the south.

  3. Repetitive element transcripts are elevated in the brain of C9orf72 ALS/FTLD patients.

    Science.gov (United States)

    Prudencio, Mercedes; Gonzales, Patrick K; Cook, Casey N; Gendron, Tania F; Daughrity, Lillian M; Song, Yuping; Ebbert, Mark T W; van Blitterswijk, Marka; Zhang, Yong-Jie; Jansen-West, Karen; Baker, Matthew C; DeTure, Michael; Rademakers, Rosa; Boylan, Kevin B; Dickson, Dennis W; Petrucelli, Leonard; Link, Christopher D

    2017-09-01

    Significant transcriptome alterations are detected in the brain of patients with amyotrophic lateral sclerosis (ALS), including carriers of the C9orf72 repeat expansion and C9orf72-negative sporadic cases. Recently, the expression of repetitive element transcripts has been associated with toxicity and, while increased repetitive element expression has been observed in several neurodegenerative diseases, little is known about their contribution to ALS. To assess whether aberrant expression of repetitive element sequences are observed in ALS, we analysed RNA sequencing data from C9orf72-positive and sporadic ALS cases, as well as healthy controls. Transcripts from multiple classes and subclasses of repetitive elements (LINEs, endogenous retroviruses, DNA transposons, simple repeats, etc.) were significantly increased in the frontal cortex of C9orf72 ALS patients. A large collection of patient samples, representing both C9orf72 positive and negative ALS, ALS/FTLD, and FTLD cases, was used to validate the levels of several repetitive element transcripts. These analyses confirmed that repetitive element expression was significantly increased in C9orf72-positive compared to C9orf72-negative or control cases. While previous studies suggest an important link between TDP-43 and repetitive element biology, our data indicate that TDP-43 pathology alone is insufficient to account for the observed changes in repetitive elements in ALS/FTLD. Instead, we found that repetitive element expression positively correlated with RNA polymerase II activity in postmortem brain, and pharmacologic modulation of RNA polymerase II activity altered repetitive element expression in vitro. We conclude that increased RNA polymerase II activity in ALS/FTLD may lead to increased repetitive element transcript expression, a novel pathological feature of ALS/FTLD. © The Author 2017. Published by Oxford University Press.

  4. Rhipicephalus (Boophilus) microplus strain Deutsch, whole genome shotgun sequencing project first submission of genome sequence

    Science.gov (United States)

    The size and repetitive nature of the Rhipicephalus microplus genome makes obtaining a full genome sequence difficult. Cot filtration/selection techniques were used to reduce the repetitive fraction of the tick genome and enrich for the fraction of DNA with gene-containing regions. The Cot-selected ...

  5. Whole exome re-sequencing implicates CCDC38 and cilia structure and function in resistance to smoking related airflow obstruction.

    Directory of Open Access Journals (Sweden)

    Louise V Wain

    2014-05-01

    Full Text Available Chronic obstructive pulmonary disease (COPD is a leading cause of global morbidity and mortality and, whilst smoking remains the single most important risk factor, COPD risk is heritable. Of 26 independent genomic regions showing association with lung function in genome-wide association studies, eleven have been reported to show association with airflow obstruction. Although the main risk factor for COPD is smoking, some individuals are observed to have a high forced expired volume in 1 second (FEV1 despite many years of heavy smoking. We hypothesised that these "resistant smokers" may harbour variants which protect against lung function decline caused by smoking and provide insight into the genetic determinants of lung health. We undertook whole exome re-sequencing of 100 heavy smokers who had healthy lung function given their age, sex, height and smoking history and applied three complementary approaches to explore the genetic architecture of smoking resistance. Firstly, we identified novel functional variants in the "resistant smokers" and looked for enrichment of these novel variants within biological pathways. Secondly, we undertook association testing of all exonic variants individually with two independent control sets. Thirdly, we undertook gene-based association testing of all exonic variants. Our strongest signal of association with smoking resistance for a non-synonymous SNP was for rs10859974 (P = 2.34 × 10(-4 in CCDC38, a gene which has previously been reported to show association with FEV1/FVC, and we demonstrate moderate expression of CCDC38 in bronchial epithelial cells. We identified an enrichment of novel putatively functional variants in genes related to cilia structure and function in resistant smokers. Ciliary function abnormalities are known to be associated with both smoking and reduced mucociliary clearance in patients with COPD. We suggest that genetic influences on the development or function of cilia in the bronchial

  6. Repetitive Bibliographical Information in Relational Databases.

    Science.gov (United States)

    Brooks, Terrence A.

    1988-01-01

    Proposes a solution to the problem of loading repetitive bibliographic information in a microcomputer-based relational database management system. The alternative design described is based on a representational redundancy design and normalization theory. (12 references) (Author/CLB)

  7. Analysis of full coding sequence of the TP53 gene in invasive vulvar cancers: Implications for therapy.

    Science.gov (United States)

    Kashofer, Karl; Regauer, Sigrid

    2017-08-01

    This study evaluates the frequency and type of TP53 gene mutations and HPV status in 72 consecutively diagnosed primary invasive vulvar squamous cell carcinomas (SCC) during the past 5years. DNA of formalin-fixed and paraffin embedded tumour tissue was analysed for 32 HPV subtypes and the full coding sequence of the TP53 gene, and correlated with results of p53 immunohistochemistry. 13/72 (18%) cancers were HPV-induced squamous cell carcinomas, of which 1/13 (8%) carcinoma harboured a somatic TP53 mutation. Among the 59/72 (82%) HPV-negative cancers, 59/72 (82%) SCC were HPV-negative with wild-type gene in 14/59 (24%) SCC and somatic TP53 mutations in 45/59 (76%) SCC. 28/45 (62%) SCC carried one (n=20) or two (n=8) missense mutations. 11/45 (24%) carcinomas showed a single disruptive mutation (3× frame shift, 7× stop codon, 1× deletion), 3/45 SCC a splice site mutation. 3/45 (7%) carcinomas had 2 or 3 different mutations. 18 different "hot spot" mutations were observed in 22/45 cancers (49%; 5× R273, 3× R282; 2× each Y220, R278, R248). Immunohistochemical p53 over expression was identified in most SCC with missense mutations, but not in SCC with disruptive TP53 mutations or TP53 wild-type. 14/45 (31%) patients with TP53 mutated SCC died of disease within 12months (range 2-24months) versus 0/13 patients with HPV-induced carcinomas and 0/14 patients with HPV-negative, TP53 wild-type carcinomas. 80% of primary invasive vulvar SCC were HPV-negative carcinomas with a high frequency of disruptive mutations and "hot spot" TP53 gene mutations, which have been linked to chemo- and radioresistance. The death rate of patients with p53 mutated vulvar cancers was 31%. Immunohistochemical p53 over expression could not reliably identify SCC with TP53 gene mutation. Pharmacological therapies targeting mutant p53 will be promising strategies for personalized therapy in patients with TP53 mutated vulvar cancers. Copyright © 2017. Published by Elsevier Inc.

  8. Document retrieval on repetitive string collections.

    Science.gov (United States)

    Gagie, Travis; Hartikainen, Aleksi; Karhu, Kalle; Kärkkäinen, Juha; Navarro, Gonzalo; Puglisi, Simon J; Sirén, Jouni

    2017-01-01

    Most of the fastest-growing string collections today are repetitive, that is, most of the constituent documents are similar to many others. As these collections keep growing, a key approach to handling them is to exploit their repetitiveness, which can reduce their space usage by orders of magnitude. We study the problem of indexing repetitive string collections in order to perform efficient document retrieval operations on them. Document retrieval problems are routinely solved by search engines on large natural language collections, but the techniques are less developed on generic string collections. The case of repetitive string collections is even less understood, and there are very few existing solutions. We develop two novel ideas, interleaved LCPs and precomputed document lists , that yield highly compressed indexes solving the problem of document listing (find all the documents where a string appears), top- k document retrieval (find the k documents where a string appears most often), and document counting (count the number of documents where a string appears). We also show that a classical data structure supporting the latter query becomes highly compressible on repetitive data. Finally, we show how the tools we developed can be combined to solve ranked conjunctive and disjunctive multi-term queries under the simple [Formula: see text] model of relevance. We thoroughly evaluate the resulting techniques in various real-life repetitiveness scenarios, and recommend the best choices for each case.

  9. A characterization of linearly repetitive cut and project sets

    Science.gov (United States)

    Haynes, Alan; Koivusalo, Henna; Walton, James

    2018-02-01

    For the development of a mathematical theory which can be used to rigorously investigate physical properties of quasicrystals, it is necessary to understand regularity of patterns in special classes of aperiodic point sets in Euclidean space. In one dimension, prototypical mathematical models for quasicrystals are provided by Sturmian sequences and by point sets generated by substitution rules. Regularity properties of such sets are well understood, thanks mostly to well known results by Morse and Hedlund, and physicists have used this understanding to study one dimensional random Schrödinger operators and lattice gas models. A key fact which plays an important role in these problems is the existence of a subadditive ergodic theorem, which is guaranteed when the corresponding point set is linearly repetitive. In this paper we extend the one-dimensional model to cut and project sets, which generalize Sturmian sequences in higher dimensions, and which are frequently used in mathematical and physical literature as models for higher dimensional quasicrystals. By using a combination of algebraic, geometric, and dynamical techniques, together with input from higher dimensional Diophantine approximation, we give a complete characterization of all linearly repetitive cut and project sets with cubical windows. We also prove that these are precisely the collection of such sets which satisfy subadditive ergodic theorems. The results are explicit enough to allow us to apply them to known classical models, and to construct linearly repetitive cut and project sets in all pairs of dimensions and codimensions in which they exist. Research supported by EPSRC grants EP/L001462, EP/J00149X, EP/M023540. HK also gratefully acknowledges the support of the Osk. Huttunen foundation.

  10. Independent and additive repetition priming of motion direction and color in visual search.

    Science.gov (United States)

    Kristjánsson, Arni

    2009-03-01

    Priming of visual search for Gabor patch stimuli, varying in color and local drift direction, was investigated. The task relevance of each feature varied between the different experimental conditions compared. When the target defining dimension was color, a large effect of color repetition was seen as well as a smaller effect of the repetition of motion direction. The opposite priming pattern was seen when motion direction defined the target--the effect of motion direction repetition was this time larger than for color repetition. Finally, when neither was task relevant, and the target defining dimension was the spatial frequency of the Gabor patch, priming was seen for repetition of both color and motion direction, but the effects were smaller than in the previous two conditions. These results show that features do not necessarily have to be task relevant for priming to occur. There is little interaction between priming following repetition of color and motion, these two features show independent and additive priming effects, most likely reflecting that the two features are processed at separate processing sites in the nervous system, consistent with previous findings from neuropsychology & neurophysiology. The implications of the findings for theoretical accounts of priming in visual search are discussed.

  11. Tactile Ranschburg effects: facilitation and inhibitory repetition effects analogous to verbal memory.

    Science.gov (United States)

    Roe, Daisy; Miles, Christopher; Johnson, Andrew J

    2017-07-01

    The present paper examines the effect of within-sequence item repetitions in tactile order memory. Employing an immediate serial recall procedure, participants reconstructed a six-item sequence tapped upon their fingers by moving those fingers in the order of original stimulation. In Experiment 1a, within-sequence repetition of an item separated by two-intervening items resulted in a significant reduction in recall accuracy for that repeated item (i.e., the Ranschburg effect). In Experiment 1b, within-sequence repetition of an adjacent item resulted in significant recall facilitation for that repeated item. These effects mirror those reported for verbal stimuli (e.g., Henson, 1998a . Item repetition in short-term memory: Ranschburg repeated. Journal of Experimental Psychology: Learning, Memory, and Cognition, 24(5), 1162-1181. doi:doi.org/10.1037/0278-7393.24.5.1162). These data are the first to demonstrate the Ranschburg effect with non-verbal stimuli and suggest further cross-modal similarities in order memory.

  12. Subjective duration distortions mirror neural repetition suppression.

    Directory of Open Access Journals (Sweden)

    Vani Pariyadath

    Full Text Available Subjective duration is strongly influenced by repetition and novelty, such that an oddball stimulus in a stream of repeated stimuli appears to last longer in duration in comparison. We hypothesize that this duration illusion, called the temporal oddball effect, is a result of the difference in expectation between the oddball and the repeated stimuli. Specifically, we conjecture that the repeated stimuli contract in duration as a result of increased predictability; these duration contractions, we suggest, result from decreased neural response amplitude with repetition, known as repetition suppression.Participants viewed trials consisting of lines presented at a particular orientation (standard stimuli followed by a line presented at a different orientation (oddball stimulus. We found that the size of the oddball effect correlates with the number of repetitions of the standard stimulus as well as the amount of deviance from the oddball stimulus; both of these results are consistent with a repetition suppression hypothesis. Further, we find that the temporal oddball effect is sensitive to experimental context--that is, the size of the oddball effect for a particular experimental trial is influenced by the range of duration distortions seen in preceding trials.Our data suggest that the repetition-related duration contractions causing the oddball effect are a result of neural repetition suppression. More generally, subjective duration may reflect the prediction error associated with a stimulus and, consequently, the efficiency of encoding that stimulus. Additionally, we emphasize that experimental context effects need to be taken into consideration when designing duration-related tasks.

  13. Concreteness of Positive, Negative, and Neutral Repetitive Thinking About the Future

    Science.gov (United States)

    Behar, Evelyn; McGowan, Sarah Kate; McLaughlin, Katie A.; Borkovec, T.D.; Goldwin, Michelle; Bjorkquist, Olivia

    2014-01-01

    Consistent with assertions that the adaptiveness of repetitive thinking is influenced by both its valence and style, Stöber (e.g., Stöber & Borkovec, 2002) has argued that worry is characterized by a reduced concreteness of thought content and that the resulting abstractness contributes to its inhibition of some aspects of anxious responding. However, extant research does not provide a direct test of Stöber’s reduced concreteness theory of worry. We sought to test Stöber’s theory and to examine the adaptiveness of repetitive worrisome thinking by randomly assigning 108 participants to engage in five consecutive periods of repetitive thinking about positively, negatively, or neutrally valenced potential future events. Results based on coding of thought data indicated that (a) repetitive thinking became increasingly less concrete as periods progressed; (b) contrary to Stöber’s theory, both negative and positive repetitive future thinking were more concrete than neutral repetitive future thinking (and did not differ from each other); and (c) abstractness of thought during negative repetitive future thinking was associated with reduced reports of imagery-based activity. Results based on self-reported affect indicated that negatively valenced repetitive future thinking was uniquely associated with initial decreases in anxious affect, followed by increased anxious affect that coincided with increased imagery-based activity. This suggests that worry is associated with a sequential mitigation of anxious meaning followed by a strengthening of anxious meaning over time. Theoretical and clinical implications of these findings are discussed. PMID:22440067

  14. Structurally Complex Organization of Repetitive DNAs in the Genome of Cobia (Rachycentron canadum).

    Science.gov (United States)

    Costa, Gideão W W F; Cioffi, Marcelo de B; Bertollo, Luiz A C; Molina, Wagner F

    2015-06-01

    Repetitive DNAs comprise the largest fraction of the eukaryotic genome. They include microsatellites or simple sequence repeats (SSRs), which play an important role in the chromosome differentiation among fishes. Rachycentron canadum is the only representative of the family Rachycentridae. This species has been focused on several multidisciplinary studies in view of its important potential for marine fish farming. In the present study, distinct classes of repetitive DNAs, with emphasis on SSRs, were mapped in the chromosomes of this species to improve the knowledge of its genome organization. Microsatellites exhibited a diversified distribution, both dispersed in euchromatin and clustered in the heterochromatin. The multilocus location of SSRs strengthened the heterochromatin heterogeneity in this species, as suggested by some previous studies. The colocalization of SSRs with retrotransposons and transposons pointed to a close evolutionary relationship between these repetitive sequences. A number of heterochromatic regions highlighted a greater complex organization than previously supposed, harboring a diversity of repetitive elements. In this sense, there was also evidence of colocalization of active genetic regions and different classes of repetitive DNAs in a common heterochromatic region, which offers a potential opportunity for further researches regarding the interaction of these distinct fractions in fish genomes.

  15. Neural dynamics during repetitive visual stimulation

    Science.gov (United States)

    Tsoneva, Tsvetomira; Garcia-Molina, Gary; Desain, Peter

    2015-12-01

    Objective. Steady-state visual evoked potentials (SSVEPs), the brain responses to repetitive visual stimulation (RVS), are widely utilized in neuroscience. Their high signal-to-noise ratio and ability to entrain oscillatory brain activity are beneficial for their applications in brain-computer interfaces, investigation of neural processes underlying brain rhythmic activity (steady-state topography) and probing the causal role of brain rhythms in cognition and emotion. This paper aims at analyzing the space and time EEG dynamics in response to RVS at the frequency of stimulation and ongoing rhythms in the delta, theta, alpha, beta, and gamma bands. Approach.We used electroencephalography (EEG) to study the oscillatory brain dynamics during RVS at 10 frequencies in the gamma band (40-60 Hz). We collected an extensive EEG data set from 32 participants and analyzed the RVS evoked and induced responses in the time-frequency domain. Main results. Stable SSVEP over parieto-occipital sites was observed at each of the fundamental frequencies and their harmonics and sub-harmonics. Both the strength and the spatial propagation of the SSVEP response seem sensitive to stimulus frequency. The SSVEP was more localized around the parieto-occipital sites for higher frequencies (>54 Hz) and spread to fronto-central locations for lower frequencies. We observed a strong negative correlation between stimulation frequency and relative power change at that frequency, the first harmonic and the sub-harmonic components over occipital sites. Interestingly, over parietal sites for sub-harmonics a positive correlation of relative power change and stimulation frequency was found. A number of distinct patterns in delta (1-4 Hz), theta (4-8 Hz), alpha (8-12 Hz) and beta (15-30 Hz) bands were also observed. The transient response, from 0 to about 300 ms after stimulation onset, was accompanied by increase in delta and theta power over fronto-central and occipital sites, which returned to baseline

  16. Refining borders of genome-rearrangements including repetitions

    Directory of Open Access Journals (Sweden)

    JA Arjona-Medina

    2016-10-01

    Full Text Available Abstract Background DNA rearrangement events have been widely studied in comparative genomic for many years. The importance of these events resides not only in the study about relatedness among different species, but also to determine the mechanisms behind evolution. Although there are many methods to identify genome-rearrangements (GR, the refinement of their borders has become a huge challenge. Until now no accepted method exists to achieve accurate fine-tuning: i.e. the notion of breakpoint (BP is still an open issue, and despite repeated regions are vital to understand evolution they are not taken into account in most of the GR detection and refinement methods. Methods and results We propose a method to refine the borders of GR including repeated regions. Instead of removing these repetitions to facilitate computation, we take advantage of them using a consensus alignment sequence of the repeated region in between two blocks. Using the concept of identity vectors for Synteny Blocks (SB and repetitions, a Finite State Machine is designed to detect transition points in the difference between such vectors. The method does not force the BP to be a region or a point but depends on the alignment transitions within the SBs and repetitions. Conclusion The accurate definition of the borders of SB and repeated genomic regions and consequently the detection of BP might help to understand the evolutionary model of species. In this manuscript we present a new proposal for such a refinement. Features of the SBs borders and BPs are different and fit with what is expected. SBs with more diversity in annotations and BPs short and richer in DNA replication and stress response, which are strongly linked with rearrangements.

  17. Targeted next-generation sequencing reveals novel USH2A mutations associated with diverse disease phenotypes: implications for clinical and molecular diagnosis.

    Science.gov (United States)

    Chen, Xue; Sheng, Xunlun; Liu, Xiaoxing; Li, Huiping; Liu, Yani; Rong, Weining; Ha, Shaoping; Liu, Wenzhou; Kang, Xiaoli; Zhao, Kanxing; Zhao, Chen

    2014-01-01

    USH2A mutations have been implicated in the disease etiology of several inherited diseases, including Usher syndrome type 2 (USH2), nonsyndromic retinitis pigmentosa (RP), and nonsyndromic deafness. The complex genetic and phenotypic spectrums relevant to USH2A defects make it difficult to manage patients with such mutations. In the present study, we aim to determine the genetic etiology and to characterize the correlated clinical phenotypes for three Chinese pedigrees with nonsyndromic RP, one with RP sine pigmento (RPSP), and one with USH2. Family histories and clinical details for all included patients were reviewed. Ophthalmic examinations included best corrected visual acuities, visual field measurements, funduscopy, and electroretinography. Targeted next-generation sequencing (NGS) was applied using two sequence capture arrays to reveal the disease causative mutations for each family. Genotype-phenotype correlations were also annotated. Seven USH2A mutations, including four missense substitutions (p.P2762A, p.G3320C, p.R3719H, and p.G4763R), two splice site variants (c.8223+1G>A and c.8559-2T>C), and a nonsense mutation (p.Y3745*), were identified as disease causative in the five investigated families, of which three reported to have consanguineous marriage. Among all seven mutations, six were novel, and one was recurrent. Two homozygous missense mutations (p.P2762A and p.G3320C) were found in one individual family suggesting a potential double hit effect. Significant phenotypic divergences were revealed among the five families. Three families of the five families were affected with early, moderated, or late onset RP, one with RPSP, and the other one with USH2. Our study expands the genotypic and phenotypic variability relevant to USH2A mutations, which would help with a clear insight into the complex genetic and phenotypic spectrums relevant to USH2A defects, and is complementary for a better management of patients with such mutations. We have also

  18. Targeted next-generation sequencing reveals novel USH2A mutations associated with diverse disease phenotypes: implications for clinical and molecular diagnosis.

    Directory of Open Access Journals (Sweden)

    Xue Chen

    Full Text Available USH2A mutations have been implicated in the disease etiology of several inherited diseases, including Usher syndrome type 2 (USH2, nonsyndromic retinitis pigmentosa (RP, and nonsyndromic deafness. The complex genetic and phenotypic spectrums relevant to USH2A defects make it difficult to manage patients with such mutations. In the present study, we aim to determine the genetic etiology and to characterize the correlated clinical phenotypes for three Chinese pedigrees with nonsyndromic RP, one with RP sine pigmento (RPSP, and one with USH2. Family histories and clinical details for all included patients were reviewed. Ophthalmic examinations included best corrected visual acuities, visual field measurements, funduscopy, and electroretinography. Targeted next-generation sequencing (NGS was applied using two sequence capture arrays to reveal the disease causative mutations for each family. Genotype-phenotype correlations were also annotated. Seven USH2A mutations, including four missense substitutions (p.P2762A, p.G3320C, p.R3719H, and p.G4763R, two splice site variants (c.8223+1G>A and c.8559-2T>C, and a nonsense mutation (p.Y3745*, were identified as disease causative in the five investigated families, of which three reported to have consanguineous marriage. Among all seven mutations, six were novel, and one was recurrent. Two homozygous missense mutations (p.P2762A and p.G3320C were found in one individual family suggesting a potential double hit effect. Significant phenotypic divergences were revealed among the five families. Three families of the five families were affected with early, moderated, or late onset RP, one with RPSP, and the other one with USH2. Our study expands the genotypic and phenotypic variability relevant to USH2A mutations, which would help with a clear insight into the complex genetic and phenotypic spectrums relevant to USH2A defects, and is complementary for a better management of patients with such mutations. We have

  19. Storytelling and Repetitive Narratives for Design Empathy

    DEFF Research Database (Denmark)

    Fritsch, Jonas; Judice, Andrea; Soini, Katja

    2007-01-01

    study. In this paper, we show how we attained an empathic understanding through storytelling and aroused empathy to others using repetitive narratives in an experimental presentation bringing forth factual, reflective and experiential aspects of the user information. Taking as a starting point our...

  20. Universal data compression and repetition times

    NARCIS (Netherlands)

    Willems, Frans M J

    1989-01-01

    A new universal data compression algorithm is described. This algorithm encodes L source symbols at a time. For the class of binary stationary sources, its rate does not exceed [formula omitted] [formula omitted] bits per source symbol. In our analysis, a property of repetition times turns out to be

  1. Matriculation Research Report: Course Repetition Data & Analysis.

    Science.gov (United States)

    Gerda, Joe

    Due to concerns that its policy on class repetition was not promoting student success, California's College of the Canyons (CoC) undertook a project to analyze student course-taking patterns and make recommendations to modify the policy. Existing college policy did not follow Section 58161 of the State Educational Code that allows colleges to…

  2. Reducing Repetitive Speech: Effects of Strategy Instruction.

    Science.gov (United States)

    Dipipi, Caroline M.; Jitendra, Asha K.; Miller, Judith A.

    2001-01-01

    This article describes an intervention with an 18-year-old young woman with mild mental retardation and a seizure disorder, which focused on her repetitive echolalic verbalizations. The intervention included time delay, differential reinforcement of other behaviors, and self-monitoring. Overall, the intervention was successful in facilitating…

  3. Neurobehavioural Correlates of Abnormal Repetitive Behaviour

    Directory of Open Access Journals (Sweden)

    R. A. Ford

    1991-01-01

    Full Text Available Conditions in which echolalia and echopraxia occur are reviewed, followed by an attempt to elicit possible mechanisms of these phenomena. A brief description of stereotypical and perseverative behaviour and obsessional phenomena is given. It is suggested that abnormal repetitive behaviour may occur partly as a result of central dopaminergic dysfunction.

  4. Verbal Repetitions and Echolalia in Alzheimer's Discourse

    Science.gov (United States)

    Da Cruz, Fernanda Miranda

    2010-01-01

    This article reports on an investigation of echolalic repetition in Alzheimer's disease (AD). A qualitative analysis of data from spontaneous conversations with MHI, a woman with AD, is presented. The data come from the DALI Corpus, a corpus of spontaneous conversations involving subjects with AD. This study argues that echolalic effects can be…

  5. Bystanders' Reactions to Witnessing Repetitive Abuse Experiences

    Science.gov (United States)

    Janson, Gregory R.; Carney, JoLynn V.; Hazler, Richard J.; Oh, Insoo

    2009-01-01

    The Impact of Event Scale-Revised (D. S. Weiss & C. R. Marmar, 1997) was used to obtain self-reported trauma levels from 587 young adults recalling childhood or adolescence experiences as witnesses to common forms of repetitive abuse defined as bullying. Mean participant scores were in a range suggesting potential need for clinical assessment…

  6. Effects of modality and repetition in a continuous recognition memory task: Repetition has no effect on auditory recognition memory.

    Science.gov (United States)

    Amir Kassim, Azlina; Rehman, Rehan; Price, Jessica M

    2018-04-01

    Previous research has shown that auditory recognition memory is poorer compared to visual and cross-modal (visual and auditory) recognition memory. The effect of repetition on memory has been robust in showing improved performance. It is not clear, however, how auditory recognition memory compares to visual and cross-modal recognition memory following repetition. Participants performed a recognition memory task, making old/new discriminations to new stimuli, stimuli repeated for the first time after 4-7 intervening items (R1), or repeated for the second time after 36-39 intervening items (R2). Depending on the condition, participants were either exposed to visual stimuli (2D line drawings), auditory stimuli (spoken words), or cross-modal stimuli (pairs of images and associated spoken words). Results showed that unlike participants in the visual and cross-modal conditions, participants in the auditory recognition did not show improvements in performance on R2 trials compared to R1 trials. These findings have implications for pedagogical techniques in education, as well as for interventions and exercises aimed at boosting memory performance. Copyright © 2018 Elsevier B.V. All rights reserved.

  7. Corrigendum to "Three climatic cycles recorded in a loess-palaeosol sequence at Semlac (Romania)-Implications for dust accumulation in south-eastern Europe" [Quat. Sci. Rev. 154C (2016) 130-142

    Science.gov (United States)

    Zeeden, C.; Kels, H.; Hambach, U.; Schulte, P.; Protze, J.; Eckmeier, E.; Marković, S. B.; Klasen, N.; Lehmkuhl, F.

    2018-05-01

    In the article 'Three climatic cycles recorded in a loess-palaeosol sequence at Semlac (Romania)-Implications for dust accumulation in south-eastern Europe' (Zeeden et al., 2016) we employed rock magnetic and grain size proxy data in combination with OSL- and correlative age models. The data and dating is combined to discuss glacial-interglacial paleoclimate variability in an Eurasian context. This dataset was also interpreted regarding the dust source in the eastern Carpathian (Middle Danube) Basin.

  8. Assembly of highly repetitive genomes using short reads: the genome of discrete typing unit III Trypanosoma cruzi strain 231.

    Science.gov (United States)

    Baptista, Rodrigo P; Reis-Cunha, Joao Luis; DeBarry, Jeremy D; Chiari, Egler; Kissinger, Jessica C; Bartholomeu, Daniella C; Macedo, Andrea M

    2018-02-14

    Next-generation sequencing (NGS) methods are low-cost high-throughput technologies that produce thousands to millions of sequence reads. Despite the high number of raw sequence reads, their short length, relative to Sanger, PacBio or Nanopore reads, complicates the assembly of genomic repeats. Many genome tools are available, but the assembly of highly repetitive genome sequences using only NGS short reads remains challenging. Genome assembly of organisms responsible for important neglected diseases such as Trypanosoma cruzi, the aetiological agent of Chagas disease, is known to be challenging because of their repetitive nature. Only three of six recognized discrete typing units (DTUs) of the parasite have their draft genomes published and therefore genome evolution analyses in the taxon are limited. In this study, we developed a computational workflow to assemble highly repetitive genomes via a combination of de novo and reference-based assembly strategies to better overcome the intrinsic limitations of each, based on Illumina reads. The highly repetitive genome of the human-infecting parasite T. cruzi 231 strain was used as a test subject. The combined-assembly approach shown in this study benefits from the reference-based assembly ability to resolve highly repetitive sequences and from the de novo capacity to assemble genome-specific regions, improving the quality of the assembly. The acceptable confidence obtained by analyzing our results showed that our combined approach is an attractive option to assemble highly repetitive genomes with NGS short reads. Phylogenomic analysis including the 231 strain, the first representative of DTU III whose genome was sequenced, was also performed and provides new insights into T. cruzi genome evolution.

  9. Exact and conceptual repetition dissociate conceptual memory tests: problems for transfer appropriate processing theory.

    Science.gov (United States)

    McDermott, K B; Roediger, H L

    1996-03-01

    Three experiments examined whether a conceptual implicit memory test (specifically, category instance generation) would exhibit repetition effects similar to those found in free recall. The transfer appropriate processing account of dissociations among memory tests led us to predict that the tests would show parallel effects; this prediction was based upon the theory's assumption that conceptual tests will behave similarly as a function of various independent variables. In Experiment 1, conceptual repetition (i.e., following a target word [e.g., puzzles] with an associate [e.g., jigsaw]) did not enhance priming on the instance generation test relative to the condition of simply presenting the target word once, although this manipulation did affect free recall. In Experiment 2, conceptual repetition was achieved by following a picture with its corresponding word (or vice versa). In this case, there was an effect of conceptual repetition on free recall but no reliable effect on category instance generation or category cued recall. In addition, we obtained a picture superiority effect in free recall but not in category instance generation. In the third experiment, when the same study sequence was used as in Experiment 1, but with instructions that encouraged relational processing, priming on the category instance generation task was enhanced by conceptual repetition. Results demonstrate that conceptual memory tests can be dissociated and present problems for Roediger's (1990) transfer appropriate processing account of dissociations between explicit and implicit tests.

  10. Repetitive muscle compression reduces vascular mechano-sensitivity and the hyperemic response to muscle contraction.

    Science.gov (United States)

    Messere, A; Turturici, M; Millo, G; Roatta, S

    2017-06-01

    Animal studies have shown that the rapid hyperemic response to external muscle compression undergoes inactivation upon repetitive stimulation, but this phenomenon has never been observed in humans. The aim of the present study was to determine whether 1) the vascular mechano-sensitivity underlying muscle compression-induced hyperemia is inactivated in an inter-stimulus interval (ISI)-dependent fashion upon repetitive stimulation, as suggested by animal studies, and 2) whether such inactivation also attenuates contraction-induced hyperemia. Brachial artery blood flow was measured by echo Doppler sonography in 13 healthy adults in response to 1) single and repetitive cuff muscle compression (CMC) of the forearm (20 CMCs, 1 s ISI); 2) a sequence of CMC delivered at decreasing ISI from 120 to 2 s; and 3) electrically-stimulated contraction of the forearm muscles before and after repetitive CMC. The peak amplitude of hyperemia in response to CMC normalized to baseline decreased from 2.2 ± 0.6 to 1.4 ± 0.4 after repetitive CMC and, in general, was decreased at ISI < 240 s. The peak amplitude of contraction-induced hyperemia was attenuated after as compared to before repeated CMC (1.7 ± 0.4 and 2.6 ± 0.6, respectively). Mechano-sensitivity of the vascular network can be conditioned by previous mechanical stimulation, and such preconditioning may substantially decrease contraction-induced hyperemia.

  11. Nonword repetition in adults who stutter: The effects of stimuli stress and auditory-orthographic cues.

    Directory of Open Access Journals (Sweden)

    Geoffrey A Coalson

    Full Text Available Adults who stutter (AWS are less accurate in their immediate repetition of novel phonological sequences compared to adults who do not stutter (AWNS. The present study examined whether manipulation of the following two aspects of traditional nonword repetition tasks unmask distinct weaknesses in phonological working memory in AWS: (1 presentation of stimuli with less-frequent stress patterns, and (2 removal of auditory-orthographic cues immediately prior to response.Fifty-two participants (26 AWS, 26 AWNS produced 12 bisyllabic nonwords in the presence of corresponding auditory-orthographic cues (i.e., immediate repetition task, and the absence of auditory-orthographic cues (i.e., short-term recall task. Half of each cohort (13 AWS, 13 AWNS were exposed to the stimuli with high-frequency trochaic stress, and half (13 AWS, 13 AWNS were exposed to identical stimuli with lower-frequency iambic stress.No differences in immediate repetition accuracy for trochaic or iambic nonwords were observed for either group. However, AWS were less accurate when recalling iambic nonwords than trochaic nonwords in the absence of auditory-orthographic cues.Manipulation of two factors which may minimize phonological demand during standard nonword repetition tasks increased the number of errors in AWS compared to AWNS. These findings suggest greater vulnerability in phonological working memory in AWS, even when producing nonwords as short as two syllables.

  12. Prediction of the Maximum Number of Repetitions and Repetitions in Reserve From Barbell Velocity.

    Science.gov (United States)

    García-Ramos, Amador; Torrejón, Alejandro; Feriche, Belén; Morales-Artacho, Antonio J; Pérez-Castilla, Alejandro; Padial, Paulino; Haff, Guy Gregory

    2018-03-01

    To provide 2 general equations to estimate the maximum possible number of repetitions (XRM) from the mean velocity (MV) of the barbell and the MV associated with a given number of repetitions in reserve, as well as to determine the between-sessions reliability of the MV associated with each XRM. After determination of the bench-press 1-repetition maximum (1RM; 1.15 ± 0.21 kg/kg body mass), 21 men (age 23.0 ± 2.7 y, body mass 72.7 ± 8.3 kg, body height 1.77 ± 0.07 m) completed 4 sets of as many repetitions as possible against relative loads of 60%1RM, 70%1RM, 80%1RM, and 90%1RM over 2 separate sessions. The different loads were tested in a randomized order with 10 min of rest between them. All repetitions were performed at the maximum intended velocity. Both the general equation to predict the XRM from the fastest MV of the set (CV = 15.8-18.5%) and the general equation to predict MV associated with a given number of repetitions in reserve (CV = 14.6-28.8%) failed to provide data with acceptable between-subjects variability. However, a strong relationship (median r 2  = .984) and acceptable reliability (CV  .85) were observed between the fastest MV of the set and the XRM when considering individual data. These results indicate that generalized group equations are not acceptable methods for estimating the XRM-MV relationship or the number of repetitions in reserve. When attempting to estimate the XRM-MV relationship, one must use individualized relationships to objectively estimate the exact number of repetitions that can be performed in a training set.

  13. Sequencing of BAC pools by different next generation sequencing platforms and strategies

    Directory of Open Access Journals (Sweden)

    Scholz Uwe

    2011-10-01

    Full Text Available Abstract Background Next generation sequencing of BACs is a viable option for deciphering the sequence of even large and highly repetitive genomes. In order to optimize this strategy, we examined the influence of read length on the quality of Roche/454 sequence assemblies, to what extent Illumina/Solexa mate pairs (MPs improve the assemblies by scaffolding and whether barcoding of BACs is dispensable. Results Sequencing four BACs with both FLX and Titanium technologies revealed similar sequencing accuracy, but showed that the longer Titanium reads produce considerably less misassemblies and gaps. The 454 assemblies of 96 barcoded BACs were improved by scaffolding 79% of the total contig length with MPs from a non-barcoded library. Assembly of the unmasked 454 sequences without separation by barcodes revealed chimeric contig formation to be a major problem, encompassing 47% of the total contig length. Masking the sequences reduced this fraction to 24%. Conclusion Optimal BAC pool sequencing should be based on the longest available reads, with barcoding essential for a comprehensive assessment of both repetitive and non-repetitive sequence information. When interest is restricted to non-repetitive regions and repeats are masked prior to assembly, barcoding is non-essential. In any case, the assemblies can be improved considerably by scaffolding with non-barcoded BAC pool MPs.

  14. Interspersion of highly repetitive DNA with single copy DNA in the genome of the red crab, Geryon quinquedens

    Energy Technology Data Exchange (ETDEWEB)

    Christie, N.T. (Univ. of Tennessee, Oak Ridge); Skinner, D.M.

    1979-02-01

    Kinetic analysis of the reassociation of 420 nucleotide (NT) long fragments has shown that essentially all of the repetitive sequences of the DNA of the red crab Geryon quinquedens are highly repetitive. There are negligible amounts of low and intermediate repetitive DNAs. Though atypical of most eukaryotes, this pattern has been observed in al other brachyurans (true crabs) studied. The major repetitive component is subdivided into short runs of 300 NT and longer runs of greater than 1200 NT while the minor component has an average sequence length of 400 NT. Both components reassociate at rates commonly observed for satellite DNAs. Unique among eukaryotes the organization of the genome includes single copy DNA contiguous to short runs (300 NT) of both repetitive components. Although patent satellites are not present, subsets of the repetitive DNA have been isolated by either restriction endonuclease digestion or by centrifugation in Ag/sup +/ or Hg/sup 2 +//Cs/sub 2/SO/sub 4/ density gradients.

  15. High power, repetitive stacked Blumlein pulse generators

    Energy Technology Data Exchange (ETDEWEB)

    Davanloo, F; Borovina, D L; Korioth, J L; Krause, R K; Collins, C B [Univ. of Texas at Dallas, Richardson, TX (United States). Center for Quantum Electronics; Agee, F J [US Air Force Phillips Lab., Kirtland AFB, NM (United States); Kingsley, L E [US Army CECOM, Ft. Monmouth, NJ (United States)

    1997-12-31

    The repetitive stacked Blumlein pulse power generators developed at the University of Texas at Dallas consist of several triaxial Blumleins stacked in series at one end. The lines are charged in parallel and synchronously commuted with a single switch at the other end. In this way, relatively low charging voltages are multiplied to give a high discharge voltage across an arbitrary load. Extensive characterization of these novel pulsers have been performed over the past few years. Results indicate that they are capable of producing high power waveforms with rise times and repetition rates in the range of 0.5-50 ns and 1-300 Hz, respectively, using a conventional thyratron, spark gap, or photoconductive switch. The progress in the development and use of stacked Blumlein pulse generators is reviewed. The technology and the characteristics of these novel pulsers driving flash x-ray diodes are discussed. (author). 4 figs., 5 refs.

  16. A repetitive elements perspective in Polycomb epigenetics.

    Directory of Open Access Journals (Sweden)

    Valentina eCasa

    2012-10-01

    Full Text Available Repetitive elements comprise over two-thirds of the human genome. For a long time, these elements have received little attention since they were considered non functional. On the contrary, recent evidence indicates that they play central roles in genome integrity, gene expression and disease. Indeed, repeats display meiotic instability associated with disease and are located within common fragile sites, which are hotspots of chromosome rearrangements in tumors. Moreover, a variety of diseases have been associated with aberrant transcription of repetitive elements. Overall this indicates that appropriate regulation of repetitive elements’ activity is fundamental.Polycomb group (PcG proteins are epigenetic regulators that are essential for the normal development of multicellular organisms. Mammalian PcG proteins are involved in fundamental processes, such as cellular memory, cell proliferation, genomic imprinting, X-inactivation, and cancer development. PcG proteins can convey their activity through long-distance interactions also on different chromosomes. This indicates that the 3D organization of PcG proteins contributes significantly to their function. However, it is still unclear how these complex mechanisms are orchestrated and which role PcG proteins play in the multi-level organization of gene regulation. Intriguingly, the greatest proportion of Polycomb-mediated chromatin modifications is located in genomic repeats and it has been suggested that they could provide a binding platform for Polycomb proteins.Here, these lines of evidence are woven together to discuss how repetitive elements could contribute to chromatin organization in the 3D nuclear space.

  17. High repetition rate intense ion beam source

    International Nuclear Information System (INIS)

    Hammer, D.A.; Glidden, S.C.; Noonan, B.

    1992-01-01

    This final report describes a ≤ 150kV, 40kA, 100ns high repetition rate pulsed power system and intense ion beam source which is now in operation at Cornell University. Operation of the Magnetically-controlled Anode Plasma (MAP) ion diode at > 100Hz (burst mode for up to 10 pulse bursts) provides an initial look at repetition rate limitations of both the ion diode and beam diagnostics. The pulsed power systems are capable of ≥ 1kHz operation (up to 10 pulse bursts), but ion diode operation was limited to ∼100Hz because of diagnostic limitations. By varying MAP diode operating parameters, ion beams can be extracted at a few 10s of keV or at up to 150keV, the corresponding accelerating gap impedance ranging from about 1Ω to about 10Ω. The ability to make hundreds of test pulses per day at an average repetition rate of about 2 pulses per minute permits statistical analysis of diode operation as a function of various parameters. Most diode components have now survived more than 10 4 pulses, and the design and construction of the various pulsed power components of the MAP diode which have enabled us to reach this point are discussed. A high speed data acquisition system and companion analysis software capable of acquiring pulse data at 1ms intervals (in bursts of up to 10 pulses) and processing it in ≤ min is described

  18. Feature-based motion control for near-repetitive structures

    NARCIS (Netherlands)

    Best, de J.J.T.H.

    2011-01-01

    In many manufacturing processes, production steps are carried out on repetitive structures which consist of identical features placed in a repetitive pattern. In the production of these repetitive structures one or more consecutive steps are carried out on the features to create the final product.

  19. Lingual Kinematics during Rapid Syllable Repetition in Parkinson's Disease

    Science.gov (United States)

    Wong, Min Ney; Murdoch, Bruce E.; Whelan, Brooke-Mai

    2012-01-01

    Background: Rapid syllable repetition tasks are commonly used in the assessment of motor speech disorders. However, little is known about the articulatory kinematics during rapid syllable repetition in individuals with Parkinson's disease (PD). Aims: To investigate and compare lingual kinematics during rapid syllable repetition in dysarthric…

  20. Grade Repetition and Primary School Dropout in Uganda

    Science.gov (United States)

    Kabay, Sarah

    2016-01-01

    Research on education in low-income countries rarely focuses on grade repetition. When addressed, repetition is typically presented along with early school dropout as the "wasting" of educational resources. Simplifying grade repetition in this way often fails to recognize significant methodological concerns and also overlooks the unique…

  1. A phenomenographic study of the ways of understanding conditional and repetition structures in computer programming languages

    Science.gov (United States)

    Bucks, Gregory Warren

    exploring the different ways of understanding held by individuals of two programming concepts: conditional structures and repetition structures. This work lays the foundation for the development of language independent assessment instruments, which can ultimately be used to assess the pedagogical implications of various programming environments.

  2. The novel primers for mammal species identification-based mitochondrial cytochrome b sequence: implication for reserved wild animals in Thailand and endangered mammal species in Southeast Asia.

    Science.gov (United States)

    Muangkram, Yuttamol; Wajjwalku, Worawidh; Amano, Akira; Sukmak, Manakorn

    2018-01-01

    We presented the powerful techniques for species identification using the short amplicon of mitochondrial cytochrome b gene sequence. Two faecal samples and one single hair sample of the Asian tapir were tested using the new cytochrome b primers. The results showed a high sequence similarity with the mainland Asian tapir group. The comparative sequence analysis of the reserved wild mammals in Thailand and the other endangered mammal species from Southeast Asia comprehensibly verified the potential of our novel primers. The forward and reverse primers were 94.2 and 93.2%, respectively, by the average value of the sequence identity among 77 species sequences, and the overall mean distance was 35.9%. This development technique could provide rapid, simple, and reliable tools for species confirmation. Especially, it could recognize the problematic biological specimens contained less DNA material from illegal products and assist with wildlife crime investigation of threatened species and related forensic casework.

  3. Imbalance between abstract and concrete repetitive thinking modes in schizophrenia.

    Science.gov (United States)

    Maurage, Pierre; Philippot, Pierre; Grynberg, Delphine; Leleux, Dominique; Delatte, Benoît; Mangelinckx, Camille; Belge, Jan-Baptist; Constant, Eric

    2017-10-01

    Repetitive thoughts can be divided in two modes: abstract/analytic (decontextualized and dysfunctional) and concrete/experiential (problem-focused and adaptive). They constitute a transdiagnostic process involved in many psychopathological states but have received little attention in schizophrenia, as earlier studies only indexed increased ruminations (related to dysfunctional repetitive thoughts) without jointly exploring both modes. This study explored the two repetitive thinking modes, beyond ruminations, to determine their imbalance in schizophrenia. Thirty stabilized patients with schizophrenia and 30 matched controls completed the Repetitive Response Scale and the Mini Cambridge-Exeter Repetitive Thought Scale, both measuring repetitive thinking modes. Complementary measures related to schizophrenic symptomatology, depression and anxiety were also conducted. Compared to controls, patients with schizophrenia presented an imbalance between repetitive thinking modes, with increased abstract/analytic and reduced concrete/experiential thoughts, even after controlling for comorbidities. Schizophrenia is associated with stronger dysfunctional repetitive thoughts (i.e. abstract thinking) and impaired ability to efficiently use repetitive thinking for current problem-solving (i.e. concrete thinking). This imbalance confirms the double-faced nature of repetitive thinking modes, whose influence on schizophrenia's symptomatology should be further investigated. The present results also claim for evaluating these processes in clinical settings and for rehabilitating the balance between opposite repetitive thinking modes. Copyright © 2017 Elsevier Inc. All rights reserved.

  4. Repetitive thinking, executive functioning, and depressive mood in the elderly.

    Science.gov (United States)

    Philippot, Pierre; Agrigoroaei, Stefan

    2017-11-01

    Previous findings and the depressive-executive dysfunction hypothesis suggest that the established association between executive functioning and depression is accounted for by repetitive thinking. Investigating the association between executive functioning, repetitive thinking, and depressive mood, the present study empirically tested this mediational model in a sample of older adults, while focusing on both concrete and abstract repetitive thinking. This latter distinction is important given the potential protective role of concrete repetitive thinking, in contrast to the depletive effect of abstract repetitive thinking. A sample of 43 elderly volunteers, between 75 and 95 years of age, completed tests of executive functioning (the Stroop test, the Trail Making test, and the Fluency test), and questionnaires of repetitive thinking and depression. Positive correlations were observed between abstract repetitive thinking and depressive mood, and between concrete repetitive thinking and executive functioning; a negative correlation was observed between depressive mood and executive functioning. Further, mediational analysis evidenced that the relation between executive functioning and depressive mood was mediated by abstract repetitive thinking. The present data provide, for the first time, empirical support to the depressive-executive dysfunction hypothesis: the lack of executive resources would favor a mode of abstract repetitive thinking, which in turn would deplete mood. It suggests that clinical intervention targeting depression in the elderly should take into consideration repetitive thinking modes and the executive resources needed to disengage from rumination.

  5. Repeated DNA sequences in fungi

    Energy Technology Data Exchange (ETDEWEB)

    Dutta, S K

    1974-11-01

    Several fungal species, representatives of all broad groups like basidiomycetes, ascomycetes and phycomycetes, were examined for the nature of repeated DNA sequences by DNA:DNA reassociation studies using hydroxyapatite chromatography. All of the fungal species tested contained 10 to 20 percent repeated DNA sequences. There are approximately 100 to 110 copies of repeated DNA sequences of approximately 4 x 10/sup 7/ daltons piece size of each. Repeated DNA sequence homoduplexes showed on average 5/sup 0/C difference of T/sub e/50 (temperature at which 50 percent duplexes dissociate) values from the corresponding homoduplexes of unfractionated whole DNA. It is suggested that a part of repetitive sequences in fungi constitutes mitochondrial DNA and a part of it constitutes nuclear DNA. (auth)

  6. Annotation, submission and screening of repetitive elements in Repbase: RepbaseSubmitter and Censor

    Directory of Open Access Journals (Sweden)

    Hankus Lukasz

    2006-10-01

    Full Text Available Abstract Background Repbase is a reference database of eukaryotic repetitive DNA, which includes prototypic sequences of repeats and basic information described in annotations. Updating and maintenance of the database requires specialized tools, which we have created and made available for use with Repbase, and which may be useful as a template for other curated databases. Results We describe the software tools RepbaseSubmitter and Censor, which are designed to facilitate updating and screening the content of Repbase. RepbaseSubmitter is a java-based interface for formatting and annotating Repbase entries. It eliminates many common formatting errors, and automates actions such as calculation of sequence lengths and composition, thus facilitating curation of Repbase sequences. In addition, it has several features for predicting protein coding regions in sequences; searching and including Pubmed references in Repbase entries; and searching the NCBI taxonomy database for correct inclusion of species information and taxonomic position. Censor is a tool to rapidly identify repetitive elements by comparison to known repeats. It uses WU-BLAST for speed and sensitivity, and can conduct DNA-DNA, DNA-protein, or translated DNA-translated DNA searches of genomic sequence. Defragmented output includes a map of repeats present in the query sequence, with the options to report masked query sequence(s, repeat sequences found in the query, and alignments. Conclusion Censor and RepbaseSubmitter are available as both web-based services and downloadable versions. They can be found at http://www.girinst.org/repbase/submission.html (RepbaseSubmitter and http://www.girinst.org/censor/index.php (Censor.

  7. Reduced representation approaches to interrogate genome diversity in large repetitive plant genomes.

    Science.gov (United States)

    Hirsch, Cory D; Evans, Joseph; Buell, C Robin; Hirsch, Candice N

    2014-07-01

    Technology and software improvements in the last decade now provide methodologies to access the genome sequence of not only a single accession, but also multiple accessions of plant species. This provides a means to interrogate species diversity at the genome level. Ample diversity among accessions in a collection of species can be found, including single-nucleotide polymorphisms, insertions and deletions, copy number variation and presence/absence variation. For species with small, non-repetitive rich genomes, re-sequencing of query accessions is robust, highly informative, and economically feasible. However, for species with moderate to large sized repetitive-rich genomes, technical and economic barriers prevent en masse genome re-sequencing of accessions. Multiple approaches to access a focused subset of loci in species with larger genomes have been developed, including reduced representation sequencing, exome capture and transcriptome sequencing. Collectively, these approaches have enabled interrogation of diversity on a genome scale for large plant genomes, including crop species important to worldwide food security. © The Author 2014. Published by Oxford University Press. All rights reserved. For permissions, please email: journals.permissions@oup.com.

  8. Pull-production in repetitive remanufacturing

    Energy Technology Data Exchange (ETDEWEB)

    McCaskey, D.W. Jr.

    1992-09-01

    In the past, production activity control practices in most repetitive remanufacturing facilities resembled those used in intermittent production operations. These operations were characterized by large amounts of work-in-process (WIP), frequent work stoppages due to part shortages, excessive overtime, low product velocity, informal scheduling between dependent operations, low employee and management moral, and a lot of wasted time, material, labor, and space. Improvement in production activity control (PAC) methods for repetitive remanufactures has been hampered by uncertainty in: supply of incoming assets, configuration of assets, process times to refurbish assets, and yields in reclamation processes. collectively these uncertainties make shop floor operations seem uncontrollable. However, one United States Army depot has taken on the challenge. Through management supported, cross-functional teams, the Tooele Army Depot has designed and implemented pull-production systems for two of its major products, with several others to follow. This article presents a generalized version of Tooele`s pull-production system and highlights design characteristics which are specific to remanufacturing applications.

  9. Pull-production in repetitive remanufacturing

    Energy Technology Data Exchange (ETDEWEB)

    McCaskey, D.W. Jr.

    1992-09-01

    In the past, production activity control practices in most repetitive remanufacturing facilities resembled those used in intermittent production operations. These operations were characterized by large amounts of work-in-process (WIP), frequent work stoppages due to part shortages, excessive overtime, low product velocity, informal scheduling between dependent operations, low employee and management moral, and a lot of wasted time, material, labor, and space. Improvement in production activity control (PAC) methods for repetitive remanufactures has been hampered by uncertainty in: supply of incoming assets, configuration of assets, process times to refurbish assets, and yields in reclamation processes. collectively these uncertainties make shop floor operations seem uncontrollable. However, one United States Army depot has taken on the challenge. Through management supported, cross-functional teams, the Tooele Army Depot has designed and implemented pull-production systems for two of its major products, with several others to follow. This article presents a generalized version of Tooele's pull-production system and highlights design characteristics which are specific to remanufacturing applications.

  10. Synergy Repetition Training versus Task Repetition Training in Acquiring New Skill.

    Science.gov (United States)

    Patel, Vrajeshri; Craig, Jamie; Schumacher, Michelle; Burns, Martin K; Florescu, Ionut; Vinjamuri, Ramana

    2017-01-01

    Traditionally, repetitive practice of a task is used to learn a new skill, exhibiting as immediately improved performance. Research suggests, however, that a more experience-based rather than exposure-based training protocol may allow for better transference of the skill to related tasks. In synergy-based motor control theory, fundamental motor skills, such as hand grasping, are represented with a synergy subspace that captures essential motor patterns. In this study, we propose that motor-skill learning through synergy-based mechanisms may provide advantages over traditional task repetition learning. A new task was designed to highlight the range of motion and dexterity of the human hand. Two separate training strategies were tested in healthy subjects: task repetition training and synergy training versus a control. All three groups showed improvements when retested on the same task. When tested on a similar, but different set of tasks, only the synergy group showed improvements in accuracy (9.27% increase) compared to the repetition (3.24% decline) and control (3.22% decline) groups. A kinematic analysis revealed that although joint angular peak velocities decreased, timing benefits stemmed from the initial feed-forward portion of the task (reaction time). Accuracy improvements may have derived from general improved coordination among the four involved fingers. These preliminary results warrant further investigation of synergy-based motor training in healthy individuals, as well as in individuals undergoing hand-based rehabilitative therapy.

  11. The complete genomic sequence of pepper yellow leaf curl virus (PYLCV and its implications for our understanding of evolution dynamics in the genus polerovirus.

    Directory of Open Access Journals (Sweden)

    Aviv Dombrovsky

    Full Text Available We determined the complete sequence and organization of the genome of a putative member of the genus Polerovirus tentatively named Pepper yellow leaf curl virus (PYLCV. PYLCV has a wider host range than Tobacco vein-distorting virus (TVDV and has a close serological relationship with Cucurbit aphid-borne yellows virus (CABYV (both poleroviruses. The extracted viral RNA was subjected to SOLiD next-generation sequence analysis and used as a template for reverse transcription synthesis, which was followed by PCR amplification. The ssRNA genome of PYLCV includes 6,028 nucleotides encoding six open reading frames (ORFs, which is typical of the genus Polerovirus. Comparisons of the deduced amino acid sequences of the PYLCV ORFs 2-4 and ORF5, indicate that there are high levels of similarity between these sequences to ORFs 2-4 of TVDV (84-93% and to ORF5 of CABYV (87%. Both PYLCV and Pepper vein yellowing virus (PeVYV contain sequences that point to a common ancestral polerovirus. The recombination breakpoint which is located at CABYV ORF3, which encodes the viral coat protein (CP, may explain the CABYV-like sequences found in the genomes of the pepper infecting viruses PYLCV and PeVYV. Two additional regions unique to PYLCV (PY1 and PY2 were identified between nucleotides 4,962 and 5,061 (ORF 5 and between positions 5,866 and 6,028 in the 3' NCR. Sequence analysis of the pepper-infecting PeVYV revealed three unique regions (Pe1-Pe3 with no similarity to other members of the genus Polerovirus. Genomic analyses of PYLCV and PeVYV suggest that the speciation of these viruses occurred through putative recombination event(s between poleroviruses co-infecting a common host(s, resulting in the emergence of PYLCV, a novel pathogen with a wider host range.

  12. The complete genomic sequence of pepper yellow leaf curl virus (PYLCV) and its implications for our understanding of evolution dynamics in the genus polerovirus.

    Science.gov (United States)

    Dombrovsky, Aviv; Glanz, Eyal; Lachman, Oded; Sela, Noa; Doron-Faigenboim, Adi; Antignus, Yehezkel

    2013-01-01

    We determined the complete sequence and organization of the genome of a putative member of the genus Polerovirus tentatively named Pepper yellow leaf curl virus (PYLCV). PYLCV has a wider host range than Tobacco vein-distorting virus (TVDV) and has a close serological relationship with Cucurbit aphid-borne yellows virus (CABYV) (both poleroviruses). The extracted viral RNA was subjected to SOLiD next-generation sequence analysis and used as a template for reverse transcription synthesis, which was followed by PCR amplification. The ssRNA genome of PYLCV includes 6,028 nucleotides encoding six open reading frames (ORFs), which is typical of the genus Polerovirus. Comparisons of the deduced amino acid sequences of the PYLCV ORFs 2-4 and ORF5, indicate that there are high levels of similarity between these sequences to ORFs 2-4 of TVDV (84-93%) and to ORF5 of CABYV (87%). Both PYLCV and Pepper vein yellowing virus (PeVYV) contain sequences that point to a common ancestral polerovirus. The recombination breakpoint which is located at CABYV ORF3, which encodes the viral coat protein (CP), may explain the CABYV-like sequences found in the genomes of the pepper infecting viruses PYLCV and PeVYV. Two additional regions unique to PYLCV (PY1 and PY2) were identified between nucleotides 4,962 and 5,061 (ORF 5) and between positions 5,866 and 6,028 in the 3' NCR. Sequence analysis of the pepper-infecting PeVYV revealed three unique regions (Pe1-Pe3) with no similarity to other members of the genus Polerovirus. Genomic analyses of PYLCV and PeVYV suggest that the speciation of these viruses occurred through putative recombination event(s) between poleroviruses co-infecting a common host(s), resulting in the emergence of PYLCV, a novel pathogen with a wider host range.

  13. Repetitive elements may comprise over two-thirds of the human genome.

    Directory of Open Access Journals (Sweden)

    A P Jason de Koning

    2011-12-01

    Full Text Available Transposable elements (TEs are conventionally identified in eukaryotic genomes by alignment to consensus element sequences. Using this approach, about half of the human genome has been previously identified as TEs and low-complexity repeats. We recently developed a highly sensitive alternative de novo strategy, P-clouds, that instead searches for clusters of high-abundance oligonucleotides that are related in sequence space (oligo "clouds". We show here that P-clouds predicts >840 Mbp of additional repetitive sequences in the human genome, thus suggesting that 66%-69% of the human genome is repetitive or repeat-derived. To investigate this remarkable difference, we conducted detailed analyses of the ability of both P-clouds and a commonly used conventional approach, RepeatMasker (RM, to detect different sized fragments of the highly abundant human Alu and MIR SINEs. RM can have surprisingly low sensitivity for even moderately long fragments, in contrast to P-clouds, which has good sensitivity down to small fragment sizes (∼25 bp. Although short fragments have a high intrinsic probability of being false positives, we performed a probabilistic annotation that reflects this fact. We further developed "element-specific" P-clouds (ESPs to identify novel Alu and MIR SINE elements, and using it we identified ∼100 Mb of previously unannotated human elements. ESP estimates of new MIR sequences are in good agreement with RM-based predictions of the amount that RM missed. These results highlight the need for combined, probabilistic genome annotation approaches and suggest that the human genome consists of substantially more repetitive sequence than previously believed.

  14. REPETITION AS A SPECIAL TYPE OF SYNTACTIC RELATIONS IN REPRESENTED SPEECH: BASED ON THE PROSE BY MARINA TSVETAEVA

    Directory of Open Access Journals (Sweden)

    Olga Pavlovna Puchinina

    2017-03-01

    text field of the writer. Results. The author concludes that in the structure of represented speech the writer builds a unique set of multi-level types of repetition, being one of the characteristic features of her individual style. In Marina Tsvetaeva’s texts, especially in the framework of represented speech, repetition performs a variety of functions, i.e., emphatic, intensifying, rhythmic and connective ones. Practical implications. The results of the study can be used by students of philological departments, while taking such courses as stylistics and syntax.

  15. Molecular structure and chromosome distribution of three repetitive DNA families in Anemone hortensis L. (Ranunculaceae).

    Science.gov (United States)

    Mlinarec, Jelena; Chester, Mike; Siljak-Yakovlev, Sonja; Papes, Drazena; Leitch, Andrew R; Besendorfer, Visnja

    2009-01-01

    The structure, abundance and location of repetitive DNA sequences on chromosomes can characterize the nature of higher plant genomes. Here we report on three new repeat DNA families isolated from Anemone hortensis L.; (i) AhTR1, a family of satellite DNA (stDNA) composed of a 554-561 bp long EcoRV monomer; (ii) AhTR2, a stDNA family composed of a 743 bp long HindIII monomer and; (iii) AhDR, a repeat family composed of a 945 bp long HindIII fragment that exhibits some sequence similarity to Ty3/gypsy-like retroelements. Fluorescence in-situ hybridization (FISH) to metaphase chromosomes of A. hortensis (2n = 16) revealed that both AhTR1 and AhTR2 sequences co-localized with DAPI-positive AT-rich heterochromatic regions. AhTR1 sequences occur at intercalary DAPI bands while AhTR2 sequences occur at 8-10 terminally located heterochromatic blocks. In contrast AhDR sequences are dispersed over all chromosomes as expected of a Ty3/gypsy-like element. AhTR2 and AhTR1 repeat families include polyA- and polyT-tracks, AT/TA-motifs and a pentanucleotide sequence (CAAAA) that may have consequences for chromatin packing and sequence homogeneity. AhTR2 repeats also contain TTTAGGG motifs and degenerate variants. We suggest that they arose by interspersion of telomeric repeats with subtelomeric repeats, before hybrid unit(s) amplified through the heterochromatic domain. The three repetitive DNA families together occupy approximately 10% of the A. hortensis genome. Comparative analyses of eight Anemone species revealed that the divergence of the A. hortensis genome was accompanied by considerable modification and/or amplification of repeats.

  16. Repetitive urges to inflict burns: An unusual presentation of impulse control disorder.

    Science.gov (United States)

    Pal, Arghya; Parmar, Arpit; Pattanayak, Raman Deep

    2016-01-01

    Impulse control disorders (ICDs) are characterized by an inability to resist an intense impulse or drive to perform a particular act that is excessive and/or harmful to self/others. Till date, there is no published report of an ICD presenting with repetitive urges to inflict burns. We describe the case of an adult male in regular follow-up for 6 months who presented with intense, irresistible, and repetitive urges and acts of causing burns on his skin for past 1 year. The phenomenology shared the core qualities described for ICDs and patient showed adequate response to treatment. The case report describes an unusual type of ICD classifiable as not otherwise specified. More clinical and research attention is warranted toward ICDs in general, with implications for ICD-11.

  17. Repetitive urges to inflict burns: An unusual presentation of impulse control disorder

    Directory of Open Access Journals (Sweden)

    Arghya Pal

    2016-01-01

    Full Text Available Impulse control disorders (ICDs are characterized by an inability to resist an intense impulse or drive to perform a particular act that is excessive and/or harmful to self/others. Till date, there is no published report of an ICD presenting with repetitive urges to inflict burns. We describe the case of an adult male in regular follow-up for 6 months who presented with intense, irresistible, and repetitive urges and acts of causing burns on his skin for past 1 year. The phenomenology shared the core qualities described for ICDs and patient showed adequate response to treatment. The case report describes an unusual type of ICD classifiable as not otherwise specified. More clinical and research attention is warranted toward ICDs in general, with implications for ICD-11.

  18. Transcribing nonsense words: The effect of numbers of voices and repetitions.

    Science.gov (United States)

    Knight, Rachael-Anne

    2010-06-01

    Transcription skills are crucially important to all phoneticians, and particularly for speech and language therapists who may use transcriptions to make decisions about diagnosis and intervention. Whilst interest in factors affecting transcription accuracy is increasing, there are still a number of issues that are yet to be investigated. The present paper considers how the number of voices and the number of repetitions affects the transcription of nonsense words. Thirty-two students in their second year of study for a BSc in Speech and Language Therapy were participants in an experiment. They heard two nonsense words presented 10 times in either one or two voices. Results show that the number of voices did not affect accuracy, but that accuracy increased between six and ten repetitions. The reasons behind these findings, and implications for teaching and learning, and further research are discussed.

  19. Repetitive transcranial magnetic stimulation over the right dorsolateral prefrontal cortex affects strategic decision-making.

    Science.gov (United States)

    van 't Wout, Mascha; Kahn, René S; Sanfey, Alan G; Aleman, André

    2005-11-07

    Although decision-making is typically seen as a rational process, emotions play a role in tasks that include unfairness. Recently, activation in the right dorsolateral prefrontal cortex during offers experienced as unfair in the Ultimatum Game was suggested to subserve goal maintenance in this task. This is restricted to correlational evidence, however, and it remains unclear whether the dorsolateral prefrontal cortex is crucial for strategic decision-making. The present study used repetitive transcranial magnetic stimulation in order to investigate the causal role of the dorsolateral prefrontal cortex in strategic decision-making in the Ultimatum Game. The results showed that repetitive transcranial magnetic stimulation over the right dorsolateral prefrontal cortex resulted in an altered decision-making strategy compared with sham stimulation. We conclude that the dorsolateral prefrontal cortex is causally implicated in strategic decision-making in healthy human study participants.

  20. Repetition Priming Magnitude Depends on Affirmative Prime Responses: A Test of Two Congruity Explanations.

    Science.gov (United States)

    Fiet, Paula; Sorensen, Linda; Mayne, Zachary; Corgiat, Damon; Woltz, Dan

    2016-01-01

    We conducted 2 experiments to evaluate the impact of positive prime responses on repetition priming effects while decoupling this impact from content congruity and specific evaluation operations. Our first experiment consisted of word-meaning comparison trials that required participants to evaluate synonyms or antonyms. A crossing of evaluation operation with semantic content allowed us to test the goal-content congruity hypothesis against the semantic congruity explanation for greater facilitation from positive response primes. Results suggested that operation-based priming is affected by goal-content congruity. A second experiment tested the observed effect of positive responses on repetition priming using mental rotation of irregular shapes, affording a test of the impact of congruity in evaluation goals and content in a nonverbal stimulus domain. Both experiments produced a pattern of results inconsistent with Schulman's (1974) semantic congruity account and instead implicated a different form of congruity that affects memory for prior operations rather than memory for semantic and episodic content.

  1. PROJECT IMPLEMENTATION IN ORGANISATIONS OF REPETITIVE ACTIVITIES

    Directory of Open Access Journals (Sweden)

    Marek WIRKUS

    2015-04-01

    Full Text Available The study presents the implementation of projects in organisations that achieve business objectives through the imple-mentation of repetitive actions. Projects in these organisations are, on the one hand, treated as marginal activities, while the results of these projects have significant impact on the delivery of main processes, e.g. through the introduction of new products. Human capital and solutions in this field bear impact on the success of projects in these organisations, which is not always conducive to smooth implementation of projects. Conflict results from the nature of a project, which is a one-time and temporary process, so organisational solutions are also temporary. It influences on attitudes and com-mitment of the project contractors. The paper identifies and analyses factors which affect the success of the projects.

  2. Low-Intensity Repetitive Exercise Induced Rhabdomyolysis

    Directory of Open Access Journals (Sweden)

    Mina Tran

    2015-01-01

    Full Text Available Rhabdomyolysis is a rare condition caused by the proteins of damaged muscle cells entering the bloodstream and damaging the kidneys. Common symptoms of rhabdomyolysis are muscle pain and fatigue in conjunction with dark urine; kidney damage is a common symptom among these patients. We present a case of a 23-year-old woman who displayed myalgia in the upper extremities caused by low-intensity and high-repetition exercise. She was successfully diagnosed and treated for exertional rhabdomyolysis. This patient had no significant medical history that would induce this condition. We urge the emergency medical community to observe and monitor patients that complain of myalgia to ensure they are not suffering from rhabdomyolysis even in atypical cases.

  3. Repetitively pulsed power for meat pasteurization

    International Nuclear Information System (INIS)

    Patterson, E.L.; Kaye, R.J.; Neau, E.L.

    1994-01-01

    Electronic pasteurization of meat offers the potential for drastically reducing the incidence of food poisoning caused by biological pathogens accidentally introduced into meat products. Previous work has shown that γ-rays are an effective method of destroying E. coli 0157:H7, Salmonella, C. jejuni, L. monocytogenes, Listeria, and S. aureus bacteria types. The concern with the use of γ-rays is that radioactive material must be used in the pasteurization process that can lead to some market resistance and activist pressure on the meat industry. The use of accelerator generated high average power electron beams, at energies less than 10 MeV, or X-rays, with energies below 5 MeV, have been approved by the FDA for use in pasteurizing foods. Accelerator produced electronic pasteurization has the advantage that no radioactive material inventory is required. Electronic pasteurization has the additional benefit that it removes bacterial pathogens on the meat surface as well as within the volume of the meat product. High average power, repetitively-pulsed, broad-area electron beam sources being developed in the RHEPP program are suitable for large scale meat treatment in packing plant environments. RHEPP-II, which operates at 2.5 MeV and 25 kA at pulse repetition frequencies up to 120 Hz has adequate electron energy to penetrate hamburger patties which comprise about half of the beef consumption in the United States. Ground beef also has the highest potential for contamination since considerable processing is required in its production. A meat pasteurization facility using this size of accelerator source should be capable of treating 10 6 pounds of hamburger patties per hour to a dose of up to 3 kGy (300 kilorads). The RHEPP modular accelerator technology can easily be modified for other production rates and types of products

  4. An integrated rock-magnetic and geochemical approach to loess/paleosol sequences from Bohemia and Moravia (Czech Republic): Implications for the Upper Pleistocene paleoenvironment in central Europe

    Czech Academy of Sciences Publication Activity Database

    Hošek, J.; Hambach, U.; Lisá, Lenka; Matys Grygar, Tomáš; Horáček, I.; Meszner, S.; Knésl, I.

    2015-01-01

    Roč. 418, 15 January (2015), s. 344-358 ISSN 0031-0182 Institutional support: RVO:67985831 ; RVO:61388980 Keywords : loess/paleosols sequences * rock-magnetism * geochemical proxies * Upper Pleistocene * paleoclimate * Central Europe Subject RIV: DB - Geology ; Mineralogy; DD - Geochemistry (UACH-T) Impact factor: 2.525, year: 2015

  5. The nucleotide sequence of the right-hand terminus of adenovirus type 5 DNA: Implications for the mechanism of DNA replication

    NARCIS (Netherlands)

    Steenbergh, P.H.; Sussenbach, J.S.

    The nucleotide sequence of the right-hand terminal 3% of adenovirus type 5 (Ad5) DNA has been determined, using the chemical degradation technique developed by Maxam and Gilbert (1977). This region of the genome comprises the 1003 basepair long HindIII-I fragment and the first 75 nucleotides of the

  6. FEMA Hazard Mitigation Assistance Severe Repetitive Loss (SRL) Data

    Data.gov (United States)

    Department of Homeland Security — This dataset contains closed and obligated projects funded under the following Hazard Mitigation Assistance (HMA) grant programs: Severe Repetitive Loss (SRL). The...

  7. FEMA Hazard Mitigation Assistance Repetitive Flood Claims (RFC) Data

    Data.gov (United States)

    Department of Homeland Security — This dataset contains closed and obligated projects funded under the following Hazard Mitigation Assistance (HMA) grant programs: Repetitive Flood Claims (RFC). The...

  8. A cross-linguistic study of real-word and non-word repetition as predictors of grammatical competence in children with typical language development

    Science.gov (United States)

    Dispaldro, Marco; Deevy, Patricia; Altoe, Gianmarco; Benelli, Beatrice; Leonard Purdue, Laurence B.

    2013-01-01

    Background Although relationships among non-word repetition, real-word repetition and grammatical ability have been documented, it is important to study whether the specific nature of these relationships is tied to the characteristics of a given language. Aims The aim of this study is to explore the potential cross-linguistic differences (Italian and English) in the relationship among non-word repetition, real-word repetition, and grammatical ability in three- and four-year-old children with typical language development. Methods & Procedures To reach this goal, two repetition tasks (one real-word list and one non-word list for each language) were used. In Italian the grammatical categories were the third person plural inflection and the direct-object clitic pronouns, while in English they were the third person singular present tense inflection and the past tense in regular and irregular forms. Outcomes & Results A cross-linguistic comparison showed that in both Italian and English, non-word repetition was a significant predictor of grammatical ability. However, performance on real-word repetition explained children’s grammatical ability in Italian but not in English. Conclusions & Implications Abilities underlying non-word repetition performance (e.g., the processing and/or storage of phonological material) play an important role in the development of children’s grammatical abilities in both languages. Lexical ability (indexed by real-word repetition) showed a close relationship to grammatical ability in Italian but not in English. Implications of the findings are discussed in terms of cross-linguistic differences, genetic research, clinical intervention and methodological issues. PMID:21899673

  9. Biosynthesis and characterization of a non-repetitive polypeptide derived from silk fibroin heavy chain

    Energy Technology Data Exchange (ETDEWEB)

    Yang, Gaoqiang; Wu, Mingyang; Yi, Honggen; Wang, Jiannan, E-mail: wangjn@suda.edu.cn

    2016-02-01

    Silk fibroin heavy chain is the major protein component of Bombyx mori silk fibroin and is composed of 12 repetitive and 11 non-repetitive regions, with the non-repetitive domain consisting of a hydrophilic polypeptide chain. In order to determine the biomedical function of the non-repetitive domain or potentially use it to modify hydrophobic biomaterials, high-purity isolation is necessary. Previously, we cloned and extended a gene motif (f(1)) encoding the non-repetitive domain. Here, this motif and its multimers are inserted into a glutathione S-transferase (GST)-tagged fusion-protein expression vector. Motif f(1) and multimers f(4) and f(8) were expressed in Escherichia coli BL21 cells following isopropyl β-D-1-thiogalactopyranoside induction, purified by GST-affinity chromatography, and single bands of purified fusion proteins GST-F(1), GST-F(4), and GST-F(8), were visualized by sodium dodecyl sulfate-polyacrylamide gel electrophoresis. Target polypeptides F(1), F(4), and F(8), were cleaved clearly from the GST-fusion tag following thrombin digestion. Mass spectrometry results indicate that the molecular weights associated with fusion proteins GST-F(1), GST-F(4), and GST-F(8) are 31.5, 43.8, and 59.0 kDa, respectively, and with the cleaved polypeptides F(1), F(4), and F(8) are 4.8, 16.8, and 32.8 kDa, respectively. The F(1), F(4), and F(8) polypeptide chains are negatively charged with isoelectric points (pI) of 3.3, 3.2, and 3.0, respectively. The molecular weight and pI values of the polypeptide chains are consistent with the predicted values and the amino acid compositions similar to predicted sequences. FTIR and CD results show the molecular conformation of F(1) was mainly random coil, and more stable α-helix structure formed in longer molecular chain. - Highlights: • A non-repetitive domain and its multimers of silk fibroin were expressed by E. coli. • The corresponding target polypeptides F(1), F(4) and F(8) were cleaved clearly. • Their

  10. The Golden Ratio of Gait Harmony: Repetitive Proportions of Repetitive Gait Phases

    Directory of Open Access Journals (Sweden)

    Marco Iosa

    2013-01-01

    Full Text Available In nature, many physical and biological systems have structures showing harmonic properties. Some of them were found related to the irrational number known as the golden ratio that has important symmetric and harmonic properties. In this study, the spatiotemporal gait parameters of 25 healthy subjects were analyzed using a stereophotogrammetric system with 25 retroreflective markers located on their skin. The proportions of gait phases were compared with , the value of which is about 1.6180. The ratio between the entire gait cycle and stance phase resulted in 1.620 ± 0.058, that between stance and the swing phase was 1.629 ± 0.173, and that between swing and the double support phase was 1.684 ± 0.357. All these ratios did not differ significantly from each other (, , repeated measure analysis of variance or from (, resp., t-tests. The repetitive gait phases of physiological walking were found in turn in repetitive proportions with each other, revealing an intrinsic harmonic structure. Harmony could be the key for facilitating the control of repetitive walking. Harmony is a powerful unifying factor between seemingly disparate fields of nature, including human gait.

  11. Structural Conservation Despite Huge Sequence Diversity Allows EPCR Binding by the PfEMP1 Family Implicated in Severe Childhood Malaria

    DEFF Research Database (Denmark)

    Lau, Clinton K.Y.; Turner, Louise; Jespersen, Jakob S.

    2015-01-01

    with severe childhood malaria. We combine crystal structures of CIDRa1:EPCR complexes with analysis of 885 CIDRa1 sequences, showing that the EPCR-binding surfaces of CIDRa1 domains are conserved in shape and bonding potential, despite dramatic sequence diversity. Additionally, these domains mimic features...... of the natural EPCR ligand and can block this ligand interaction. Using peptides corresponding to the EPCR-binding region, antibodies can be purified from individuals in malaria-endemic regions that block EPCR binding of diverse CIDRa1 variants. This highlights the extent to which such a surface protein family......The PfEMP1 family of surface proteins is central for Plasmodium falciparum virulence and must retain the ability to bind to host receptors while also diversifying to aid immune evasion. The interaction between CIDRa1 domains of PfEMP1 and endothelial protein C receptor (EPCR) is associated...

  12. Cloning and sequencing of V genes from anti-osteosarcoma monoclonal antibodies TP-1 and TP-3: Location of lysine residues and implications for radiolabeling

    International Nuclear Information System (INIS)

    Olafsen, Tove; Bruland, Oeyvind S.; Zalutsky, Michael R.; Sandlie, Inger

    1995-01-01

    Monoclonal antibodies TP-1 and TP-3 are of potential utility for the radioimmunodiagnosis of osteosarcoma in both human and canine patients. The V genes of these antibodies were cloned and sequenced and to facilitate radiolabeling of these proteins, the location of the lysine residues within these sequences have been determined. The V-domains of TP-1 contain a total of 12 lysines, 10 in the framework region and 2 in the CDR region, while the V-domains of TP-3 contain a total of 14 lysines, 11 in the framework region and 3 in the CDR regions. Using space-filling models, the availability of each lysine residue for radiolabeling, and potential interference with antigen binding was predicted

  13. Cloning and sequencing of V genes from anti-osteosarcoma monoclonal antibodies TP-1 and TP-3: Location of lysine residues and implications for radiolabeling

    Energy Technology Data Exchange (ETDEWEB)

    Olafsen, Tove; Bruland, Oeyvind S.; Zalutsky, Michael R.; Sandlie, Inger

    1995-08-01

    Monoclonal antibodies TP-1 and TP-3 are of potential utility for the radioimmunodiagnosis of osteosarcoma in both human and canine patients. The V genes of these antibodies were cloned and sequenced and to facilitate radiolabeling of these proteins, the location of the lysine residues within these sequences have been determined. The V-domains of TP-1 contain a total of 12 lysines, 10 in the framework region and 2 in the CDR region, while the V-domains of TP-3 contain a total of 14 lysines, 11 in the framework region and 3 in the CDR regions. Using space-filling models, the availability of each lysine residue for radiolabeling, and potential interference with antigen binding was predicted.

  14. Complete plastome sequences of Equisetum arvense and Isoetes flaccida: implications for phylogeny and plastid genome evolution of early land plant lineages

    OpenAIRE

    Karol, Kenneth G; Arumuganathan, Kathiravetpillai; Boore, Jeffrey L; Duffy, Aaron M; Everett, Karin DE; Hall, John D; Hansen, S Kellon; Kuehl, Jennifer V; Mandoli, Dina F; Mishler, Brent D; Olmstead, Richard G; Renzaglia, Karen S; Wolf, Paul G

    2010-01-01

    Abstract Background Despite considerable progress in our understanding of land plant phylogeny, several nodes in the green tree of life remain poorly resolved. Furthermore, the bulk of currently available data come from only a subset of major land plant clades. Here we examine early land plant evolution using complete plastome sequences including two previously unexamined and phylogenetically critical lineages. To better understand the evolution of land plants and their plastomes, we examined...

  15. Complete plastome sequences of Equisetum arvense and Isoetes flaccida: implications for phylogeny and plastid genome evolution of early land plant lineages

    Directory of Open Access Journals (Sweden)

    Mandoli Dina F

    2010-10-01

    Full Text Available Abstract Background Despite considerable progress in our understanding of land plant phylogeny, several nodes in the green tree of life remain poorly resolved. Furthermore, the bulk of currently available data come from only a subset of major land plant clades. Here we examine early land plant evolution using complete plastome sequences including two previously unexamined and phylogenetically critical lineages. To better understand the evolution of land plants and their plastomes, we examined aligned nucleotide sequences, indels, gene and nucleotide composition, inversions, and gene order at the boundaries of the inverted repeats. Results We present the plastome sequences of Equisetum arvense, a horsetail, and of Isoetes flaccida, a heterosporous lycophyte. Phylogenetic analysis of aligned nucleotides from 49 plastome genes from 43 taxa supported monophyly for the following clades: embryophytes (land plants, lycophytes, monilophytes (leptosporangiate ferns + Angiopteris evecta + Psilotum nudum + Equisetum arvense, and seed plants. Resolution among the four monilophyte lineages remained moderate, although nucleotide analyses suggested that P. nudum and E. arvense form a clade sister to A. evecta + leptosporangiate ferns. Results from phylogenetic analyses of nucleotides were consistent with the distribution of plastome gene rearrangements and with analysis of sequence gaps resulting from insertions and deletions (indels. We found one new indel and an inversion of a block of genes that unites the monilophytes. Conclusions Monophyly of monilophytes has been disputed on the basis of morphological and fossil evidence. In the context of a broad sampling of land plant data we find several new pieces of evidence for monilophyte monophyly. Results from this study demonstrate resolution among the four monilophytes lineages, albeit with moderate support; we posit a clade consisting of Equisetaceae and Psilotaceae that is sister to the "true ferns

  16. Implications of sequence and timing of exposure for synergy between the pyrethroid insecticide alpha-cypermethrin and the entomopathogenic fungus Beauveria bassiana.

    Science.gov (United States)

    Meyling, Nicolai V; Arthur, Samuel; Pedersen, Kathrine E; Dhakal, Suraj; Cedergreen, Nina; Fredensborg, Brian L

    2018-03-30

    Combining low doses of chemical insecticides with entomopathogens constitutes a sustainable pest control method, but the significance of the timing and sequence of exposures needs clarification. We studied lethal effects of combinations of the entomopathogenic fungus Beauveria bassiana (KVL03-122) and the pyrethroid alpha-cypermethrin on the beetle Tenebrio molitor under varying timing and sequence of exposure. Synergy over time was evaluated in relation to the model of independent action (IA). We expected that increased progression of disease caused by B. bassiana would make beetles more susceptible to the insecticide, leading to enhanced synergy. Synergistic effects between B. bassiana and alpha-cypermethrin were observed when B. bassiana was applied first, but only when the interval between applications was >48 h. With 72 h between exposures, mortality had increased to 100% after 8 days, in contrast to the 60% mortality expected. No synergy was observed when the insecticide was applied prior to fungal exposure within 24 h. The sequence and timing of exposure do matter to achieve synergistic mortality by combining B. bassiana and alpha-cypermethrin, and the IA model proved to be a strong tool with which to evaluate the interactions of the two stressors over time. Pest control strategies could include B. bassiana followed by low-dose exposures to alpha-cypermethrin after 2-3 days. © 2018 Society of Chemical Industry. © 2018 Society of Chemical Industry.

  17. Mixed-frame and stationary-frame repetitive control schemes for compensating typical load and grid harmonics

    DEFF Research Database (Denmark)

    Loh, P.; Tang, Y.; Blaabjerg, Frede

    2011-01-01

    In this study, repetitive current controllers operating in either the mixed or stationary frame are proposed for high-precision reference tracking and disturbance rejection of power converters. Both controllers use a proportional-resonant regulator in the stationary frame for regulating...... the positive- and negative-sequence fundamental currents, which are known to directly influence the flow of active and reactive power in most energy conversion systems. Moreover, for the tracking or compensation of harmonics, the controllers include a repetitive control path in either the synchronous...... or stationary frame, whose inherent feedback and feedforward structure is proven to resemble a bank of resonant filters in either reference frames. Unlike other existing controllers, the proposed repetitive controllers function by introducing multiple resonant peaks at only those harmonic frequencies typically...

  18. Photocathodes for High Repetition Rate Light Sources

    Energy Technology Data Exchange (ETDEWEB)

    Ben-Zvi, Ilan [Stony Brook Univ., NY (United States). Dept. of Physics and Astronomy. Center for Accelerator Science and Education

    2014-04-20

    This proposal brought together teams at Brookhaven National Laboratory (BNL), Lawrence Berkeley National Laboratory (LBNL) and Stony Brook University (SBU) to study photocathodes for high repetition rate light sources such as Free Electron Lasers (FEL) and Energy Recovery Linacs (ERL). Below details the Principal Investigators and contact information. Each PI submits separately for a budget through his corresponding institute. The work done under this grant comprises a comprehensive program on critical aspects of the production of the electron beams needed for future user facilities. Our program pioneered in situ and in operando diagnostics for alkali antimonide growth. The focus is on development of photocathodes for high repetition rate Free Electron Lasers (FELs) and Energy Recovery Linacs (ERLs), including testing SRF photoguns, both normal-­conducting and superconducting. Teams from BNL, LBNL and Stony Brook University (SBU) led this research, and coordinated their work over a range of topics. The work leveraged a robust infrastructure of existing facilities and the support was used for carrying out the research at these facilities. The program concentrated in three areas: a) Physics and chemistry of alkali-­antimonide cathodes (BNL – LBNL) b) Development and testing of a diamond amplifier for photocathodes (SBU -­ BNL) c) Tests of both cathodes in superconducting RF photoguns (SBU) and copper RF photoguns (LBNL) Our work made extensive use of synchrotron radiation materials science techniques, such as powder-­ and single-­crystal diffraction, x-­ray fluorescence, EXAFS and variable energy XPS. BNL and LBNL have many complementary facilities at the two light sources associated with these laboratories (NSLS and ALS, respectively); use of these will be a major thrust of our program and bring our understanding of these complex materials to a new level. In addition, CHESS at Cornell will be used to continue seamlessly throughout the NSLS dark period and

  19. Visual attention to advertising : The impact of motivation and repetition

    NARCIS (Netherlands)

    Pieters, RGM; Rosbergen, E; Hartog, M; Corfman, KP; Lynch, JG

    1996-01-01

    Using eye-tracking data, we examine the impact of motivation and repetition on visual attention to advertisements differing in argument quality. Our analyses indicate that repetition leads to an overall decrease in the amount of attention. However, while at first high motivation subjects attend to

  20. Repetitively pulsed, double discharge TEA CO/sub 2/ laser

    Energy Technology Data Exchange (ETDEWEB)

    Hamilton, D C; James, D J; Ramsden, S A

    1975-10-01

    The design and operation of a repetitively pulsed TEA CO/sub 2/ laser is described. Average powers of up to 400 W at a repetition frequency of 200 pulses/s have been obtained. The system has also been used to provide long pulses (over 20 ..mu..s) and tunable single axial mode pulses.

  1. Effects of repetition and temperature on Contingent Electrical Stimulation

    DEFF Research Database (Denmark)

    Castrillon, Eduardo E.; Zhou, Xinwen; Svensson, Peter

    ) activity associated with bruxism. Repetition of the electrical stimulus and skin surface temperature (ST) may affect the perception of CES and possibly also the inhibitory EMG effects.Objectives: To determine the effects of stimulus repetition and skin ST on the perception of CES.  Methods: Healthy...

  2. Repetition Blindness: Out of Sight or Out of Mind?

    Science.gov (United States)

    Morris, Alison L.; Harris, Catherine L.

    2004-01-01

    Does repetition blindness represent a failure of perception or of memory? In Experiment 1, participants viewed rapid serial visual presentation (RSVP) sentences. When critical words (C1 and C2) were orthographically similar, C2 was frequently omitted from serial report; however, repetition priming for C2 on a postsentence lexical decision task was…

  3. Evidence-Based Behavioral Interventions for Repetitive Behaviors in Autism

    Science.gov (United States)

    Boyd, Brian A.; McDonough, Stephen G.; Bodfish, James W.

    2012-01-01

    Restricted and repetitive behaviors (RRBs) are a core symptom of autism spectrum disorders (ASD). There has been an increased research emphasis on repetitive behaviors; however, this research primarily has focused on phenomenology and mechanisms. Thus, the knowledge base on interventions is lagging behind other areas of research. The literature…

  4. Pre-Lexical Disorders in Repetition Conduction Aphasia

    Science.gov (United States)

    Sidiropoulos, Kyriakos; de Bleser, Ria; Ackermann, Hermann; Preilowski, Bruno

    2008-01-01

    At the level of clinical speech/language evaluation, the repetition type of conduction aphasia is characterized by repetition difficulties concomitant with reduced short-term memory capacities, in the presence of fluent spontaneous speech as well as unimpaired naming and reading abilities. It is still unsettled which dysfunctions of the…

  5. Local repeat sequence organization of an intergenic spacer

    Indian Academy of Sciences (India)

    The amplification yielded the same uniquely ``sequence-scrambled” product, whether the template used for PCR was total cellular DNA, chloroplast DNA or a plasmid clone DNA corresponding to that region. The PCR product, a ``unique” new sequence, had lost the repetitive organization of the template genome where it ...

  6. Repetitive exposure: Brain and reflex measures of emotion and attention

    Science.gov (United States)

    Ferrari, Vera; Bradley, Margaret M.; Codispoti, Maurizio; Lang, Peter J.

    2010-01-01

    Effects of massed repetition on the modulation of the late positive potential elicited during affective picture viewing were investigated in two experiments. Despite a difference in the number of repetitions across studies (from 5 to 30), results were quite similar: the late positive potential continued to be enhanced when viewing emotional, compared to neutral, pictures. On the other hand, massed repetition did prompt a reduction in the late positive potential that was most pronounced for emotional pictures. Startle probe P3 amplitude generally increased with repetition, suggesting diminished attention allocation to repeated pictures. The blink reflex, however, continued to be modulated by hedonic valence, despite massive massed repetition. Taken together, the data suggest that the amplitude of the late positive potential during picture viewing reflects both motivational significance and attention allocation. PMID:20701711

  7. Repetition and Emotive Communication in Music Versus Speech

    Directory of Open Access Journals (Sweden)

    Elizabeth Hellmuth eMargulis

    2013-04-01

    Full Text Available Music and speech are often placed alongside one another as comparative cases. Their relative overlaps and disassociations have been well explored (e.g. Patel, 2010. But one key attribute distinguishing these two domains has often been overlooked: the greater preponderance of repetition in music in comparison to speech. Recent fMRI studies have shown that familiarity – achieved through repetition – is a critical component of emotional engagement with music (Pereira et al., 2011. If repetition is fundamental to emotional responses to music, and repetition is a key distinguisher between the domains of music and speech, then close examination of the phenomenon of repetition might help clarify the ways that music elicits emotion differently than speech.

  8. Transgenerational effects of environmental enrichment on repetitive motor behavior development.

    Science.gov (United States)

    Bechard, Allison R; Lewis, Mark H

    2016-07-01

    The favorable consequences of environmental enrichment (EE) on brain and behavior development are well documented. Much less is known, however, about transgenerational benefits of EE on non-enriched offspring. We explored whether transgenerational effects of EE might extend to the development of repetitive motor behaviors in deer mice. Repetitive motor behaviors are invariant patterns of movement that, across species, can be reduced by EE. We found that EE not only attenuated the development of repetitive behavior in dams, but also in their non-enriched offspring. Moreover, maternal behavior did not seem to mediate the transgenerational effect we found, although repetitive behavior was affected by reproductive experience. These data support a beneficial transgenerational effect of EE on repetitive behavior development and suggest a novel benefit of reproductive experience. Copyright © 2016 Elsevier B.V. All rights reserved.

  9. The complete mitochondrial sequence of the"living fossil" Tricholepidion gertschi: structure, phylogenetic implications, and the description of a novel A/T asymmetrical bias

    Energy Technology Data Exchange (ETDEWEB)

    Nardi, F.; Frati, F.; Carapelli, A.; Dallai, R.; Boore, J.

    2002-06-23

    mitochondrial genome sequences to study the evolution and differentiation of the most basal hexapod groups, including Tricholepidion. Mitochondrial genomics, that is analysis of various features of the mitochondrial genome such as gene order and the analysis of the concatenated sequence of its genes, has proved to be a very powerful tool for the study of ancient phylogenetic relationships (Boore, 2000; Boore and Brown, 1995; Boore and Brown, 1998; Garcia-Machado et al., 1999; Hwang et al., 2001; Nardi et al., 2001), and its application seems to be appropriate for the problem under study ((Nardi et al., 2001), this study). In addition, complete mitochondrial sequences, with the advent of automatic sequencing tools, are accumulating rapidly, but there is a strong bias towards the better known or economically important groups, while only two sequences have been produced for the more basal, and evolutionarily more intriguing, hexapod orders. The complete sequence of the mitochondrial genome of Tricholepidion gertschi is the second among apterygotans, following the collembolan T.bielanensis (Nardi et al., 2001).

  10. The Complete Plastid Genome Sequence of Madagascar Periwinkle Catharanthus roseus (L.) G. Don: Plastid Genome Evolution, Molecular Marker Identification, and Phylogenetic Implications in Asterids

    Science.gov (United States)

    Ku, Chuan; Chung, Wan-Chia; Chen, Ling-Ling; Kuo, Chih-Horng

    2013-01-01

    The Madagascar periwinkle ( Catharanthus roseus in the family Apocynaceae) is an important medicinal plant and is the source of several widely marketed chemotherapeutic drugs. It is also commonly grown for its ornamental values and, due to ease of infection and distinctiveness of symptoms, is often used as the host for studies on phytoplasmas, an important group of uncultivated plant pathogens. To gain insights into the characteristics of apocynaceous plastid genomes (plastomes), we used a reference-assisted approach to assemble the complete plastome of C . roseus , which could be applied to other C . roseus -related studies. The C . roseus plastome is the second completely sequenced plastome in the asterid order Gentianales. We performed comparative analyses with two other representative sequences in the same order, including the complete plastome of Coffea arabica (from the basal Gentianales family Rubiaceae) and the nearly complete plastome of Asclepias syriaca (Apocynaceae). The results demonstrated considerable variations in gene content and plastome organization within Apocynaceae, including the presence/absence of three essential genes (i.e., accD, clpP, and ycf1) and large size changes in non-coding regions (e.g., rps2-rpoC2 and IRb-ndhF). To find plastome markers of potential utility for Catharanthus breeding and phylogenetic analyses, we identified 41 C . roseus -specific simple sequence repeats. Furthermore, five intergenic regions with high divergence between C . roseus and three other euasterids I taxa were identified as candidate markers. To resolve the euasterids I interordinal relationships, 82 plastome genes were used for phylogenetic inference. With the addition of representatives from Apocynaceae and sampling of most other asterid orders, a sister relationship between Gentianales and Solanales is supported. PMID:23825699

  11. Pooled Sequencing of 531 Genes in Inflammatory Bowel Disease Identifies an Associated Rare Variant in BTNL2 and Implicates Other Immune Related Genes

    Science.gov (United States)

    Prescott, Natalie J.; Lehne, Benjamin; Stone, Kristina; Lee, James C.; Taylor, Kirstin; Knight, Jo; Papouli, Efterpi; Mirza, Muddassar M.; Simpson, Michael A.; Spain, Sarah L.; Lu, Grace; Fraternali, Franca; Bumpstead, Suzannah J.; Gray, Emma; Amar, Ariella; Bye, Hannah; Green, Peter; Chung-Faye, Guy; Hayee, Bu’Hussain; Pollok, Richard; Satsangi, Jack; Parkes, Miles; Barrett, Jeffrey C.; Mansfield, John C.; Sanderson, Jeremy; Lewis, Cathryn M.; Weale, Michael E.; Schlitt, Thomas; Mathew, Christopher G.

    2015-01-01

    The contribution of rare coding sequence variants to genetic susceptibility in complex disorders is an important but unresolved question. Most studies thus far have investigated a limited number of genes from regions which contain common disease associated variants. Here we investigate this in inflammatory bowel disease by sequencing the exons and proximal promoters of 531 genes selected from both genome-wide association studies and pathway analysis in pooled DNA panels from 474 cases of Crohn’s disease and 480 controls. 80 variants with evidence of association in the sequencing experiment or with potential functional significance were selected for follow up genotyping in 6,507 IBD cases and 3,064 population controls. The top 5 disease associated variants were genotyped in an extension panel of 3,662 IBD cases and 3,639 controls, and tested for association in a combined analysis of 10,147 IBD cases and 7,008 controls. A rare coding variant p.G454C in the BTNL2 gene within the major histocompatibility complex was significantly associated with increased risk for IBD (p = 9.65x10−10, OR = 2.3[95% CI = 1.75–3.04]), but was independent of the known common associated CD and UC variants at this locus. Rare (T) or decreased risk (IL12B p.V298F, and NICN p.H191R) of IBD. These results provide additional insights into the involvement of the inhibition of T cell activation in the development of both sub-phenotypes of inflammatory bowel disease. We suggest that although rare coding variants may make a modest overall contribution to complex disease susceptibility, they can inform our understanding of the molecular pathways that contribute to pathogenesis. PMID:25671699

  12. Repetitive switching for an electromagnetic rail gun

    Science.gov (United States)

    Gruden, J. M.

    1983-12-01

    Previous testing on a repetitive opening switch for inductive energy storage has proved the feasibility of the rotary switch concept. The concept consists of a rotating copper disk (rotor) with a pie-shaped insulator section and brushes which slide along each of the rotor surfaces. While on top of the copper surface, the brushes and rotor conduct current allowing the energy storage inductor to charge. When the brushes slide onto the insulator section, the current cannot pass through the rotor and is diverted into the load. This study investigates two new brush designs and a rotor modification designed to improve the current commutating capabilities of the switch. One brush design (fringe fiber) employs carbon fibers on the leading and trailing edge of the brush to increase the resistive commutating action as the switch opens and closes. The other brush design uses fingers to conduct current to the rotor surface, effectively increasing the number of brush contact points. The rotor modification was the placement of tungsten inserts at the copper-insulator interfaces.

  13. Repetitive Interrogation of 2-Level Quantum Systems

    Science.gov (United States)

    Prestage, John D.; Chung, Sang K.

    2010-01-01

    Trapped ion clocks derive information from a reference atomic transition by repetitive interrogations of the same quantum system, either a single ion or ionized gas of many millions of ions. Atomic beam frequency standards, by contrast, measure reference atomic transitions in a continuously replenished "flow through" configuration where initial ensemble atomic coherence is zero. We will describe some issues and problems that can arise when atomic state selection and preparation of the quantum atomic system is not completed, that is, optical pumping has not fully relaxed the coherence and also not fully transferred atoms to the initial state. We present a simple two-level density matrix analysis showing how frequency shifts during the state-selection process can cause frequency shifts of the measured clock transition. Such considerations are very important when a low intensity lamp light source is used for state selection, where there is relatively weak relaxation and re-pumping of ions to an initial state and much weaker 'environmental' relaxation of the atomic coherence set-up in the atomic sample.

  14. Pigs in sequence space: A 0.66X coverage pig genome survey based on shotgun sequencing

    DEFF Research Database (Denmark)

    Wernersson, Rasmus; Schierup, M.H.; Jorgensen, F.G.

    2005-01-01

    sequences (0.66X coverage) from the pig genome. The data are hereby released (NCBI Trace repository with center name "SDJVP", and project name "Sino-Danish Pig Genome Project") together with an initial evolutionary analysis. The non-repetitive fraction of the sequences was aligned to the UCSC human...

  15. LINEAR RELATION FOR WIND-BLOWN BUBBLE SIZES OF MAIN-SEQUENCE OB STARS IN A MOLECULAR ENVIRONMENT AND IMPLICATION FOR SUPERNOVA PROGENITORS

    Energy Technology Data Exchange (ETDEWEB)

    Chen Yang; Zhou Ping [Department of Astronomy, Nanjing University, Nanjing 210093 (China); Chu Youhua [Department of Astronomy, University of Illinois at Urbana-Champaign, 1002 West Green Street, Urbana, IL 61801 (United States)

    2013-05-20

    We find a linear relationship between the size of a massive star's main-sequence bubble in a molecular environment and the star's initial mass: R{sub b} Almost-Equal-To 1.22 M/M{sub Sun} - 9.16 pc, assuming a constant interclump pressure. Since stars in the mass range of 8 to 25-30 M{sub Sun} will end their evolution in the red supergiant phase without launching a Wolf-Rayet wind, the main-sequence wind-blown bubbles are mainly responsible for the extent of molecular gas cavities, while the effect of the photoionization is comparatively small. This linear relation can thus be used to infer the masses of the massive star progenitors of supernova remnants (SNRs) that are discovered to evolve in molecular cavities, while few other means are available for inferring the properties of SNR progenitors. We have used this method to estimate the initial masses of the progenitors of eight SNRs: Kes 69, Kes 75, Kes 78, 3C 396, 3C 397, HC 40, Vela, and RX J1713-3946.

  16. Hierarchy of sedimentary discontinuity surfaces and condensed beds from the middle Paleozoic of eastern North America: Implications for cratonic sequence stratigraphy

    Science.gov (United States)

    McLaughlin, P.I.; Brett, Carlton E.; Wilson, M.A.

    2008-01-01

    Sedimentological analyses of middle Paleozoic epeiric sea successions in North America suggest a hierarchy of discontinuity surfaces and condensed beds of increasing complexity. Simple firmgrounds and hardgrounds, which are comparatively ephemeral features, form the base of the hierarchy. Composite hardgrounds, reworked concretions, authigenic mineral crusts and monomictic intraformational conglomerates indicate more complex histories. Polymictic intraformational conglomerates, ironstones and phosphorites form the most complex discontinuity surfaces and condensed beds. Complexity of discontinuities is closely linked to depositional environments duration of sediment starvation and degree of reworking which in turn show a relationship to stratigraphic cyclicity. A model of cratonic sequence stratigraphy is generated by combining data on the complexity and lateral distribution of discontinuities in the context of facies successions. Lowstand, early transgressive and late transgressive systems tracts are representative of sea-level rise. Early and late transgressive systems tracts are separated by the maximum starvation surface (typically a polymictic intraformational conglomerate or condensed phosphorite), deposited during the peak rate of sea-level rise. Conversely the maximum flooding surface, representing the highest stand of sea level, is marked by little to no break in sedimentation. The highstand and falling stage systems tracts are deposited during relative sea-level fall. They are separated by the forced-regression surface, a thin discontinuity surface or condensed bed developed during the most rapid rate of sea-level fall. The lowest stand of sea level is marked by the sequence boundary. In subaerially exposed areas it is occasionally modified as a rockground or composite hardground.

  17. Homologous alpha satellite sequences on human acrocentric chromosomes with selectivity for chromosomes 13, 14, and 21: implications for recombination between nonhomologues and Robertsonian translocations

    Energy Technology Data Exchange (ETDEWEB)

    Choo, K H; Vissel, B; Brown, R; Filby, R G; Earle, E

    1988-02-25

    The authors report a new subfamily of alpha satellite DNA (pTRA-2) which is found on all the human acrocentric chromosomes. The alphoid nature of the cloned DNA was established by partial sequencing. Southern analysis of restriction enzyme-digested DNA fragments from mouse/human hybrid cells containing only human chromosome 21 showed that the predominant higher-order repeating unit for pTRA-2 is a 3.9 kb structure. Analysis of a consensus in situ hybridization profile derived from 13 normal individuals revealed the localization of 73% of all centromeric autoradiographic grains over the five acrocentric chromosomes, with the following distribution: 20.4%, 21.5%, 17.1%, 7.3% and 6.5% on chromosomes 13, 14, 21, 15 and 22 respectively. An average of 1.4% of grains was found on the centromere of each of the remaining 19 nonacrocentric chromosomes. These results indicate the presence of a common subfamily of alpha satellite DNA on the five acrocentric chromosomes and suggest an evolutionary process consistent with recombination exchange of sequences between the nonhomologues. The results further suggests that such exchanges are more selective for chromosomes 13, 14 and 21 than for chromosomes 15 and 22. The possible role of centromeric alpha satellite DNA in the aetiology of 13q14q and 14q21q Robertsonian translocation involving the common and nonrandom association of chromosomes 13 and 14, and 14 and 21 is discussed.

  18. Novel arenavirus sequences in Hylomyscus sp. and Mus (Nannomys setulosus from Côte d'Ivoire: implications for evolution of arenaviruses in Africa.

    Directory of Open Access Journals (Sweden)

    David Coulibaly-N'Golo

    Full Text Available This study aimed to identify new arenaviruses and gather insights in the evolution of arenaviruses in Africa. During 2003 through 2005, 1,228 small mammals representing 14 different genera were trapped in 9 villages in south, east, and middle west of Côte d'Ivoire. Specimens were screened by pan-Old World arenavirus RT-PCRs targeting S and L RNA segments as well as immunofluorescence assay. Sequences of two novel tentative species of the family Arenaviridae, Menekre and Gbagroube virus, were detected in Hylomyscus sp. and Mus (Nannomys setulosus, respectively. Arenavirus infection of Mus (Nannomys setulosus was also demonstrated by serological testing. Lassa virus was not found, although 60% of the captured animals were Mastomys natalensis. Complete S RNA and partial L RNA sequences of the novel viruses were recovered from the rodent specimens and subjected to phylogenetic analysis. Gbagroube virus is a closely related sister taxon of Lassa virus, while Menekre virus clusters with the Ippy/Mobala/Mopeia virus complex. Reconstruction of possible virus-host co-phylogeny scenarios suggests that, within the African continent, signatures of co-evolution might have been obliterated by multiple host-switching events.

  19. Breakpoint of an inversion of chromosome 14 in a T-cell leukemia: sequences downstream of the immunoglobulin heavy chain locus are implicated in tumorigenesis

    International Nuclear Information System (INIS)

    Baer, R.; Heppell, A.; Taylor, A.M.R.; Rabbitts, P.H.; Boullier, B.; Rabbitts, T.H.

    1987-01-01

    T-cell tumors are characterized by inversions or translocations of chromosome 14. The breakpoints of these karyotypic abnormalities occur in chromosome bands 14q11 and 14q32 - the same bands in which the T-cell receptor (TCR) α-chain and immunoglobulin heavy chain genes have been mapped, respectively. Patients with ataxia-telangiectasia are particularly prone to development of T-cell chronic lymphocytic leukemia with such chromosomal abnormalities. The authors describe DNA rearrangements of the TCR α-chain gene in an ataxia-telangiectasia-associated leukemia containing both a normal and an inverted chromosome 14. The normal chromosome 14 has undergone a productive join of TCR α-chain variable (V/sub α/) and joining (J/sub α/) gene segments. The other allele of the TCR α-chain gene features a DNA rearrangement, about 50 kilobases from the TCR α-chain constant (C/sub α/) gene, that represents the breakpoint of the chromosome 14 inversion; this breakpoint is comprised of a TCR J/sub α/) segment (from 14q11) fused to sequences derived from 14q32 but on the centromeric side of C/sub μ/. These results imply that 14q32 sequences located at an undetermined distance downstream of immunoglobulin C/sub μ/ locus can contribute to the development of T-cell tumors

  20. Control method of Three-phase Four-leg converter based on repetitive control

    Science.gov (United States)

    Hui, Wang

    2018-03-01

    The research chose the magnetic levitation force of wind power generation system as the object. In order to improve the power quality problem caused by unbalanced load in power supply system, we combined the characteristics and repetitive control principle of magnetic levitation wind power generation system, and then an independent control strategy for three-phase four-leg converter was proposed. In this paper, based on the symmetric component method, the second order generalized integrator was used to generate the positive and negative sequence of signals, and the decoupling control was carried out under the synchronous rotating reference frame, in which the positive and negative sequence voltage is PI double closed loop, and a PI regulator with repetitive control was introduced to eliminate the static error regarding the fundamental frequency fluctuation characteristic of zero sequence component. The simulation results based on Matlab/Simulink show that the proposed control project can effectively suppress the disturbance caused by unbalanced loads and maintain the load voltage balance. The project is easy to be achieved and remarkably improves the quality of the independent power supply system.

  1. Chromosomal organization of repetitive DNAs in Hordeum bogdanii and H. brevisubulatum (Poaceae

    Directory of Open Access Journals (Sweden)

    Quanwen Dou

    2016-10-01

    Full Text Available Molecular karyotypes of H. bogdanii Wilensky, 1918 (2n = 14, and H. brevisubulatum Link, 1844 ssp. brevisubulatum (2n = 28, were characterized by physical mapping of several repetitive sequences. A total of 18 repeats, including all possible di- or trinucleotide SSR (simple sequence repeat motifs and satellite DNAs, such as pAs1, 5S rDNA, 45S rDNA, and pSc119.2, were used as probes for fluorescence in situ hybridization on root-tip metaphase chromosomes. Except for the SSR motifs AG, AT and GC, all the repeats we examined produced detectable hybridization signals on chromosomes of both species. A detailed molecular karyotype of the I genome of H. bogdanii is described for the first time, and each repetitive sequence is physically mapped. A high degree of chromosome variation, including aneuploidy and structural changes, was observed in H. brevisubulatum. Although the distribution of repeats in the chromosomes of H. brevisubulatum is different from that of H. bogdanii, similar patterns between the two species imply that the autopolyploid origin of H. brevisubulatum is from a Hordeum species with an I genome. A comparison of the I genome and the other Hordeum genomes, H, Xa and Xu, shows that colocalization of motifs AAC, ACT and CAT and colocalization of motifs AAG and AGG are characteristic of the I genome. In addition, we discuss the evolutionary significance of repeats in the genome during genome differentiation.

  2. Impulsive sounds change European seabass swimming patterns: Influence of pulse repetition interval

    International Nuclear Information System (INIS)

    Neo, Y.Y.; Ufkes, E.; Kastelein, R.A.; Winter, H.V.; Cate, C. ten; Slabbekoorn, H.

    2015-01-01

    Highlights: • We exposed impulsive sounds of different repetition intervals to European seabass. • Immediate behavioural changes mirrored previous indoor & outdoor studies. • Repetition intervals influenced the impacts differentially but not the recovery. • Sound temporal patterns may be more important than some standard metrics. - Abstract: Seismic shootings and offshore pile-driving are regularly performed, emitting significant amounts of noise that may negatively affect fish behaviour. The pulse repetition interval (PRI) of these impulsive sounds may vary considerably and influence the behavioural impact and recovery. Here, we tested the effect of four PRIs (0.5–4.0 s) on European seabass swimming patterns in an outdoor basin. At the onset of the sound exposures, the fish swam faster and dived deeper in tighter shoals. PRI affected the immediate and delayed behavioural changes but not the recovery time. Our study highlights that (1) the behavioural changes of captive European seabass were consistent with previous indoor and outdoor studies; (2) PRI could influence behavioural impact differentially, which may have management implications; (3) some acoustic metrics, e.g. SEL cum , may have limited predictive power to assess the strength of behavioural impacts of noise. Noise impact assessments need to consider the contribution of sound temporal structure

  3. Memory and learning with rapid audiovisual sequences

    Science.gov (United States)

    Keller, Arielle S.; Sekuler, Robert

    2015-01-01

    We examined short-term memory for sequences of visual stimuli embedded in varying multisensory contexts. In two experiments, subjects judged the structure of the visual sequences while disregarding concurrent, but task-irrelevant auditory sequences. Stimuli were eight-item sequences in which varying luminances and frequencies were presented concurrently and rapidly (at 8 Hz). Subjects judged whether the final four items in a visual sequence identically replicated the first four items. Luminances and frequencies in each sequence were either perceptually correlated (Congruent) or were unrelated to one another (Incongruent). Experiment 1 showed that, despite encouragement to ignore the auditory stream, subjects' categorization of visual sequences was strongly influenced by the accompanying auditory sequences. Moreover, this influence tracked the similarity between a stimulus's separate audio and visual sequences, demonstrating that task-irrelevant auditory sequences underwent a considerable degree of processing. Using a variant of Hebb's repetition design, Experiment 2 compared musically trained subjects and subjects who had little or no musical training on the same task as used in Experiment 1. Test sequences included some that intermittently and randomly recurred, which produced better performance than sequences that were generated anew for each trial. The auditory component of a recurring audiovisual sequence influenced musically trained subjects more than it did other subjects. This result demonstrates that stimulus-selective, task-irrelevant learning of sequences can occur even when such learning is an incidental by-product of the task being performed. PMID:26575193

  4. Memory and learning with rapid audiovisual sequences.

    Science.gov (United States)

    Keller, Arielle S; Sekuler, Robert

    2015-01-01

    We examined short-term memory for sequences of visual stimuli embedded in varying multisensory contexts. In two experiments, subjects judged the structure of the visual sequences while disregarding concurrent, but task-irrelevant auditory sequences. Stimuli were eight-item sequences in which varying luminances and frequencies were presented concurrently and rapidly (at 8 Hz). Subjects judged whether the final four items in a visual sequence identically replicated the first four items. Luminances and frequencies in each sequence were either perceptually correlated (Congruent) or were unrelated to one another (Incongruent). Experiment 1 showed that, despite encouragement to ignore the auditory stream, subjects' categorization of visual sequences was strongly influenced by the accompanying auditory sequences. Moreover, this influence tracked the similarity between a stimulus's separate audio and visual sequences, demonstrating that task-irrelevant auditory sequences underwent a considerable degree of processing. Using a variant of Hebb's repetition design, Experiment 2 compared musically trained subjects and subjects who had little or no musical training on the same task as used in Experiment 1. Test sequences included some that intermittently and randomly recurred, which produced better performance than sequences that were generated anew for each trial. The auditory component of a recurring audiovisual sequence influenced musically trained subjects more than it did other subjects. This result demonstrates that stimulus-selective, task-irrelevant learning of sequences can occur even when such learning is an incidental by-product of the task being performed.

  5. Multineuronal Spike Sequences Repeat with Millisecond Precision

    Directory of Open Access Journals (Sweden)

    Koki eMatsumoto

    2013-06-01

    Full Text Available Cortical microcircuits are nonrandomly wired by neurons. As a natural consequence, spikes emitted by microcircuits are also nonrandomly patterned in time and space. One of the prominent spike organizations is a repetition of fixed patterns of spike series across multiple neurons. However, several questions remain unsolved, including how precisely spike sequences repeat, how the sequences are spatially organized, how many neurons participate in sequences, and how different sequences are functionally linked. To address these questions, we monitored spontaneous spikes of hippocampal CA3 neurons ex vivo using a high-speed functional multineuron calcium imaging technique that allowed us to monitor spikes with millisecond resolution and to record the location of spiking and nonspiking neurons. Multineuronal spike sequences were overrepresented in spontaneous activity compared to the statistical chance level. Approximately 75% of neurons participated in at least one sequence during our observation period. The participants were sparsely dispersed and did not show specific spatial organization. The number of sequences relative to the chance level decreased when larger time frames were used to detect sequences. Thus, sequences were precise at the millisecond level. Sequences often shared common spikes with other sequences; parts of sequences were subsequently relayed by following sequences, generating complex chains of multiple sequences.

  6. The polydeoxyadenylate tract of Alu repetitive elements is polymorphic in the human genome

    International Nuclear Information System (INIS)

    Economou, E.P.; Bergen, A.W.; Warren, A.C.; Antonarakis, S.E.

    1990-01-01

    To identify DNA polymorphisms that are abundant in the human genome and are detectable by polymerase chain reaction amplification of genomic DNA, the authors hypothesize that the polydeoxyadenylate tract of the Alu family of repetitive elements is polymorphic among human chromosomes. Analysis of the 3' ends of three specific Alu sequences showed two occurrences, one in the adenosine deaminase gene and other in the β-globin pseudogene, were polymorphic. This novel class of polymorphism, termed AluVpA [Alu variable poly(A)] may represent one of the most useful and informative group of DNA markers in the human genome

  7. Sediment sequence and site formation processes at the Arbreda Cave, NE Iberian Peninsula, and implications on human occupation and climate change during the Last Glacial

    Directory of Open Access Journals (Sweden)

    M. Kehl

    2014-09-01

    Full Text Available The Arbreda Cave provides a detailed archaeological record of the Middle to Upper Palaeolithic and is a key site for studying human occupation and cultural transitions in NE Iberia. Recently, studies of lake archives and archaeological sites presented new evidence on climate changes in NE Iberia correlating with Heinrich events. It, therefore, needs to be determined whether climate signals can be identified in the cave sequence of Arbreda, and if so, whether these signals can be correlated with stratigraphic indicators suggesting the continuity or discontinuity of human occupation. We conducted a high-resolution sedimentological and geochemical study, including micromorphological investigations, to shed light on stratigraphy, processes of sediment accumulation and post-depositional alteration in the cave. Seven major sediment units were distinguished which partly correlate with archaeological levels. The lower part of the sequence including Mousterian levels J and K consists of fluvial deposits truncated by a sharp erosional disconformity between Mousterian levels J and I. Strong enrichment with phosphorus and strontium reflect zoogenic inputs. The transition from Mousterian to Archaic Aurignacian in levels I and H, respectively, is reflected by more gradual changes in colour, grain size and geochemical composition. However, a peak in potentially wind-blown particles (40–125 μm in diameter reflects higher aeolian input, and banded microstructure suggests reworking of sediments at the interface. Both properties correlate with low density of finds suggesting low intensity of human occupation related to a dry spell. More arid conditions than during the Holocene are indicated for the Gravettian to Solutrean levels. These findings are in agreement with previous palaeoclimatic interpretations as based on palaeontological proxies. The detailed multi-proxy analyses of the sequence adds to our understanding on sediment accumulation and alteration in

  8. Differential preparation intervals modulate repetition processes in task switching: an ERP study

    Directory of Open Access Journals (Sweden)

    Min eWang

    2016-02-01

    Full Text Available In task-switching paradigms, reaction times (RTs switch cost (SC and the neural correlates underlying the SC are affected by different preparation intervals. However, little is known about the effect of the preparation interval on the repetition processes in task-switching. To examine this effect we utilized a cued task-switching paradigm with long sequences of repeated trials. Response-stimulus intervals (RSI and cue-stimulus intervals (CSI were manipulated in short and long conditions. Electroencephalography (EEG and behavioral data were recorded. We found that with increasing repetitions, RTs were faster in the short CSI conditions, while P3 amplitudes decreased in the LS (long RSI and short CSI conditions. Positive correlations between RT benefit and P3 activation decrease (repeat 1 minus repeat 5, and between the slope of the RT and P3 regression lines were observed only in the LS condition. Our findings suggest that differential preparation intervals modulate repetition processes in task switching.

  9. Repetitive transcranial magnetic stimulation in psychiatry

    Directory of Open Access Journals (Sweden)

    Biswa Ranjan Mishra

    2011-01-01

    Full Text Available Repetitive transcranial magnetic stimulation (rTMS is a non-invasive and relatively painless tool that has been used to study various cognitive functions as well as to understand the brain-behavior relationship in normal individuals as well as in those with various neuropsychiatric disorders. It has also been used as a therapeutic tool in various neuropsychiatric disorders because of its ability to specifically modulate distinct brain areas. Studies have shown that repeated stimulation at low frequency produces long-lasting inhibition, which is called as long-term depression, whereas repeated high-frequency stimulation can produce excitation through long-term potentiation. This paper reviews the current status of rTMS as an investigative and therapeutic modality in various neuropsychiatric disorders. It has been used to study the cortical and subcortical functions, neural plasticity and brain mapping in normal individuals and in various neuropsychiatric disorders. rTMS has been most promising in the treatment of depression, with an overall milder adverse effect profile compared with electroconvulsive therapy. In other neuropsychiatric disorders such as schizophrenia, mania, epilepsy and substance abuse, it has been found to be useful, although further studies are required to establish therapeutic efficacy. It appears to be ineffective in the treatment of obsessive compulsive disorder. There is a paucity of studies of efficacy and safety of rTMS in pediatric and geriatric population. Although it appears safe, further research is required to optimize its efficacy and reduce the side-effects. Magnetic seizure therapy, which involves producing seizures akin to electroconvulsive therapy, appears to be of comparable efficacy in the treatment of depression with less cognitive adverse effects.

  10. Repetition-based Interactive Facade Modeling

    KAUST Repository

    AlHalawani, Sawsan

    2012-07-01

    Modeling and reconstruction of urban environments has gained researchers attention throughout the past few years. It spreads in a variety of directions across multiple disciplines such as image processing, computer graphics and computer vision as well as in architecture, geoscience and remote sensing. Having a virtual world of our real cities is very attractive in various directions such as entertainment, engineering, governments among many others. In this thesis, we address the problem of processing a single fa cade image to acquire useful information that can be utilized to manipulate the fa cade and generate variations of fa cade images which can be later used for buildings\\' texturing. Typical fa cade structures exhibit a rectilinear distribution where in windows and other elements are organized in a grid of horizontal and vertical repetitions of similar patterns. In the firt part of this thesis, we propose an efficient algorithm that exploits information obtained from a single image to identify the distribution grid of the dominant elements i.e. windows. This detection method is initially assisted with the user marking the dominant window followed by an automatic process for identifying its repeated instances which are used to define the structure grid. Given the distribution grid, we allow the user to interactively manipulate the fa cade by adding, deleting, resizing or repositioning the windows in order to generate new fa cade structures. Having the utility for the interactive fa cade is very valuable to create fa cade variations and generate new textures for building models. Ultimately, there is a wide range of interesting possibilities of interactions to be explored.

  11. Complete chloroplast genome sequences of Drimys, Liriodendron, andPiper: Implications for the phylogeny of magnoliids and the evolution ofGC content

    Energy Technology Data Exchange (ETDEWEB)

    Zhengqiu, C.; Penaflor, C.; Kuehl, J.V.; Leebens-Mack, J.; Carlson, J.; dePamphilis, C.W.; Boore, J.L.; Jansen, R.K.

    2006-06-01

    The magnoliids represent the largest basal angiosperm clade with four orders, 19 families and 8,500 species. Although several recent angiosperm molecular phylogenies have supported the monophyly of magnoliids and suggested relationships among the orders, the limited number of genes examined resulted in only weak support, and these issues remain controversial. Furthermore, considerable incongruence has resulted in phylogenies supporting three different sets of relationships among magnoliids and the two large angiosperm clades, monocots and eudicots. This is one of the most important remaining issues concerning relationships among basal angiosperms. We sequenced the chloroplast genomes of three magnoliids, Drimys (Canellales), Liriodendron (Magnoliales), and Piper (Piperales), and used these data in combination with 32 other completed angiosperm chloroplast genomes to assess phylogenetic relationships among magnoliids. The Drimys and Piper chloroplast genomes are nearly identical in size at 160,606 and 160,624 bp, respectively. The genomes include a pair of inverted repeats of 26,649 bp (Drimys) and 27,039 (Piper), separated by a small single copy region of 18,621 (Drimys) and 18,878 (Piper) and a large single copy region of 88,685 bp (Drimys) and 87,666 bp (Piper). The gene order of both taxa is nearly identical to many other unrearranged angiosperm chloroplast genomes, including Calycanthus, the other published magnoliid genome. Comparisons of angiosperm chloroplast genomes indicate that GC content is not uniformly distributed across the genome. Overall GC content ranges from 34-39%, and coding regions have a substantially higher GC content than non-coding regions (both intergenic spacers and introns). Among protein-coding genes, GC content varies by codon position with 1st codon > 2nd codon > 3rd codon, and it varies by functional group with photosynthetic genes having the highest percentage and NADH genes the lowest. Across the genome, GC content is highest in

  12. Sequence analysis and characterization of pyruvate kinase from Clonorchis sinensis, a 53.1-kDa homopentamer, implicated immune protective efficacy against clonorchiasis

    Directory of Open Access Journals (Sweden)

    Tingjin Chen

    2017-11-01

    Full Text Available Abstract Background Clonorchis sinensis, the causative agent of clonorchiasis, is classified as one of the most neglected tropical diseases and affects more than 15 million people globally. This hepatobiliary disease is highly associated with cholangiocarcinoma. As key molecules in the infectivity and subsistence of trematodes, glycolytic enzymes have been targets for drug and vaccine development. Clonorchis sinensis pyruvate kinase (CsPK, a crucial glycolytic enzyme, was characterized in this research. Results Differences were observed in the sequences and spatial structures of CsPK and PKs from humans, rats, mice and rabbits. CsPK possessed a characteristic active site signature (IKLIAKIENHEGV and some unique sites but lacked the N-terminal domain. The predicted subunit molecular mass (Mr of CsPK was 53.1 kDa. Recombinant CsPK (rCsPK was a homopentamer with a Mr. of approximately 290 kDa by both native PAGE and gel filtration chromatography. Significant differences in the protein and mRNA levels of CsPK were observed among four life stages of C. sinensis (egg, adult worm, excysted metacercaria and metacercaria, suggesting that these developmental stages may be associated with diverse energy demands. CsPK was widely distributed in adult worms. Moreover, an intense Th1-biased immune response was persistently elicited in rats immunized with rCsPK. Also, rat anti-rCsPK sera suppressed C. sinensis adult subsistence both in vivo and in vitro. Conclusions The sequences and spatial structures, molecular mass, and expression profile of CsPK have been characterized. rCsPK was indicated to be a homopentamer. Rat anti-rCsPK sera suppressed C. sinensis adult subsistence both in vivo and in vitro. CsPK is worthy of further study as a promising target for drug and vaccine development.

  13. Sequence analysis and characterization of pyruvate kinase from Clonorchis sinensis, a 53.1-kDa homopentamer, implicated immune protective efficacy against clonorchiasis.

    Science.gov (United States)

    Chen, Tingjin; Jiang, Hongye; Sun, Hengchang; Xie, Zhizhi; Ren, Pengli; Zhao, Lu; Dong, Huimin; Shi, Mengchen; Lv, Zhiyue; Wu, Zhongdao; Li, Xuerong; Yu, Xinbing; Huang, Yan; Xu, Jin

    2017-11-09

    Clonorchis sinensis, the causative agent of clonorchiasis, is classified as one of the most neglected tropical diseases and affects more than 15 million people globally. This hepatobiliary disease is highly associated with cholangiocarcinoma. As key molecules in the infectivity and subsistence of trematodes, glycolytic enzymes have been targets for drug and vaccine development. Clonorchis sinensis pyruvate kinase (CsPK), a crucial glycolytic enzyme, was characterized in this research. Differences were observed in the sequences and spatial structures of CsPK and PKs from humans, rats, mice and rabbits. CsPK possessed a characteristic active site signature (IKLIAKIENHEGV) and some unique sites but lacked the N-terminal domain. The predicted subunit molecular mass (Mr) of CsPK was 53.1 kDa. Recombinant CsPK (rCsPK) was a homopentamer with a Mr. of approximately 290 kDa by both native PAGE and gel filtration chromatography. Significant differences in the protein and mRNA levels of CsPK were observed among four life stages of C. sinensis (egg, adult worm, excysted metacercaria and metacercaria), suggesting that these developmental stages may be associated with diverse energy demands. CsPK was widely distributed in adult worms. Moreover, an intense Th1-biased immune response was persistently elicited in rats immunized with rCsPK. Also, rat anti-rCsPK sera suppressed C. sinensis adult subsistence both in vivo and in vitro. The sequences and spatial structures, molecular mass, and expression profile of CsPK have been characterized. rCsPK was indicated to be a homopentamer. Rat anti-rCsPK sera suppressed C. sinensis adult subsistence both in vivo and in vitro. CsPK is worthy of further study as a promising target for drug and vaccine development.

  14. Influence of repetitive mechanical loading on MMP2 activity in tendon fibroblasts.

    Science.gov (United States)

    Huisman, Elise; Lu, Alex; Jamil, Sarwat; Mousavizadeh, Rouhollah; McCormack, Robert; Roberts, Clive; Scott, Alex

    2016-11-01

    Matrix metalloproteinase2 has been implicated in tendon pathology caused by repetitive movements. However, its activity in the early stages of the tendon's response to overuse, and its presence in the circulation as a possible indicator of tendon degradation, remain unknown. Human tendon cells were repetitively stretched for 5 days, and the rabbit Achilles tendon complex underwent repetitive motion 3× per week for 2 weeks. Quantitative polymer chain reaction analysis was performed to detect matrix metalloproteinase2/14 and tissue inhibitor of matrix metalloproteinase2 messenger ribonucleic acid of cells and rabbit tissue, and matrix metalloproteinase2 protein levels were determined with an enzyme linked immunoassay. Matrix metalloproteinase2 activity was examined using zymography of the conditioned media, tendon and serum. Immunohistochemistry was used to localize matrix metalloproteinase2 in tendon tissue, and the density of fibrillar collagen in tendons was examined using second harmonic generation microscopy. Tendon cells stretched with high strain or high frequency demonstrated increased matrix metalloproteinase2 messenger ribonucleic acid and protein levels. Matrix metalloproteinase2 activity was increased in the rabbit Achilles tendon tissue at weeks 1 and 2; however, serum activity was only increased at week 1. After 2 weeks of exercise, the collagen density was lower in specific regions of the exercised rabbit Achilles tendon complex. Matrix metalloproteinase2 expression in exercised rabbit Achilles tendons was detected surrounding tendon fibroblasts. Repetitive mechanical stimulation of tendon cells results in a small increase in matrix metalloproteinase2 levels, but it appears unlikely that serum matrix metalloproteinase2 will be a useful indicator of tendon overuse injury. © 2016 Orthopaedic Research Society. Published by Wiley Periodicals, Inc. J Orthop Res 34:1991-2000, 2016. © 2016 Orthopaedic Research Society. Published by Wiley Periodicals, Inc.

  15. A cross-linguistic study of real-word and non-word repetition as predictors of grammatical competence in children with typical language development.

    Science.gov (United States)

    Dispaldro, Marco; Deevy, Patricia; Altoé, Gianmarco; Benelli, Beatrice; Leonard, Laurence B

    2011-01-01

    Although relationships among non-word repetition, real-word repetition and grammatical ability have been documented, it is important to study whether the specific nature of these relationships is tied to the characteristics of a given language. The aim of this study is to explore the potential cross-linguistic differences (Italian and English) in the relationship among non-word repetition, real-word repetition, and grammatical ability in three-and four-year-old children with typical language development. To reach this goal, two repetition tasks (one real-word list and one non-word list for each language) were used. In Italian the grammatical categories were the third person plural inflection and the direct-object clitic pronouns, while in English they were the third person singular present tense inflection and the past tense in regular and irregular forms. A cross-linguistic comparison showed that in both Italian and English, non-word repetition was a significant predictor of grammatical ability. However, performance on real-word repetition explained children's grammatical ability in Italian but not in English. Abilities underlying non-word repetition performance (e.g., the processing and/or storage of phonological material) play an important role in the development of children's grammatical abilities in both languages. Lexical ability (indexed by real-word repetition) showed a close relationship to grammatical ability in Italian but not in English. Implications of the findings are discussed in terms of cross-linguistic differences, genetic research, clinical intervention and methodological issues. © 2011 Royal College of Speech & Language Therapists.

  16. Progress in developing repetitive pulse systems utilizing inductive energy storage

    Energy Technology Data Exchange (ETDEWEB)

    Honig, E.M.

    1983-01-01

    High-power, fast-recovery vacuum switches were used in a new repetitive counterpulse and transfer circuit to deliver a 5-kHz pulse train with a peak power of 75 MW (at 8.6 kA) to a 1-..cap omega.. load, resulting in the first demonstration of fully controlled, high-power, high-repetition-rate operation of an inductive energy-storage and transfer system with nondestructive switches. New circuits, analytical and experimental results, and feasibility of 100-kV repetitive pulse generation are discussed. A new switching concept for railgun loads is presented.

  17. Electrical strength of vacuum gap at repetitive breakdown

    International Nuclear Information System (INIS)

    Dubinin, N.P.; Chistyakov, N.P.

    1983-01-01

    The investigation of repetitive pulse breakdown of vacuum space, which electrodes have been subjected to various treatment in vacuum and inert gas, is carried out. In case of electrode warm-up in vacuum up to 400 deg C as well as electronic heating up to 900 deg C the voltage in case of repetitive breakdown hasncreased approximately twice and in case of a through treatment, which is accomplished by a high-current glow discharge in inert gas, the maximum high voltage in case of the first breakdown at repetitive breakdown has decreased by 30...40%, remaining 2-3 times higher than in the first case

  18. Entropic fluctuations in DNA sequences

    Science.gov (United States)

    Thanos, Dimitrios; Li, Wentian; Provata, Astero

    2018-03-01

    The Local Shannon Entropy (LSE) in blocks is used as a complexity measure to study the information fluctuations along DNA sequences. The LSE of a DNA block maps the local base arrangement information to a single numerical value. It is shown that despite this reduction of information, LSE allows to extract meaningful information related to the detection of repetitive sequences in whole chromosomes and is useful in finding evolutionary differences between organisms. More specifically, large regions of tandem repeats, such as centromeres, can be detected based on their low LSE fluctuations along the chromosome. Furthermore, an empirical investigation of the appropriate block sizes is provided and the relationship of LSE properties with the structure of the underlying repetitive units is revealed by using both computational and mathematical methods. Sequence similarity between the genomic DNA of closely related species also leads to similar LSE values at the orthologous regions. As an application, the LSE covariance function is used to measure the evolutionary distance between several primate genomes.

  19. Savings for visuomotor adaptation require prior history of error, not prior repetition of successful actions.

    Science.gov (United States)

    Leow, Li-Ann; de Rugy, Aymar; Marinovic, Welber; Riek, Stephan; Carroll, Timothy J

    2016-10-01

    When we move, perturbations to our body or the environment can elicit discrepancies between predicted and actual outcomes. We readily adapt movements to compensate for such discrepancies, and the retention of this learning is evident as savings, or faster readaptation to a previously encountered perturbation. The mechanistic processes contributing to savings, or even the necessary conditions for savings, are not fully understood. One theory suggests that savings requires increased sensitivity to previously experienced errors: when perturbations evoke a sequence of correlated errors, we increase our sensitivity to the errors experienced, which subsequently improves error correction (Herzfeld et al. 2014). An alternative theory suggests that a memory of actions is necessary for savings: when an action becomes associated with successful target acquisition through repetition, that action is more rapidly retrieved at subsequent learning (Huang et al. 2011). In the present study, to better understand the necessary conditions for savings, we tested how savings is affected by prior experience of similar errors and prior repetition of the action required to eliminate errors using a factorial design. Prior experience of errors induced by a visuomotor rotation in the savings block was either prevented at initial learning by gradually removing an oppositely signed perturbation or enforced by abruptly removing the perturbation. Prior repetition of the action required to eliminate errors in the savings block was either deprived or enforced by manipulating target location in preceding trials. The data suggest that prior experience of errors is both necessary and sufficient for savings, whereas prior repetition of a successful action is neither necessary nor sufficient for savings. Copyright © 2016 the American Physiological Society.

  20. Amino acid and nucleotide recurrence in aligned sequences: synonymous substitution patterns in association with global and local base compositions.

    Science.gov (United States)

    Nishizawa, M; Nishizawa, K

    2000-10-01

    The tendency for repetitiveness of nucleotides in DNA sequences has been reported for a variety of organisms. We show that the tendency for repetitive use of amino acids is widespread and is observed even for segments conserved between human and Drosophila melanogaster at the level of >50% amino acid identity. This indicates that repetitiveness influences not only the weakly constrained segments but also those sequence segments conserved among phyla. Not only glutamine (Q) but also many of the 20 amino acids show a comparable level of repetitiveness. Repetitiveness in bases at codon position 3 is stronger for human than for D.melanogaster, whereas local repetitiveness in intron sequences is similar between the two organisms. While genes for immune system-specific proteins, but not ancient human genes (i.e. human homologs of Escherichia coli genes), have repetitiveness at codon bases 1 and 2, repetitiveness at codon base 3 for these groups is similar, suggesting that the human genome has at least two mechanisms generating local repetitiveness. Neither amino acid nor nucleotide repetitiveness is observed beyond the exon boundary, denying the possibility that such repetitiveness could mainly stem from natural selection on mRNA or protein sequences. Analyses of mammalian sequence alignments show that while the 'between gene' GC content heterogeneity, which is linked to 'isochores', is a principal factor associated with the bias in substitution patterns in human, 'within gene' heterogeneity in nucleotide composition is also associated with such bias on a more local scale. The relationship amongst the various types of repetitiveness is discussed.

  1. DNA sequences of troglobitic nicoletiid insects support Sierra de El Abra and the Sierra de Guatemala as a single biogeographical area: Implications for Astyanax

    Directory of Open Access Journals (Sweden)

    Luis Espinasa

    2014-03-01

    Full Text Available The blind Mexican tetra fish, Astyanax mexicanus, has become the most influential model for research of cave adapted organisms. Many authors assume that the Sierra de Guatemala populations and the Sierra de El Abra populations are derived from two independent colonizations. This assumption arises in part from biogeography. The 100 m high, 100 m wide Servilleta Canyon of the Boquillas River separates both mountain ranges and is an apparent barrier for troglobite dispersion. Anelpistina quinterensis (Nicoletiidae, Zygentoma, Insecta is one of the most troglomorphic nicoletiid silverfish insects ever described. 16S rRNA sequences support that this species migrated underground to reach both mountain ranges within less than 12,000 years. Furthermore, literature shows a plethora of aquatic and terrestrial cave restricted species that inhabit both mountain ranges. Thus, the Servilleta canyon has not been an effective biological barrier that prevented underground migration of troglobites between the Sierra de Guatemala and the Sierra de El Abra. The Boquillas River has changed its course throughout time. Caves that in the past connected the two Sierras were only recently geologically truncated by the erosion of the new river course. It is likely that, with the geological changes of the area and throughout the 2-8 million years of evolutionary history of cave Astyanax, there have been opportunities to migrate across the Servilleta canyon.

  2. Eukaryotic Plankton Species Diversity in the Western Channel of the Korea Strait using 18S rDNA Sequences and its Implications for Water Masses

    Science.gov (United States)

    Lee, Sang-Rae; Song, Eun Hye; Lee, Tongsup

    2018-03-01

    Organisms entering the East Sea (Sea of Japan) through the Korea Strait, together with water, salt, and energy, affect the East Sea ecosystem. In this study, we report on the biodiversity of eukaryotic plankton found in the Western Channel of the Korea Strait for the first time using small subunit ribosomal RNA gene (18S rDNA) sequences. We also discuss the characteristics of water masses and their physicochemical factors. Diverse taxonomic groups were recovered from 18S rDNA clone libraries, including putative novel, higher taxonomic entities affiliated with Cercozoa, Raphidophyceae, Picozoa, and novel marine Stramenopiles. We also found that there was cryptic genetic variation at both the intraspecific and interspecific levels among arthropods, diatoms, and green algae. Specific plankton assemblages were identified at different sampling depths and they may provide useful information that could be used to interpret the origin and the subsequent mixing history of the water masses that contribute to the Tsushima Warm Current waters. Furthermore, the biological information highlighted in this study may help improve our understanding about the complex water mass interactions that were highlighted in the Korea Strait.

  3. Reservoir characteristics of coal-shale sedimentary sequence in coal-bearing strata and their implications for the accumulation of unconventional gas

    Science.gov (United States)

    Wang, Yang; Zhu, Yanming; Liu, Yu; Chen, Shangbin

    2018-04-01

    Shale gas and coalbed methane (CBM) are both considered unconventional natural gas and are becoming increasingly important energy resources. In coal-bearing strata, coal and shale are vertically adjacent as coal and shale are continuously deposited. Research on the reservoir characteristics of coal-shale sedimentary sequences is important for CBM and coal-bearing shale gas exploration. In this study, a total of 71 samples were collected, including coal samples (total organic carbon (TOC) content >40%), carbonaceous shale samples (TOC content: 6%-10%), and shale samples (TOC content TOC content. Clay and quartz also have a great effect on the porosity of shale samples. According to the FE-SEM image technique, nanoscale pores in the organic matter of coal samples are much more developed compared with shale samples. For shales with low TOC, inorganic minerals provide more pores than organic matter. In addition, TOC content has a positive relationship with methane adsorption capacity, and the adsorption capacity of coal samples is more sensitive than the shale samples to temperature.

  4. Binding of cholesterol and inhibitory peptide derivatives with the fusogenic hydrophobic sequence of F-glycoprotein of HVJ (Sendai virus): possible implication in the fusion reaction

    International Nuclear Information System (INIS)

    Asano, K.; Asano, A.

    1988-01-01

    Specificity of the binding of sterols and related compounds with purified F-protein (fusion protein) of the HVJ (Sendai virus) was studied by binding competition with [ 3 H] cholesterol. Requirement for cholesterol or the A/B ring trans structure and nonrequirement for the 3-hydroxyl group were found in this binding. Binding of 125 I-labeled Z-Phe-Tyr, an inhibitory peptide of viral membrane-cell membrane fusion, was studied by using purified proteins and virions. F-Protein and virions showed a specific binding with the peptide, whereas the result was negative with hemagglutinin and neuraminidase protein. Thermolysin-truncated F-protein (an F-protein derivative deprived of a 2.5-kDa fragment from the N-terminal of the F 1 subunit and without fusogenic activity) exhibited a considerably diminished binding ability both to cholesterol and to inhibitory peptides. Therefore, the N-terminal hydrophobic sequence that was previously assigned as fusogenic seems to be the binding site of these molecules. In support of this, the binding of cholesterol with F-protein was inhibited by Z-Phe-Tyr and other fusion inhibitory peptides, whereas it was not affected with non-fusion-inhibitory Z-Gly-Phe. These results are discussed in relation to the notion that the binding of the N-terminal portion of the F 1 subunit of F-protein with cholesterol in the target cell membranes facilitiates the fusion reaction

  5. Sequence assembly

    DEFF Research Database (Denmark)

    Scheibye-Alsing, Karsten; Hoffmann, S.; Frankel, Annett Maria

    2009-01-01

    Despite the rapidly increasing number of sequenced and re-sequenced genomes, many issues regarding the computational assembly of large-scale sequencing data have remain unresolved. Computational assembly is crucial in large genome projects as well for the evolving high-throughput technologies and...... in genomic DNA, highly expressed genes and alternative transcripts in EST sequences. We summarize existing comparisons of different assemblers and provide a detailed descriptions and directions for download of assembly programs at: http://genome.ku.dk/resources/assembly/methods.html....

  6. Genome Sequencing

    DEFF Research Database (Denmark)

    Sato, Shusei; Andersen, Stig Uggerhøj

    2014-01-01

    The current Lotus japonicus reference genome sequence is based on a hybrid assembly of Sanger TAC/BAC, Sanger shotgun and Illumina shotgun sequencing data generated from the Miyakojima-MG20 accession. It covers nearly all expressed L. japonicus genes and has been annotated mainly based on transcr......The current Lotus japonicus reference genome sequence is based on a hybrid assembly of Sanger TAC/BAC, Sanger shotgun and Illumina shotgun sequencing data generated from the Miyakojima-MG20 accession. It covers nearly all expressed L. japonicus genes and has been annotated mainly based...

  7. The Effect of Repetition on Tempo Preferences of Elementary Children.

    Science.gov (United States)

    Moskovitz, Elisa M.

    1992-01-01

    Reports on a study of children's preferences between slow and fast tempo classical music excerpts. Finds that students preferred music with a slow tempo. Concludes that repetition had a positive effect on children's preferences. (CFR)

  8. Antagonistic control of social versus repetitive self-grooming behaviors by separable amygdala neuronal subsets.

    Science.gov (United States)

    Hong, Weizhe; Kim, Dong-Wook; Anderson, David J

    2014-09-11

    Animals display a range of innate social behaviors that play essential roles in survival and reproduction. While the medial amygdala (MeA) has been implicated in prototypic social behaviors such as aggression, the circuit-level mechanisms controlling such behaviors are not well understood. Using cell-type-specific functional manipulations, we find that distinct neuronal populations in the MeA control different social and asocial behaviors. A GABAergic subpopulation promotes aggression and two other social behaviors, while neighboring glutamatergic neurons promote repetitive self-grooming, an asocial behavior. Moreover, this glutamatergic subpopulation inhibits social interactions independently of its effect to promote self-grooming, while the GABAergic subpopulation inhibits self-grooming, even in a nonsocial context. These data suggest that social versus repetitive asocial behaviors are controlled in an antagonistic manner by inhibitory versus excitatory amygdala subpopulations, respectively. These findings provide a framework for understanding circuit-level mechanisms underlying opponency between innate behaviors, with implications for their perturbation in psychiatric disorders. Copyright © 2014 Elsevier Inc. All rights reserved.

  9. Transcription of highly repetitive tandemly organized DNA in amphibians and birds: A historical overview and modern concepts.

    Science.gov (United States)

    Trofimova, Irina; Krasikova, Alla

    2016-12-01

    Tandemly organized highly repetitive DNA sequences are crucial structural and functional elements of eukaryotic genomes. Despite extensive evidence, satellite DNA remains an enigmatic part of the eukaryotic genome, with biological role and significance of tandem repeat transcripts remaining rather obscure. Data on tandem repeats transcription in amphibian and avian model organisms is fragmentary despite their genomes being thoroughly characterized. Review systematically covers historical and modern data on transcription of amphibian and avian satellite DNA in somatic cells and during meiosis when chromosomes acquire special lampbrush form. We highlight how transcription of tandemly repetitive DNA sequences is organized in interphase nucleus and on lampbrush chromosomes. We offer LTR-activation hypotheses of widespread satellite DNA transcription initiation during oogenesis. Recent explanations are provided for the significance of high-yield production of non-coding RNA derived from tandemly organized highly repetitive DNA. In many cases the data on the transcription of satellite DNA can be extrapolated from lampbrush chromosomes to interphase chromosomes. Lampbrush chromosomes with applied novel technical approaches such as superresolution imaging, chromosome microdissection followed by high-throughput sequencing, dynamic observation in life-like conditions provide amazing opportunities for investigation mechanisms of the satellite DNA transcription.

  10. RNA Sequencing and Bioinformatics Analysis Implicate the Regulatory Role of a Long Noncoding RNA-mRNA Network in Hepatic Stellate Cell Activation.

    Science.gov (United States)

    Guo, Can-Jie; Xiao, Xiao; Sheng, Li; Chen, Lili; Zhong, Wei; Li, Hai; Hua, Jing; Ma, Xiong

    2017-01-01

    To analyze the long noncoding (lncRNA)-mRNA expression network and potential roles in rat hepatic stellate cells (HSCs) during activation. LncRNA expression was analyzed in quiescent and culture-activated HSCs by RNA sequencing, and differentially expressed lncRNAs verified by quantitative reverse transcription polymerase chain reaction (qRT-PCR) were subjected to bioinformatics analysis. In vivo analyses of differential lncRNA-mRNA expression were performed on a rat model of liver fibrosis. We identified upregulation of 12 lncRNAs and 155 mRNAs and downregulation of 12 lncRNAs and 374 mRNAs in activated HSCs. Additionally, we identified the differential expression of upregulated lncRNAs (NONRATT012636.2, NONRATT016788.2, and NONRATT021402.2) and downregulated lncRNAs (NONRATT007863.2, NONRATT019720.2, and NONRATT024061.2) in activated HSCs relative to levels observed in quiescent HSCs, and Gene Ontology and Kyoto Encyclopedia of Genes and Genomes pathway analyses showed that changes in lncRNAs associated with HSC activation revealed 11 significantly enriched pathways according to their predicted targets. Moreover, based on the predicted co-expression network, the relative dynamic levels of NONRATT013819.2 and lysyl oxidase (Lox) were compared during HSC activation both in vitro and in vivo. Our results confirmed the upregulation of lncRNA NONRATT013819.2 and Lox mRNA associated with the extracellular matrix (ECM)-related signaling pathway in HSCs and fibrotic livers. Our results detailing a dysregulated lncRNA-mRNA network might provide new treatment strategies for hepatic fibrosis based on findings indicating potentially critical roles for NONRATT013819.2 and Lox in ECM remodeling during HSC activation. © 2017 The Author(s). Published by S. Karger AG, Basel.

  11. Is perfectionism associated with academic burnout through repetitive negative thinking?

    Science.gov (United States)

    Garratt-Reed, David; Howell, Joel; Hayes, Lana; Boyes, Mark

    2018-01-01

    Academic burnout is prevalent among university students, although understanding of what predicts burnout is limited. This study aimed to test the direct and indirect relationship between two dimensions of perfectionism (Perfectionistic Concerns and Perfectionistic Strivings) and the three elements of Academic Burnout (Exhaustion, Inadequacy, and Cynicism) through Repetitive Negative Thinking. In a cross-sectional survey, undergraduate students ( n  = 126, M age = 23.64, 79% female) completed well-validated measures of Perfectionism, Repetitive Negative Thinking, and Academic Burnout. Perfectionistic Concerns was directly associated with all elements of burnout, as well as indirectly associated with Exhaustion and Cynicism via Repetitive Negative Thinking. Perfectionistic Strivings was directly associated with less Inadequacy and Cynicism; however, there were no indirect associations between Perfectionistic Strivings and Academic Burnout operating through Repetitive Negative Thinking. Repetitive Negative Thinking was also directly related to more burnout Exhaustion and Inadequacy, but not Cynicism. It is concluded that future research should investigate whether interventions targeting Perfectionistic Concerns and Repetitive Negative Thinking can reduce Academic Burnout in university students.

  12. Negative effects of item repetition on source memory.

    Science.gov (United States)

    Kim, Kyungmi; Yi, Do-Joon; Raye, Carol L; Johnson, Marcia K

    2012-08-01

    In the present study, we explored how item repetition affects source memory for new item-feature associations (picture-location or picture-color). We presented line drawings varying numbers of times in Phase 1. In Phase 2, each drawing was presented once with a critical new feature. In Phase 3, we tested memory for the new source feature of each item from Phase 2. Experiments 1 and 2 demonstrated and replicated the negative effects of item repetition on incidental source memory. Prior item repetition also had a negative effect on source memory when different source dimensions were used in Phases 1 and 2 (Experiment 3) and when participants were explicitly instructed to learn source information in Phase 2 (Experiments 4 and 5). Importantly, when the order between Phases 1 and 2 was reversed, such that item repetition occurred after the encoding of critical item-source combinations, item repetition no longer affected source memory (Experiment 6). Overall, our findings did not support predictions based on item predifferentiation, within-dimension source interference, or general interference from multiple traces of an item. Rather, the findings were consistent with the idea that prior item repetition reduces attention to subsequent presentations of the item, decreasing the likelihood that critical item-source associations will be encoded.

  13. Recency, repetition, and the multidimensional basis of recognition memory.

    Science.gov (United States)

    Buchsbaum, Bradley R; Lemire-Rodger, Sabrina; Bondad, Ashley; Chepesiuk, Alexander

    2015-02-25

    Recency and repetition are two factors that have large effects on human memory performance. One way of viewing the beneficial impact of these variables on recognition memory is to assume that both factors modulate a unidimensional memory trace strength. Although previous functional neuroimaging studies have indicated that recency and repetition may modulate similar brain structures, particularly in the region of the inferior parietal cortex, there is extensive behavioral evidence that human subjects can make independent and accurate recognition memory judgments about both an item's recency and its frequency. In the present study, we used fMRI to examine patterns of brain activity during recognition memory for auditory-verbal stimuli that were parametrically and orthogonally manipulated in terms of recency and number of repetitions. We found in a continuous recognition paradigm that the lateral inferior parietal cortex, a region that has previously been associated with recollective forms of memory, is highly sensitive to recency but not repetition. In a multivariate analysis of whole-brain activation patterns, we found orthogonal components that dissociated recency and repetition variables, indicating largely independent neural bases underlying these two factors. The results demonstrate that although both recency and repetition dramatically improve recognition memory performance, the neural bases for this improvement are dissociable, and thus are difficult to explain in terms of access to a unitary memory trace. Copyright © 2015 the authors 0270-6474/15/353544-11$15.00/0.

  14. Properties of water surface discharge at different pulse repetition rates

    International Nuclear Information System (INIS)

    Ruma,; Yoshihara, K.; Hosseini, S. H. R.; Sakugawa, T.; Akiyama, H.; Akiyama, M.; Lukeš, P.

    2014-01-01

    The properties of water surface discharge plasma for variety of pulse repetition rates are investigated. A magnetic pulse compression (MPC) pulsed power modulator able to deliver pulse repetition rates up to 1000 Hz, with 0.5 J per pulse energy output at 25 kV, was used as the pulsed power source. Positive pulse with a point-to-plane electrode configuration was used for the experiments. The concentration and production yield of hydrogen peroxide (H 2 O 2 ) were quantitatively measured and orange II organic dye was treated, to evaluate the chemical properties of the discharge reactor. Experimental results show that the physical and chemical properties of water surface discharge are not influenced by pulse repetition rate, very different from those observed for under water discharge. The production yield of H 2 O 2 and degradation rate per pulse of the dye did not significantly vary at different pulse repetition rates under a constant discharge mode on water surface. In addition, the solution temperature, pH, and conductivity for both water surface and underwater discharge reactors were measured to compare their plasma properties for different pulse repetition rates. The results confirm that surface discharge can be employed at high pulse repetition rates as a reliable and advantageous method for industrial and environmental decontamination applications.

  15. Deep-sequencing protocols influence the results obtained in small-RNA sequencing.

    Directory of Open Access Journals (Sweden)

    Joern Toedling

    Full Text Available Second-generation sequencing is a powerful method for identifying and quantifying small-RNA components of cells. However, little attention has been paid to the effects of the choice of sequencing platform and library preparation protocol on the results obtained. We present a thorough comparison of small-RNA sequencing libraries generated from the same embryonic stem cell lines, using different sequencing platforms, which represent the three major second-generation sequencing technologies, and protocols. We have analysed and compared the expression of microRNAs, as well as populations of small RNAs derived from repetitive elements. Despite the fact that different libraries display a good correlation between sequencing platforms, qualitative and quantitative variations in the results were found, depending on the protocol used. Thus, when comparing libraries from different biological samples, it is strongly recommended to use the same sequencing platform and protocol in order to ensure the biological relevance of the comparisons.

  16. Structure characterization of the central repetitive domain of high molecular weight gluten proteins .1. Model studies using cyclic and linear peptides

    NARCIS (Netherlands)

    VanDijk, AA; VanWijk, LL; VanVliet, A; Haris, P; VanSwieten, E; Tesser, GI; Robillard, GT

    The high molecular weight (HMW) proteins from wheat contain a repetitive domain that forms 60-80% of their sequence. The consensus peptides PGQGQQ and GYYPTSPQQ form more than 90% of the domain; both are predicted to adopt beta-turn structure. This paper describes the structural characterization of

  17. The effects of previewing questions, repetition of input, and topic preparation on listening comprehension of Iranian EFL learners

    Directory of Open Access Journals (Sweden)

    Afsar Rouhi

    2014-07-01

    Full Text Available In this study, an attempt was made to examine the effects of previewing questions, repetition of input, and topic preparation on listening comprehension of Iranian learners of English. The study was conducted with 104 high school students in 3 experimental and one control groups. The participants in the previewing questions group read the comprehension questions before hearing the text and answering the questions. The topic preparation group took advantage of topic-related texts in Persian followed by previewing questions; then they listened to the texts and answered the questions. The repetition of input group had two hearings with previewing before each hearing that preceded answering the comprehension questions. The control group, however, only had one hearing before answering the questions. The results obtained from data analysis showed that the topic preparation group performed better than the other participating groups. The repetition group, in turn, did better than the previewing group. There was, however, no statistically significant difference between the previewing and repetition groups. Based on the results obtained, it can be argued that providing and/or activating background knowledge and repeating a listening task might facilitate listening comprehension in EFL classroom settings. The findings and pedagogical implications of the study are discussed in detail.

  18. Vibrational sum-frequency generation spectroscopy of lipid bilayers at repetition rates up to 100 kHz

    Science.gov (United States)

    Yesudas, Freeda; Mero, Mark; Kneipp, Janina; Heiner, Zsuzsanna

    2018-03-01

    Broadband vibrational sum-frequency generation (BB-VSFG) spectroscopy has become a well-established surface analytical tool capable of identifying the orientation and structure of molecular layers. A straightforward way to boost the sensitivity of the technique could be to increase the laser repetition rate beyond that of standard BB-VSFG spectrometers, which rely on Ti:sapphire lasers operating at repetition rates of 1-5 kHz. Nevertheless, possible thermally induced artifacts in the vibrational spectra due to higher laser average powers are unexplored. Here, we discuss laser power induced temperature accumulation effects that distort the BB-VSFG spectra of 1,2-diacyl-sn-glycero-3-phosphocholine at an interface between two transparent phases at repetition rates of 5, 10, 50, and 100 kHz at constant pulse energy. No heat-induced distortions were found in the spectra, suggesting that the increase in the laser repetition rate provides a feasible route to an improved signal-to-noise ratio or shorter data acquisition times in BB-VSFG spectroscopy for thin films on transparent substrates. The results have implications for future BB-VSFG spectrometers pushing the detection limit for molecular layers with low surface coverage.

  19. Dog Y chromosomal DNA sequence: identification, sequencing and SNP discovery

    Directory of Open Access Journals (Sweden)

    Kirkness Ewen

    2006-10-01

    Full Text Available Abstract Background Population genetic studies of dogs have so far mainly been based on analysis of mitochondrial DNA, describing only the history of female dogs. To get a picture of the male history, as well as a second independent marker, there is a need for studies of biallelic Y-chromosome polymorphisms. However, there are no biallelic polymorphisms reported, and only 3200 bp of non-repetitive dog Y-chromosome sequence deposited in GenBank, necessitating the identification of dog Y chromosome sequence and the search for polymorphisms therein. The genome has been only partially sequenced for one male dog, disallowing mapping of the sequence into specific chromosomes. However, by comparing the male genome sequence to the complete female dog genome sequence, candidate Y-chromosome sequence may be identified by exclusion. Results The male dog genome sequence was analysed by Blast search against the human genome to identify sequences with a best match to the human Y chromosome and to the female dog genome to identify those absent in the female genome. Candidate sequences were then tested for male specificity by PCR of five male and five female dogs. 32 sequences from the male genome, with a total length of 24 kbp, were identified as male specific, based on a match to the human Y chromosome, absence in the female dog genome and male specific PCR results. 14437 bp were then sequenced for 10 male dogs originating from Europe, Southwest Asia, Siberia, East Asia, Africa and America. Nine haplotypes were found, which were defined by 14 substitutions. The genetic distance between the haplotypes indicates that they originate from at least five wolf haplotypes. There was no obvious trend in the geographic distribution of the haplotypes. Conclusion We have identified 24159 bp of dog Y-chromosome sequence to be used for population genetic studies. We sequenced 14437 bp in a worldwide collection of dogs, identifying 14 SNPs for future SNP analyses, and

  20. Snake Genome Sequencing: Results and Future Prospects.

    Science.gov (United States)

    Kerkkamp, Harald M I; Kini, R Manjunatha; Pospelov, Alexey S; Vonk, Freek J; Henkel, Christiaan V; Richardson, Michael K

    2016-12-01

    Snake genome sequencing is in its infancy-very much behind the progress made in sequencing the genomes of humans, model organisms and pathogens relevant to biomedical research, and agricultural species. We provide here an overview of some of the snake genome projects in progress, and discuss the biological findings, with special emphasis on toxinology, from the small number of draft snake genomes already published. We discuss the future of snake genomics, pointing out that new sequencing technologies will help overcome the problem of repetitive sequences in assembling snake genomes. Genome sequences are also likely to be valuable in examining the clustering of toxin genes on the chromosomes, in designing recombinant antivenoms and in studying the epigenetic regulation of toxin gene expression.

  1. Snake Genome Sequencing: Results and Future Prospects

    Directory of Open Access Journals (Sweden)

    Harald M. I. Kerkkamp

    2016-12-01

    Full Text Available Snake genome sequencing is in its infancy—very much behind the progress made in sequencing the genomes of humans, model organisms and pathogens relevant to biomedical research, and agricultural species. We provide here an overview of some of the snake genome projects in progress, and discuss the biological findings, with special emphasis on toxinology, from the small number of draft snake genomes already published. We discuss the future of snake genomics, pointing out that new sequencing technologies will help overcome the problem of repetitive sequences in assembling snake genomes. Genome sequences are also likely to be valuable in examining the clustering of toxin genes on the chromosomes, in designing recombinant antivenoms and in studying the epigenetic regulation of toxin gene expression.

  2. Transcription of tandemly repetitive DNA: functional roles.

    Science.gov (United States)

    Biscotti, Maria Assunta; Canapa, Adriana; Forconi, Mariko; Olmo, Ettore; Barucca, Marco

    2015-09-01

    A considerable fraction of the eukaryotic genome is made up of satellite DNA constituted of tandemly repeated sequences. These elements are mainly located at centromeres, pericentromeres, and telomeres and are major components of constitutive heterochromatin. Although originally satellite DNA was thought silent and inert, an increasing number of studies are providing evidence on its transcriptional activity supporting, on the contrary, an unexpected dynamicity. This review summarizes the multiple structural roles of satellite noncoding RNAs at chromosome level. Indeed, satellite noncoding RNAs play a role in the establishment of a heterochromatic state at centromere and telomere. These highly condensed structures are indispensable to preserve chromosome integrity and genome stability, preventing recombination events, and ensuring the correct chromosome pairing and segregation. Moreover, these RNA molecules seem to be involved also in maintaining centromere identity and in elongation, capping, and replication of telomere. Finally, the abnormal variation of centromeric and pericentromeric DNA transcription across major eukaryotic lineages in stress condition and disease has evidenced the critical role that these transcripts may play and the potentially dire consequences for the organism.

  3. Word and nonword repetition in patients with Schizophrenia

    Directory of Open Access Journals (Sweden)

    Alireza Farnam

    2015-08-01

    Full Text Available Introduction: The assessment of the verbal repetition is important in the study of acquired language disorders and neuropsychology. It is helpful in differential diagnosis of aphasia subtypes, auditory breakdowns, and working memory (WM performance. Though different linguistic disorders have been identified in patients with schizophrenia, very little is known about their verbal repetition ability. Methods: The present study was conducted in the inpatient ward of Razi Psychiatric Hospital, Tabriz University of Medical Sciences, Iran, during the year 2013. Participants were: 30 patients diagnosed with schizophrenia during the maintenance phase of treatment and 30 healthy people as control group. They were asked to repeat 15 words and 15 nonwords immediately. The stimuli were 1, 2, and 3 syllabic in Turkish language. Any incorrect repetition scored 1 and correct repetitions scored 0. Lexicalization errors were compared between groups too. Results: Both groups repeated words better than nonwords. Patients showed lower ability to repeat nonwords than controls, especially in 3 syllabics. There was no significant difference in the repetition of words between groups though it was better in controls. Patients with schizophrenia made more errors in both words and nonwords and lexicalization errors were twice more. Conclusion: Lower ability to repeat nonwords (than words in patients with schizophrenia may show the involvement of phonological loop of WM. More lexicalization errors may take place because of dis-inhibition.

  4. Quantifying repetitive speech in autism spectrum disorders and language impairment.

    Science.gov (United States)

    van Santen, Jan P H; Sproat, Richard W; Hill, Alison Presmanes

    2013-10-01

    We report on an automatic technique for quantifying two types of repetitive speech: repetitions of what the child says him/herself (self-repeats) and of what is uttered by an interlocutor (echolalia). We apply this technique to a sample of 111 children between the ages of four and eight: 42 typically developing children (TD), 19 children with specific language impairment (SLI), 25 children with autism spectrum disorders (ASD) plus language impairment (ALI), and 25 children with ASD with normal, non-impaired language (ALN). The results indicate robust differences in echolalia between the TD and ASD groups as a whole (ALN + ALI), and between TD and ALN children. There were no significant differences between ALI and SLI children for echolalia or self-repetitions. The results confirm previous findings that children with ASD repeat the language of others more than other populations of children. On the other hand, self-repetition does not appear to be significantly more frequent in ASD, nor does it matter whether the child's echolalia occurred within one (immediate) or two turns (near-immediate) of the adult's original utterance. Furthermore, non-significant differences between ALN and SLI, between TD and SLI, and between ALI and TD are suggestive that echolalia may not be specific to ALN or to ASD in general. One important innovation of this work is an objective fully automatic technique for assessing the amount of repetition in a transcript of a child's utterances. © 2013 International Society for Autism Research, Wiley Periodicals, Inc.

  5. Autism and exergaming: effects on repetitive behaviors and cognition

    Directory of Open Access Journals (Sweden)

    Anderson-Hanley C

    2011-09-01

    Full Text Available Cay Anderson-Hanley, Kimberly Tureck, Robyn L Schneiderman Department of Psychology, Union College, Schenectady, NY, USA Abstract: Autism is a neurodevelopmental disorder that leads to impairment in social skills and delay in language development, and results in repetitive behaviors and restricted interests that impede academic and social involvement. Physical exercise has been shown to decrease repetitive behaviors in autistic children and improve cognitive function across the life-span. Exergaming combines physical and mental exercise simultaneously by linking physical activity movements to video game control and may yield better compliance with exercise. In this investigation, two pilot studies explored the potential behavioral and cognitive benefits of exergaming. In Pilot I, twelve children with autism spectrum disorders completed a control task and an acute bout of Dance Dance Revolution (DDR; in Pilot II, ten additional youths completed an acute bout of cyber cycling. Repetitive behaviors and executive function were measured before and after each activity. Repetitive behaviors significantly decreased, while performance on Digits Backwards improved following the exergaming conditions compared with the control condition. Additional research is needed to replicate these findings, and to explore the application of exergaming for the management of behavioral disturbance and to increase cognitive control in children on the autism spectrum. Keywords: autism, repetitive behaviors, exergaming, exercise, executive function

  6. Nanosecond radar system based on repetitive pulsed relativistic BWO

    International Nuclear Information System (INIS)

    Bunkin, B.V.; Gaponov-Grekhov, A.V.; Eltchaninov, A.S.; Zagulov, F.Ya.; Korovin, S.D.; Mesyats, G.A.; Osipov, M.L.; Otlivantchik, E.A.; Petelin, M.I.; Prokhorov, A.M.

    1993-01-01

    The paper presents the results of studies of a nanosecond radar system based on repetitive pulsed relativistic BWO. A pulsed power repetitive accelerator producing electron beams of electron energy 500-700 keV and current 5 kA in pulses of duraction 10 ns with a repetition rate of 100 pps is described. The results of experiments with a high-voltage gas-filled spark gap and a cold-cathode vacuum diode under the conditions of high repetition rates are given. Also presented are the results of studies of a relativistic BWO operating with a wavelength of 3 cm. It is shown that for a high-current beam electron energy of 500-700 keV, the BWO efficiency can reach 35%, the microwave power being 10 9 W. A superconducting solenoid creating a magnetic field of 30 kOe was used for the formation and transportation of the high-current electron beam. In conclusion, the outcome of tests of a nanosecond radar station based on a pulsed power repetitive accelerator and a relativistic BWO is reported

  7. RPERT: Repetitive-Projects Evaluation and Review Technique

    Directory of Open Access Journals (Sweden)

    Remon Fayek Aziz

    2014-03-01

    Full Text Available Estimating expected completion probability of any repetitive construction project with a specified/certain duration including repetitive identical activities by using program evaluation and review technique is the most essential part in construction areas since the activities were had optimistic, most likely and pessimistic durations. This paper focuses on the calculation of expected completion probability of any repetitive construction project within a specified/certain duration (contract duration by using Line Of Balance technique (LOB in case of single or multiple number of crews integrated with Program Evaluation and Review Technique (PERT. Repetitive-Projects Evaluation and Review Technique (RPERT, which is a simplified software, will generate the expected project completion probability of a specified/certain duration (contract duration. RPERT software is designed by java programming code system to provide a number of new and unique capabilities, including: (1 Viewing the expected project completion probability according to a set of specified durations per each identical activity (optimistic time, most likely time, and pessimistic time in the analyzed project; (2 Providing seamless integration with available project time calculations. In order to provide the aforementioned capabilities of RPERT, the system is implemented and developed in four main modules: (1 A user interface module; (2 A database module; (3 A running module; and (4 A processing module. At the end, an illustrative example will be presented to demonstrate and verify the applications of proposed software (RPERT, by using probabilistic calculations for repetitive construction projects.

  8. solation, characterization and chromosome localization of repetitive DNA sequences in bananas (Musa spp.)

    Czech Academy of Sciences Publication Activity Database

    Valárik, Miroslav; Šimková, Hana; Šafář, Jan; Doleželová, Marie; Doležel, Jaroslav

    2002-01-01

    Roč. 10, - (2002), s. 89-100 ISSN 0967-3849 R&D Projects: GA AV ČR IAA6038204; GA AV ČR IBS5038104 Institutional research plan: CEZ:AV0Z5038910 Keywords : chromosome structure * genome size * in situ hybridization Subject RIV: EB - Genetics ; Molecular Biology Impact factor: 1.828, year: 2002

  9. Comparative genomics and repetitive sequence divergence in the species of diploid Nicotiana section Alatae

    Czech Academy of Sciences Publication Activity Database

    Lim, Y.K.; Kovařík, Aleš; Matyášek, Roman; Chase, M.W.; Knapp, S.; McCarthy, E.; Clarkson, J.; Leitch, A.R.

    2006-01-01

    Roč. 48, č. 6 (2006), s. 907-919 ISSN 0960-7412 R&D Projects: GA ČR(CZ) GA521/04/0775 Institutional research plan: CEZ:AV0Z50040507 Keywords : comparative genomics * DNA phylogenetics * tandem repeats Subject RIV: BO - Biophysics Impact factor: 6.565, year: 2006

  10. Mutations detected in the repetitive sequences in the children of the atomic bomb survivors

    International Nuclear Information System (INIS)

    Satoh, Chiyoko; Kodaira, Mieko

    1994-01-01

    We have been examining genetic effects of radiation in the children of the atomic bomb survivors. In a pilot study, 50 exposed families with 64 children and 50 control families with 60 children were examined for trinucleotide repeat expansion mutations at 3 loci and mutations at 6 minisatellite loci. Average dose of the 51 exposed parents was 1.8 Sv. By examining 124 children of 100 families, 65 germ cells derived from exposed parents and 183 germ cells of non-exposed parents were examined. The trinucleotide repeat expansions in genes of certain human genetic diseases show remarkable variation both within the cells of a single individual and among affected members of a single family which have been interpreted as mitotic and meiotic instability. We examined the regions with triplet repeats in the FMR-1, AR and DM genes causative for fragile X syndrome, spinobulbar muscular atrophy and myotonic dystrophy. No mutations were detected in 177 regions derived from 65 germ cells of exposed parents and 443 regions from 183 germ cells of non-exposed parents. No effects on the instability of the triplet repeats in the germ cells derived from exposed or unexposed individuals were observed. In the examinations of the 6 minisatellite loci of Pc-1, λTM-18, ChdTC-15, pλg3, λMS-1, and CEB-1, we detected single mutations at each of the pλg3 and λMS-1, and 4 mutations at the CEB-1 locus which had occurred in the 65 gametes in the exposed parents. Thus, mutation rates per gamete at the pλg3, λMS-1 and CEB-1 were 1.5%, 1.5% and 6.2%. On the other hand, mutations in these 3 loci in the 183 gametes of non-exposed parents were 0, 11 and 11, that is, the mutation rates per gamete were 0%, 6.0% and 6.0%. No significant difference was observed in the mutation rate at each of the 3 loci between 2 groups of parents. These preliminary results suggest that A-bomb exposure seems not to affect the germline instability at these 3 loci. (J.P.N)

  11. Molecular Cytogenetics in Artificial Hybrid and Highly Polyploid Sturgeons: An Evolutionary Story Narrated by Repetitive Sequences

    Czech Academy of Sciences Publication Activity Database

    Symonová, Radka; Flajšhans, M.; Sember, Alexandr; Havelka, M.; Gela, D.; Kořínková, Tereza; Rodina, M.; Rábová, Marie; Ráb, Petr

    2013-01-01

    Roč. 141, 2-3 (2013), s. 153-162 ISSN 1424-8581 R&D Projects: GA ČR GA523/08/0824; GA ČR(CZ) GPP506/11/P596 Institutional support: RVO:67985904 Keywords : Acipenser * GISH * Hybridization * Macrochromosomes Subject RIV: EG - Zoology Impact factor: 1.905, year: 2013

  12. Potato Genome Sequencing: A Short Glimpse of the Non-Repetitive.

    Science.gov (United States)

    Potato is the world’s number one vegetable crop. The potato is a member of the Solanaceae family that contains other crops such tomato pepper and eggplant as well as model species tobacco and petunia. Tomato is both an important crop as well as a model species for genetic and physical genomic info...

  13. Body-focused repetitive behavior disorders in ICD-11

    Directory of Open Access Journals (Sweden)

    Jon E. Grant

    2014-01-01

    Full Text Available This article addresses the question of how body-focused repetitive behavior disorders (e.g., trichotillomania and skin-picking disorder should be characterized in ICD-11. The article reviews the historical nosology of the two disorders and the current approaches in DSM-5 and ICD-10. Although data are limited and mixed regarding the optimal relationship between body-focused repetitive behavior disorders and nosological categories, these conditions should be included within the obsessive-compulsive and related disorders category, as this is how most clinicians see these behaviors, and as this may optimize clinical utility. The descriptions of these disorders should largely mirror those in DSM-5, given the evidence from recent field surveys. The recommendations regarding ICD-11 and body-focused repetitive behavior disorders should promote the global identification and treatment of these conditions in primary care settings.

  14. Repetitive control of an electrostatic microbridge actuator: theory and simulation

    International Nuclear Information System (INIS)

    Zhao, Haiyu; Rahn, Christopher D

    2010-01-01

    Electrostatic microactuators are used extensively in MEMS sensors, RF switches and microfluidic pumps. The high bandwidth operation required by these applications complicates the implementation of feedback controllers. This paper designs, proves stability and simulates a feedforward repetitive controller for an electrostatic microbridge. High residual stress creates tension in the microbridge that dominates bending stiffness so a pinned string model with uniform electrostatic force loading is used for model-based control. The control objective is to force the microbridge displacement to follow prescribed spatial and periodic time trajectories. Viscous damping ensures boundedness of the distributed transverse displacement in response to bounded inputs. The average displacement is measured by capacitive sensing and processed offline using a repetitive control algorithm that updates a high speed waveform generator's parameters. Simulations show that the performance depends on the amount of damping. With less than 1% damping in a representative microbridge structure, repetitive control reduces the midspan displacement overshoot by 83%

  15. Illusory sensation of movement induced by repetitive transcranial magnetic stimulation

    DEFF Research Database (Denmark)

    Christensen, Mark Schram; Lundbye-Jensen, Jesper; Grey, Michael James

    2010-01-01

    Human movement sense relies on both somatosensory feedback and on knowledge of the motor commands used to produce the movement. We have induced a movement illusion using repetitive transcranial magnetic stimulation over primary motor cortex and dorsal premotor cortex in the absence of limb movement...... and its associated somatosensory feedback. Afferent and efferent neural signalling was abolished in the arm with ischemic nerve block, and in the leg with spinal nerve block. Movement sensation was assessed following trains of high-frequency repetitive transcranial magnetic stimulation applied over...... premotor cortex stimulation was less affected by sensory and motor deprivation than was primary motor cortex stimulation. We propose that repetitive transcranial magnetic stimulation over dorsal premotor cortex produces a corollary discharge that is perceived as movement....

  16. Risk factors for hand-wrist disorders in repetitive work

    DEFF Research Database (Denmark)

    Thomsen, J. F.; Mikkelsen, S.; Andersen, JH

    2007-01-01

    OBJECTIVES: To identify the risk of hand-wrist disorders related to repetitive movements, use of hand force and wrist position in repetitive monotonous work. METHODS: Using questionnaires and physical examinations, the prevalence and incidence of hand-wrist pain and possible extensor tendonitis...... (wrist pain and palpation tenderness) were determined in 3123 employees in 19 industrial settings. With the use of questionnaires and video recordings of homogenous work tasks number of wrist movements, hand force requirements and wrist position were analysed as risk factors for hand-wrist disorders......, controlling for potential personal and psychosocial confounders. All participants were re-examined three times during a follow-up period of three years. RESULTS: Force but not repetition and position was related to hand-wrist pain and possible tendonitis in the baseline analyses showing an exposure...

  17. Reliability of one-repetition maximum performance in people with chronic heart failure.

    Science.gov (United States)

    Ellis, Rachel; Holland, Anne E; Dodd, Karen; Shields, Nora

    2018-02-24

    Evaluate intra-rater and inter-rater reliability of the one-repetition maximum strength test in people with chronic heart failure. Intra-rater and inter-rater reliability study. A public tertiary hospital in northern metropolitan Melbourne. Twenty-four participants (nine female, mean age 71.8 ± 13.1 years) with mild to moderate heart failure of any aetiology. Lower limb strength was assessed by determining the maximum weight that could be lifted using a leg press. Intra-rater reliability was tested by one assessor on two separate occasions . Inter-rater reliability was tested by two assessors in random order. Intra-class correlation coefficients and 95% confidence intervals were calculated. Bland and Altman analyses were also conducted, including calculation of mean differences between measures ([Formula: see text]) and limits of agreement . Ten intra-rater and 21 inter-rater assessments were completed. Excellent intra-rater (intra-class correlation coefficient 2,1 0.96) and inter-rater (intra-class correlation coefficient 2,1 0.93) reliability was found. Intra-rater assessment showed less variability (mean difference 4.5 kg, limits of agreement -8.11 to 17.11 kg) than inter-rater agreement (mean difference -3.81 kg, limits of agreement -23.39 to 15.77 kg). One-repetition maximum determined using a leg press is a reliable measure in people with heart failure. Given its smaller limits of agreement, intra-rater testing is recommended. Implications for Rehabilitation Using a leg press to determine a one-repetition maximum we were able to demonstrate excellent inter-rater and intra-rater reliability using an intra-class correlation coefficient. The Bland and Altman levels of agreement were wide for inter-rater reliability and so we recommend using one assessor if measuring change in strength within an individual over time.

  18. Identification and chromosome mapping of repetitive elements in the Astyanax scabripinnis (Teleostei: Characidae) species complex.

    Science.gov (United States)

    Barbosa, Patrícia; de Oliveira, Luiz Antonio; Pucci, Marcela Baer; Santos, Mateus Henrique; Moreira-Filho, Orlando; Vicari, Marcelo Ricardo; Nogaroto, Viviane; de Almeida, Mara Cristina; Artoni, Roberto Ferreira

    2015-02-01

    Most part of the eukaryotic genome is composed of repeated sequences or multiple copies of DNA, which were considered as "junk DNA", and may be associated to the heterochromatin. In this study, three populations of Astyanax aff. scabripinnis from Brazilian rivers of Guaratinguetá and Pindamonhangaba (São Paulo) and a population from Maringá (Paraná) were analyzed concerning the localization of the nucleolar organizer regions (Ag-NORs), the As51 satellite DNA, the 18S ribosomal DNA (rDNA), and the 5S rDNA. Repeated sequences were also isolated and identified by the Cot - 1 method, which indicated similarity (90%) with the LINE UnaL2 retrotransposon. The fluorescence in situ hybridization (FISH) showed the retrotransposon dispersed and more concentrated markers in centromeric and telomeric chromosomal regions. These sequences were co-localized and interspaced with 18S and 5S rDNA and As51, confirmed by fiber-FISH essay. The B chromosome found in these populations pointed to a conspicuous hybridization with LINE probe, which is also co-located in As51 sequences. The NORs were active at unique sites of a homologous pair in the three populations. There were no evidences that transposable elements and repetitive DNA had influence in the transcriptional regulation of ribosomal genes in our analyses.

  19. Comparison of concentric and eccentric bench press repetitions to failure.

    Science.gov (United States)

    Kelly, Stephen B; Brown, Lee E; Hooker, Steven P; Swan, Pamela D; Buman, Matthew P; Alvar, Brent A; Black, Laurie E

    2015-04-01

    Eccentric muscle actions (ECC) are characterized by muscle lengthening, despite actin-myosin crossbridge formation. Muscles acting eccentrically are capable of producing higher levels of force compared with muscles acting concentrically. The purpose of this study was to determine whether ECC bench press yields greater strength than concentric (CON) as determined by 1 repetition maximum (1RM). Additionally, a comparison was made examining differences in the number of repetitions to failure at different relative intensities of 1RM. Thirty healthy men (age = 24.63 ± 5.6 years) were tested for 1RM in CON and ECC bench press and the number of repetitions completed at 60, 70, 80, and 90% 1RM. For CON repetitions, the weight was mechanically lowered to the chest, and the participant pressed it up until the elbows were fully extended. The ECC bench press consisted of lowering a barbell from a fully extended elbow position to the chest in a continuous controlled manner for 3 seconds as determined by electronic metronome. Paired t-tests showed that ECC 1RM (115.99 ± 31.08 kg) was significantly (p ≤ 0.05) greater than CON 1RM (93.56 ± 26.56 kg), and the number of repetitions completed at 90% 1RM was significantly (p ≤ 0.05) greater in ECC (7.67 ± 3.24) as compared with CON (4.57 ± 2.21). There were no significant differences in number of completed repetitions during CON and ECC bench press at 60, 70, and 80% 1RM. These data indicate that ECC actions yield increased force capabilities (∼120%) as compared with CON in the bench press and may be less prone to fatigue, especially at higher intensities. These differences suggest a need to develop unique strategies for training eccentrically.

  20. The relationships within the mathematical content of teachers’ lesson sequences

    Science.gov (United States)

    Shahrill, M.; Prahmana, R. C. I.; Roslan, R.

    2017-12-01

    This study explored how mathematics content is carried through by means of the problems presented during lessons. Following the definitions and the coding criteria from the TIMSS 1999 Video Study, a total of 163 mathematics problems were identified in the video- recorded lesson sequences of four Bruneian mathematics teachers teaching at the Year 8 level. These problems were classified according to the four basic kinds of relationships: mathematically related, thematically related, repetition and unrelated. Drawing on the mathematical content of the teachers’ lesson sequences, the findings revealed variations among the mathematical problems coded as repetition and thematically related, between the four Brunei classes. The aggregated results obtained from the four classes highlighted several points of discussion, such as the relatively higher proportion of repetition problems (52%) from one teacher in particular; the percentage similarities of thematically related problems for all four classes (ranging from 26% to 33%); and the incredibly varied results for mathematically related problems across the four Brunei classes.

  1. Negative effects of item repetition on source memory

    OpenAIRE

    Kim, Kyungmi; Yi, Do-Joon; Raye, Carol L.; Johnson, Marcia K.

    2012-01-01

    In the present study, we explored how item repetition affects source memory for new item–feature associations (picture–location or picture–color). We presented line drawings varying numbers of times in Phase 1. In Phase 2, each drawing was presented once with a critical new feature. In Phase 3, we tested memory for the new source feature of each item from Phase 2. Experiments 1 and 2 demonstrated and replicated the negative effects of item repetition on incidental source memory. Prior item re...

  2. High-repetition-rate short-pulse gas discharge.

    Science.gov (United States)

    Tulip, J; Seguin, H; Mace, P N

    1979-09-01

    A high-average-power short-pulse gas discharge is described. This consists of a volume-preionized transverse discharge of the type used in gas lasers driven by a Blumlein energy storage circuit. The Blumlein circuit is fabricated from coaxial cable, is pulse-charged from a high-repetition-rate Marx-bank generator, and is switched by a high-repetition-rate segmented rail gap. The operation of this discharge under conditions typical of rare-gas halide lasers is described. A maximum of 900 pps was obtained, giving a power flow into the discharge of 30 kW.

  3. The repetition effect in building and construction works

    DEFF Research Database (Denmark)

    Gottlieb, Stefan Christoffer; Haugbølle, Kim

    are then applied on the Public Transport Authorities' main account structure of units and costs, and a method for assessing the possibilities of achieving effects of repetition for each account is described. Finally, the report summarises the core conditions necessary to take into consideration in relation......This report summarises the results from the work undertaken for the Public Transport Authority on the effect of learning and repetition in building and construction works. The results are applied by the Public Transport Authority in a new budgeting model, while the agency investigates...

  4. Iodine laser of high efficiency and fast repetition rate

    Energy Technology Data Exchange (ETDEWEB)

    Hohla, K; Witte, K J

    1976-07-01

    The scaling laws of an iodine laser of high efficiency and fast repetition rate are reported. The laser is pumped with a new kind of low pressure Hg-UV-lamps which convert 32% of the electrical input in UV-light in the absorption band of the iodine laser and which can be fired up to 100 Hz. Details of a 10 kJ/1 nsec system as dimensions, energy density, repetition rate, flow velocity, gas composition and gas pressure and the overall efficiency are given which is expected to be about 2%.

  5. Repetition priming of face recognition in a serial choice reaction-time task.

    Science.gov (United States)

    Roberts, T; Bruce, V

    1989-05-01

    Marshall & Walker (1987) found that pictorial stimuli yield visual priming that is disrupted by an unpredictable visual event in the response-stimulus interval. They argue that visual stimuli are represented in memory in the form of distinct visual and object codes. Bruce & Young (1986) propose similar pictorial, structural and semantic codes which mediate the recognition of faces, yet repetition priming results obtained with faces as stimuli (Bruce & Valentine, 1985), and with objects (Warren & Morton, 1982) are quite different from those of Marshall & Walker (1987), in the sense that recognition is facilitated by pictures presented 20 minutes earlier. The experiment reported here used different views of familiar and unfamiliar faces as stimuli in a serial choice reaction-time task and found that, with identical pictures, repetition priming survives and intervening item requiring a response, with both familiar and unfamiliar faces. Furthermore, with familiar faces such priming was present even when the view of the prime was different from the target. The theoretical implications of these results are discussed.

  6. The DNA sequence and biology of human chromosome 19

    Energy Technology Data Exchange (ETDEWEB)

    Grimwood, J; Gordon, L A; Olsen, A; Terry, A; Schmutz, J; Lamerdin, J; Hellsten, U; Goodstein, D; Couronne, O; Tran-Gyamfi, M

    2004-04-06

    Chromosome 19 has the highest gene density of all human chromosomes, more than double the genome-wide average. The large clustered gene families, corresponding high GC content, CpG islands and density of repetitive DNA indicate a chromosome rich in biological and evolutionary significance. Here we describe 55.8 million base pairs of highly accurate finished sequence representing 99.9% of the euchromatin portion of the chromosome. Manual curation of gene loci reveals 1,461 protein-coding genes and 321 pseudogenes. Among these are genes directly implicated in Mendelian disorders, including familial hypercholesterolemia and insulin-resistant diabetes. Nearly one quarter of these genes belong to tandemly arranged families, encompassing more than 25% of the chromosome. Comparative analyses show a fascinating picture of conservation and divergence, revealing large blocks of gene orthology with rodents, scattered regions with more recent gene family expansions and deletions, and segments of coding and non-coding conservation with the distant fish species Takifugu.

  7. Analogous selection processes in declarative and procedural working memory: N-2 list-repetition and task-repetition costs.

    Science.gov (United States)

    Gade, Miriam; Souza, Alessandra S; Druey, Michel D; Oberauer, Klaus

    2017-01-01

    Working memory (WM) holds and manipulates representations for ongoing cognition. Oberauer (Psychology of Learning and Motivation, 51, 45-100, 2009) distinguishes between two analogous WM sub-systems: a declarative WM which handles the objects of thought, and a procedural WM which handles the representations of (cognitive) actions. Here, we assessed whether analogous effects are observed when participants switch between memory sets (declarative representations) and when they switch between task sets (procedural representations). One mechanism assumed to facilitate switching in procedural WM is the inhibition of previously used, but currently irrelevant task sets, as indexed by n-2 task-repetition costs (Mayr & Keele, Journal of Experimental Psychology: General, 129(1), 4-26, 2000). In this study we tested for an analogous effect in declarative WM. We assessed the evidence for n-2 list-repetition costs across eight experiments in which participants switched between memory lists to perform speeded classifications, mental arithmetic, or a local recognition test. N-2 list-repetition costs were obtained consistently in conditions assumed to increase interference between memory lists, and when lists formed chunks in long-term memory. Further analyses across experiments revealed a substantial contribution of episodic memory to n-2 list-repetition costs, thereby questioning the interpretation of n-2 repetition costs as reflecting inhibition. We reanalyzed the data of eight task-switching experiments, and observed that episodic memory also contributes to n-2 task-repetition costs. Taken together, these results show analogous processing principles in declarative and procedural WM, and question the relevance of inhibitory processes for efficient switching between mental sets.

  8. S1 satellite DNA repetitive units display identical structure and overall variability in all Anatolian brown frog taxa.

    Science.gov (United States)

    Picariello, Orfeo; Feliciello, Isidoro; Chinali, Gianni

    2016-02-01

    S1 satellite DNA from Palearctic brown frogs has a species-specific structure in all European species. We characterized S1 satellite DNA from the Anatolian brown frogs Rana macrocnemis, R. camerani, and R. holtzi in order to define their taxonomic rank and the structure of this satellite in this frog lineage. Southern blots of genomic DNA digested with KpnI, EcoRV, NdeI, NheI, or StuI produced the same pattern of satellite DNA bands. Moreover, quantitative dot blots showed that this satellite DNA accounts for 0.1 % of the genome in all taxa. Analysis of the overall genomic variability of the S1a repeat sequence in specimens from various populations demonstrated that this repetitive unit also has the same size (476 bp), the same most common sequence (MCS) and the same overall variability in all three taxa, and also in R. macrocnemis tavasensis. The S1a repetitive unit presents three deletions of 9, 8 and 1 bp compared to the 494-bp S1a repeat from European frogs. The S1a MCS has three variable positions (sequence WWTK in positions 183-186), due to the presence of two repeat subpopulations with motifs AATG and WWTT in all taxa. Unlike previously analyzed mitochondrial and nuclear sequences that show considerable variations among these taxa, no difference could be detected in the structure and variability of the S1 satellite repetitive units. This suggests that these taxa should belong to a single species. Our results indicate that this satellite DNA variety probably formed when the Anatolian lineage radiated from common ancestor about 4 mya, and since then has maintained its structure in all four taxa examined.

  9. Rhipicephalus microplus strain Deutsch, 10 BAC clone sequences

    Science.gov (United States)

    The cattle tick, Rhipicephalus (Boophilus) microplus, has a genome over 2.4 times the size of the human genome, and with over 70% of repetitive DNA, this genome would prove very costly to sequence at today's prices and difficult to assemble and analyze. We used labeled DNA probes from the coding reg...

  10. Repetitive Domain-Referenced Testing Using Computers: the TITA System.

    Science.gov (United States)

    Olympia, P. L., Jr.

    The TITA (Totally Interactive Testing and Analysis) System algorithm for the repetitive construction of domain-referenced tests utilizes a compact data bank, is highly portable, is useful in any discipline, requires modest computer hardware, and does not present a security problem. Clusters of related keyphrases, statement phrases, and distractors…

  11. Repetitive endoscopic sinus surgery failure: a role for radical surgery?

    NARCIS (Netherlands)

    Videler, Ward J. M.; Wreesmann, Volkert B.; van der Meulen, Freerk W.; Knegt, Paul P.; Fokkens, Wytske J.

    2006-01-01

    OBJECTIVES: Endoscopic sinus surgery (ESS) is considered to be the golden standard for surgery in patients with chronic rhinosinusitis and nasal polyposis. However, there is still a small group of patients unresponsive despite repetitive surgery. Radical surgery aimed at reduction of the

  12. Nonword Repetition and Language Learning Disorders: A Developmental Contingency Framework

    Science.gov (United States)

    Snowling, Margaret J.

    2006-01-01

    In 1990 Gathercole and Baddeley proposed a strong hypothesis that has generated a wealth of research in the field of language development and disorder. The hypothesis was that phonological memory, as indexed by nonword repetition, is causally related to vocabulary development. Support for the hypothesis came from an impressive range of…

  13. Software-engineering-based model for mitigating Repetitive Strain ...

    African Journals Online (AJOL)

    The incorporation of Information and Communication Technology (ICT) in virtually all facets of human endeavours has fostered the use of computers. This has induced Repetitive Stress Injury (RSI) for continuous and persistent computer users. Proposing a software engineering model capable of enacted RSI force break ...

  14. Intrinsic and Extrinsic Motivation for Stereotypic and Repetitive Behavior

    Science.gov (United States)

    Joosten, Annette V.; Bundy, Anita C.; Einfeld, Stewart L.

    2009-01-01

    This study provides evidence for intrinsic and extrinsic motivators for stereotypical and repetitive behavior in children with autism and intellectual disability and children with intellectual disability alone. We modified the Motivation Assessment Scale (MAS) (1988b); dividing it into intrinsic and extrinsic measures and adding items to assess…

  15. Temporal dynamics of high repetition rate pulsed single longitudinal ...

    Indian Academy of Sciences (India)

    ing (GIG) cavity, single-mode dye laser pumped by high repetition rate ... in a high loss cavity, a detailed theoretical study and optimization of cavity ..... rate for high conversion efficiency and longer pulse width of the single-mode dye laser.

  16. Context-Dependent Repetition Effects on Recognition Memory

    Science.gov (United States)

    Opitz, Bertram

    2010-01-01

    One widely acknowledged way to improve our memory performance is to repeatedly study the to be learned material. One aspect that has received little attention in past research regards the context sensitivity of this repetition effect, that is whether the item is repeated within the same or within different contexts. The predictions of a…

  17. Autism and exergaming: effects on repetitive behaviors and cognition.

    Science.gov (United States)

    Anderson-Hanley, Cay; Tureck, Kimberly; Schneiderman, Robyn L

    2011-01-01

    Autism is a neurodevelopmental disorder that leads to impairment in social skills and delay in language development, and results in repetitive behaviors and restricted interests that impede academic and social involvement. Physical exercise has been shown to decrease repetitive behaviors in autistic children and improve cognitive function across the life-span. Exergaming combines physical and mental exercise simultaneously by linking physical activity movements to video game control and may yield better compliance with exercise. In this investigation, two pilot studies explored the potential behavioral and cognitive benefits of exergaming. In Pilot I, twelve children with autism spectrum disorders completed a control task and an acute bout of Dance Dance Revolution (DDR); in Pilot II, ten additional youths completed an acute bout of cyber cycling. Repetitive behaviors and executive function were measured before and after each activity. Repetitive behaviors significantly decreased, while performance on Digits Backwards improved following the exergaming conditions compared with the control condition. Additional research is needed to replicate these findings, and to explore the application of exergaming for the management of behavioral disturbance and to increase cognitive control in children on the autism spectrum.

  18. Heavy-duty high-repetition-rate generators

    NARCIS (Netherlands)

    Heesch, van E.J.M.; Yan, K.; Pemen, A.J.M.

    2002-01-01

    We present our results on high-power repetitive pulse sources for continuous operation. Two 1-10-kW systems using advanced spark gap technology and a transmission line transformer have been tested for several hundred hours at a 60-MW pulse level. High reliability and above 90% overall efficiency are

  19. Post-exercise cortical depression following repetitive passive finger movement.

    Science.gov (United States)

    Otsuka, Ryohei; Sasaki, Ryoki; Tsuiki, Shota; Kojima, Sho; Onishi, Hideaki

    2017-08-24

    This study aimed to clarify the influence of range of repetitive passive finger movement on corticospinal excitability. Thirteen healthy subjects participated in this study. Passive index finger adduction-abduction movements were performed from 15° abduction to 15° adduction, 15° abduction to 0°, 0° to 15° adduction, and 15° adduction to 30° adduction, each at 15°/s for 10min on separate days. Motor evoked potentials (MEPs) elicited by transcranial magnetic stimulation and M- and F-waves were measured before and after each repetitive passive index finger movement protocol to evaluate changes in corticospinal excitability. MEP amplitude significantly decreased after all passive movements, while F-wave amplitude, F-wave persistence, and M-wave amplitude remained stable. These results suggest that cortical excitability decreases after repetitive passive movement. However, the range of repetitive passive movement does not markedly influence the magnitude of cortical depression. Copyright © 2017 Elsevier B.V. All rights reserved.

  20. Use of Repetitive Transcranial Magnetic Stimulation for Treatment in Psychiatry

    NARCIS (Netherlands)

    Aleman, Andre

    The potential of noninvasive neurostimulation by repetitive transcranial magnetic stimulation (rTMS) for improving psychiatric disorders has been studied increasingly over the past two decades. This is especially the case for major depression and for auditory verbal hallucinations in schizophrenia.

  1. Repetitive controller for improving grid-connected photovoltaic systems

    NARCIS (Netherlands)

    Almeida, de P.M.; Duarte, J.L.; Ribeiro, P.F.; Barbosa, P.G.

    2014-01-01

    This study presents the modelling and design steps of a discrete time recursive repetitive controller (RC) to be used in a grid-connected photovoltaic (PV) system. It is shown that the linear synchronous reference frame proportional-integral controller, originally designed to control the converter's

  2. Task type and incidental L2 vocabulary learning: Repetition versus ...

    African Journals Online (AJOL)

    This study investigated the effect of task type on incidental L2 vocabulary learning. The different tasks investigated in this study differed in terms of repetition of encounters and task involvement load. In a within-subjects design, 72 Iranian learners of English practised 18 target words in three exercise conditions: three ...

  3. Exact Repetition as Input Enhancement in Second Language Acquisition.

    Science.gov (United States)

    Jensen, Eva Dam; Vinther, Thora

    2003-01-01

    Reports on two studies on input enhancement used to support learners' selection of focus of attention in Spanish second language listening material. Input consisted of video recordings of dialogues between native speakers. Exact repetition and speech rate reduction were examined for effect on comprehension, acquisition of decoding strategies, and…

  4. Repetition of Attempted Suicide Among Immigrants in Europe

    Science.gov (United States)

    Lipsicas, Cendrine Bursztein; Mäkinen, Ilkka Henrik; Wasserman, Danuta; Apter, Alan; Kerkhof, Ad; Michel, Konrad; Renberg, Ellinor Salander; van Heeringen, Kees; Värnik, Airi; Schmidtke, Armin

    2014-01-01

    Objectives To compare frequencies of suicide attempt repetition in immigrants and local European populations, and the timing of repetition in these groups. Method: Data from 7 European countries, comprising 10 574 local and 3032 immigrant subjects, were taken from the World Health Organization European Multicentre Study on Suicidal Behaviour and the ensuing Monitoring Suicidal Behaviour in Europe (commonly referred to as MONSUE) project. The relation between immigrant status and repetition of suicide attempt within 12-months following first registered attempt was analyzed with binary logistic regression, controlling for sex, age, and method of attempt. Timing of repetition was controlled for sex, age, and the recommended type of aftercare. Results: Lower odds of repeating a suicide attempt were found in Eastern European (OR 0.50; 95% CI 0.41 to 0.61, P Europe stands in contrast to their markedly higher tendency to attempt suicide in general, possibly pointing to situational stress factors related to their suicidal crisis that are less persistent over time. Our findings also raise the possibility that suicide attempters and repeaters constitute only partially overlapping populations. PMID:25565687

  5. Understanding the relationship between repetition priming and mere exposure.

    Science.gov (United States)

    Butler, Laurie T; Berry, Dianne C

    2004-11-01

    Over the last two decades interest in implicit memory, most notably repetition priming, has grown considerably. During the same period, research has also focused on the mere exposure effect. Although the two areas have developed relatively independently, a number of studies has described the mere exposure effect as an example of implicit memory. Tacit in their comparisons is the assumption that the effect is more specifically a demonstration of repetition priming. Having noted that this assumption has attracted relatively little attention, this paper reviews current evidence and shows that it is by no means conclusive. Although some evidence is suggestive of a common underlying mechanism, even a modified repetition priming (perceptual fluency/attribution) framework cannot accommodate all of the differences between the two phenomena. Notwithstanding this, it seems likely that a version of this theoretical framework still offers the best hope of a comprehensive explanation for the mere exposure effect and its relationship to repetition priming. As such, the paper finishes by offering some initial guidance as to ways in which the perceptual fluency/attribution framework might be extended, as well as outlining important areas for future research.

  6. Instruction, Repetition, Discovery: Restoring the Historical Educational Role of Practice

    Science.gov (United States)

    Trninic, Dragan

    2018-01-01

    This conceptual paper considers what it would mean to take seriously Freudenthal's suggestion that mathematics should be taught like swimming. The general claim being made is that "direct instruction" and "discovery" are not opposite but complementary, linked by repetitive yet explorative practice. This claim is elaborated…

  7. Pulsed electron beam generation with fast repetitive double pulse system

    Energy Technology Data Exchange (ETDEWEB)

    Sharma, Surender Kumar; Deb, Pankaj; Shyam, Anurag, E-mail: surender80@gmail.com [Energetics and Electromagnetics Division, Bhabha Atomic Research Centre, Visakhapatnam (India); Sharma, Archana [Accelerator and Pulse Power Division, Bhabha Atomic Research Centre, Mumbai (India)

    2014-07-01

    Longer duration high voltage pulse (∼ 100 kV, 260 ns) is generated and reported using helical pulse forming line in compact geometry. The transmission line characteristics of the helical pulse forming line are also used to develop fast repetition double pulse system with very short inter pulse interval. It overcomes the limitations caused due to circuit parameters, power supplies and load characteristics for fast repetitive high voltage pulse generation. The high voltage double pulse of 100 kV, 100 ns with an inter pulse repetition interval of 30 ns is applied across the vacuum field emission diode for pulsed electron beam generation. The electron beam is generated from cathode material by application of negative high voltage (> 100 kV) across the diode by explosive electron emission process. The vacuum field emission diode is made of 40 mm diameter graphite cathode and SS mesh anode. The anode cathode gap was 6 mm and the drift tube diameter was 10 cm. The initial experimental results of pulsed electron beam generation with fast repetitive double pulse system are reported and discussed. (author)

  8. Evidence for the involvement of a nonlexical route in the repetition of familiar words: A comparison of single and dual route models of auditory repetition.

    Science.gov (United States)

    Hanley, J Richard; Dell, Gary S; Kay, Janice; Baron, Rachel

    2004-03-01

    In this paper, we attempt to simulate the picture naming and auditory repetition performance of two patients reported by Hanley, Kay, and Edwards (2002), who were matched for picture naming score but who differed significantly in their ability to repeat familiar words. In Experiment 1, we demonstrate that the model of naming and repetition put forward by Foygel and Dell (2000) is better able to accommodate this pattern of performance than the model put forward by Dell, Schwartz, Martin, Saffran, and Gagnon (1997). Nevertheless, Foygel and Dell's model underpredicted the repetition performance of both patients. In Experiment 2, we attempt to simulate their performance using a new dual route model of repetition in which Foygel and Dell's model is augmented by an additional nonlexical repetition pathway. The new model provided a more accurate fit to the real-word repetition performance of both patients. It is argued that the results provide support for dual route models of auditory repetition.

  9. By-product formation in repetitive PCR amplification of DNA libraries during SELEX.

    Science.gov (United States)

    Tolle, Fabian; Wilke, Julian; Wengel, Jesper; Mayer, Günter

    2014-01-01

    The selection of nucleic acid aptamers is an increasingly important approach to generate specific ligands binding to virtually any molecule of choice. However, selection-inherent amplification procedures are prone to artificial by-product formation that prohibits the enrichment of target-recognizing aptamers. Little is known about the formation of such by-products when employing nucleic acid libraries as templates. We report on the formation of two different forms of by-products, named ladder- and non-ladder-type observed during repetitive amplification in the course of in vitro selection experiments. Based on sequence information and the amplification behaviour of defined enriched nucleic acid molecules we suppose a molecular mechanism through which these amplification by-products are built. Better understanding of these mechanisms might help to find solutions minimizing by-product formation and improving the success rate of aptamer selection.

  10. High repetition rate tunable femtosecond pulses and broadband amplification from fiber laser pumped parametric amplifier.

    Science.gov (United States)

    Andersen, T V; Schmidt, O; Bruchmann, C; Limpert, J; Aguergaray, C; Cormier, E; Tünnermann, A

    2006-05-29

    We report on the generation of high energy femtosecond pulses at 1 MHz repetition rate from a fiber laser pumped optical parametric amplifier (OPA). Nonlinear bandwidth enhancement in fibers provides the intrinsically synchronized signal for the parametric amplifier. We demonstrate large tunability extending from 700 nm to 1500 nm of femtosecond pulses with pulse energies as high as 1.2 muJ when the OPA is seeded by a supercontinuum generated in a photonic crystal fiber. Broadband amplification over more than 85 nm is achieved at a fixed wavelength. Subsequent compression in a prism sequence resulted in 46 fs pulses. With an average power of 0.5 W these pulses have a peak-power above 10 MW. In particular, the average power and pulse energy scalability of both involved concepts, the fiber laser and the parametric amplifier, will enable easy up-scaling to higher powers.

  11. Low-pass shotgun sequencing of the barley genome facilitates rapid identification of genes, conserved non-coding sequences and novel repeats

    Directory of Open Access Journals (Sweden)

    Graner Andreas

    2008-10-01

    Full Text Available Abstract Background Barley has one of the largest and most complex genomes of all economically important food crops. The rise of new short read sequencing technologies such as Illumina/Solexa permits such large genomes to be effectively sampled at relatively low cost. Based on the corresponding sequence reads a Mathematically Defined Repeat (MDR index can be generated to map repetitive regions in genomic sequences. Results We have generated 574 Mbp of Illumina/Solexa sequences from barley total genomic DNA, representing about 10% of a genome equivalent. From these sequences we generated an MDR index which was then used to identify and mark repetitive regions in the barley genome. Comparison of the MDR plots with expert repeat annotation drawing on the information already available for known repetitive elements revealed a significant correspondence between the two methods. MDR-based annotation allowed for the identification of dozens of novel repeat sequences, though, which were not recognised by hand-annotation. The MDR data was also used to identify gene-containing regions by masking of repetitive sequences in eight de-novo sequenced bacterial artificial chromosome (BAC clones. For half of the identified candidate gene islands indeed gene sequences could be identified. MDR data were only of limited use, when mapped on genomic sequences from the closely related species Triticum monococcum as only a fraction of the repetitive sequences was recognised. Conclusion An MDR index for barley, which was obtained by whole-genome Illumina/Solexa sequencing, proved as efficient in repeat identification as manual expert annotation. Circumventing the labour-intensive step of producing a specific repeat library for expert annotation, an MDR index provides an elegant and efficient resource for the identification of repetitive and low-copy (i.e. potentially gene-containing sequences regions in uncharacterised genomic sequences. The restriction that a particular

  12. Cenozoic global sea level, sequences, and the New Jersey transect: Results from coastal plain and continental slope drilling

    Science.gov (United States)

    Miller, K.G.; Mountain, Gregory S.; Browning, J.V.; Kominz, M.; Sugarman, P.J.; Christie-Blick, N.; Katz, M.E.; Wright, J.D.

    1998-01-01

    The New Jersey Sea Level Transect was designed to evaluate the relationships among global sea level (eustatic) change, unconformity-bounded sequences, and variations in subsidence, sediment supply, and climate on a passive continental margin. By sampling and dating Cenozoic strata from coastal plain and continental slope locations, we show that sequence boundaries correlate (within ??0.5 myr) regionally (onshore-offshore) and interregionally (New Jersey-Alabama-Bahamas), implicating a global cause. Sequence boundaries correlate with ??18O increases for at least the past 42 myr, consistent with an ice volume (glacioeustatic) control, although a causal relationship is not required because of uncertainties in ages and correlations. Evidence for a causal connection is provided by preliminary Miocene data from slope Site 904 that directly link ??18O increases with sequence boundaries. We conclude that variation in the size of ice sheets has been a primary control on the formation of sequence boundaries since ~42 Ma. We speculate that prior to this, the growth and decay of small ice sheets caused small-amplitude sea level changes (changes on mid-ocean ridges. Although our results are consistent with the general number and timing of Paleocene to middle Miocene sequences published by workers at Exxon Production Research Company, our estimates of sea level amplitudes are substantially lower than theirs. Lithofacies patterns within sequences follow repetitive, predictable patterns: (1) coastal plain sequences consist of basal transgressive sands overlain by regressive highstand silts and quartz sands; and (2) although slope lithofacies variations are subdued, reworked sediments constitute lowstand deposits, causing the strongest, most extensive seismic reflections. Despite a primary eustatic control on sequence boundaries, New Jersey sequences were also influenced by changes in tectonics, sediment supply, and climate. During the early to middle Eocene, low siliciclastic and

  13. Active power filter for harmonic compensation using a digital dual-mode-structure repetitive control approach

    DEFF Research Database (Denmark)

    Zou, Zhixiang; Wang, Zheng; Cheng, Ming

    2012-01-01

    This paper presents an digital dual-mode-structure repetitive control approach for the single-phase shunt active power filter (APF), which aims to enhance the tracking ability and eliminate arbitrary order harmonic. The proposed repetitive control scheme blends the characteristics of both odd......-harmonic repetitive control and even-harmonic repetitive control. Moreover, the convergence rate is faster than conventional repetitive controller. Additionally, the parameters have been designed and optimized for the dual-mode structure repetitive control to improve the performance of APF system. Experimental...

  14. Modulation of repetitive genes in the parent forms of heterozygous corn hybrids

    International Nuclear Information System (INIS)

    Gilyazetdinov, S.Ya.; Zimnitskii, A.N.; Yakhin, I.A.; Bikbaeva, E.S.

    1987-01-01

    The number of copies of the genes of high-molecular-weight rRNA, 5 S r RNA, and certain other families of repetitive sequences of DNA in the genome of different forms of corn is not coordinated but is stably inherited in the same strains. The authors present the results of their investigations into the repetition of the genes of tRNA, 5 S rRNA, histones, and the controlling element Ds of corn for the highly heterozygous hybrid Slava (VIR 44 x VIR 38), the medium-heterozygous hybrid Svetoch (VIR 40 x VIR 43), the low heterozygous hybrid Iskra (VIR 26 x VIR 27), and their parent strains. The relative content of these sequences was studied by the molecular hybridization of DNA immobilized on nitrocellulose filters with [ 125 I]tRNA labeled in vitro, 5 S rRNA, histone DNA of Drosophila, and the Ds-element of corn. The DNA preparations were isolated from the zones of the meristem (1.5-2mm), elongation (4-5mm), differentiation of the roots (3 cm), of 3-4 day seedlings, and from isolated embryos of 4 h and 24 h seedlings. The DNA of the embryos immobilized on the filters was preliminarily incubated with unlabeled high-molecular-weight rRNA in the experiments with tRNA and 5 S rRNA, while when histone DNA and the Ds element of corn were used in the hybridization reaction, it was preliminary incubated with plasmid DNA

  15. Genetic variation in the Staphylococcus aureus 8325 strain lineage revealed by whole-genome sequencing.

    Directory of Open Access Journals (Sweden)

    Kristoffer T Bæk

    Full Text Available Staphylococcus aureus strains of the 8325 lineage, especially 8325-4 and derivatives lacking prophage, have been used extensively for decades of research. We report herein the results of our deep sequence analysis of strain 8325-4. Assignment of sequence variants compared with the reference strain 8325 (NRS77/PS47 required correction of errors in the 8325 reference genome, and reassessment of variation previously attributed to chemical mutagenesis of the restriction-defective RN4220. Using an extensive strain pedigree analysis, we discovered that 8325-4 contains 16 single nucleotide polymorphisms (SNP arising prior to the construction of RN4220. We identified 5 indels in 8325-4 compared with 8325. Three indels correspond to expected Φ11, 12, 13 excisions, one indel is explained by a sequence assembly artifact, and the final indel (Δ63bp in the spa-sarS intergenic region is common to only a sub-lineage of 8325-4 strains including SH1000. This deletion was found to significantly decrease (75% steady state sarS but not spa transcript levels in post-exponential phase. The sub-lineage 8325-4 was also found to harbor 4 additional SNPs. We also found large sequence variation between 8325, 8325-4 and RN4220 in a cluster of repetitive hypothetical proteins (SA0282 homologs near the Ess secretion cluster. The overall 8325-4 SNP set results in 17 alterations within coding sequences. Remarkably, we discovered that all tested strains of the 8325-4 lineage lack phenol soluble modulin α3 (PSMα3, a virulence determinant implicated in neutrophil chemotaxis, biofilm architecture and surface spreading. Collectively, our results clarify and define the 8325-4 pedigree and reveal clear evidence that mutations existing throughout all branches of this lineage, including the widely used RN6390 and SH1000 strains, could conceivably impact virulence regulation.

  16. Competitive repair by naturally dispersed repetitive DNA during non-allelic homologous recombination

    Energy Technology Data Exchange (ETDEWEB)

    Hoang, Margaret L.; Tan, Frederick J.; Lai, David C.; Celniker, Sue E.; Hoskins, Roger A.; Dunham, Maitreya J.; Zheng, Yixian; Koshland, Douglas

    2010-08-27

    Genome rearrangements often result from non-allelic homologous recombination (NAHR) between repetitive DNA elements dispersed throughout the genome. Here we systematically analyze NAHR between Ty retrotransposons using a genome-wide approach that exploits unique features of Saccharomyces cerevisiae purebred and Saccharomyces cerevisiae/Saccharomyces bayanus hybrid diploids. We find that DNA double-strand breaks (DSBs) induce NAHR-dependent rearrangements using Ty elements located 12 to 48 kilobases distal to the break site. This break-distal recombination (BDR) occurs frequently, even when allelic recombination can repair the break using the homolog. Robust BDR-dependent NAHR demonstrates that sequences very distal to DSBs can effectively compete with proximal sequences for repair of the break. In addition, our analysis of NAHR partner choice between Ty repeats shows that intrachromosomal Ty partners are preferred despite the abundance of potential interchromosomal Ty partners that share higher sequence identity. This competitive advantage of intrachromosomal Tys results from the relative efficiencies of different NAHR repair pathways. Finally, NAHR generates deleterious rearrangements more frequently when DSBs occur outside rather than within a Ty repeat. These findings yield insights into mechanisms of repeat-mediated genome rearrangements associated with evolution and cancer.

  17. Competitive repair by naturally dispersed repetitive DNA during non-allelic homologous recombination.

    Directory of Open Access Journals (Sweden)

    Margaret L Hoang

    2010-12-01

    Full Text Available Genome rearrangements often result from non-allelic homologous recombination (NAHR between repetitive DNA elements dispersed throughout the genome. Here we systematically analyze NAHR between Ty retrotransposons using a genome-wide approach that exploits unique features of Saccharomyces cerevisiae purebred and Saccharomyces cerevisiae/Saccharomyces bayanus hybrid diploids. We find that DNA double-strand breaks (DSBs induce NAHR-dependent rearrangements using Ty elements located 12 to 48 kilobases distal to the break site. This break-distal recombination (BDR occurs frequently, even when allelic recombination can repair the break using the homolog. Robust BDR-dependent NAHR demonstrates that sequences very distal to DSBs can effectively compete with proximal sequences for repair of the break. In addition, our analysis of NAHR partner choice between Ty repeats shows that intrachromosomal Ty partners are preferred despite the abundance of potential interchromosomal Ty partners that share higher sequence identity. This competitive advantage of intrachromosomal Tys results from the relative efficiencies of different NAHR repair pathways. Finally, NAHR generates deleterious rearrangements more frequently when DSBs occur outside rather than within a Ty repeat. These findings yield insights into mechanisms of repeat-mediated genome rearrangements associated with evolution and cancer.

  18. Chromosomal Mapping of Repetitive DNAs in the Grasshopper Abracris flavolineata Reveal Possible Ancestry of the B Chromosome and H3 Histone Spreading

    Science.gov (United States)

    Bueno, Danilo; Palacios-Gimenez, Octavio Manuel; Cabral-de-Mello, Diogo Cavalcanti

    2013-01-01

    Supernumerary chromosomes (B chromosomes) occur in approximately 15% of eukaryote species. Although these chromosomes have been extensively studied, knowledge concerning their specific molecular composition is lacking in most cases. The accumulation of repetitive DNAs is one remarkable characteristic of B chromosomes, and the occurrence of distinct types of multigene families, satellite DNAs and some transposable elements have been reported. Here, we describe the organization of repetitive DNAs in the A complement and B chromosome system in the grasshopper species Abracris flavolineata using classical cytogenetic techniques and FISH analysis using probes for five multigene families, telomeric repeats and repetitive C0t-1 DNA fractions. The 18S rRNA and H3 histone multigene families are highly variable and well distributed in A. flavolineata chromosomes, which contrasts with the conservation of U snRNA genes and less variable distribution of 5S rDNA sequences. The H3 histone gene was an extensively distributed with clusters occurring in all chromosomes. Repetitive DNAs were concentrated in C-positive regions, including the pericentromeric region and small chromosomal arms, with some occurrence in C-negative regions, but abundance was low in the B chromosome. Finally, the first demonstration of the U2 snRNA gene in B chromosomes in A. flavolineata may shed light on its possible origin. These results provide new information regarding chromosomal variability for repetitive DNAs in grasshoppers and the specific molecular composition of B chromosomes. PMID:23826099

  19. Repetitive 'snakes' and their damping effect on core toroidal rotation in EAST plasmas with multiple H-L-H transitions

    International Nuclear Information System (INIS)

    Xu Liqing; Hu Liqun

    2015-01-01

    Repetitive impurity snake-modes have been observed after H-L mode transitions (high to low confinement modes) in EAST plasmas exhibiting multiple H-L-H transitions. Such snake-modes have been observed to lower the core plasma toroidal rotation. A critical impurity strength factor associated with snake-mode formation has been estimated to be as high as α_Z_,_c =n_Z_,_cZ"2 / n_e ∼0.75. These observations have implications for ITER H-mode sustainability when the heating power is only slightly above the H-mode power threshold. (author)

  20. An investigation of fMRI time series stationarity during motor sequence learning foot tapping tasks.

    Science.gov (United States)

    Muhei-aldin, Othman; VanSwearingen, Jessie; Karim, Helmet; Huppert, Theodore; Sparto, Patrick J; Erickson, Kirk I; Sejdić, Ervin

    2014-04-30

    Understanding complex brain networks using functional magnetic resonance imaging (fMRI) is of great interest to clinical and scientific communities. To utilize advanced analysis methods such as graph theory for these investigations, the stationarity of fMRI time series needs to be understood as it has important implications on the choice of appropriate approaches for the analysis of complex brain networks. In this paper, we investigated the stationarity of fMRI time series acquired from twelve healthy participants while they performed a motor (foot tapping sequence) learning task. Since prior studies have documented that learning is associated with systematic changes in brain activation, a sequence learning task is an optimal paradigm to assess the degree of non-stationarity in fMRI time-series in clinically relevant brain areas. We predicted that brain regions involved in a "learning network" would demonstrate non-stationarity and may violate assumptions associated with some advanced analysis approaches. Six blocks of learning, and six control blocks of a foot tapping sequence were performed in a fixed order. The reverse arrangement test was utilized to investigate the time series stationarity. Our analysis showed some non-stationary signals with a time varying first moment as a major source of non-stationarity. We also demonstrated a decreased number of non-stationarities in the third block as a result of priming and repetition. Most of the current literature does not examine stationarity prior to processing. The implication of our findings is that future investigations analyzing complex brain networks should utilize approaches robust to non-stationarities, as graph-theoretical approaches can be sensitive to non-stationarities present in data. Copyright © 2014 Elsevier B.V. All rights reserved.

  1. Perseveration and other repetitive verbal behaviors: functional dissociations.

    Science.gov (United States)

    Christman, Sarah S; Boutsen, Frank R; Buckingham, Hugh W

    2004-11-01

    This article will review types of perseveration from a neurolinguistic perspective. During the course of the article, continuous, stuck-in-set, and recurrent perseveration will be placed in contradistinction to several other types of repetitive behaviors commonly associated with neurogenic communication disorders. These include echolalia in mixed transcortical aphasia; conduite d'approche and conduite d'ecart in fluent aphasias; lexical and nonlexical automatisms in nonfluent aphasias; palilalia in neuromotor disorders, such as Parkinson's disease (PD); and sound, syllable, word, and phrase repetitions in neurogenic stuttering. When differentiating these phenomena from perseveration, it is helpful to consider the salient factors that condition observed behaviors in individual patients, such as overall speech fluency, inventory of available utterances, nature of eliciting tasks, and propositionality of responses. Information such as communication disorder diagnosis, underlying etiology, and known sites of lesion from each patient's total clinical profile may also assist with differentiation.

  2. Repetitive motion planning and control of redundant robot manipulators

    CERN Document Server

    Zhang, Yunong

    2013-01-01

    Repetitive Motion Planning and Control of Redundant Robot Manipulators presents four typical motion planning schemes based on optimization techniques, including the fundamental RMP scheme and its extensions. These schemes are unified as quadratic programs (QPs), which are solved by neural networks or numerical algorithms. The RMP schemes are demonstrated effectively by the simulation results based on various robotic models; the experiments applying the fundamental RMP scheme to a physical robot manipulator are also presented. As the schemes and the corresponding solvers presented in the book have solved the non-repetitive motion problems existing in redundant robot manipulators, it is of particular use in applying theoretical research based on the quadratic program for redundant robot manipulators in industrial situations. This book will be a valuable reference work for engineers, researchers, advanced undergraduate and graduate students in robotics fields. Yunong Zhang is a professor at The School of Informa...

  3. Interaction of Repetitively Pulsed High Energy Laser Radiation With Matter

    Science.gov (United States)

    Hugenschmidt, Manfred

    1986-10-01

    The paper is concerned with laser target interaction processes involving new methods of improving the overall energy balance. As expected theoretically, this can be achieved with high repetition rate pulsed lasers even for initially highly reflecting materials, such as metals. Experiments were performed by using a pulsed CO2 laser at mean powers up to 2 kW and repetition rates up to 100 Hz. The rates of temperature rise of aluminium for example were thereby increased by lore than a factor of 3 as compared to cw-radiation of comparable power density. Similar improvements were found for the overall absorptivities that were increased by this method by more than an order of magnitude.

  4. Long-term repetition priming with symmetrical polygons and words.

    Science.gov (United States)

    Kersteen-Tucker, Z

    1991-01-01

    In two different tasks, subjects were asked to make lexical decisions (word or nonword) and symmetry judgments (symmetrical or nonsymmetrical) about two-dimensional polygons. In both tasks, every stimulus was repeated at one of four lags (0, 1, 4, or 8 items interposed between the first and second stimulus presentations). This paradigm, known as repetition priming, revealed comparable short-term priming (Lag 0) and long-term priming (Lags 1, 4, and 8) both for symmetrical polygons and for words. A shorter term component (Lags 0 and 1) of priming was observed for nonwords, and only very short-term priming (Lag 0) was observed for nonsymmetrical polygons. These results indicate that response facilitation accruing from repeated exposure can be observed for stimuli that have no preexisting memory representations and suggest that perceptual factors contribute to repetition-priming effects.

  5. Closed cycle high-repetition-rate pulsed HF laser

    Science.gov (United States)

    Harris, Michael R.; Morris, A. V.; Gorton, Eric K.

    1997-04-01

    The design and performance of a closed cycle high repetition rate HF laser is described. A short pulse, glow discharge is formed in a 10 SF6:1 H2 gas mixture at a total pressure of approximately 110 torr within a 15 by 0.5 by 0.5 cm3 volume. Transverse, recirculated gas flow adequate to enable repetitive operation up to 3 kHz is imposed by a centrifugal fan. The fan also forces the gas through a scrubber cell to eliminate ground state HF from the gas stream. An automated gas make-up system replenishes spent gas removed by the scrubber. Typical mean laser output powers up to 3 W can be maintained for extended periods of operation.

  6. High repetition rate burst-mode spark gap

    International Nuclear Information System (INIS)

    Faltens, A.; Reginato, L.; Hester, R.; Chesterman, A.; Cook, E.; Yokota, T.; Dexter, W.

    1978-01-01

    Results are presented on the design and testing of a pressurized gas blown spark gap switch capable of high repetition rates in a burst mode of operation. The switch parameters which have been achieved are as follows: 220-kV, 42-kA, a five pulse burst at 1-kHz, 12-ns risetime, 2-ns jitter at a pulse width of 50-ns

  7. Context-dependent repetition effects on recognition memory.

    OpenAIRE

    Opitz, B

    2010-01-01

    One widely acknowledged way to improve our memory performance is to repeatedly study the to be learned material. One aspect that has received little attention in past research regards the context sensitivity of this repetition effect, that is whether the item is repeated within the same or within different contexts. The predictions of a neuro-computational model (O'Reilly & Norman, 2002) were tested in an experiment requiring participants to study visual objects either once or three times. Cr...

  8. Repetitive nanosecond electron accelerators type URT-1 for radiation technology

    Science.gov (United States)

    Sokovnin, S. Yu.; Balezin, M. E.

    2018-03-01

    The electron accelerator URT-1М-300 for mobile installation was created for radiation disinfecting to correct drawbacks that were found the URT-1M electron accelerator operation (the accelerating voltage up to 1 МV, repetition rate up to 300 pps, electron beam size 400 × 100 mm, the pulse width about 100 ns). Accelerator configuration was changed that allowed to reduce significantly by 20% tank volume with oil where is placed the system of formation high-voltage pulses, thus the average power of the accelerator is increased by 6 times at the expense of increase in pulses repetition rate. Was created the system of the computerized monitoring parameters (output parameters and thermal mode) and remote control of the accelerator (charge voltage, pulse repetition rate), its elements and auxiliary systems (heat of the thyratron, vacuum system), the remote control panel is connected to the installation by the fiber-optical channel, what lightens the work for service personnel. For generating an electron beam up to 400 mm wide there are used metal- ceramic] and metal-dielectric cold cathodes of several emission elements (plates) with a non-uniform distribution of the electron beam current density on the output foil ± 15%. It was found that emission drop of both type of cathodes, during the operation at the high repetition rate (100 pps) is substantial at the beginning of the process, and then proceeds rather slowly that allows for continuous operation up to 40 h. Experiments showed that linear dependence of the voltage and a signal from the pin-diode remains within the range of the charge voltage 45-65 kV. Thus, voltage increases from 690 to 950 kV, and the signal from the pin-diode - from (2,8-4,6)*104 Gy/s. It allows to select electron energy quite precisely with consideration of the radiation technology requirements.

  9. Progress toward a microsecond duration, repetitively pulsed, intense- ion beam

    International Nuclear Information System (INIS)

    Davis, H.A.; Olson, J.C.; Reass, W.A.; Coates, D.M.; Hunt, J.W.; Schleinitz, H.M.; Greenly, J.B.

    1996-01-01

    A number of intense ion beams applications are emerging requiring repetitive high-average-power beams. These applications include ablative deposition of thin films, rapid melt and resolidification for surface property enhancement, advanced diagnostic neutral beams for the next generation of Tokamaks, and intense pulsed-neutron sources. We are developing a 200-250 keV, 15 kA, 1 μs duration, 1-30 Hz intense ion beam accelerator to address these applications

  10. Effects of Navigated Repetitive Transcranial Magnetic Stimulation After Stroke.

    Science.gov (United States)

    Chervyakov, Alexander V; Poydasheva, Alexandra G; Lyukmanov, Roman H; Suponeva, Natalia A; Chernikova, Ludmila A; Piradov, Michael A; Ustinova, Ksenia I

    2018-03-01

    The purpose of this study was to test the effects of navigated repetitive transcranial magnetic stimulation, delivered in different modes, on motor impairments and functional limitations after stroke. The study sample included 42 patients (58.5 ± 10.7 years; 26 males) who experienced a single unilateral stroke (1-12 months previously) in the area of the middle cerebral artery. Patients completed a course of conventional rehabilitation, together with 10 sessions of navigated repetitive transcranial magnetic stimulation or sham stimulation. Stimulation was scheduled five times a week over two consecutive weeks in an inpatient clinical setting. Patients were randomly assigned to one of four groups and received sham stimulation (n = 10), low-frequency (1-Hz) stimulation of the nonaffected hemisphere (n = 11), high-frequency (10-Hz) stimulation of the affected hemisphere (n = 13), or sequential combination of low- and high-frequency stimulations (n = 8). Participants were evaluated before and after stimulation with clinical tests, including the arm and hand section of the Fugl-Meyer Assessment Scale, modified Ashworth Scale of Muscle Spasticity, and Barthel Index of Activities of Daily Living. Participants in the three groups receiving navigated repetitive transcranial magnetic stimulation showed improvements in arm and hand functions on the Fugl-Meyer Stroke Assessment Scale. Ashworth Scale of Muscle Spasticity and Barthel Index scores were significantly reduced in groups receiving low- or high-frequency stimulation alone. Including navigated repetitive transcranial magnetic stimulation in a conventional rehabilitation program positively influenced motor and functional recovery in study participants, demonstrating the clinical potential of the method. The results of this study will be used for designing a large-scale clinical trial.

  11. Repetitive display system of line profiles for Doppler broadening measurement

    International Nuclear Information System (INIS)

    Mohri, A.; Narihara, K.; Haba, K.

    1982-10-01

    Line profiles of impurities in visible and ultraviolet regions are repetitively displayed on a CRT with an interval of 250 mu s or 500 mu s, using a system composed of a Czerny-Turner monochromator with 1 m F.L., a self-resonant optical scanner, a photomultiplier shielded against hard X-rays and electronic circuits. The profile resolution is 0.035 nm FWHM. This system can be used in the environment of strong hard X-rays. (author)

  12. Repetitive Observation of Coniferous Samples in ESEM and SEM

    Czech Academy of Sciences Publication Activity Database

    Tihlaříková, Eva; Neděla, Vilém

    2015-01-01

    Roč. 21, S3 (2015), s. 1695-1696 ISSN 1431-9276 R&D Projects: GA ČR(CZ) GA14-22777S; GA MŠk(CZ) LO1212; GA MŠk ED0017/01/01 Institutional support: RVO:68081731 Keywords : SEM * ESEM * biological samples * repetitive observation Subject RIV: JA - Electronics ; Optoelectronics, Electrical Engineering Impact factor: 1.730, year: 2015

  13. The Influence of Level of Processing on Advertising Repetition Effects.

    OpenAIRE

    Nordhielm, Christie L

    2002-01-01

    This research examines whether or not repetition of features of a stimulus are subject to wear-out effects that have until now only been tested for the stimulus as a whole. When consumers process features in either a shallower or deeper manner, the level of processing performed dictates the effect of repeated feature exposure on their judgments. When repeated exposures to features are processed in a shallower fashion, there is an enhancement in evaluations with no subsequent downturn, whereas...

  14. High repetition rate ultrashort laser cuts a path through fog

    Science.gov (United States)

    de la Cruz, Lorena; Schubert, Elise; Mongin, Denis; Klingebiel, Sandro; Schultze, Marcel; Metzger, Thomas; Michel, Knut; Kasparian, Jérôme; Wolf, Jean-Pierre

    2016-12-01

    We experimentally demonstrate that the transmission of a 1030 nm, 1.3 ps laser beam of 100 mJ energy through fog increases when its repetition rate increases to the kHz range. Due to the efficient energy deposition by the laser filaments in the air, a shockwave ejects the fog droplets from a substantial volume of the beam, at a moderate energy cost. This process opens prospects for applications requiring the transmission of laser beams through fogs and clouds.

  15. High-repetition-rate hydrogen chamber: Preliminary studies

    International Nuclear Information System (INIS)

    1967-01-01

    This report is a conclusion to the tests realised with an experimental bubbles chamber in view to study the possibilities to increase the repetition rate. The more important parameters (the evolution of the bubbles, the expansion system) are considered in a theoretical way. Then the hardware is described. To end, experimental results are compared with the first evaluations. The calculations and the experimentation are against an oscillation system for the expansion. A system with a locking is to he considered. (authors) [fr

  16. Effect of repetitive transcranial magnetic stimulation on reducing spasticity in patients suffering from HTLV-1-associated myelopathy.

    Science.gov (United States)

    Amiri, Mostafa; Nafissi, Shahriar; Jamal-Omidi, Shirin; Amiri, Motahareh; Fatehi, Farzad

    2014-12-01

    Human T-lymphotropic virus type 1 has been implicated in human T-lymphotropic virus type 1-associated myelopathy/tropical spastic paraparesis (HAM/TSP). Regarding its endemicity in Iran and the role of repetitive transcranial magnetic stimulation in reducing spasticity, we decided to evaluate the efficacy of repetitive transcranial magnetic stimulation in reducing spasticity (as primary outcome) and pain, muscle power, and quality of life (as secondary outcomes) in patients suffering from HAM/TSP. In this pretest-posttest study, nine definite patients with HAM/TSP (according to WHO guidelines) were recruited. All patients underwent five consecutive daily sessions of active repetitive transcranial magnetic stimulation (each session consisting of 20 trains of 10 pulses at 5 Hz and an intensity of 90% of resting motor threshold for the biceps brachii muscle). Main outcome measures including spasticity (by modified Ashworth scale), pain (by visual analog scale), muscle power, and quality of life (by SF 36) were measured before the study and days 5, 7, 30 after the termination of the sessions. Seven (77.8%) females and 2 (22.2%) males were recruited with the mean age of 52 ± 12.67 years, and the mean duration of the disease was 5 ± 3.94. Comparison of the repeated measures showed a statistically significant decrease in pain and spasticity in lower limbs. The decrement in spasticity was persistent even 30 days after the intervention; however, the pain reduction was seen only 5 days after the procedure. No change in quality of life, and muscle power was detected. It seems that repetitive transcranial magnetic stimulation could decrease spasticity and pain in patients with HAM/TSP, and this effect could persistently continue by 1 month, but it did not influence patients' muscle power and quality of life, and it could be used as an adjuvant therapy in patients suffering from human T-lymphotropic virus type 1-associated HAM/TSP.

  17. Modulation of social deficits and repetitive behaviors in a mouse model of autism: the role of the nicotinic cholinergic system.

    Science.gov (United States)

    Wang, Li; Almeida, Luis E F; Spornick, Nicholas A; Kenyon, Nicholas; Kamimura, Sayuri; Khaibullina, Alfia; Nouraie, Mehdi; Quezado, Zenaide M N

    2015-12-01

    Accumulating evidence implicates the nicotinic cholinergic system in autism spectrum disorder (ASD) pathobiology. Neuropathologic studies suggest that nicotinic acetylcholine (ACh) receptor (nAChR) subtypes are altered in brain of autistic individuals. In addition, strategies that increase ACh, the neurotransmitter for nicotinic and muscarinic receptors, appear to improve cognitive deficits in neuropsychiatric disorders and ASD. The aim of this study is to examine the role of the nicotinic cholinergic system on social and repetitive behavior abnormalities and exploratory physical activity in a well-studied model of autism, the BTBR T(+) Itpr3 (tf) /J (BTBR) mouse. Using a protocol known to up-regulate expression of brain nAChR subtypes, we measured behavior outcomes before and after BTBR and C57BL/6J (B6) mice were treated (4 weeks) with vehicle or nicotine (50, 100, 200, or 400 μg/ml). Increasing nicotine doses were associated with decreases in water intake, increases in plasma cotinine levels, and at the higher dose (400 μg/ml) with weight loss in BTBR mice. At lower (50, 100 μg/ml) but not higher (200, 400 μg/ml) doses, nicotine increased social interactions in BTBR and B6 mice and at higher, but not lower doses, it decreased repetitive behavior in BTBR. In the open-field test, nicotine at 200 and 400 μg/ml, but not 100 μg/ml compared with vehicle, decreased overall physical activity in BTBR mice. These findings support the hypotheses that the nicotinic cholinergic system modulates social and repetitive behaviors and may be a therapeutic target to treat behavior deficits in ASD. Further, the BTBR mouse may be valuable for investigations of the role of nAChRs in social deficits and repetitive behavior.

  18. A compact, repetitive accelerator for military and industrial applications

    International Nuclear Information System (INIS)

    Zutavern, F.J.; O'Malley, M.W.; Ruebush, M.H.; Rinehart, L.F.; Loubriel, G.M.; Babcock, S.R.; Denison, G.J.

    1998-04-01

    A compact, short pulse, repetitive accelerator has many useful military and commercial applications in biological counter proliferation, materials processing, radiography, and sterilization (medical instruments, waste, and food). The goal of this project was to develop and demonstrate a small, 700 kV accelerator, which can produce 7 kA particle beams with pulse lengths of 10--30 ns at rates up to 50 Hz. At reduced power levels, longer pulses or higher repetition rates (up to 10 kHz) could be achieved. Two switching technologies were tested: (1) spark gaps, which have been used to build low repetition rate accelerators for many years; and (2) high gain photoconductive semiconductor switches (PCSS), a new solid state switching technology. This plan was economical, because it used existing hardware for the accelerator, and the PCSS material and fabrication for one module was relatively inexpensive. It was research oriented, because it provided a test bed to examine the utility of other emerging switching technologies, such as magnetic switches. At full power, the accelerator will produce 700 kV and 7 kA with either the spark gap or PCSS pulser

  19. Sound segregation via embedded repetition is robust to inattention.

    Science.gov (United States)

    Masutomi, Keiko; Barascud, Nicolas; Kashino, Makio; McDermott, Josh H; Chait, Maria

    2016-03-01

    The segregation of sound sources from the mixture of sounds that enters the ear is a core capacity of human hearing, but the extent to which this process is dependent on attention remains unclear. This study investigated the effect of attention on the ability to segregate sounds via repetition. We utilized a dual task design in which stimuli to be segregated were presented along with stimuli for a "decoy" task that required continuous monitoring. The task to assess segregation presented a target sound 10 times in a row, each time concurrent with a different distractor sound. McDermott, Wrobleski, and Oxenham (2011) demonstrated that repetition causes the target sound to be segregated from the distractors. Segregation was queried by asking listeners whether a subsequent probe sound was identical to the target. A control task presented similar stimuli but probed discrimination without engaging segregation processes. We present results from 3 different decoy tasks: a visual multiple object tracking task, a rapid serial visual presentation (RSVP) digit encoding task, and a demanding auditory monitoring task. Load was manipulated by using high- and low-demand versions of each decoy task. The data provide converging evidence of a small effect of attention that is nonspecific, in that it affected the segregation and control tasks to a similar extent. In all cases, segregation performance remained high despite the presence of a concurrent, objectively demanding decoy task. The results suggest that repetition-based segregation is robust to inattention. (c) 2016 APA, all rights reserved).

  20. Repetitive, small-bore two-stage light gas gun

    International Nuclear Information System (INIS)

    Combs, S.K.; Foust, C.R.; Fehling, D.T.; Gouge, M.J.; Milora, S.L.

    1991-01-01

    A repetitive two-stage light gas gun for high-speed pellet injection has been developed at Oak Ridge National Laboratory. In general, applications of the two-stage light gas gun have been limited to only single shots, with a finite time (at least minutes) needed for recovery and preparation for the next shot. The new device overcomes problems associated with repetitive operation, including rapidly evacuating the propellant gases, reloading the gun breech with a new projectile, returning the piston to its initial position, and refilling the first- and second-stage gas volumes to the appropriate pressure levels. In addition, some components are subjected to and must survive severe operating conditions, which include rapid cycling to high pressures and temperatures (up to thousands of bars and thousands of kelvins) and significant mechanical shocks. Small plastic projectiles (4-mm nominal size) and helium gas have been used in the prototype device, which was equipped with a 1-m-long pump tube and a 1-m-long gun barrel, to demonstrate repetitive operation (up to 1 Hz) at relatively high pellet velocities (up to 3000 m/s). The equipment is described, and experimental results are presented. 124 refs., 6 figs., 5 tabs

  1. Inverted U-shaped model: How frequent repetition affects perceived risk

    OpenAIRE

    Xi Lu; Xiaofei Xie; Lu Liu

    2015-01-01

    We asked how repeated media reports on technological hazards influence an individual's risk perception. We looked for two contradictory effects, an increasing effect of repetition on perceived risk with the first few repetitions and a decreasing effect with later repetitions, leading to the inverted U-shaped pattern. In an experiment, we demonstrated the inverted U-shaped relationship between the repetition and perceived risk in the context of food risk. The finding broaden...

  2. Don't Throw out the Baby with the Bathwater: Verbal Repetition, Mnemonics, and Active Learning

    Science.gov (United States)

    Saber, Jane Lee; Johnson, Richard D.

    2008-01-01

    The effectiveness of using verbal repetition and first-letter acronyms to teach a common marketing framework was examined in two experiments. In Experiment 1, 345 undergraduate students were exposed to the framework using one of four conditions: control, verbal repetition, acronym, and verbal repetition plus acronym in a traditional learning…

  3. Repetition suppression and multi-voxel pattern similarity differentially track implicit and explicit visual memory.

    Science.gov (United States)

    Ward, Emily J; Chun, Marvin M; Kuhl, Brice A

    2013-09-11

    Repeated exposure to a visual stimulus is associated with corresponding reductions in neural activity, particularly within visual cortical areas. It has been argued that this phenomenon of repetition suppression is related to increases in processing fluency or implicit memory. However, repetition of a visual stimulus can also be considered in terms of the similarity of the pattern of neural activity elicited at each exposure--a measure that has recently been linked to explicit memory. Despite the popularity of each of these measures, direct comparisons between the two have been limited, and the extent to which they differentially (or similarly) relate to behavioral measures of memory has not been clearly established. In the present study, we compared repetition suppression and pattern similarity as predictors of both implicit and explicit memory. Using functional magnetic resonance imaging, we scanned 20 participants while they viewed and categorized repeated presentations of scenes. Repetition priming (facilitated categorization across repetitions) was used as a measure of implicit memory, and subsequent scene recognition was used as a measure of explicit memory. We found that repetition priming was predicted by repetition suppression in prefrontal, parietal, and occipitotemporal regions; however, repetition priming was not predicted by pattern similarity. In contrast, subsequent explicit memory was predicted by pattern similarity (across repetitions) in some of the same occipitotemporal regions that exhibited a relationship between priming and repetition suppression; however, explicit memory was not related to repetition suppression. This striking double dissociation indicates that repetition suppression and pattern similarity differentially track implicit and explicit learning.

  4. The mitochondrial genomes of sponges provide evidence for multiple invasions by Repetitive Hairpin-forming Elements (RHE

    Directory of Open Access Journals (Sweden)

    Lavrov Dennis V

    2009-12-01

    Full Text Available Abstract Background The mitochondrial (mt genomes of sponges possess a variety of features, which appear to be intermediate between those of Eumetazoa and non-metazoan opisthokonts. Among these features is the presence of long intergenic regions, which are common in other eukaryotes, but generally absent in Eumetazoa. Here we analyse poriferan mitochondrial intergenic regions, paying particular attention to repetitive sequences within them. In this context we introduce the mitochondrial genome of Ircinia strobilina (Lamarck, 1816; Demospongiae: Dictyoceratida and compare it with mtDNA of other sponges. Results Mt genomes of dictyoceratid sponges are identical in gene order and content but display major differences in size and organization of intergenic regions. An even higher degree of diversity in the structure of intergenic regions was found among different orders of demosponges. One interesting observation made from such comparisons was of what appears to be recurrent invasions of sponge mitochondrial genomes by repetitive hairpin-forming elements, which cause large genome size differences even among closely related taxa. These repetitive hairpin-forming elements are structurally and compositionally divergent and display a scattered distribution throughout various groups of demosponges. Conclusion Large intergenic regions of poriferan mt genomes are targets for insertions of repetitive hairpin- forming elements, similar to the ones found in non-metazoan opisthokonts. Such elements were likely present in some lineages early in animal mitochondrial genome evolution but were subsequently lost during the reduction of intergenic regions, which occurred in the Eumetazoa lineage after the split of Porifera. Porifera acquired their elements in several independent events. Patterns of their intra-genomic dispersal can be seen in the mt genome of Vaceletia sp.

  5. Repetition suppression and repetition enhancement underlie auditory memory-trace formation in the human brain: an MEG study.

    Science.gov (United States)

    Recasens, Marc; Leung, Sumie; Grimm, Sabine; Nowak, Rafal; Escera, Carles

    2015-03-01

    The formation of echoic memory traces has traditionally been inferred from the enhanced responses to its deviations. The mismatch negativity (MMN), an auditory event-related potential (ERP) elicited between 100 and 250ms after sound deviation is an indirect index of regularity encoding that reflects a memory-based comparison process. Recently, repetition positivity (RP) has been described as a candidate ERP correlate of direct memory trace formation. RP consists of repetition suppression and enhancement effects occurring in different auditory components between 50 and 250ms after sound onset. However, the neuronal generators engaged in the encoding of repeated stimulus features have received little interest. This study intends to investigate the neuronal sources underlying the formation and strengthening of new memory traces by employing a roving-standard paradigm, where trains of different frequencies and different lengths are presented randomly. Source generators of repetition enhanced (RE) and suppressed (RS) activity were modeled using magnetoencephalography (MEG) in healthy subjects. Our results show that, in line with RP findings, N1m (~95-150ms) activity is suppressed with stimulus repetition. In addition, we observed the emergence of a sustained field (~230-270ms) that showed RE. Source analysis revealed neuronal generators of RS and RE located in both auditory and non-auditory areas, like the medial parietal cortex and frontal areas. The different timing and location of neural generators involved in RS and RE points to the existence of functionally separated mechanisms devoted to acoustic memory-trace formation in different auditory processing stages of the human brain. Copyright © 2014 Elsevier Inc. All rights reserved.

  6. The development of interactive multimedia based on auditory, intellectually, repetition in repetition algorithm learning to increase learning outcome

    Science.gov (United States)

    Munir; Sutarno, H.; Aisyah, N. S.

    2018-05-01

    This research aims to find out how the development of interactive multimedia based on auditory, intellectually, and repetition can improve student learning outcomes. This interactive multimedia is developed through 5 stages. Analysis stages include the study of literature, questionnaire, interviews and observations. The design phase is done by the database design, flowchart, storyboards and repetition algorithm material while the development phase is done by the creation of web-based framework. Presentation material is adapted to the model of learning such as auditory, intellectually, repetition. Auditory points are obtained by recording the narrative material that presented by a variety of intellectual points. Multimedia as a product is validated by material and media experts. Implementation phase conducted on grade XI-TKJ2 SMKN 1 Garut. Based on index’s gain, an increasing of student learning outcomes in this study is 0.46 which is fair due to interest of student in using interactive multimedia. While the multimedia assessment earned 84.36% which is categorized as very well.

  7. PRESCHOOL SPEECH ARTICULATION AND NONWORD REPETITION ABILITIES MAY HELP PREDICT EVENTUAL RECOVERY OR PERSISTENCE OF STUTTERING

    Science.gov (United States)

    Spencer, Caroline; Weber-Fox, Christine

    2014-01-01

    Purpose In preschool children, we investigated whether expressive and receptive language, phonological, articulatory, and/or verbal working memory proficiencies aid in predicting eventual recovery or persistence of stuttering. Methods Participants included 65 children, including 25 children who do not stutter (CWNS) and 40 who stutter (CWS) recruited at age 3;9–5;8. At initial testing, participants were administered the Test of Auditory Comprehension of Language, 3rd edition (TACL-3), Structured Photographic Expressive Language Test, 3rd edition (SPELT-3), Bankson-Bernthal Test of Phonology-Consonant Inventory subtest (BBTOP-CI), Nonword Repetition Test (NRT; Dollaghan & Campbell, 1998), and Test of Auditory Perceptual Skills-Revised (TAPS-R) auditory number memory and auditory word memory subtests. Stuttering behaviors of CWS were assessed in subsequent years, forming groups whose stuttering eventually persisted (CWS-Per; n=19) or recovered (CWS-Rec; n=21). Proficiency scores in morphosyntactic skills, consonant production, verbal working memory for known words, and phonological working memory and speech production for novel nonwords obtained at the initial testing were analyzed for each group. Results CWS-Per were less proficient than CWNS and CWS-Rec in measures of consonant production (BBTOP-CI) and repetition of novel phonological sequences (NRT). In contrast, receptive language, expressive language, and verbal working memory abilities did not distinguish CWS-Rec from CWS-Per. Binary logistic regression analysis indicated that preschool BBTOP-CI scores and overall NRT proficiency significantly predicted future recovery status. Conclusion Results suggest that phonological and speech articulation abilities in the preschool years should be considered with other predictive factors as part of a comprehensive risk assessment for the development of chronic stuttering. PMID:25173455

  8. High-speed repetitive pellet injector for plasma fueling of magnetic confinement fusion devices

    International Nuclear Information System (INIS)

    Combs, S.K.; Baylor, L.R.; Foust, C.R.

    1993-01-01

    The projected fueling requirements of future magnetic confinement devices for controlled thermonuclear research [e.g., the International Thermonuclear Experimental Reactor (ITER)] indicate that a flexible plasma fueling capability is required. This includes a mix of traditional gas puffing and low- and high-velocity deuterium-tritium pellets. Conventional pellet injectors (based on light gas guns or centrifugal accelerators) can reliably provide frozen hydrogen pellets (1- to 6-mm-diam sizes tested) up to ∼1.3-km/s velocity at the appropriate pellet fueling rates (1 to 10 Hz or greater). For long-pulse operation in a higher velocity regime (>2 km/s), an experiment in collaboration between Oak Ridge National Laboratory (ORNL) and ENEA Frascati is under way. This activity will be carried out in the framework of a collaborative agreement between the US Department of Energy and European Atomic Energy Community -- ENEA Association. In this experiment, an existing ORNL hydrogen extruder (equipped with a pellet chambering mechanism/gun barrel assembly) and a Frascati two-stage light gas gun driver have been combined on a test facility at ORNL. Initial testing has been carried out with single deuterium pellets accelerated up to 2.05 km/s with the two-stage driver; in addition, some preliminary repetitive testing (to commission the diagnostics) was performed at reduced speeds, including sequences at 0.5 to 1 Hz and 10 to 30 pellets. The primary objective of this study is to demonstrate repetitive operation (up to ∼1 Hz) with speeds in the 2- to 3-km/s range. In addition, the strength of extruded hydrogen ice as opposed to that produced in situ by direct condensation in pipe guns can be investigated. The equipment and initial experimental results are described

  9. Periventricular white matter abnormalities and restricted repetitive behavior in autism spectrum disorder

    Directory of Open Access Journals (Sweden)

    Karen Blackmon

    2016-01-01

    Full Text Available Malformations of cortical development are found at higher rates in autism spectrum disorder (ASD than in healthy controls on postmortem neuropathological evaluation but are more variably observed on visual review of in-vivo MRI brain scans. This may be due to the visually elusive nature of many malformations on MRI. Here, we utilize a quantitative approach to determine whether a volumetric measure of heterotopic gray matter in the white matter is elevated in people with ASD, relative to typically developing controls (TDC. Data from a primary sample of 48 children/young adults with ASD and 48 age-, and gender-matched TDCs, selected from the Autism Brain Imaging Data Exchange (ABIDE open-access database, were analyzed to compare groups on (1 blinded review of high-resolution T1-weighted research sequences; and (2 quantitative measurement of white matter hypointensity (WMH volume calculated from the same T1-weighted scans. Groupwise WMH volume comparisons were repeated in an independent, multi-site sample (80 ASD/80 TDC, also selected from ABIDE. Visual review resulted in equivalent proportions of imaging abnormalities in the ASD and TDC group. However, quantitative analysis revealed elevated periventricular and deep subcortical WMH volumes in ASD. This finding was replicated in the independent, multi-site sample. Periventricular WMH volume was not associated with age but was associated with greater restricted repetitive behaviors on both parent-reported and clinician-rated assessment inventories. Thus, findings demonstrate that periventricular WMH volume is elevated in ASD and associated with a higher degree of repetitive behaviors and restricted interests. Although the etiology of focal WMH clusters is unknown, the absence of age effects suggests that they may reflect a static anomaly.

  10. Increased tissue oxygenation explains the attenuation of hyperemia upon repetitive pneumatic compression of the lower leg.

    Science.gov (United States)

    Messere, Alessandro; Ceravolo, Gianluca; Franco, Walter; Maffiodo, Daniela; Ferraresi, Carlo; Roatta, Silvestro

    2017-12-01

    The rapid hyperemia evoked by muscle compression is short lived and was recently shown to undergo a rapid decrease even in spite of continuing mechanical stimulation. The present study aims at investigating the mechanisms underlying this attenuation, which include local metabolic mechanisms, desensitization of mechanosensitive pathways, and reduced efficacy of the muscle pump. In 10 healthy subjects, short sequences of mechanical compressions ( n = 3-6; 150 mmHg) of the lower leg were delivered at different interstimulus intervals (ranging from 20 to 160 s) through a customized pneumatic device. Hemodynamic monitoring included near-infrared spectroscopy, detecting tissue oxygenation and blood volume in calf muscles, and simultaneous echo-Doppler measurement of arterial (superficial femoral artery) and venous (femoral vein) blood flow. The results indicate that 1 ) a long-lasting (>100 s) increase in local tissue oxygenation follows compression-induced hyperemia, 2 ) compression-induced hyperemia exhibits different patterns of attenuation depending on the interstimulus interval, 3 ) the amplitude of the hyperemia is not correlated with the amount of blood volume displaced by the compression, and 4 ) the extent of attenuation negatively correlates with tissue oxygenation ( r  = -0,78, P < 0.05). Increased tissue oxygenation appears to be the key factor for the attenuation of hyperemia upon repetitive compressive stimulation. Tissue oxygenation monitoring is suggested as a useful integration in medical treatments aimed at improving local circulation by repetitive tissue compression. NEW & NOTEWORTHY This study shows that 1 ) the hyperemia induced by muscle compression produces a long-lasting increase in tissue oxygenation, 2 ) the hyperemia produced by subsequent muscle compressions exhibits different patterns of attenuation at different interstimulus intervals, and 3 ) the extent of attenuation of the compression-induced hyperemia is proportional to the level of

  11. Understanding work related musculoskeletal pain: does repetitive work cause stress symptoms?

    DEFF Research Database (Denmark)

    Bonde, J. P.; Mikkelsen, S.; Andersen, JH

    2005-01-01

    for development of regional pain in repetitive work, stress symptoms would likely be on the causal path. AIMS: To examine whether objective measures of repetitive monotonous work are related to occurrence and development of stress symptoms. METHODS: In 1994-95, 2033 unskilled workers with continuous repetitive...... Profile Inventory. RESULTS: Repetitive work, task cycle time, and quantified measures of repetitive upper extremity movements including force requirements were not related to occurrence of stress symptoms at baseline or development of stress symptoms during three years of follow up. CONCLUSIONS......: The findings do not indicate that repetitive work is associated with stress symptoms, but small effects cannot be ruled out. Thus the results question the importance of mental stress mechanisms in the causation of regional pain related to repetitive work. However, the findings should be interpreted...

  12. Exploring repetitive DNA landscapes using REPCLASS, a tool that automates the classification of transposable elements in eukaryotic genomes.

    Science.gov (United States)

    Feschotte, Cédric; Keswani, Umeshkumar; Ranganathan, Nirmal; Guibotsy, Marcel L; Levine, David

    2009-07-23

    Eukaryotic genomes contain large amount of repetitive DNA, most of which is derived from transposable elements (TEs). Progress has been made to develop computational tools for ab initio identification of repeat families, but there is an urgent need to develop tools to automate the annotation of TEs in genome sequences. Here we introduce REPCLASS, a tool that automates the classification of TE sequences. Using control repeat libraries, we show that the program can classify accurately virtually any known TE types. Combining REPCLASS to ab initio repeat finding in the genomes of Caenorhabditis elegans and Drosophila melanogaster allowed us to recover the contrasting TE landscape characteristic of these species. Unexpectedly, REPCLASS also uncovered several novel TE families in both genomes, augmenting the TE repertoire of these model species. When applied to the genomes of distant Caenorhabditis and Drosophila species, the approach revealed a remarkable conservation of TE composition profile within each genus, despite substantial interspecific covariations in genome size and in the number of TEs and TE families. Lastly, we applied REPCLASS to analyze 10 fungal genomes from a wide taxonomic range, most of which have not been analyzed for TE content previously. The results showed that TE diversity varies widely across the fungi "kingdom" and appears to positively correlate with genome size, in particular for DNA transposons. Together, these data validate REPCLASS as a powerful tool to explore the repetitive DNA landscapes of eukaryotes and to shed light onto the evolutionary forces shaping TE diversity and genome architecture.

  13. Repetitive DNAs highlight the role of chromosomal fusions in the karyotype evolution of Dascyllus species (Pomacentridae, Perciformes).

    Science.gov (United States)

    Getlekha, Nuntaporn; Molina, Wagner Franco; de Bello Cioffi, Marcelo; Yano, Cassia Fernanda; Maneechot, Nuntiya; Bertollo, Luiz Antonio Carlos; Supiwong, Weerayuth; Tanomtong, Alongklod

    2016-04-01

    The Dascyllus genus consists of 11 species spread over vast regions of the Indo-Pacific, showing remarkable reductions in the diploid chromosome numbers (2n). The present study analyzed the karyotypes and other chromosomal characteristics of D. trimaculatus (2n = 48; 2st + 46a; NF = 50), D. carneus (2n = 48; 2st + 46a; NF = 50) and D. aruanus (2n = 30; 18m + 2st + 10a; NF = 50) from the Thailand Gulf (Pacific Ocean) and D. melanurus (2n = 48; 2st + 46a; NF = 50) from the Andaman Sea (Indian Ocean), employing conventional cytogenetic analyses and the chromosomal mapping of repetitive DNAs, using 18S and 5S rDNA, telomeric sequences and (CA)15, (GA)15, and (CAA)10 microsatellites as probes. The C-positive heterochromatin was found in the centromeric regions of most chromosomal pairs and 18S rDNA phenotypes were single in all species. However, in D. aruanus (2n = 30), which harbors nine metacentric pairs; the 5S rDNA sites were located in the centromeric region of the shortest one. The mapping of the telomeric sequences in D. aruanus revealed the presence of interstitial telomeric sites (ITS) in the centromeric region of four metacentric pairs, with one of these pairs also displaying an additional ITS in the long arms. Distinct chromosomal markers confirmed the reduction of the 2n by chromosomal fusions, highlighting the precise characterization of these rearrangements by the cytogenetic mapping of the repetitive DNAs.

  14. Comparative Analysis of Repetitive DNA between the Main Vectors of Chagas Disease: Triatoma infestans and Rhodnius prolixus.

    Science.gov (United States)

    Pita, Sebastián; Mora, Pablo; Vela, Jesús; Palomeque, Teresa; Sánchez, Antonio; Panzera, Francisco; Lorite, Pedro

    2018-04-24

    Chagas disease or American trypanosomiasis affects six to seven million people worldwide, mostly in Latin America. This disease is transmitted by hematophagous insects known as "kissing bugs" (Hemiptera, Triatominae), with Triatoma infestans and Rhodnius prolixus being the two most important vector species. Despite the fact that both species present the same diploid chromosome number (2 n = 22), they have remarkable differences in their total DNA content, chromosome structure and genome organization. Variations in the DNA genome size are expected to be due to differences in the amount of repetitive DNA sequences. The T. infestans genome-wide analysis revealed the existence of 42 satellite DNA families. BLAST searches of these sequences against the R. prolixus genome assembly revealed that only four of these satellite DNA families are shared between both species, suggesting a great differentiation between the Triatoma and Rhodnius genomes. Fluorescence in situ hybridization (FISH) location of these repetitive DNAs in both species showed that they are dispersed on the euchromatic regions of all autosomes and the X chromosome. Regarding the Y chromosome, these common satellite DNAs are absent in T. infestans but they are present in the R. prolixus Y chromosome. These results support a different origin and/or evolution in the Y chromosome of both species.

  15. Relationship to carcinogenesis of repetitive low-dose radiation exposure

    International Nuclear Information System (INIS)

    Ootsuyama, Akira

    2016-01-01

    We studied the carcinogenic effects caused by repetitive irradiation at a low dose, which has received attention in recent years, and examined the experimental methods used to evaluate radiation-induced carcinogenesis. For this experiment, we selected a mouse with as few autochthonous cancers as possible. Skin cancer was selected as the target for analysis, because it is a rare cancer in mice. Beta-rays were selected as the radiation source. The advantage of using beta-rays is weaker penetration power into tissues, thus protecting organs, such as the digestive and hematogenous organs. The benefit of our experimental method is that only skin cancer requires monitoring, and it is possible to perform long-term experiments. The back skin of mice was exposed repetitively to beta-rays three times a week until the occurrence of cancer or death, and the dose per exposure ranged from 0.5 to 11.8 Gy. With the high-dose range (2.5-11.8 Gy), the latency period and carcinogenic rate were almost the same in each experimental group. When the dose was reduced to 1-1.5 Gy, the latency period increased, but the carcinogenic rate remained. When the dose was further reduced to 0.5 Gy, skin cancer never happened, even though we continued irradiation until death of the last mouse in this group. The lifespan of 0.5 Gy group mice was the same as that of the controls. We showed that the 0.5 Gy dose did not cause cancer, even in mice exposed repetitively throughout their life span, and thus refer to 0.5 Gy as the threshold-like dose. (author)

  16. High-repetition intra-cavity source of Compton radiation

    International Nuclear Information System (INIS)

    Pogorelsky, I; Polyanskiy, M; Agustsson, R; Campese, T; Murokh, A; Ovodenko, A; Shaftan, T

    2014-01-01

    We report our progress in developing a high-power Compton source for a diversity of applications ranging from university-scale compact x-ray light sources and metrology tools for EUV lithography, to high-brilliance gamma-sources for nuclear analysis. Our conceptual approach lies in multiplying the source’s repetition rate and increasing its average brightness by placing the Compton interaction point inside the optical cavity of an active laser. We discuss considerations in its design, our simulations, and tests of the laser’s cavity that confirm the feasibility of the proposed concept. (paper)

  17. Repetitive Transcranial Magnetic Stimulation in Patients with Hereditary Spastic Paraplegia

    Directory of Open Access Journals (Sweden)

    Mehmet Ağırman

    2011-06-01

    Full Text Available Hereditary spastic paraplegia (HSPP is a heterogeneous genetic disease characterized by progressive spasticity of lower extremities. Spasticity is a major cause of long-term disability in HSPP and significantly affects the functional life of patients. Repetitive transcranial magnetic stimulation (rTMS is widely used in diagnosis and treatment of many neurological and psychiatric diseases. Although the positive impacts of rTMS for spasticity have been reported, no study has been found on HSPP. We present two HSPP patients treated with low frequency rTMS (20 minutes at a frequency of 1 Hz (1200 pulses, for a period of 10 treatment sessions.

  18. Repetitive Transcranial Magnetic Stimulation in Patients with Hereditary Spastic Paraplegia

    Directory of Open Access Journals (Sweden)

    Mehmet Ağırman

    2011-06-01

    Full Text Available Hereditary spastic paraplegia (HSPP is a heterogeneous genetic disease characterized by progressive spasticity of lower extremities. Spasticity is a major cause of long-term disability in HSPP and significantly affects the functional life of patients. Repetitive transcranial magnetic stimulation (rTMS is widely used in diagnosis and treatment of many neurological and psychiatric diseases. Although the positive impacts of rTMS for spasticity have been reported, no study has been found on HSPP. We present two HSPP patients treated with low frequency rTMS (20 minutes at a frequency of 1 Hz (1200 pulses, for a period of 10 treatment sessions

  19. About the Infinite Repetition of Histories in Space

    Directory of Open Access Journals (Sweden)

    Manuel Alfonseca

    2014-08-01

    Full Text Available This paper analyzes two different proposals, one by Ellis and Brundrit, based on classical relativistic cosmology, the other by Garriga and Vilenkin, based on the DH interpretation of quantum mechanics, both concluding that, in an infinite universe, planets and beings must be repeated an infinite number of times. We point to possible shortcomings in these arguments. We conclude that the idea of an infinite repetition of histories in space cannot be considered strictly speaking a consequence of current physics and cosmology. Such ideas should be seen rather as examples of «ironic science» in the terminology of John Horgan.

  20. ARCA II - a new apparatus for fast, repetitive HPLC separations

    International Nuclear Information System (INIS)

    Schaedel, M.; Bruechle, W.; Jaeger, E.; Schimpf, E.; Kratz, J.V.; Scherer, U.W.; Zimmermann, H.P.

    1989-04-01

    The microcomputer controlled Automated Rapid Chemistry Apparatus, ARCA, is described in its newly designed version for the study of chemical properties of element 105 in aqueous solutions. This improved version, ARCA II, is adapted to the needs of fast and repetitive separations to be carried out in a chemically inert automated micro high performance liquid chromatography system. As an example, the separation of several group IIIB, IVB, and VB elements in the system triisooctylamine/hydrochloric acid within 30 s is demonstrated. Furthermore, a new method for the fast preparation of samples for α-particle spectroscopy by evaporation of the aqueous effluent with an intense light source is presented. (orig.)

  1. Design of a repetitively pulsed megajoule dense-plasma focus

    International Nuclear Information System (INIS)

    Zucker, O.; Bostick, W.; Gullickson, R.; Long, J.; Luce, J.; Sahlin, H.

    1975-01-01

    This report describes a 1 pulse per second, dense-plasma-focus (DPF) materials-testing device capable of delivering a minimum of 10 15 neutrons per pulse. Moderate scaling up from existing designs is shown to be sufficient to provide 2 x 10 13 neutrons/ cm 2 . s to a suitable target. The average power consumption, which has become a major issue due to the energy crisis, is analyzed with respect to other plasma devices and is shown to be highly favorable. Also discussed is a novel approach to capacitor-bank and switch design with respect to repetitive-pulse operation. (auth)

  2. Environmentally stable picosecond Yb fiber laser with low repetition rate

    Science.gov (United States)

    Baumgartl, M.; Abreu-Afonso, J.; Díez, A.; Rothhardt, M.; Limpert, J.; Tünnermann, A.

    2013-04-01

    A SESAM-mode-locked, all-polarization-maintaining Ytterbium fiber laser producing picosecond pulses with narrow spectral bandwidth is presented. A simple linear all-fiber cavity without dispersion compensation is realized using a uniform fiber Bragg grating (FBG). Different cavity lengths are investigated and repetition rates down to 0.7 MHz are obtained. Bandwidth and pulse duration of the output pulses are mainly determined by the choice of FBG. Pulses between 30 and 200 ps are generated employing different FBGs with bandwidths between 17 and 96 pm. The experimental results are in good agreement with numerical simulations. The laser holds great potential for simple amplification setups without pulse picking.

  3. A Unified Theoretical Framework for Cognitive Sequencing.

    Science.gov (United States)

    Savalia, Tejas; Shukla, Anuj; Bapi, Raju S

    2016-01-01

    The capacity to sequence information is central to human performance. Sequencing ability forms the foundation stone for higher order cognition related to language and goal-directed planning. Information related to the order of items, their timing, chunking and hierarchical organization are important aspects in sequencing. Past research on sequencing has emphasized two distinct and independent dichotomies: implicit vs. explicit and goal-directed vs. habits. We propose a theoretical framework unifying these two streams. Our proposal relies on brain's ability to implicitly extract statistical regularities from the stream of stimuli and with attentional engagement organizing sequences explicitly and hierarchically. Similarly, sequences that need to be assembled purposively to accomplish a goal require engagement of attentional processes. With repetition, these goal-directed plans become habits with concomitant disengagement of attention. Thus, attention and awareness play a crucial role in the implicit-to-explicit transition as well as in how goal-directed plans become automatic habits. Cortico-subcortical loops basal ganglia-frontal cortex and hippocampus-frontal cortex loops mediate the transition process. We show how the computational principles of model-free and model-based learning paradigms, along with a pivotal role for attention and awareness, offer a unifying framework for these two dichotomies. Based on this framework, we make testable predictions related to the potential influence of response-to-stimulus interval (RSI) on developing awareness in implicit learning tasks.

  4. A Unified Theoretical Framework for Cognitive Sequencing

    Directory of Open Access Journals (Sweden)

    Tejas Savalia

    2016-11-01

    Full Text Available The capacity to sequence information is central to human performance. Sequencing ability forms the foundation stone for higher order cognition related to language and goal-directed planning. Information related to the order of items, their timing, chunking and hierarchical organization are important aspects in sequencing. Past research on sequencing has emphasized two distinct and independent dichotomies: implicit versus explicit and goal-directed versus habits. We propose a theoretical framework unifying these two streams. Our proposal relies on brain's ability to implicitly extract statistical regularities from the stream of stimuli and with attentional engagement organizing sequences explicitly and hierarchically. Similarly, sequences that need to be assembled purposively to accomplish a goal require engagement of attentional processes. With repetition, these goal-directed plans become habits with concomitant disengagement of attention. Thus attention and awareness play a crucial role in the implicit-to-explicit transition as well as in how goal-directed plans become automatic habits. Cortico-subcortical loops ─ basal ganglia-frontal cortex and hippocampus-frontal cortex loops ─ mediate the transition process. We show how the computational principles of model-free and model-based learning paradigms, along with a pivotal role for attention and awareness, offer a unifying framework for these two dichotomies. Based on this framework, we make testable predictions related to the potential influence of response-to-stimulus interval (RSI on developing awareness in implicit learning tasks.

  5. Implicative Algebras

    African Journals Online (AJOL)

    Tadesse

    In this paper we introduce the concept of implicative algebras which is an equivalent definition of lattice implication algebra of Xu (1993) and further we prove that it is a regular Autometrized. Algebra. Further we remark that the binary operation → on lattice implicative algebra can never be associative. Key words: Implicative ...

  6. Repetitive pulse accelerator technology for light ion inertial confinement fusion

    International Nuclear Information System (INIS)

    Buttram, M.T.

    1985-01-01

    Successful ignition of an inertial confinement fusion (ICF) pellet is calculated to require that several megajoules of energy be deposited in the pellet's centimeter-sized shell within 10 ns. This implies a driver power of several hundreds of terawatts and power density around 100 TW/cm 2 . The Sandia ICF approach is to deposit the energy with beams of 30 MV lithium ions. The first accelerator capable of producing these beams (PBFA II, 100 TW) will be used to study beam formation and target physics on a single pulse basis. To utilize this technology for power production, repetitive pulsing at rates that may be as high as 10 Hz will be required. This paper will overview the technologies being studied for a repetitively pulsed ICF accelerator. As presently conceived, power is supplied by rotating machinery providing 16 MJ in 1 ms. The generator output is transformed to 3 MV, then switched into a pulse compression system using laser triggered spark gaps. These must be synchronized to about 1 ns. Pulse compression is performed with saturable inductor switches, the output being 40 ns, 1.5 MV pulses. These are transformed to 30 MV in a self-magnetically insulated cavity adder structure. Space charge limited ion beams are drawn from anode plasmas with electron counter streaming being magnetically inhibited. The ions are ballistically focused into the entrances of guiding discharge channels for transport to the pellet. The status of component development from the prime power to the ion source will be reviewed

  7. Verbal behavior in Alzheimer's disease patients: Analysis of phrase repetition.

    Science.gov (United States)

    Cecato, Juliana Francisca; Martinellil, José Eduardo; Bartholomeu, Luana Luz; Basqueira, Ana Paula; Yassuda, Mônica Sanches; Aprahamian, Ivan

    2010-01-01

    Language problems in the elderly with AD are due to the fact that deterioration occurs not only in semantic memory, but in a group of cognitive factors, evidenced by a deficiency in search strategies for linguistic information. To evaluate phrase repetition in two cognitive tests, the MMSE and MoCA, in a group of Alzheimer disease patients (AD) and normal controls. A Cross-sectional study was conducted involving 20 patients who sought medical assistance at a geriatric institute in Jundiaí, São Paulo. The subjects underwent a detailed clinical examination and neuropsychometric evaluation. All subjects with AD met DSM-IV and NINCDS-ADRDA criteria. Ten patients received a diagnosis of AD and 10 were healthy subjects, forming the control group (CG). All participants correctly answered the phrase from the MMSE (phrase 1). The MoCA phrases (phrases 2 and 3) were correct in 80% and 90%, respectively in the CG and in 40% and 50%, respectively in the AD group. The MoCA test proved more effective in evaluating the echoic behavior in AD patients compared to the MMSE. The simpler phrase repetition task in the MMSE was found to be less sensitive in detecting mild language decline in AD patients.

  8. Identification of multiple modes of axisymmetric or circularly repetitive structures

    International Nuclear Information System (INIS)

    Kopff, P.

    1983-01-01

    The axisymmetric structures, or those composed with circularly repetitive elements, often display multiple modes, which are not easy to separate by modal identification of experimental responses. To be able to solve in situ some problems related to the vibrational behaviour of reactor vessels or other such huge structures, ELECTRICITY DE FRANCE developed a few years ago, experimental capabilities providing heavy harmonic driving forces, and elaborate data acquisition, signal processing and modal identification software, self-contained in an integrated mobile test facility. The modal analysis techniques we have developed with the LABORATOIRE DE MECANIQUE Appliquee of University of BESANCON (FRANCE) were especially suited for identification of multiple or separation of quasi-multiple modes, i.e. very close and strongly coupled resonances. Besides, the curve fitting methods involved, compute the same complex eigen-frequencies for all the vibration pick-ups, for better accuracy of the related eigen-vector components. Moreover, the latest extensions of these algorithms give us the means to deal with non-linear behaviour. The performances of these programs are drawn from some experimental results on axisymmetric or circularly repetitive structure, we tested in our laboratory to validate the computational hypothesis used in models for seismic responses of breeder reactor vessels. (orig.)

  9. Verbal behavior in Alzheimer disease patients: Analysis of phrase repetition

    Directory of Open Access Journals (Sweden)

    Juliana Francisca Cecato

    Full Text Available Abstract Language problems in the elderly with AD are due to the fact that deterioration occurs not only in semantic memory, but in a group of cognitive factors, evidenced by a deficiency in search strategies for linguistic information. Objectives: To evaluate phrase repetition in two cognitive tests, the MMSE and MoCA, in a group of Alzheimer disease patients (AD and normal controls. Methods: A Cross-sectional study was conducted involving 20 patients who sought medical assistance at a geriatric institute in Jundiaí, São Paulo. The subjects underwent a detailed clinical examination and neuropsychometric evaluation. All subjects with AD met DSM-IV and NINCDS-ADRDA criteria. Ten patients received a diagnosis of AD and 10 were healthy subjects, forming the control group (CG. Results: All participants correctly answered the phrase from the MMSE (phrase 1. The MoCA phrases (phrases 2 and 3 were correct in 80% and 90%, respectively in the CG and in 40% and 50%, respectively in the AD group. Conclusions: The MoCA test proved more effective in evaluating the echoic behavior in AD patients compared to the MMSE. The simpler phrase repetition task in the MMSE was found to be less sensitive in detecting mild language decline in AD patients.

  10. Rotated balance in humans due to repetitive rotational movement

    Science.gov (United States)

    Zakynthinaki, M. S.; Madera Milla, J.; López Diaz De Durana, A.; Cordente Martínez, C. A.; Rodríguez Romo, G.; Sillero Quintana, M.; Sampedro Molinuevo, J.

    2010-03-01

    We show how asymmetries in the movement patterns during the process of regaining balance after perturbation from quiet stance can be modeled by a set of coupled vector fields for the derivative with respect to time of the angles between the resultant ground reaction forces and the vertical in the anteroposterior and mediolateral directions. In our model, which is an adaption of the model of Stirling and Zakynthinaki (2004), the critical curve, defining the set of maximum angles one can lean to and still correct to regain balance, can be rotated and skewed so as to model the effects of a repetitive training of a rotational movement pattern. For the purposes of our study a rotation and a skew matrix is applied to the critical curve of the model. We present here a linear stability analysis of the modified model, as well as a fit of the model to experimental data of two characteristic "asymmetric" elite athletes and to a "symmetric" elite athlete for comparison. The new adapted model has many uses not just in sport but also in rehabilitation, as many work place injuries are caused by excessive repetition of unaligned and rotational movement patterns.

  11. New solid state opening switches for repetitive pulsed power technology

    Energy Technology Data Exchange (ETDEWEB)

    Lyubutin, S K; Mesyats, G A; Rukin, S N; Slovikovskii, B G; Turov, A M [Russian Academy of Sciences, Ekaterinburg (Russian Federation). Inst. of Electrophysics

    1997-12-31

    In 1991 the authors discovered a semiconductor opening switch (SOS) effect that occurs in p{sup +}-p-n-n{sup +} silicon structures at a current density of up to 60 kA/cm{sup 2}. This effect was used to develop high-power semiconductor opening switches in intermediate inductive storage circuits. The breaking power of the opening switches was as high as 5 GW, the interrupted current being up to 45 kA, reverse voltage up to 1 MV and the current interruption time between 10 and 60 ns. The opening switches were assembled from quantity-produced Russian-made rectifying diodes type SDL with hard recovery characteristic. On the basis of experimental and theoretical investigations of the SOS effect, new SOS diodes were designed and manufactured by the Electrophysical Institute. The paper gives basic parameters of the SOS diodes. The new diodes offer higher values of interrupted current and shorter times of current interruption together with a considerable increase in the energy switching efficiency. The new SOS diodes were used to develop repetitive all-solid-state pulsed generators with an output voltage of up to 250 kV, pulse repetition rate up to 5 kHz, and pulse duration between 10 and 30 ns. (author). 2 tabs., 3 figs., 4 refs.

  12. Application of repetitive pulsed power technology to chemical processing

    International Nuclear Information System (INIS)

    Kaye, R.J.; Hamil, R.

    1995-01-01

    The numerous sites of soil and water contaminated with organic chemicals present an urgent environmental concern that continues to grow. Electron and x-ray irradiation have been shown to be effective methods to destroy a wide spectrum of organic chemicals, nitrates, nitrites, and cyanide in water by breaking molecules to non-toxic products or entirely mineralizing the by-products to gas, water, and salts. Sandia National Laboratories is developing Repetitive High Energy Pulsed Power (RHEPP) technology capable of producing high average power, broad area electron or x-ray beams. The 300 kW RHEPP-II facility accelerates electrons to 2.5 MeV at 25 kA over 1,000 cm 2 in 60 ns pulses at repetition rates of over 100 Hz. Linking this modular treatment capability with the rapid optical-sensing diagnostics and neutral network characterization software algorithms will provide a Smart Waste Treatment (SWaT) system. Such a system would also be applicable for chemical manufacture and processing of industrial waste for reuse or disposal. This talk describes both the HREPP treatment capability and sensing technologies. Measurements of the propagated RHEPP-II beam and dose profiles are presented. Sensors and rapid detection software are discussed with application toward chemical treatment

  13. Evolution of repetitive explosive instabilities in space and time

    International Nuclear Information System (INIS)

    Wilhelmsson, H.

    1984-01-01

    A nonlinear rate equation describing nonlinear, explosive type interaction of waves in plasmas is studied, assuming that amplitude saturation occurs due to nonlinear frequency shifts. Emphasis is put on the space dependence of the solution caused by the assumption of a given initial amplitude distribution in space. An analysis is given of the problem of repetitive peaks governed by the nonlinear rate equation for the time development of the amplitudes of plasma waves and by a Lorentzian shape distribution of the initial amplitudes. For the one-dimensional case, the peaks developed by explosive instability move in the direction of lower initial amplitude values, and the speed and the repetition rate of the peaks are determined. The possible forms of equilibria for the nonlinear rate equation in the explosive case are also studied, including, in addition to the quadratic nonlinearity, diffusion and linear damping effects. A solution to the nonlinear rate equation including diffusion is also given for the case where the quadratic nonlinearity represents recombination. (Auth.)

  14. Effect of parallel magnetic field on repetitively unipolar nanosecond pulsed dielectric barrier discharge under different pulse repetition frequencies

    Science.gov (United States)

    Liu, Yidi; Yan, Huijie; Guo, Hongfei; Fan, Zhihui; Wang, Yuying; Wu, Yun; Ren, Chunsheng

    2018-03-01

    A magnetic field, with the direction parallel to the electric field, is applied to the repetitively unipolar positive nanosecond pulsed dielectric barrier discharge. The effect of the parallel magnetic field on the plasma generated between two parallel-plate electrodes in quiescent air is experimentally studied under different pulse repetition frequencies (PRFs). It is indicated that only the current pulse in the rising front of the voltage pulse occurs, and the value of the current is increased by the parallel magnetic field under different PRFs. The discharge uniformity is improved with the decrease in PRF, and this phenomenon is also observed in the discharge with the parallel magnetic field. By using the line-ratio technique of optical emission spectra, it is found that the average electron density and electron temperature under the considered PRFs are both increased when the parallel magnetic field is applied. The incremental degree of average electron density is basically the same under the considered PRFs, while the incremental degree of electron temperature under the higher-PRFs is larger than that under the lower-PRFs. All the above phenomena are explained by the effect of parallel magnetic field on diffusion and dissipation of electrons.

  15. High-repetition-rate hydrogen chamber: Preliminary studies; Chambre a hydrogene a haut taux de repetition: Etudes preliminaires

    Energy Technology Data Exchange (ETDEWEB)

    NONE

    1967-01-01

    This report is a conclusion to the tests realised with an experimental bubbles chamber in view to study the possibilities to increase the repetition rate. The more important parameters (the evolution of the bubbles, the expansion system) are considered in a theoretical way. Then the hardware is described. To end, experimental results are compared with the first evaluations. The calculations and the experimentation are against an oscillation system for the expansion. A system with a locking is to he considered. (authors) [French] Ce rapport est une conclusion aux essais realises avec une chambre a bulles experimentale en vue d'etudier les possibilites d'accroitre les taux de repetition. Les parametres les plus importants (evolution des bulles, mecanique de la detente) sont etudies par voie theorique. Puis l'appareillage est decrit. Enfin, les resultats experimentaux sont compares aux evaluations donnees au debut. Ces calculs et cette experimentation ne sont pas en faveur d'un systeme oscillant pour la detente et il faut envisager un systeme avec verrouillage. (auteurs)

  16. Relationship between the number of repetitions and selected percentages of one repetition maximum in free weight exercises in trained and untrained men.

    Science.gov (United States)

    Shimano, Tomoko; Kraemer, William J; Spiering, Barry A; Volek, Jeff S; Hatfield, Disa L; Silvestre, Ricardo; Vingren, Jakob L; Fragala, Maren S; Maresh, Carl M; Fleck, Steven J; Newton, Robert U; Spreuwenberg, Luuk P B; Häkkinen, Keijo

    2006-11-01

    Resistance exercise intensity is commonly prescribed as a percent of 1 repetition maximum (1RM). However, the relationship between percent 1RM and the number of repetitions allowed remains poorly studied, especially using free weight exercises. The purpose of this study was to determine the maximal number of repetitions that trained (T) and untrained (UT) men can perform during free weight exercises at various percentages of 1RM. Eight T and 8 UT men were tested for 1RM strength. Then, subjects performed 1 set to failure at 60, 80, and 90% of 1RM in the back squat, bench press, and arm curl in a randomized, balanced design. There was a significant (p squat than the bench press or arm curl at 60% 1RM for T and UT. At 80 and 90% 1RM, there were significant differences between the back squat and other exercises; however, differences were much less pronounced. No differences in number of repetitions performed at a given exercise intensity were noted between T and UT (except during bench press at 90% 1RM). In conclusion, the number of repetitions performed at a given percent of 1RM is influenced by the amount of muscle mass used during the exercise, as more repetitions can be performed during the back squat than either the bench press or arm curl. Training status of the individual has a minimal impact on the number of repetitions performed at relative exercise intensity.

  17. Two discharge modes of a repetitive nanosecond pulsed helium glow discharge under sub-atmospheric pressure in the repetition frequency range of 20 to 600 kHz

    Science.gov (United States)

    Kikuchi, Yusuke; Maegawa, Takuya; Otsubo, Akira; Nishimura, Yoshimi; Nagata, Masayoshi; Yatsuzuka, Mitsuyasu

    2018-05-01

    Two discharge modes, α and γ, of a repetitive nanosecond pulsed helium glow discharge at a gas pressure of 10 kPa in the repetition frequency range from 20 to 600 kHz are reported for the first time. The pulsed glow discharge is produced in a pair of parallel plate metal electrodes without insertion of dielectrics. The α mode discharge is volumetrically produced in the electrode gap at a low-repetition frequency, whereas the γ mode discharge is localized at the cathode surface at a high-repetition frequency. At high-repetition frequency, the time interval between voltage pulses is shorter than the lifetime of the afterglow produced by the preceding discharge. Then, the γ mode discharge is maintained by a large number of secondary electrons emitted from the cathode exposed to high-density ions and metastable helium atoms in the afterglow. In the α mode discharge with a low-repetition frequency operation, primary electrons due to gas ionization dominate the ionization process. Thus, a large discharge voltage is needed for the excitation of the α mode discharge. It is established that the bifurcation of α-γ discharge mode, accompanied by a decrease in the discharge voltage, occurs at the high-repetition frequency of ∼120 kHz.

  18. Optimality based repetitive controller design for track-following servo system of optical disk drives.

    Science.gov (United States)

    Chen, Wentao; Zhang, Weidong

    2009-10-01

    In an optical disk drive servo system, to attenuate the external periodic disturbances induced by inevitable disk eccentricity, repetitive control has been used successfully. The performance of a repetitive controller greatly depends on the bandwidth of the low-pass filter included in the repetitive controller. However, owing to the plant uncertainty and system stability, it is difficult to maximize the bandwidth of the low-pass filter. In this paper, we propose an optimality based repetitive controller design method for the track-following servo system with norm-bounded uncertainties. By embedding a lead compensator in the repetitive controller, both the system gain at periodic signal's harmonics and the bandwidth of the low-pass filter are greatly increased. The optimal values of the repetitive controller's parameters are obtained by solving two optimization problems. Simulation and experimental results are provided to illustrate the effectiveness of the proposed method.

  19. Mosaic structure of intragenic repetitive elements in histone H1-like protein Hc2 varies within serovars of Chlamydia trachomatis

    Directory of Open Access Journals (Sweden)

    Nilsson Anders

    2010-03-01

    Full Text Available Abstract Background The histone-like protein Hc2 binds DNA in Chlamydia trachomatis and is known to vary in size between 165 and 237 amino acids, which is caused by different numbers of lysine-rich pentamers. A more complex structure was seen in this study when sequences from 378 specimens covering the hctB gene, which encodes Hc2, were compared. Results This study shows that the size variation is due to different numbers of 36-amino acid long repetitive elements built up of five pentamers and one hexamer. Deletions and amino acid substitutions result in 14 variants of repetitive elements and these elements are combined into 22 configurations. A protein with similar structure has been described in Bordetella but was now also found in other genera, including Burkholderia, Herminiimonas, Minibacterium and Ralstonia. Sequence determination resulted in 41 hctB variants that formed four clades in phylogenetic analysis. Strains causing the eye disease trachoma and strains causing invasive lymphogranuloma venereum infections formed separate clades, while strains from urogenital infections were more heterogeneous. Three cases of recombination were identified. The size variation of Hc2 has previously been attributed to deletions of pentamers but we show that the structure is more complex with both duplication and deletions of 36-amino acid long elements. Conclusions The polymorphisms in Hc2 need to be further investigated in experimental studies since DNA binding is essential for the unique biphasic life cycle of the Chlamydiacae. The high sequence variation in the corresponding hctB gene enables phylogenetic analysis and provides a suitable target for the genotyping of C. trachomatis.

  20. Non-word repetition in children with specific language impairment: a deficit in phonological working memory or in long-term verbal knowledge?

    Science.gov (United States)

    Casalini, Claudia; Brizzolara, Daniela; Chilosi, Anna; Cipriani, Paola; Marcolini, Stefania; Pecini, Chiara; Roncoli, Silvia; Burani, Cristina

    2007-08-01

    In this study we investigated the effects of long-term memory (LTM) verbal knowledge on short-term memory (STM) verbal recall in a sample of Italian children affected by different subtypes of specific language impairment (SLI). The aim of the study was to evaluate if phonological working memory (PWM) abilities of SLI children can be supported by LTM linguistic representations and if PWM performances can be differently affected in the various subtypes of SLI. We tested a sample of 54 children affected by Mixed Receptive-Expressive (RE), Expressive (Ex) and Phonological (Ph) SLI (DSM-IV - American Psychiatric Association, 1994) by means of a repetition task of words (W) and non-words (NW) differing in morphemic structure [morphological non-words (MNW), consisting of combinations of roots and affixes - and simple non-words - with no morphological constituency]. We evaluated the effects of lexical and morpho-lexical LTM representations on STM recall by comparing the repetition accuracy across the three types of stimuli. Results indicated that although SLI children, as a group, showed lower repetition scores than controls, their performance was affected similarly to controls by the type of stimulus and the experimental manipulation of the non-words (better repetition of W than MNW and NW, and of MNW than NW), confirming the recourse to LTM verbal representations to support STM recall. The influence of LTM verbal knowledge on STM recall in SLI improved with age and did not differ among the three types of SLI. However, the three types of SLI differed in the accuracy of their repetition performances (PMW abilities), with the Phonological group showing the best scores. The implications for SLI theory and practice are discussed.

  1. Functions of repetition in the discourse of elderly speakers: The role of prosody and gesture

    OpenAIRE

    Bolly, Catherine; Gerstenberg, Annette; 14th International Pragmatics Conference (IPra), Panel session "Age and language use"

    2015-01-01

    Cognitively speaking, repetition can work as a facilitator for both the planning and the understanding of spoken language. It can work as a cohesive and interactive device or, at a higher-level function of discourse, to engage in interaction by creating interpersonal involvement: repetition always conveys altered meaning, as it has to be re-interpreted by the interlocutor “in light of the accretion, juxtaposition, or expansion” (Tannen 2007: 62). Repetition is thus useful for the building of ...

  2. Nonword repetition in lexical decision: support for two opposing processes.

    Science.gov (United States)

    Wagenmakers, Eric-Jan; Zeelenberg, René; Steyvers, Mark; Shiffrin, Richard; Raaijmakers, Jeroen

    2004-10-01

    We tested and confirmed the hypothesis that the prior presentation of nonwords in lexical decision is the net result of two opposing processes: (1) a relatively fast inhibitory process based on global familiarity; and (2) a relatively slow facilitatory process based on the retrieval of specific episodic information. In three studies, we manipulated speed-stress to influence the balance between the two processes. Experiment 1 showed item-specific improvement for repeated nonwords in a standard "respond-when-ready" lexical decision task. Experiment 2 used a 400-ms deadline procedure and showed performance for nonwords to be unaffected by up to four prior presentations. In Experiment 3 we used a signal-to-respond procedure with variable time intervals and found negative repetition priming for repeated nonwords. These results can be accounted for by dual-process models of lexical decision.

  3. Repetitive Bunches from RF-Photo Gun Radiate Coherently

    CERN Document Server

    Van der Geer, C A J; Van der Geer, S B

    2004-01-01

    We consider to feed the laser wake field accelerator of the alpha-X project by a train of low charge pancake electron bunches to reduce undesired expansion due to space-charge forces. To this purpose the photo excitation laser of the rf-injector is split into a train of sub-pulses, such that each of the produced electron bunches falls into a successive ponderomotive well of the plasma accelerator. This way the total accelerated charge is not reduced. The repetitive photo gun can be tested, at low energy, by connecting it directly to the undulator and monitoring the radiation. The assertions are based on the results of new GPT simulations.

  4. Report on computation of repetitive hyperbaric-hypobaric decompression tables

    Science.gov (United States)

    Edel, P. O.

    1975-01-01

    The tables were constructed specifically for NASA's simulated weightlessness training program; they provide for 8 depth ranges covering depths from 7 to 47 FSW, with exposure times of 15 to 360 minutes. These tables were based up on an 8 compartment model using tissue half-time values of 5 to 360 minutes and Workmanline M-values for control of the decompression obligation resulting from hyperbaric exposures. Supersaturation ratios of 1.55:1 to 2:1 were used for control of ascents to altitude following such repetitive dives. Adequacy of the method and the resultant tables were determined in light of past experience with decompression involving hyperbaric-hypobaric interfaces in human exposures. Using these criteria, the method showed conformity with empirically determined values. In areas where a discrepancy existed, the tables would err in the direction of safety.

  5. [Repetitive impulse-associated behavioral disorders in Parkinson's disease].

    Science.gov (United States)

    Katzenschlager, R; Goerlich, K S; van Eimeren, T

    2012-12-01

    Parkinson's disease (PD) is associated with a number of behavioral disorders which may cause considerable social, professional or financial problems. Impulse control disorders (ICDs), such as pathological gambling, binge eating, compulsive shopping and hypersexuality occur in approximately 13-14% of PD patients. Further behavioral disorders are the dopamine dysregulation syndrome (DDS), a substance dependence characterized by craving for dopaminergic substances and punding (prolonged repetitive activities which are not goal-oriented).Treatment-related risk factors are dopamine agonists for ICDs and a high total dopaminergic dose for DDS and punding. Shared risk factors are young age at onset, impulsive personality traits, depression and possibly dyskinesia. At the neuronal level these behavioral disorders seem to be associated with changes in the reward system and dysfunction of the orbitofrontal cortex. The evidence level for management strategies is at present insufficient. For ICDs current clinical practice consists of discontinuation or reduction of dopamine agonists.

  6. Repetitive pulse accelerator technology for light ion inertial confinement fusion

    International Nuclear Information System (INIS)

    Buttram, M.T.

    1985-01-01

    This paper will overview the technologies being studied for a repetitively pulsed ICF accelerator. As presently conceived, power is supplied by rotating machinery providing 16 MJ in 1 ms. The generator output is transformed to 3 MV, then switched into a pulse compression system using laser triggered spark gaps. These must be synchronized to about 1 ns. Pulse compression is performed with saturable inductor switches, the output being 40 ns, 1.5 MV pulses. These are transformed to 30 MV in a self-magnetically insulated cavity adder structure. Space charge limited ion beams are drawn from anode plasmas with electron counter streaming being magnetically inhibited. The ions are ballistically focused into the entrances of guiding discharge channels for transport to the pellet. The status of component development from the prime power to the ion source will be reviewed

  7. High repetition rate driver circuit for modulation of injection lasers

    International Nuclear Information System (INIS)

    Dornan, B.R.; Goel, J.; Wolkstein, H.J.

    1981-01-01

    An injection laser modulator comprises a self-biased field effect transistor (FET) and an injection laser to provide a quiescent state during which lasing of the injection laser occurs in response to a high repetition rate signal of pulse coded modulation (pcm). The modulator is d.c. coupled to an input pulse source of pcm rendering it compatible with an input pulse referenced to ground and not being subject to voltage level shifting of the input pulse. The modulator circuit in its preferred and alternate embodiments provides various arrangements for high impedance input and low impedance output matching. In addition, means are provided for adjusting the bias of the FET as well as the bias of the injection laser

  8. A high repetition rate XUV seeding source for FLASH2

    International Nuclear Information System (INIS)

    Willner, Arik

    2012-05-01

    Improved performance of free-electron laser (FEL) light sources in terms of timing stability, pulse shape and spectral properties of the amplified FEL pulses is of interest in material science, the fields of ultrafast dynamics, biology, chemistry and even special branches in industry. A promising scheme for such an improvement is direct seeding with high harmonic generation (HHG) in a noble gas target. A free-electron laser seeded by an external extreme ultraviolet (XUV) source is planned for FLASH2 at DESY in Hamburg. The requirements for the XUV/soft X-ray source can be summarized as follows: A repetition rate of at least 100 kHz in a 10 Hz burst is needed at variable wavelengths from 10 to 40 nm and pulse energies of several nJ within a single laser harmonic. This application requires a laser amplifier system with exceptional parameters, mJ-level pulse energy, 10-15 fs pulse duration at 100 kHz (1 MHz) burst repetition rate. A new optical parametric chirped-pulse amplification (OPCPA) system is under development in order to meet these requirements, and very promising results have been achieved in the last three years. In parallel to this development, a new HHG concept is necessary to sustain high average power of the driving laser system and to generate harmonics with high conversion efficiencies. Currently, the highest conversion efficiency with HHG has been demonstrated using gas-filled capillary targets. For our application, only a free-jet target can be used for HHG, in order to overcome damage threshold limitations of HHG target optics at a high repetition rate. A novel dual-gas multijet gas target has been developed and first experiments show remarkable control of the degree of phase matching forming the basis for improved control of the harmonic photon flux and the XUV pulse characteristics. The basic idea behind the dual-gas concept is the insertion of matching zones in between multiple HHG sources. These matching sections are filled with hydrogen which

  9. A high repetition rate XUV seeding source for FLASH2

    Energy Technology Data Exchange (ETDEWEB)

    Willner, Arik

    2012-05-15

    Improved performance of free-electron laser (FEL) light sources in terms of timing stability, pulse shape and spectral properties of the amplified FEL pulses is of interest in material science, the fields of ultrafast dynamics, biology, chemistry and even special branches in industry. A promising scheme for such an improvement is direct seeding with high harmonic generation (HHG) in a noble gas target. A free-electron laser seeded by an external extreme ultraviolet (XUV) source is planned for FLASH2 at DESY in Hamburg. The requirements for the XUV/soft X-ray source can be summarized as follows: A repetition rate of at least 100 kHz in a 10 Hz burst is needed at variable wavelengths from 10 to 40 nm and pulse energies of several nJ within a single laser harmonic. This application requires a laser amplifier system with exceptional parameters, mJ-level pulse energy, 10-15 fs pulse duration at 100 kHz (1 MHz) burst repetition rate. A new optical parametric chirped-pulse amplification (OPCPA) system is under development in order to meet these requirements, and very promising results have been achieved in the last three years. In parallel to this development, a new HHG concept is necessary to sustain high average power of the driving laser system and to generate harmonics with high conversion efficiencies. Currently, the highest conversion efficiency with HHG has been demonstrated using gas-filled capillary targets. For our application, only a free-jet target can be used for HHG, in order to overcome damage threshold limitations of HHG target optics at a high repetition rate. A novel dual-gas multijet gas target has been developed and first experiments show remarkable control of the degree of phase matching forming the basis for improved control of the harmonic photon flux and the XUV pulse characteristics. The basic idea behind the dual-gas concept is the insertion of matching zones in between multiple HHG sources. These matching sections are filled with hydrogen which

  10. Intrinsic and extrinsic motivation for stereotypic and repetitive behavior.

    Science.gov (United States)

    Joosten, Annette V; Bundy, Anita C; Einfeld, Stewart L

    2009-03-01

    This study provides evidence for intrinsic and extrinsic motivators for stereotypical and repetitive behavior in children with autism and intellectual disability and children with intellectual disability alone. We modified the Motivation Assessment Scale (MAS) (1988b); dividing it into intrinsic and extrinsic measures and adding items to assess anxiety as an intrinsic motivator. Rasch analysis of data from 279 MASs (74 children) revealed that the items formed two unidimensional scales. Anxiety was a more likely intrinsic motivator than sensory seeking for children with dual diagnoses; the reverse was true for children with intellectual disability only. Escape and gaining a tangible object were the most common extrinsic motivators for those with dual diagnoses and attention and escape for children with intellectual disability.

  11. Repetitive elements dynamics in cell identity programming, maintenance and disease

    KAUST Repository

    Bodega, Beatrice

    2014-12-01

    The days of \\'junk DNA\\' seem to be over. The rapid progress of genomics technologies has been unveiling unexpected mechanisms by which repetitive DNA and in particular transposable elements (TEs) have evolved, becoming key issues in understanding genome structure and function. Indeed, rather than \\'parasites\\', recent findings strongly suggest that TEs may have a positive function by contributing to tissue specific transcriptional programs, in particular as enhancer-like elements and/or modules for regulation of higher order chromatin structure. Further, it appears that during development and aging genomes experience several waves of TEs activation, and this contributes to individual genome shaping during lifetime. Interestingly, TEs activity is major target of epigenomic regulation. These findings are shedding new light on the genome-phenotype relationship and set the premises to help to explain complex disease manifestation, as consequence of TEs activity deregulation.

  12. Repetition blindness for natural images of objects with viewpoint changes

    Directory of Open Access Journals (Sweden)

    Stephane eBuffat

    2013-01-01

    Full Text Available When stimuli are repeated in a rapid serial visual presentation (RSVP, observers sometimes fail to report the second occurrence of a target. This phenomenon is referred to as repetition blindness (RB. We report an RSVP experiment with photographs in which we manipulated object viewpoints between the first and second occurrences of a target (0-, 45-, or 90-degree changes, and spatial frequency content. Natural images were spatially filtered to produce low, medium, or high spatial-frequency stimuli. RB was observed for all filtering conditions. Surprisingly, for full-spectrum images, RB increased significantly as the viewpoint reached 90 degrees. For filtered images, a similar pattern of results was found for all conditions except for medium spatial-frequency stimuli. These findings suggest that object recognition in RSVP are subtended by viewpoint-specific representations for all spatial frequencies except medium ones.

  13. Influence of Music Style and Rate on Repetitive Finger Tapping.

    Science.gov (United States)

    Stegemöller, Elizabeth L; Tatz, Joshua R; Warnecke, Alison; Hibbing, Paul; Bates, Brandon; Zaman, Andrew

    2018-03-09

    Auditory cues, including music, are commonly used in the treatment of persons with Parkinson's disease. Yet, how music style and movement rate modulate movement performance in persons with Parkinson's disease have been neglected and remain limited in healthy young populations. The purpose of this study was to determine how music style and movement rate influence movement performance in healthy young adults. Healthy participants were asked to perform repetitive finger movements at two pacing rates (70 and 140 beats per minute) for the following conditions: (a) a tone only, (b) activating music, and (c) relaxing music. Electromyography, movement kinematics, and variability were collected. Results revealed that the provision of music, regardless of style, reduced amplitude variability at both pacing rates. Intermovement interval was longer, and acceleration variability was reduced during both music conditions at the lower pacing rate only. These results may prove beneficial for designing therapeutic interventions for persons with Parkinson's disease.

  14. Repetitive fueling pellet injection in large helical device

    International Nuclear Information System (INIS)

    Yamada, H.; Sakamoto, R.; Viniar, I.; Oda, Y.; Kikuchi, K.; Lukin, A.; Skoblikov, S.; Umov, A.; Takaura, K.; Onozuka, M.; Kato, S.; Sudo, S.

    2003-01-01

    A repetitive pellet injector has been developed for investigation of fueling issues towards the steady-state operation in Large Helical Device (LHD). The goal of this approach is achievement of the plasma operation for longer than 1000 s. A principal technical element of the pellet injector is solidification of hydrogen and extrusion of a solid hydrogen rod through a cryogenic screw extruder cooled by Giffard-McMahon (GM) cryo-coolers. Continuous operation of more than 10000 pellet launches at 10 Hz has been demonstrated. The reliability of pellet launch exceeds 99%. The pellet mass and velocity, the consumption of propellant gas and quality of pellets have been successfully tested to fit the experimental requirement in LHD

  15. Repetitive fueling pellet injection in large helical device

    Energy Technology Data Exchange (ETDEWEB)

    Yamada, H. E-mail: hyamada@lhd.nifs.ac.jp; Sakamoto, R.; Viniar, I.; Oda, Y.; Kikuchi, K.; Lukin, A.; Skoblikov, S.; Umov, A.; Takaura, K.; Onozuka, M.; Kato, S.; Sudo, S

    2003-09-01

    A repetitive pellet injector has been developed for investigation of fueling issues towards the steady-state operation in Large Helical Device (LHD). The goal of this approach is achievement of the plasma operation for longer than 1000 s. A principal technical element of the pellet injector is solidification of hydrogen and extrusion of a solid hydrogen rod through a cryogenic screw extruder cooled by Giffard-McMahon (GM) cryo-coolers. Continuous operation of more than 10000 pellet launches at 10 Hz has been demonstrated. The reliability of pellet launch exceeds 99%. The pellet mass and velocity, the consumption of propellant gas and quality of pellets have been successfully tested to fit the experimental requirement in LHD.

  16. BANSHEE: High-voltage repetitively pulsed electron-beam driver

    International Nuclear Information System (INIS)

    VanHaaften, F.

    1992-01-01

    BANSHEE (Beam Accelerator for a New Source of High-Energy Electrons) this is a high-voltage modulator is used to produce a high-current relativistic electron beam for high-power microwave tube development. The goal of the BANSHEE research is first to achieve a voltage pulse of 700--750 kV with a 1-μs pulse width driving a load of ∼100 Ω, the pulse repetition frequency (PRF) of a few hertz. The ensuing goal is to increase the pulse amplitude to a level approaching 1 MV. We conducted tests using half the modulator with an output load of 200 Ω, up to a level of ∼650 kV at a PRF of 1 Hz and 525 kV at a PRF of 5 Hz. We then conducted additional testing using the complete system driving a load of ∼100 Ω

  17. Repetition rates in heavy ion beam driven fusion reactors

    Science.gov (United States)

    Peterson, Robert R.

    1986-01-01

    The limits on the cavity gas density required for beam propagation and condensation times for material vaporized by target explosions can determine the maximum repetition rate of Heavy Ion Beam (HIB) driven fusion reactors. If the ions are ballistically focused onto the target, the cavity gas must have a density below roughly 10-4 torr (3×1012 cm-3) at the time of propagation; other propagation schemes may allow densities as high as 1 torr or more. In some reactor designs, several kilograms of material may be vaporized off of the target chamber walls by the target generated x-rays, raising the average density in the cavity to 100 tor or more. A one-dimensional combined radiation hydrodynamics and vaporization and condensation computer code has been used to simulate the behavior of the vaporized material in the target chambers of HIB fusion reactors.

  18. Repetition rates in heavy ion beam driven fusion reactors

    International Nuclear Information System (INIS)

    Peterson, R.R.

    1986-01-01

    The limits on the cavity gas density required for beam propagation and condensation times for material vaporized by target explosions can determine the maximum repetition rate of Heavy Ion Beam (HIB) driven fusion reactors. If the ions are ballistically focused onto the target, the cavity gas must have a density below roughly 10 -4 torr (3 x 10 12 cm -3 ) at the time of propagation; other propagation schemes may allow densities as high as 1 torr or more. In some reactor designs, several kilograms of material may be vaporized off of the target chamber walls by the target generated x-rays, raising the average density in the cavity to 100 tor or more. A one-dimensional combined radiation hydrodynamics and vaporization and condensation computer code has been used to simulate the behavior of the vaporized material in the target chambers of HIB fusion reactors

  19. On the non-Poissonian repetition pattern of FRB121102

    Science.gov (United States)

    Oppermann, Niels; Yu, Hao-Ran; Pen, Ue-Li

    2018-04-01

    The Fast Radio Burst FRB121102 has been observed to repeat in an irregular fashion. Using published timing data of the observed bursts, we show that Poissonian statistics are not a good description of this random process. As an alternative, we suggest to describe the intervals between bursts with a Weibull distribution with a shape parameter smaller than one, which allows for the clustered nature of the bursts. We quantify the amount of clustering using the parameters of the Weibull distribution and discuss the consequences that it has for the detection probabilities of future observations and for the optimization of observing strategies. Allowing for this generalization, we find a mean repetition rate of r=5.7^{+3.0}_{-2.0} per day and index k=0.34^{+0.06}_{-0.05} for a correlation function ξ(t) = (t/t0)k - 1.

  20. Dose Measurements in a 20-J Repetitive Plasma Focus

    Science.gov (United States)

    Goudarzi, S.; Babaee, H.; Esmaeli, A.; Nasiri, A.; Mazandarani, A.

    2018-02-01

    In this article, the results of X-ray dose measurements executed using thermoluminescent dosimeters in experiments with a very small (20 J) repetitive plasma focus device named SORENA-1 are presented and analyzed. The working gas in these experiments was Argon. Also, pinch formation in experiments with this device has been observed. This device has been designed and constructed in Plasma and Nuclear Fusion Research School of Nuclear Science and Technology Research Institute of Iran. From these results, it is concluded that we can do experiments with this device using Ar as working gas all over the working days of year, and a good symmetry for measured dose around the device has been seen.