WorldWideScience

Sample records for replication timing patterns

  1. The Cell Cycle Timing of Human Papillomavirus DNA Replication.

    Science.gov (United States)

    Reinson, Tormi; Henno, Liisi; Toots, Mart; Ustav, Mart; Ustav, Mart

    2015-01-01

    Viruses manipulate the cell cycle of the host cell to optimize conditions for more efficient viral genome replication. One strategy utilized by DNA viruses is to replicate their genomes non-concurrently with the host genome; in this case, the viral genome is amplified outside S phase. This phenomenon has also been described for human papillomavirus (HPV) vegetative genome replication, which occurs in G2-arrested cells; however, the precise timing of viral DNA replication during initial and stable replication phases has not been studied. We developed a new method to quantitate newly synthesized DNA levels and used this method in combination with cell cycle synchronization to show that viral DNA replication is initiated during S phase and is extended to G2 during initial amplification but follows the replication pattern of cellular DNA during S phase in the stable maintenance phase. E1 and E2 protein overexpression changes the replication time from S only to both the S and G2 phases in cells that stably maintain viral episomes. These data demonstrate that the active synthesis and replication of the HPV genome are extended into the G2 phase to amplify its copy number and the duration of HPV genome replication is controlled by the level of the viral replication proteins E1 and E2. Using the G2 phase for genome amplification may be an important adaptation that allows exploitation of changing cellular conditions during cell cycle progression. We also describe a new method to quantify newly synthesized viral DNA levels and discuss its benefits for HPV research.

  2. Late-replicating X-chromosome: replication patterns in mammalian females

    Directory of Open Access Journals (Sweden)

    Tunin Karen

    2002-01-01

    Full Text Available The GTG-banding and 5-BrdU incorporation patterns of the late-replicating X-chromosome were studied in female dogs and cattle, and compared to human female patterns. The replication patterns of the short arm of the X-chromosomes did not show any difference between human, dog and cattle females. As to the long arm, some bands showed differences among the three studied species regarding the replication kinetics pattern. These differences were observed in a restricted region of the X-chromosome, delimited by Xq11 -> q25 in humans, by Xq1 -> q8 in dogs, and by Xq12 -> q32 in cattle. In an attempt to find out if these differences in the replication kinetics could be a reflection of differences in the localization of genes in that region of the X-chromosome, we used the probe for the human androgen receptor gene (AR localized at Xq12, which is in the region where we observed differences among the three studied species. We did not, however, observe hybridization signals. Our study goes on, using other human probes for genes located in the region Xq11 -> Xq25.

  3. A replication-time-controlling sequence element in Schizosaccharomyces pombe.

    Science.gov (United States)

    Tripathi, Vishnu P; Dubey, Dharani D

    2017-08-01

    Eukaryotic replication origins are highly variable in their activity and replication timing. The nature and role of cis-acting regulatory sequences that control chromosomal replication timing is not well defined. In the fission yeast, Schizosaccharomyces pombe, a 200-bp late-replication-enforcing element (LRE), has been shown to enforce late replication of ARS elements in plasmids. Here, we show that a short (133-bp) fragment of the LRE (shLRE) is required for causing late replication of adjoining origins in its native as well as in an ectopic early-replicating chromosomal location. Active from both sides of an early-replicating origin, the shLRE is a bona fide cis-acting regulatory element that imposes late replication timing in the chromosome.

  4. On the scattering of DNA replication completion times

    Science.gov (United States)

    Meilikhov, E. Z.; Farzetdinova, R. M.

    2015-07-01

    Stochasticity of Eukaryotes' DNA replication should not lead to large fluctuations of replication times, which could result in mitotic catastrophes. Fundamental problem that cells face is how to be ensured that entire genome is replicated on time. We develop analytic approach of calculating DNA replication times, that being simplified and approximate, leads, nevertheless, to results practically coincident with those that were obtained by some sophisticated methods. In the framework of that model we consider replication times' scattering and discuss the influence of repair stopping on kinetics of DNA replication. Our main explicit formulae for DNA replication time t r ∝ ( N is the total number of DNA base pairs) is of general character and explains basic features of DNA replication kinetics.

  5. ReplicationDomain: a visualization tool and comparative database for genome-wide replication timing data

    Directory of Open Access Journals (Sweden)

    Yokochi Tomoki

    2008-12-01

    Full Text Available Abstract Background Eukaryotic DNA replication is regulated at the level of large chromosomal domains (0.5–5 megabases in mammals within which replicons are activated relatively synchronously. These domains replicate in a specific temporal order during S-phase and our genome-wide analyses of replication timing have demonstrated that this temporal order of domain replication is a stable property of specific cell types. Results We have developed ReplicationDomain http://www.replicationdomain.org as a web-based database for analysis of genome-wide replication timing maps (replication profiles from various cell lines and species. This database also provides comparative information of transcriptional expression and is configured to display any genome-wide property (for instance, ChIP-Chip or ChIP-Seq data via an interactive web interface. Our published microarray data sets are publicly available. Users may graphically display these data sets for a selected genomic region and download the data displayed as text files, or alternatively, download complete genome-wide data sets. Furthermore, we have implemented a user registration system that allows registered users to upload their own data sets. Upon uploading, registered users may choose to: (1 view their data sets privately without sharing; (2 share with other registered users; or (3 make their published or "in press" data sets publicly available, which can fulfill journal and funding agencies' requirements for data sharing. Conclusion ReplicationDomain is a novel and powerful tool to facilitate the comparative visualization of replication timing in various cell types as well as other genome-wide chromatin features and is considerably faster and more convenient than existing browsers when viewing multi-megabase segments of chromosomes. Furthermore, the data upload function with the option of private viewing or sharing of data sets between registered users should be a valuable resource for the

  6. Replication timing: a fingerprint for cell identity and pluripotency.

    Directory of Open Access Journals (Sweden)

    Tyrone Ryba

    2011-10-01

    Full Text Available Many types of epigenetic profiling have been used to classify stem cells, stages of cellular differentiation, and cancer subtypes. Existing methods focus on local chromatin features such as DNA methylation and histone modifications that require extensive analysis for genome-wide coverage. Replication timing has emerged as a highly stable cell type-specific epigenetic feature that is regulated at the megabase-level and is easily and comprehensively analyzed genome-wide. Here, we describe a cell classification method using 67 individual replication profiles from 34 mouse and human cell lines and stem cell-derived tissues, including new data for mesendoderm, definitive endoderm, mesoderm and smooth muscle. Using a Monte-Carlo approach for selecting features of replication profiles conserved in each cell type, we identify "replication timing fingerprints" unique to each cell type and apply a k nearest neighbor approach to predict known and unknown cell types. Our method correctly classifies 67/67 independent replication-timing profiles, including those derived from closely related intermediate stages. We also apply this method to derive fingerprints for pluripotency in human and mouse cells. Interestingly, the mouse pluripotency fingerprint overlaps almost completely with previously identified genomic segments that switch from early to late replication as pluripotency is lost. Thereafter, replication timing and transcription within these regions become difficult to reprogram back to pluripotency, suggesting these regions highlight an epigenetic barrier to reprogramming. In addition, the major histone cluster Hist1 consistently becomes later replicating in committed cell types, and several histone H1 genes in this cluster are downregulated during differentiation, suggesting a possible instrument for the chromatin compaction observed during differentiation. Finally, we demonstrate that unknown samples can be classified independently using site

  7. Self-Replication of Nanoscale tiles and patterns

    Science.gov (United States)

    Chaikin, Paul

    2012-02-01

    We want to make a ``non-biological'' system which can self-replicate. The idea is to design particles with specific and reversible and irreversible interactions, introduce seed motifs, and cycle the system in such a way that a copy is made. Repeating the cycle would double the number of offspring in each generation leading to exponential growth. Using the chemistry of DNA either on colloids or on DNA tiles makes the specific recognition part easy. In the case of DNA tiles we have in fact replicated the seed at least to the third generation. The DNA linkers can also be self-protected so that particles don't interact unless they are held together for sufficient time -- a nano-contact glue. Chemical modification of the DNA allows us to permanently crosslink hybridized strands for irreversible bonds and a new type of photolithography. We have also designed and produced colloidal particles that use novel ``lock and key'' geometries to get specific and reversible physical interactions.[4pt] With Tong Wang, Ruojie Sha, Remi Dreyfus, Mirjam E. Leunissen, Corinna Maass, David J. Pine, and Nadrian C. Seeman.

  8. Defining multiple, distinct, and shared spatiotemporal patterns of DNA replication and endoreduplication from 3D image analysis of developing maize (Zea mays L.) root tip nuclei.

    Science.gov (United States)

    Bass, Hank W; Hoffman, Gregg G; Lee, Tae-Jin; Wear, Emily E; Joseph, Stacey R; Allen, George C; Hanley-Bowdoin, Linda; Thompson, William F

    2015-11-01

    Spatiotemporal patterns of DNA replication have been described for yeast and many types of cultured animal cells, frequently after cell cycle arrest to aid in synchronization. However, patterns of DNA replication in nuclei from plants or naturally developing organs remain largely uncharacterized. Here we report findings from 3D quantitative analysis of DNA replication and endoreduplication in nuclei from pulse-labeled developing maize root tips. In both early and middle S phase nuclei, flow-sorted on the basis of DNA content, replicative labeling was widely distributed across euchromatic regions of the nucleoplasm. We did not observe the perinuclear or perinucleolar replicative labeling patterns characteristic of middle S phase in mammals. Instead, the early versus middle S phase patterns in maize could be distinguished cytologically by correlating two quantitative, continuous variables, replicative labeling and DAPI staining. Early S nuclei exhibited widely distributed euchromatic labeling preferentially localized to regions with weak DAPI signals. Middle S nuclei also exhibited widely distributed euchromatic labeling, but the label was preferentially localized to regions with strong DAPI signals. Highly condensed heterochromatin, including knobs, replicated during late S phase as previously reported. Similar spatiotemporal replication patterns were observed for both mitotic and endocycling maize nuclei. These results revealed that maize euchromatin exists as an intermingled mixture of two components distinguished by their condensation state and replication timing. These different patterns might reflect a previously described genome organization pattern, with "gene islands" mostly replicating during early S phase followed by most of the intergenic repetitive regions replicating during middle S phase.

  9. Evidence for sequential and increasing activation of replication origins along replication timing gradients in the human genome.

    Science.gov (United States)

    Guilbaud, Guillaume; Rappailles, Aurélien; Baker, Antoine; Chen, Chun-Long; Arneodo, Alain; Goldar, Arach; d'Aubenton-Carafa, Yves; Thermes, Claude; Audit, Benjamin; Hyrien, Olivier

    2011-12-01

    Genome-wide replication timing studies have suggested that mammalian chromosomes consist of megabase-scale domains of coordinated origin firing separated by large originless transition regions. Here, we report a quantitative genome-wide analysis of DNA replication kinetics in several human cell types that contradicts this view. DNA combing in HeLa cells sorted into four temporal compartments of S phase shows that replication origins are spaced at 40 kb intervals and fire as small clusters whose synchrony increases during S phase and that replication fork velocity (mean 0.7 kb/min, maximum 2.0 kb/min) remains constant and narrowly distributed through S phase. However, multi-scale analysis of a genome-wide replication timing profile shows a broad distribution of replication timing gradients with practically no regions larger than 100 kb replicating at less than 2 kb/min. Therefore, HeLa cells lack large regions of unidirectional fork progression. Temporal transition regions are replicated by sequential activation of origins at a rate that increases during S phase and replication timing gradients are set by the delay and the spacing between successive origin firings rather than by the velocity of single forks. Activation of internal origins in a specific temporal transition region is directly demonstrated by DNA combing of the IGH locus in HeLa cells. Analysis of published origin maps in HeLa cells and published replication timing and DNA combing data in several other cell types corroborate these findings, with the interesting exception of embryonic stem cells where regions of unidirectional fork progression seem more abundant. These results can be explained if origins fire independently of each other but under the control of long-range chromatin structure, or if replication forks progressing from early origins stimulate initiation in nearby unreplicated DNA. These findings shed a new light on the replication timing program of mammalian genomes and provide a general

  10. Timing, coordination, and rhythm: Acrobatics at the DNA replication fork

    KAUST Repository

    Hamdan, Samir

    2010-04-09

    In DNA replication, the antiparallel nature of the parental duplex imposes certain constraints on the activity of the DNA polymerases that synthesize new DNA. The leading-strand polymerase advances in a continuous fashion, but the lagging-strand polymerase is forced to restart at short intervals. In several prokaryotic systems studied so far, this problem is solved by the formation of a loop in the lagging strand of the replication fork to reorient the lagging-strand DNA polymerase so that it advances in parallel with the leading-strand polymerase. The replication loop grows and shrinks during each cycle of Okazaki fragment synthesis. The timing of Okazaki fragment synthesis and loop formation is determined by a subtle interplay of enzymatic activities at the fork. Recent developments in single-molecule techniques have enabled the direct observation of these processes and have greatly contributed to a better understanding of the dynamic nature of the replication fork. Here, we will review recent experimental advances, present the current models, and discuss some of the exciting developments in the field. 2010 by The American Society for Biochemistry and Molecular Biology, Inc.

  11. Time averages, recurrence and transience in the stochastic replicator dynamics

    CERN Document Server

    Hofbauer, Josef; 10.1214/08-AAP577

    2009-01-01

    We investigate the long-run behavior of a stochastic replicator process, which describes game dynamics for a symmetric two-player game under aggregate shocks. We establish an averaging principle that relates time averages of the process and Nash equilibria of a suitably modified game. Furthermore, a sufficient condition for transience is given in terms of mixed equilibria and definiteness of the payoff matrix. We also present necessary and sufficient conditions for stochastic stability of pure equilibria.

  12. A Replication Protocol for Real Time database System

    Directory of Open Access Journals (Sweden)

    Ashish Srivastava

    2012-06-01

    Full Text Available Database replication protocols for real time system based on a certification approach are usually the best ones for achieving good performance. The weak voting approach achieves a slightly longer transaction completion time, but with a lower abortion rate. So, both techniques can be considered as the best ones for replication when performance is a must, and both of them take advantage of the properties provided by atomic broadcast. We propose a new database replication strategy that shares many characteristics with such previous strategies. It is also based on totally ordering the application of writesets, using only an unordered reliable broadcast, instead of an atomic broadcast. Additionally, the writesets of transactions that are aborted in the final validation phase along with verification phase incorporated in the new system are not broadcast in our strategy rather than only validation phase. Thus, this new approach certainly reducesc the communication traffic and also achieves a good transaction response time (even shorter than those previous strategies associated with only validation phase in some system configurations.

  13. Difference-based clustering of short time-course microarray data with replicates

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    Kim Jihoon

    2007-07-01

    Full Text Available Abstract Background There are some limitations associated with conventional clustering methods for short time-course gene expression data. The current algorithms require prior domain knowledge and do not incorporate information from replicates. Moreover, the results are not always easy to interpret biologically. Results We propose a novel algorithm for identifying a subset of genes sharing a significant temporal expression pattern when replicates are used. Our algorithm requires no prior knowledge, instead relying on an observed statistic which is based on the first and second order differences between adjacent time-points. Here, a pattern is predefined as the sequence of symbols indicating direction and the rate of change between time-points, and each gene is assigned to a cluster whose members share a similar pattern. We evaluated the performance of our algorithm to those of K-means, Self-Organizing Map and the Short Time-series Expression Miner methods. Conclusions Assessments using simulated and real data show that our method outperformed aforementioned algorithms. Our approach is an appropriate solution for clustering short time-course microarray data with replicates.

  14. Rif1 Regulates Initiation Timing of Late Replication Origins throughout the S. cerevisiae Genome

    OpenAIRE

    Peace, Jared M.; Anna Ter-Zakarian; Aparicio, Oscar M

    2014-01-01

    Chromosomal DNA replication involves the coordinated activity of hundreds to thousands of replication origins. Individual replication origins are subject to epigenetic regulation of their activity during S-phase, resulting in differential efficiencies and timings of replication initiation during S-phase. This regulation is thought to involve chromatin structure and organization into timing domains with differential ability to recruit limiting replication factors. Rif1 has recently been identi...

  15. Imprinted chromosomal domains revealed by allele-specific replication timing of the GABRB3 and GABRA5 genes

    Energy Technology Data Exchange (ETDEWEB)

    LaSalle, J.; Flint, A.; Lalande, M. [Harvard Medical School, Boston, MA (United States)] [and others

    1994-09-01

    The GABRB3 and GABRA5 genes are organized as a cluster in chromosome 15q11-q13. The genes are separated by around 100 kb and arranged in opposite transcriptional orientations. The GABA{sub A} receptor cluster lies near the Angelman and Prader-Willi loci and displays asynchronous DNA replication, suggesting that this region is subject to parental imprinting. In order to further study the association between DNA replication and imprinting, allele-specific replication was assayed by fluorescence in situ hybridization with {lambda}-phage probes from the GABRB3/A5 region and a D15Z1 satellite probe to identify the parental origin of each chromosome. The replication kinetics of each allele was determined by using a flow sorter to fractionate mitogen-stimulated lymphocytes on the basis of cell cycle progression prior to FISH analysis. These kinetic studies reveal a 50-150 kb chromosomal domain extending from the middle of the GABRB3/A5 intergenic region into the GABRA5 5{prime}-UTR which displays maternal replication in early S with paternal replication delayed until the end of S. In contrast, genomic regions on either side of this maternal early replication domain exhibit the opposite pattern with paternal before maternal replication and both alleles replicating in the latter half of S. These results indicate that the GABRB3/A5 region is divided into domains in which replication timing is determined by parental origin. In addition to a loss of asynchronous replication, organization into replication timing domains is also lost in lymphocytes from maternal and paternal uniparental disomy 15 patients suggesting that a chromosome contribution from both parents is required for the establishment of the imprinted replication domains.

  16. DNA replication origin activation in space and time.

    Science.gov (United States)

    Fragkos, Michalis; Ganier, Olivier; Coulombe, Philippe; Méchali, Marcel

    2015-06-01

    DNA replication begins with the assembly of pre-replication complexes (pre-RCs) at thousands of DNA replication origins during the G1 phase of the cell cycle. At the G1-S-phase transition, pre-RCs are converted into pre-initiation complexes, in which the replicative helicase is activated, leading to DNA unwinding and initiation of DNA synthesis. However, only a subset of origins are activated during any S phase. Recent insights into the mechanisms underlying this choice reveal how flexibility in origin usage and temporal activation are linked to chromosome structure and organization, cell growth and differentiation, and replication stress.

  17. On the replication of genetic associations: timing can be everything!

    Science.gov (United States)

    Lasky-Su, Jessica; Lyon, Helen N; Emilsson, Valur; Heid, Iris M; Molony, Cliona; Raby, Benjamin A; Lazarus, Ross; Klanderman, Barbara; Soto-Quiros, Manuel E; Avila, Lydiana; Silverman, Edwin K; Thorleifsson, Gudmar; Thorsteinsdottir, Unnur; Kronenberg, Florian; Vollmert, Caren; Illig, Thomas; Fox, Caroline S; Levy, Daniel; Laird, Nan; Ding, Xiao; McQueen, Matt B; Butler, Johannah; Ardlie, Kristin; Papoutsakis, Constantina; Dedoussis, George; O'Donnell, Christopher J; Wichmann, H-Erich; Celedón, Juan C; Schadt, Eric; Hirschhorn, Joel; Weiss, Scott T; Stefansson, Kari; Lange, Christoph

    2008-04-01

    The failure of researchers to replicate genetic-association findings is most commonly attributed to insufficient statistical power, population stratification, or various forms of between-study heterogeneity or environmental influences.(1) Here, we illustrate another potential cause for nonreplications that has so far not received much attention in the literature. We illustrate that the strength of a genetic effect can vary by age, causing "age-varying associations." If not taken into account during the design and the analysis of a study, age-varying genetic associations can cause nonreplication. By using the 100K SNP scan of the Framingham Heart Study, we identified an age-varying association between a SNP in ROBO1 and obesity and hypothesized an age-gene interaction. This finding was followed up in eight independent samples comprising 13,584 individuals. The association was replicated in five of the eight studies, showing an age-dependent relationship (one-sided combined p = 3.92 x 10(-9), combined p value from pediatric cohorts = 2.21 x 10(-8), combined p value from adult cohorts = 0.00422). Furthermore, this study illustrates that it is difficult for cross-sectional study designs to detect age-varying associations. If the specifics of age- or time-varying genetic effects are not considered in the selection of both the follow-up samples and in the statistical analysis, important genetic associations may be missed.

  18. Replication of patterned thin-film structures for use in plasmonics and metamaterials

    Science.gov (United States)

    Norris, David J; Han, Sang Eon; Bhan, Aditya; Nagpal, Prashant; Lindquist, Nathan Charles; Oh, Sang-Hyun

    2015-02-03

    The present invention provides templating methods for replicating patterned metal films from a template substrate such as for use in plasmonic devices and metamaterials. Advantageously, the template substrate is reusable and can provide plural copies of the structure of the template substrate. Because high-quality substrates that are inherently smooth and flat are available, patterned metal films in accordance with the present invention can advantageously provide surfaces that replicate the surface characteristics of the template substrate both in the patterned regions and in the unpatterned regions.

  19. Exonuclease mutations in DNA polymerase epsilon reveal replication strand specific mutation patterns and human origins of replication.

    Science.gov (United States)

    Shinbrot, Eve; Henninger, Erin E; Weinhold, Nils; Covington, Kyle R; Göksenin, A Yasemin; Schultz, Nikolaus; Chao, Hsu; Doddapaneni, HarshaVardhan; Muzny, Donna M; Gibbs, Richard A; Sander, Chris; Pursell, Zachary F; Wheeler, David A

    2014-11-01

    Tumors with somatic mutations in the proofreading exonuclease domain of DNA polymerase epsilon (POLE-exo*) exhibit a novel mutator phenotype, with markedly elevated TCT→TAT and TCG→TTG mutations and overall mutation frequencies often exceeding 100 mutations/Mb. Here, we identify POLE-exo* tumors in numerous cancers and classify them into two groups, A and B, according to their mutational properties. Group A mutants are found only in POLE, whereas Group B mutants are found in POLE and POLD1 and appear to be nonfunctional. In Group A, cell-free polymerase assays confirm that mutations in the exonuclease domain result in high mutation frequencies with a preference for C→A mutation. We describe the patterns of amino acid substitutions caused by POLE-exo* and compare them to other tumor types. The nucleotide preference of POLE-exo* leads to increased frequencies of recurrent nonsense mutations in key tumor suppressors such as TP53, ATM, and PIK3R1. We further demonstrate that strand-specific mutation patterns arise from some of these POLE-exo* mutants during genome duplication. This is the first direct proof of leading strand-specific replication by human POLE, which has only been demonstrated in yeast so far. Taken together, the extremely high mutation frequency and strand specificity of mutations provide a unique identifier of eukaryotic origins of replication.

  20. Uncovering the genetic signature of quantitative trait evolution with replicated time series data.

    Science.gov (United States)

    Franssen, S U; Kofler, R; Schlötterer, C

    2017-01-01

    The genetic architecture of adaptation in natural populations has not yet been resolved: it is not clear to what extent the spread of beneficial mutations (selective sweeps) or the response of many quantitative trait loci drive adaptation to environmental changes. Although much attention has been given to the genomic footprint of selective sweeps, the importance of selection on quantitative traits is still not well studied, as the associated genomic signature is extremely difficult to detect. We propose 'Evolve and Resequence' as a promising tool, to study polygenic adaptation of quantitative traits in evolving populations. Simulating replicated time series data we show that adaptation to a new intermediate trait optimum has three characteristic phases that are reflected on the genomic level: (1) directional frequency changes towards the new trait optimum, (2) plateauing of allele frequencies when the new trait optimum has been reached and (3) subsequent divergence between replicated trajectories ultimately leading to the loss or fixation of alleles while the trait value does not change. We explore these 3 phase characteristics for relevant population genetic parameters to provide expectations for various experimental evolution designs. Remarkably, over a broad range of parameters the trajectories of selected alleles display a pattern across replicates, which differs both from neutrality and directional selection. We conclude that replicated time series data from experimental evolution studies provide a promising framework to study polygenic adaptation from whole-genome population genetics data.

  1. Use of lymphocyte cultures for BrdU replication banding patterns in anuran species (Amphibia

    Directory of Open Access Journals (Sweden)

    Kasahara Sanae

    1998-01-01

    Full Text Available We describe the standardization of lymphocyte culture procedures in order to improve cytological preparations of anuran species. This methodology permits the use of 5-bromodeoxyuridine (BrdU treatment to obtain replication banding patterns in the chromosomes of these species.

  2. Crystallographic orientation-dependent pattern replication in direct imprint of aluminum nanostructures

    OpenAIRE

    2015-01-01

    In the present work, we perform molecular dynamics simulations corroborated by experimental validations to elucidate the underlying deformation mechanisms of single-crystalline aluminum under direct imprint using a rigid silicon master. We investigate the influence of crystallographic orientation on the microscopic deformation behavior of the substrate materials and its correlation with the macroscopic pattern replications. Furthermore, the surface mechanical properties of the patterned struc...

  3. Replication Banding Patterns in Human Chromosomes Detected Using 5-ethynyl-2'-deoxyuridine Incorporation

    OpenAIRE

    Hoshi, Osamu; Ushiki, Tatsuo

    2011-01-01

    A novel technique using the incorporation of 5-ethynyl-2'-deoxyuridine (EdU) into replicating DNA is described for the analysis of replicating banding patterns of human metaphase chromosomes. Human lymphocytes were synchronized with excess thymidine and treated with EdU during the late S phase of the cell cycle. The incorporated EdU was then detected in metaphase chromosomes using Alexa Fluor® 488 azides, through the 1,3-dipolar cycloaddition reaction of organic azides with the terminal acety...

  4. Replication Banding Patterns in Human Chromosomes Detected Using 5-ethynyl-2'-deoxyuridine Incorporation.

    Science.gov (United States)

    Hoshi, Osamu; Ushiki, Tatsuo

    2011-10-26

    A novel technique using the incorporation of 5-ethynyl-2'-deoxyuridine (EdU) into replicating DNA is described for the analysis of replicating banding patterns of human metaphase chromosomes. Human lymphocytes were synchronized with excess thymidine and treated with EdU during the late S phase of the cell cycle. The incorporated EdU was then detected in metaphase chromosomes using Alexa Fluor® 488 azides, through the 1,3-dipolar cycloaddition reaction of organic azides with the terminal acetylene group of EdU. Chromosomes with incorporated EdU showed a banding pattern similar to G-banding of normal human chromosomes. Imaging by atomic force microscopy (AFM) in liquid conditions showed that the structure of the chromosomes was well preserved even after EdU treatment. Comparison between fluorescence microscopy and AFM images of the same chromosome 1 indicated the presence of ridges and grooves in the chromatid arm, features that have been previously reported in relation to G-banding. These results suggest an intimate relationship between EdU-induced replication bands and G- or R-bands in human chromosomes. This technique is thus useful for analyzing the structure of chromosomes in relation to their banding patterns following DNA replication in the S phase.

  5. Rif1 regulates initiation timing of late replication origins throughout the S. cerevisiae genome.

    Directory of Open Access Journals (Sweden)

    Jared M Peace

    Full Text Available Chromosomal DNA replication involves the coordinated activity of hundreds to thousands of replication origins. Individual replication origins are subject to epigenetic regulation of their activity during S-phase, resulting in differential efficiencies and timings of replication initiation during S-phase. This regulation is thought to involve chromatin structure and organization into timing domains with differential ability to recruit limiting replication factors. Rif1 has recently been identified as a genome-wide regulator of replication timing in fission yeast and in mammalian cells. However, previous studies in budding yeast have suggested that Rif1's role in controlling replication timing may be limited to subtelomeric domains and derives from its established role in telomere length regulation. We have analyzed replication timing by analyzing BrdU incorporation genome-wide, and report that Rif1 regulates the timing of late/dormant replication origins throughout the S. cerevisiae genome. Analysis of pfa4Δ cells, which are defective in palmitoylation and membrane association of Rif1, suggests that replication timing regulation by Rif1 is independent of its role in localizing telomeres to the nuclear periphery. Intra-S checkpoint signaling is intact in rif1Δ cells, and checkpoint-defective mec1Δ cells do not comparably deregulate replication timing, together indicating that Rif1 regulates replication timing through a mechanism independent of this checkpoint. Our results indicate that the Rif1 mechanism regulates origin timing irrespective of proximity to a chromosome end, and suggest instead that telomere sequences merely provide abundant binding sites for proteins that recruit Rif1. Still, the abundance of Rif1 binding in telomeric domains may facilitate Rif1-mediated repression of non-telomeric origins that are more distal from centromeres.

  6. Analysis of spatial correlations between patterns of DNA damage response and DNA replication in nuclei of cells subjected to replication stress or oxidative damage.

    Science.gov (United States)

    Bernas, Tytus; Berniak, Krzysztof; Rybak, Paulina; Zarębski, Mirosław; Zhao, Hong; Darzynkiewicz, Zbigniew; Dobrucki, Jerzy W

    2013-10-01

    Sites of DNA replication (EdU incorporation) and DNA damage signaling (γH2AX) induced by camptothecin (Cpt) or hydrogen peroxide (H2O2) form characteristic patterns of foci in cell nuclei. The overlap between these patterns is a function of the number of DNA double strand breaks (DSBs) formed in replication sites. The goal of this study was to optimize a method of quantitative assessment of a degree of correlation between these two patterns. Such a correlation can be used to estimate a probability of inducing damage in sections of replicating DNA. The damage and replication foci are imaged in 3D with confocal microscopy and their respective positions within nuclei are determined with adaptive image segmentation. Using correlation functions spatial proximity of the resultant point patterns is quantified over the range of distances in cells in early-, mid- and late S-phase. As the numbers (and nuclear densities) of γH2AX and replication foci differ significantly in the subsequent substages of S phase, the detected association values were corrected for the expected random overlap between both classes of foci. Thus, the probability of their nonrandom association was estimated. Moreover, self association (clustering) of DNA replication sites in different stages of S-phase of the cell cycle was detected and accounted for. While the analysis revealed a strong correlation between the γH2AX foci and the sites of DNA replication in cells treated with Cpt, only a low correlation was apparent in cells exposed to H2O2. © 2013 International Society for Advancement of Cytometry.

  7. Technology for fabricating micro-lens arrays utilizing lithographically replicated concave resist patterns

    Science.gov (United States)

    Kobayashi, Noa; Sasaki, Ryunosuke; Horiuchi, Toshiyuki

    2016-05-01

    Lithography has been generally used for printing two-dimensional patterns on flat wafers. Recently, however, it is also applied to a three-dimensional patterning for fabricating various MEMS (Micro Electro Mechanical Systems) components. The purpose of this research is to develop a new method for fabricating micro-lens arrays. At first, resist (Tokyo Ohka Kogyo, PMER LA-900PM) mold patterns with densely arrayed square or hexagonal concaves were replicated by intentionally shifting the focal position of projection exposure. The size of resist-mold was 2 mm square, and the initial thickness of the resist was 10 μm. Next, the wafer with the concave resist patterns was cut into small chips, and each wafer chip was fixed at the bottom of a paper cup using an adhesive tape. Then the epoxy resin (Nissin resin, Crystal resin Neo) was poured on the concave resist-mold patterns, and the resin was coagulated. Afterward, the hardened resin was grooved along the wafer chip using a cutter knife, and the wafer chip with the resist-mold patterns was forcibly removed using a pair of tweezers. Finally, both sides of the resin block were polished, and the thickness was reduced. Although the transparency and roughness of the resin block surfaces should be improved, epoxy micro-lens arrays were certainly fabricated. The mean values of curvature radius and lens height were 28.3μm and 4.9 μm, respectively.

  8. Global profiling of DNA replication timing and efficiency reveals that efficient replication/firing occurs late during S-phase in S. pombe.

    Directory of Open Access Journals (Sweden)

    Majid Eshaghi

    Full Text Available BACKGROUND: During S. pombe S-phase, initiation of DNA replication occurs at multiple sites (origins that are enriched with AT-rich sequences, at various times. Current studies of genome-wide DNA replication profiles have focused on the DNA replication timing and origin location. However, the replication and/or firing efficiency of the individual origins on the genomic scale remain unclear. METHODOLOGY/PRINCIPAL FINDINGS: Using the genome-wide ORF-specific DNA microarray analysis, we show that in S. pombe, individual origins fire with varying efficiencies and at different times during S-phase. The increase in DNA copy number plotted as a function of time is approximated to the near-sigmoidal model, when considering the replication start and end timings at individual loci in cells released from HU-arrest. Replication efficiencies differ from origin to origin, depending on the origin's firing efficiency. We have found that DNA replication is inefficient early in S-phase, due to inefficient firing at origins. Efficient replication occurs later, attributed to efficient but late-firing origins. Furthermore, profiles of replication timing in cds1Delta cells are abnormal, due to the failure in resuming replication at the collapsed forks. The majority of the inefficient origins, but not the efficient ones, are found to fire in cds1Delta cells after HU removal, owing to the firing at the remaining unused (inefficient origins during HU treatment. CONCLUSIONS/SIGNIFICANCE: Taken together, our results indicate that efficient DNA replication/firing occurs late in S-phase progression in cells after HU removal, due to efficient late-firing origins. Additionally, checkpoint kinase Cds1p is required for maintaining the efficient replication/firing late in S-phase. We further propose that efficient late-firing origins are essential for ensuring completion of DNA duplication by the end of S-phase.

  9. Youth spare time: Typical patterns of behavior

    Directory of Open Access Journals (Sweden)

    Stepanović Ivana

    2009-01-01

    Full Text Available In this research we have tried to identify typical patterns of young people's behavior in their spare time and to use these patterns in order to group our subjects regarding their interests and preferences. Main-component analysis showed that it was possible to find different patterns of secondary school students' behavior in spare time as well as that the identified models could be the criteria for grouping them. Five patterns have been identified describing youth orientations towards their free time: academic orientation, orientation towards sports, orientation towards entertainment, orientation towards spending time going out and orientation towards music and computers.

  10. Multiprocessor Real-Time Locking Protocols for Replicated Resources

    Science.gov (United States)

    2016-07-01

    Unnecessary s- blocking can be reduced by employing a cutting-ahead mechanism [8] that sometimes allows a newly issued re- quest to be ordered before...of replicas re- quested and released, respectively, up to the current time. These counters are updated atomically using fetch&add in- structions.4 As...than blocking, pro - vided we are able to reap the benfits of rare blocking analyt- ically. In particular, if worst-case s-blocking is pessimisti- cally

  11. CIRS: A State-Conscious Concurrency Control Protocol for Replicated Real-Time Databases

    Directory of Open Access Journals (Sweden)

    Vishal Pathak,

    2011-01-01

    Full Text Available Replication [5] is the technique of using multiple copies of a server or a resource for better availability and performance.Each copy is called a replica. The main goal of replication is to improve availability, since a service is available even if some of its replicas are not. This helps mission critical services, such as many financial systems or reservation systems, where even a short outage can be very disruptive and expensive.A prerequisite for realizing the banefits of replication, however, is the devlopement of high erformance concurrency machenism. Current applications, such as Web-based services, electronic commerce, mobile telecommunication system, etc., are distributed in nature and manipulate time-critical databases. In order to enhance the performance and the availability of such applications, one of the main techniques is to replicate data on multiple sites of the network. Therefore, the major issue is to develop efficient replica concurrency control protocols that are able to tolerate the overload of the distributed system. In fact, if the system is not designed to handle overloads, the effects can be catastrophic and some primordial transactions of the application can miss their deadlines. In this paper we present CIRS (Concurrency control In Replicated realtime Systems a state conscious concurrency control protocol in replicated distributed environment which is specially for firm realtime database system. CIRS mechanism uses S2PL (Static Two Phase Locking for deadlock free environment.It also includes veto power given to a cohort after receiving PREPARE message from its coordinator. Also with some more assumptions like sending an extra message in execution phase but after completionof execution at local copy which is described later in this paper the proposed mechanism has a significant increased performance over O2PL and MIRROR in decreasing execution time of the current transaction and it also decreases the waiting time of

  12. The Cultural Pattern of Time in America

    Institute of Scientific and Technical Information of China (English)

    郑艳

    2009-01-01

    The perceptions of time are influenced by different cultural background. American undmtanding of time is typical of western countries. This paper introduces and explains American cUltural pattern, thus avoiding ~om happemng unpleasant things in the process of cross-cultural communication.

  13. Mcm10 coordinates the timely assembly and activation of the replication fork helicase

    Science.gov (United States)

    Perez-Arnaiz, Patricia; Bruck, Irina; Kaplan, Daniel L.

    2016-01-01

    Mcm10 is an essential replication factor that is required for DNA replication in eukaryotes. Two key steps in the initiation of DNA replication are the assembly and activation of Cdc45–Mcm2–7-GINS (CMG) replicative helicase. However, it is not known what coordinates helicase assembly with helicase activation. We show in this manuscript, using purified proteins from budding yeast, that Mcm10 directly interacts with the Mcm2–7 complex and Cdc45. In fact, Mcm10 recruits Cdc45 to Mcm2–7 complex in vitro. To study the role of Mcm10 in more detail in vivo we used an auxin inducible degron in which Mcm10 is degraded upon addition of auxin. We show in this manuscript that Mcm10 is required for the timely recruitment of Cdc45 and GINS recruitment to the Mcm2–7 complex in vivo during early S phase. We also found that Mcm10 stimulates Mcm2 phosphorylation by DDK in vivo and in vitro. These findings indicate that Mcm10 plays a critical role in coupling replicative helicase assembly with helicase activation. Mcm10 is first involved in the recruitment of Cdc45 to the Mcm2–7 complex. After Cdc45–Mcm2–7 complex assembly, Mcm10 promotes origin melting by stimulating DDK phosphorylation of Mcm2, which thereby leads to GINS attachment to Mcm2–7. PMID:26582917

  14. The replication timing of the amplified dihydrofolate reductase genes in the Chinese hamster ovary cell line CHOC 400.

    Science.gov (United States)

    Caddle, M S; Heintz, N H

    1990-07-16

    We have examined the timing of replication of the amplified dihydrofolate reductase genes in the methotrexate-resistant Chinese hamster ovary cell line CHOC 400 using two synchronization procedures. DNA replicated in the presence of 5-bromodeoxyuridine was collected from cells of various times during the DNA synthesis phase and the extent of replication for defined sequences was determined by Southern blotting analysis of CsCl density gradient fractions. We report that under these conditions the DHFR gene replicates throughout the course of S phase in a mode similar to the bulk of the replicated genomic DNA. This contrasts with previous data that shows the non-amplified DHFR gene replicates during the first quarter of S phase. Therefore, we conclude that gene amplification alters the replication timing of the DHFR gene in CHOC 400 cells.

  15. Identifying significant temporal variation in time course microarray data without replicates

    Directory of Open Access Journals (Sweden)

    Porter Weston

    2009-03-01

    Full Text Available Abstract Background An important component of time course microarray studies is the identification of genes that demonstrate significant time-dependent variation in their expression levels. Until recently, available methods for performing such significance tests required replicates of individual time points. This paper describes a replicate-free method that was developed as part of a study of the estrous cycle in the rat mammary gland in which no replicate data was collected. Results A temporal test statistic is proposed that is based on the degree to which data are smoothed when fit by a spline function. An algorithm is presented that uses this test statistic together with a false discovery rate method to identify genes whose expression profiles exhibit significant temporal variation. The algorithm is tested on simulated data, and is compared with another recently published replicate-free method. The simulated data consists both of genes with known temporal dependencies, and genes from a null distribution. The proposed algorithm identifies a larger percentage of the time-dependent genes for a given false discovery rate. Use of the algorithm in a study of the estrous cycle in the rat mammary gland resulted in the identification of genes exhibiting distinct circadian variation. These results were confirmed in follow-up laboratory experiments. Conclusion The proposed algorithm provides a new approach for identifying expression profiles with significant temporal variation without relying on replicates. When compared with a recently published algorithm on simulated data, the proposed algorithm appears to identify a larger percentage of time-dependent genes for a given false discovery rate. The development of the algorithm was instrumental in revealing the presence of circadian variation in the virgin rat mammary gland during the estrous cycle.

  16. Modelling of Patterns in Space and Time

    CERN Document Server

    Murray, James

    1984-01-01

    This volume contains a selection of papers presented at the work­ shop "Modelling of Patterns in Space and Time", organized by the 80nderforschungsbereich 123, "8tochastische Mathematische Modelle", in Heidelberg, July 4-8, 1983. The main aim of this workshop was to bring together physicists, chemists, biologists and mathematicians for an exchange of ideas and results in modelling patterns. Since the mathe­ matical problems arising depend only partially on the particular field of applications the interdisciplinary cooperation proved very useful. The workshop mainly treated phenomena showing spatial structures. The special areas covered were morphogenesis, growth in cell cultures, competition systems, structured populations, chemotaxis, chemical precipitation, space-time oscillations in chemical reactors, patterns in flames and fluids and mathematical methods. The discussions between experimentalists and theoreticians were especially interesting and effective. The editors hope that these proceedings reflect ...

  17. How well do CMIP5 climate simulations replicate historical trends and patterns of meteorological droughts?

    Science.gov (United States)

    Nasrollahi, Nasrin; AghaKouchak, Amir; Cheng, Linyin; Damberg, Lisa; Phillips, Thomas J.; Miao, Chiyuan; Hsu, Kuolin; Sorooshian, Soroosh

    2015-04-01

    Assessing the uncertainties and understanding the deficiencies of climate models are fundamental to developing adaptation strategies. The objective of this study is to understand how well Coupled Model Intercomparison-Phase 5 (CMIP5) climate model simulations replicate ground-based observations of continental drought areas and their trends. The CMIP5 multimodel ensemble encompasses the Climatic Research Unit (CRU) ground-based observations of area under drought at all time steps. However, most model members overestimate the areas under extreme drought, particularly in the Southern Hemisphere (SH). Furthermore, the results show that the time series of observations and CMIP5 simulations of areas under drought exhibit more variability in the SH than in the Northern Hemisphere (NH). The trend analysis of areas under drought reveals that the observational data exhibit a significant positive trend at the significance level of 0.05 over all land areas. The observed trend is reproduced by about three-fourths of the CMIP5 models when considering total land areas in drought. While models are generally consistent with observations at a global (or hemispheric) scale, most models do not agree with observed regional drying and wetting trends. Over many regions, at most 40% of the CMIP5 models are in agreement with the trends of CRU observations. The drying/wetting trends calculated using the 3 months Standardized Precipitation Index (SPI) values show better agreement with the corresponding CRU values than with the observed annual mean precipitation rates. Pixel-scale evaluation of CMIP5 models indicates that no single model demonstrates an overall superior performance relative to the other models.

  18. Replication timing of human telomeres is chromosome arm-specific, influenced by subtelomeric structures and connected to nuclear localization.

    Directory of Open Access Journals (Sweden)

    Nausica Arnoult

    2010-04-01

    Full Text Available The mechanisms governing telomere replication in humans are still poorly understood. To fill this gap, we investigated the timing of replication of single telomeres in human cells. Using in situ hybridization techniques, we have found that specific telomeres have preferential time windows for replication during the S-phase and that these intervals do not depend upon telomere length and are largely conserved between homologous chromosomes and between individuals, even in the presence of large subtelomeric segmental polymorphisms. Importantly, we show that one copy of the 3.3 kb macrosatellite repeat D4Z4, present in the subtelomeric region of the late replicating 4q35 telomere, is sufficient to confer both a more peripheral localization and a later-replicating property to a de novo formed telomere. Also, the presence of beta-satellite repeats next to a newly created telomere is sufficient to delay its replication timing. Remarkably, several native, non-D4Z4-associated, late-replicating telomeres show a preferential localization toward the nuclear periphery, while several early-replicating telomeres are associated with the inner nuclear volume. We propose that, in humans, chromosome arm-specific subtelomeric sequences may influence both the spatial distribution of telomeres in the nucleus and their replication timing.

  19. Turning the hands of time again: a purely confirmatory replication study and a Bayesian analysis.

    Science.gov (United States)

    Wagenmakers, Eric-Jan; Beek, Titia F; Rotteveel, Mark; Gierholz, Alex; Matzke, Dora; Steingroever, Helen; Ly, Alexander; Verhagen, Josine; Selker, Ravi; Sasiadek, Adam; Gronau, Quentin F; Love, Jonathon; Pinto, Yair

    2015-01-01

    In a series of four experiments, Topolinski and Sparenberg (2012) found support for the conjecture that clockwise movements induce psychological states of temporal progression and an orientation toward the future and novelty. Here we report the results of a preregistered replication attempt of Experiment 2 from Topolinski and Sparenberg (2012). Participants turned kitchen rolls either clockwise or counterclockwise while answering items from a questionnaire assessing openness to experience. Data from 102 participants showed that the effect went slightly in the direction opposite to that predicted by Topolinski and Sparenberg (2012), and a preregistered Bayes factor hypothesis test revealed that the data were 10.76 times more likely under the null hypothesis than under the alternative hypothesis. Our findings illustrate the theoretical importance and practical advantages of preregistered Bayes factor replication studies, both for psychological science and for empirical work in general.

  20. Turning the Hands of Time Again: A Purely Confirmatory Replication Study and a Bayesian Analysis

    Directory of Open Access Journals (Sweden)

    Eric-Jan eWagenmakers

    2015-04-01

    Full Text Available In a series of four experiments, Topolinski and Sparenberg (2012; TS found support for the conjecture that clockwise movements induce psychological states of temporal progression and an orientation toward the future and novelty. Here we report the results of a preregistered replication attempt of Experiment 2 from TS. Participants turned kitchen rolls either clockwise or counterclockwise while answering items from a questionnaire assessing openness to experience. Data from 102 participants showed that the effect went slightly in the direction opposite to that predicted by TS, and a preregistered Bayes factor hypothesis test revealed that the data were 10.76 times more likely under the null hypothesis than under the alternative hypothesis. Our findings illustrate the theoretical importance and practical advantages of preregistered Bayes factor replication studies, both for psychological science and for empirical work in general.

  1. Globally disruptive events show predictable timing patterns

    Science.gov (United States)

    Gillman, Michael P.; Erenler, Hilary E.

    2017-01-01

    Globally disruptive events include asteroid/comet impacts, large igneous provinces and glaciations, all of which have been considered as contributors to mass extinctions. Understanding the overall relationship between the timings of the largest extinctions and their potential proximal causes remains one of science's great unsolved mysteries. Cycles of about 60 Myr in both fossil diversity and environmental data suggest external drivers such as the passage of the Solar System through the galactic plane. While cyclic phenomena are recognized statistically, a lack of coherent mechanisms and a failure to link key events has hampered wider acceptance of multi-million year periodicity and its relevance to earth science and evolution. The generation of a robust predictive model of timings, with a clear plausible primary mechanism, would signal a paradigm shift. Here, we present a model of the timings of globally disruptive events and a possible explanation of their ultimate cause. The proposed model is a symmetrical pattern of 63 Myr sequences around a central value, interpreted as the occurrence of events along, and parallel to, the galactic midplane. The symmetry is consistent with multiple dark matter disks, aligned parallel to the midplane. One implication of the precise pattern of timings and the underlying physical model is the ability to predict future events, such as a major extinction in 1-2 Myr.

  2. Multiple DNA binding proteins contribute to timing of chromosome replication in E. coli

    DEFF Research Database (Denmark)

    Riber, Leise; Frimodt-Møller, Jakob; Charbon, Godefroid

    2016-01-01

    Chromosome replication in Escherichia coli is initiated from a single origin, oriC. Initiation involves a number of DNA binding proteins, but only DnaA is essential and specific for the initiation process. DnaA is an AAA+ protein that binds both ATP and ADP with similar high affinities. Dna...... replication is initiated, or the time window in which all origins present in a single cell are initiated, i.e. initiation synchrony, or both. Overall, these DNA binding proteins modulate the initiation frequency from oriC by: (i) binding directly to oriC to affect DnaA binding, (ii) altering the DNA topology...... in or around oriC, (iii) altering the nucleotide bound status of DnaA by interacting with non-coding chromosomal sequences, distant from oriC, that are important for DnaA activity. Thus, although DnaA is the key protein for initiation of replication, other DNA-binding proteins act not only on ori...

  3. Empirically Derived Learning Disability Subtypes: A Replication Attempt and Longitudinal Patterns over 15 Years.

    Science.gov (United States)

    Spreen, Otfried; Haaf, Robert G.

    1986-01-01

    Test scores of two groups of learning disabled children (N=63 and N=96) were submitted to cluster analysis in an attempt to replicate previously described subtypes. All three subtypes (visuo-perceptual, linguistic, and articulo-graphomotor types) were identified along with minimally and severely impaired subtypes. Similar clusters in the same…

  4. Empirically Derived Learning Disability Subtypes: A Replication Attempt and Longitudinal Patterns over 15 Years.

    Science.gov (United States)

    Spreen, Otfried; Haaf, Robert G.

    1986-01-01

    Test scores of two groups of learning disabled children (N=63 and N=96) were submitted to cluster analysis in an attempt to replicate previously described subtypes. All three subtypes (visuo-perceptual, linguistic, and articulo-graphomotor types) were identified along with minimally and severely impaired subtypes. Similar clusters in the same…

  5. Useful Pattern Mining on Time Series

    DEFF Research Database (Denmark)

    Goumatianos, Nikitas; Christou, Ioannis T; Lindgren, Peter

    2013-01-01

    We present the architecture of a “useful pattern” mining system that is capable of detecting thousands of different candlestick sequence patterns at the tick or any higher granularity levels. The system architecture is highly distributed and performs most of its highly compute-intensive aggregation...... calculations as complex but efficient distributed SQL queries on the relational databases that store the time-series. We present initial results from mining all frequent candlestick sequences with the characteristic property that when they occur then, with an average at least 60% probability, they signal a 2......% or higher increase (or, alternatively, decrease) in a chosen property of the stock (e.g. close-value) within a given time-window (e.g. 5 days). Initial results from a first prototype implementation of the architecture show that after training on a large set of stocks, the system is capable of finding...

  6. Patterns of replication in the neo-sex chromosomes of Drosophila nasuta albomicans

    Indian Academy of Sciences (India)

    G Mahesh; N B Ramachandra; H A Ranganath

    2000-09-01

    Drosophila nasuta albomicans (with 2n = 6), contains a pair of metacentric neo-sex chromosomes. Phylogenetically these are products of centric fusion between ancestral sex (X, Y) chromosomes and an autosome (chromosome 3). The polytene chromosome complement of males with a neo-X- and neo-Y-chromosomes has revealed asynchrony in replication between the two arms of the neo-sex chromosomes. The arm which represents the ancestral X-chromosome is faster replicating than the arm which represents ancestral autosome. The latter arm of the neo-sex chromosome is synchronous with other autosomes of the complement. We conclude that one arm of the neo-X/Y is still mimicking the features of an autosome while the other arm has the features of a classical X/Y-chromosome. This X-autosome translocation differs from the other evolutionary X-autosome translocations known in certain species of Drosophila.

  7. Myc and Ras oncogenes engage different energy metabolism programs and evoke distinct patterns of oxidative and DNA replication stress.

    Science.gov (United States)

    Maya-Mendoza, Apolinar; Ostrakova, Jitka; Kosar, Martin; Hall, Arnaldur; Duskova, Pavlina; Mistrik, Martin; Merchut-Maya, Joanna Maria; Hodny, Zdenek; Bartkova, Jirina; Christensen, Claus; Bartek, Jiri

    2015-03-01

    Both Myc and Ras oncogenes impact cellular metabolism, deregulate redox homeostasis and trigger DNA replication stress (RS) that compromises genomic integrity. However, how are such oncogene-induced effects evoked and temporally related, to what extent are these kinetic parameters shared by Myc and Ras, and how are these cellular changes linked with oncogene-induced cellular senescence in different cell context(s) remain poorly understood. Here, we addressed the above-mentioned open questions by multifaceted comparative analyses of human cellular models with inducible expression of c-Myc and H-RasV12 (Ras), two commonly deregulated oncoproteins operating in a functionally connected signaling network. Our study of DNA replication parameters using the DNA fiber approach and time-course assessment of perturbations in glycolytic flux, oxygen consumption and production of reactive oxygen species (ROS) revealed the following results. First, overabundance of nuclear Myc triggered RS promptly, already after one day of Myc induction, causing slow replication fork progression and fork asymmetry, even before any metabolic changes occurred. In contrast, Ras overexpression initially induced a burst of cell proliferation and increased the speed of replication fork progression. However, after several days of induction Ras caused bioenergetic metabolic changes that correlated with slower DNA replication fork progression and the ensuing cell cycle arrest, gradually leading to senescence. Second, the observed oncogene-induced RS and metabolic alterations were cell-type/context dependent, as shown by comparative analyses of normal human BJ fibroblasts versus U2-OS sarcoma cells. Third, the energy metabolic reprogramming triggered by Ras was more robust compared to impact of Myc. Fourth, the detected oncogene-induced oxidative stress was due to ROS (superoxide) of non-mitochondrial origin and mitochondrial OXPHOS was reduced (Crabtree effect). Overall, our study provides novel

  8. Visual pattern discovery in timed event data

    Science.gov (United States)

    Schaefer, Matthias; Wanner, Franz; Mansmann, Florian; Scheible, Christian; Stennett, Verity; Hasselrot, Anders T.; Keim, Daniel A.

    2011-01-01

    Business processes have tremendously changed the way large companies conduct their business: The integration of information systems into the workflows of their employees ensures a high service level and thus high customer satisfaction. One core aspect of business process engineering are events that steer the workflows and trigger internal processes. Strict requirements on interval-scaled temporal patterns, which are common in time series, are thereby released through the ordinal character of such events. It is this additional degree of freedom that opens unexplored possibilities for visualizing event data. In this paper, we present a flexible and novel system to find significant events, event clusters and event patterns. Each event is represented as a small rectangle, which is colored according to categorical, ordinal or intervalscaled metadata. Depending on the analysis task, different layout functions are used to highlight either the ordinal character of the data or temporal correlations. The system has built-in features for ordering customers or event groups according to the similarity of their event sequences, temporal gap alignment and stacking of co-occurring events. Two characteristically different case studies dealing with business process events and news articles demonstrate the capabilities of our system to explore event data.

  9. ASAR15, A cis-acting locus that controls chromosome-wide replication timing and stability of human chromosome 15.

    Directory of Open Access Journals (Sweden)

    Nathan Donley

    2015-01-01

    Full Text Available DNA replication initiates at multiple sites along each mammalian chromosome at different times during each S phase, following a temporal replication program. We have used a Cre/loxP-based strategy to identify cis-acting elements that control this replication-timing program on individual human chromosomes. In this report, we show that rearrangements at a complex locus at chromosome 15q24.3 result in delayed replication and structural instability of human chromosome 15. Characterization of this locus identified long, RNA transcripts that are retained in the nucleus and form a "cloud" on one homolog of chromosome 15. We also found that this locus displays asynchronous replication that is coordinated with other random monoallelic genes on chromosome 15. We have named this locus ASynchronous replication and Autosomal RNA on chromosome 15, or ASAR15. Previously, we found that disruption of the ASAR6 lincRNA gene results in delayed replication, delayed mitotic condensation and structural instability of human chromosome 6. Previous studies in the mouse found that deletion of the Xist gene, from the X chromosome in adult somatic cells, results in a delayed replication and instability phenotype that is indistinguishable from the phenotype caused by disruption of either ASAR6 or ASAR15. In addition, delayed replication and chromosome instability were detected following structural rearrangement of many different human or mouse chromosomes. These observations suggest that all mammalian chromosomes contain similar cis-acting loci. Thus, under this scenario, all mammalian chromosomes contain four distinct types of essential cis-acting elements: origins, telomeres, centromeres and "inactivation/stability centers", all functioning to promote proper replication, segregation and structural stability of each chromosome.

  10. HIV-1 replication in central nervous system increases over time on only protease inhibitor therapy.

    Science.gov (United States)

    Donath, Maximilian; Wolf, Timo; Stürmer, Martin; Herrmann, Eva; Bickel, Markus; Khaykin, Pavel; Göpel, Siri; Gute, Peter; Haberl, Annette; de Leuw, Philipp; Schüttfort, Gundolf; Berger, Annemarie; Stephan, Christoph

    2016-12-01

    There are concerns about central nervous system (CNS)-replication of HIV-1 in patients on boosted protease inhibitors. Purpose of this study was to compare HIV-1 viral loads (VLs) from patients treated with only boosted dual protease inhibitor (bdPI), versus combination antiretroviral therapy (cART group), containing two nucleoside analogue reverse transcriptase inhibitors (NRTI) and a third partner. All patients from a large German HIV-treatment cohort with available medication, clinical and demographic data, including results from simultaneous HIV-1 viral load (VL) assessments in cerebrospinal fluid (CSF) and blood plasma, were retrospectively evaluated as controlled cross-sectional study. CSF had been obtained from patients with variable neurological symptoms during 2005-2014. Statistical analysis comprised nonparametric tests, regression and correlation techniques accounting for undetectable quantifications. Statistical analysis comprised nonparametric tests, regression and correlation techniques accounting for undetectable quantifications. Overall, 155 patients were evaluable (bdPI: 24; cART: 131). At time of CSF-collection, both groups were comparable in age, gender, CD4-cell counts, or primary HIV-transmission risks, though bdPI patients were clinically more advanced. The proportion of patients with undetectable HIV-1 (<50 copies/ml) in CSF was lower for bdPI group (25 vs 49.6 %; p = 0.026), but similar in plasma (46 vs 41 %). Median CSF-VL was higher in bdPI group (600 vs 50 copies/ml; p = 0.027) and similar in plasma. Mean VL CSF/plasma ratio was 342.91 for bdPI- and 54.48 for cART patients (p < 0.001). Pearson's regression analysis revealed a trend for an elevated VL-ratio over time within bdPI group. HIV-1 replication was higher and more frequently detectable in CSF from bdPI patients, indicating a worse CNS penetration effectiveness of used boosted PI. Within bdPI group, measured CNS-viral replication was increasing over time, suggesting an over

  11. Studying the replication history of human B lymphocytes by real-time quantitative (RQ)-PCR.

    Science.gov (United States)

    van Zelm, Menno C; Berkowska, Magdalena A; van Dongen, Jacques J M

    2013-01-01

    The cells of the adaptive immune system, B and T lymphocytes, each generate a unique antigen receptor through V(D)J recombination of their immunoglobulin (Ig) and T cell receptor (TCR) loci, respectively. Such rearrangements join coding elements to form a coding joint and delete the intervening DNA as circular excision products containing the signal joint. These excision circles are stable structures that cannot replicate and have no function in the cell. Since the coding joint in the genome is replicated with each cell division, the ratio between coding joints and signal joints in a population of B cells can be used as a measure for proliferation. This chapter describes a real-time quantitative (RQ-)PCR-based approach to quantify proliferation through calculating the ratio between coding joints and signal joints of the frequently occurring intronRSS-Kde rearrangements in the IGK light chain locus. The approach is useful to study basic B-cell biology as well as abnormal proliferation in human diseases.

  12. Mammalian chromosomes contain cis-acting elements that control replication timing, mitotic condensation, and stability of entire chromosomes.

    Science.gov (United States)

    Thayer, Mathew J

    2012-09-01

    Recent studies indicate that mammalian chromosomes contain discrete cis-acting loci that control replication timing, mitotic condensation, and stability of entire chromosomes. Disruption of the large non-coding RNA gene ASAR6 results in late replication, an under-condensed appearance during mitosis, and structural instability of human chromosome 6. Similarly, disruption of the mouse Xist gene in adult somatic cells results in a late replication and instability phenotype on the X chromosome. ASAR6 shares many characteristics with Xist, including random mono-allelic expression and asynchronous replication timing. Additional "chromosome engineering" studies indicate that certain chromosome rearrangements affecting many different chromosomes display this abnormal replication and instability phenotype. These observations suggest that all mammalian chromosomes contain "inactivation/stability centers" that control proper replication, condensation, and stability of individual chromosomes. Therefore, mammalian chromosomes contain four types of cis-acting elements, origins, telomeres, centromeres, and "inactivation/stability centers", all functioning to ensure proper replication, condensation, segregation, and stability of individual chromosomes.

  13. Rock bream iridovirus (RBIV) replication in rock bream (Oplegnathus fasciatus) exposed for different time periods to susceptible water temperatures.

    Science.gov (United States)

    Jung, Myung-Hwa; Nikapitiya, Chamilani; Vinay, Tharabenahalli-Nagaraju; Lee, Jehee; Jung, Sung-Ju

    2017-09-15

    Rock bream iridovirus (RBIV) is a member of the Megalocytivirus genus that causes severe mortality to rock bream. Water temperature is known to affect the immune system and susceptibility of fish to RBIV infection. In this study, we evaluated the time dependent virus replication pattern and time required to completely eliminate virus from the rock bream body against RBIV infection at different water temperature conditions. The rock bream was exposed to the virus and held at 7 (group A1), 4 (group A2) and 2 days (group A3) at 23 °C before the water temperature was reduced to 17 °C. A total of 28% mortality was observed 24-35 days post infection (dpi) in only the 7 day exposure group at 23 °C. In all 23 °C exposure groups, virus replication peaked at 20 to 22 dpi (10(6)-10(7)/μl). In recovery stages (30-100 dpi), the virus copy number was gradually reduced, from 10(6) to 10(1) with faster decreases in the shorter exposure period group at 23 °C. When the water temperature was increased in surviving fish from 17 to 26 °C at 70 dpi, they did not show any mortality or signs of disease and had low virus copy numbers (below 10(2)/μl). Thus, fish need at least 50 days from peaked RBIV levels (approximately 20-25 dpi) to inhibit the virus. This indicates that maintaining the fish at low water temperature (17 °C) for 70 days is sufficient to eradicate RBIV from fish body. Thus, RBIV could be eliminated slowly from the fish body and the virus may be completely eliminated under the threshold of causing mortality. Copyright © 2017 Elsevier Ltd. All rights reserved.

  14. Genome-wide mapping of human DNA-replication origins: levels of transcription at ORC1 sites regulate origin selection and replication timing.

    Science.gov (United States)

    Dellino, Gaetano Ivan; Cittaro, Davide; Piccioni, Rossana; Luzi, Lucilla; Banfi, Stefania; Segalla, Simona; Cesaroni, Matteo; Mendoza-Maldonado, Ramiro; Giacca, Mauro; Pelicci, Pier Giuseppe

    2013-01-01

    We report the genome-wide mapping of ORC1 binding sites in mammals, by chromatin immunoprecipitation and parallel sequencing (ChIP-seq). ORC1 binding sites in HeLa cells were validated as active DNA replication origins (ORIs) using Repli-seq, a method that allows identification of ORI-containing regions by parallel sequencing of temporally ordered replicating DNA. ORC1 sites were universally associated with transcription start sites (TSSs) of coding or noncoding RNAs (ncRNAs). Transcription levels at the ORC1 sites directly correlated with replication timing, suggesting the existence of two classes of ORIs: those associated with moderate/high transcription levels (≥1 RNA copy/cell), firing in early S and mapping to the TSSs of coding RNAs; and those associated with low transcription levels (<1 RNA copy/cell), firing throughout the entire S and mapping to TSSs of ncRNAs. These findings are compatible with a scenario whereby TSS expression levels influence the efficiency of ORC1 recruitment at G(1) and the probability of firing during S.

  15. Time-varying Entry Heating Profile Replication with a Rotating Arc Jet Test Article

    Science.gov (United States)

    Grinstead, Jay Henderson; Venkatapathy, Ethiraj; Noyes, Eric A.; Mach, Jeffrey J.; Empey, Daniel M.; White, Todd R.

    2014-01-01

    A new approach for arc jet testing of thermal protection materials at conditions approximating the time-varying conditions of atmospheric entry was developed and demonstrated. The approach relies upon the spatial variation of heat flux and pressure over a cylindrical test model. By slowly rotating a cylindrical arc jet test model during exposure to an arc jet stream, each point on the test model will experience constantly changing applied heat flux. The predicted temporal profile of heat flux at a point on a vehicle can be replicated by rotating the cylinder at a prescribed speed and direction. An electromechanical test model mechanism was designed, built, and operated during an arc jet test to demonstrate the technique.

  16. Patterns and predictors of ADHD persistence into adulthood: Results from the National Comorbidity Survey Replication

    Science.gov (United States)

    Kessler, Ronald C.; Adler, Lenard A.; Barkley, Russell; Biederman, Joseph; Conners, C. Keith; Faraone, Stephen V.; Greenhill, Laurence L.; Jaeger, Savina; Secnik, Kristina; Spencer, Thomas; Üstün, T. Bedirhan; Zaslavsky, Alan M.

    2010-01-01

    BACKGROUND Despite growing interest in adult ADHD, little is known about predictors of persistence of childhood cases into adulthood. METHODS A retrospective assessment of childhood ADHD, childhood risk factors, and a screen for adult ADHD were included in a sample of 3197 18–44 year old respondents in the National Comorbidity Survey Replication (NCS-R). Blinded adult ADHD clinical reappraisal interviews were administered to a sub-sample of respondents. Multiple imputation (MI) was used to estimate adult persistence of childhood ADHD. Logistic regression was used to study retrospectively reported childhood predictors of persistence. Potential predictors included socio-demographics, childhood ADHD severity, childhood adversity, traumatic life experiences, and comorbid DSM-IV child-adolescent disorders (anxiety, mood, impulse-control, and substance disorders). RESULTS 36.3% of respondents with retrospectively assessed childhood ADHD were classified by blinded clinical interviews as meeting DSM-IV criteria for current ADHD. Childhood ADHD severity and childhood treatment significantly predicted persistence. Controlling for severity and excluding treatment, none of the other variables significantly predicted persistence even though they were significantly associated with childhood ADHD. CONCLUSIONS No modifiable risk factors were found for adult persistence of ADHD. Further research, ideally based on prospective general population samples, is needed to search for modifiable determinants of adult persistence of ADHD. PMID:15950019

  17. Replication of cicada wing's nano-patterns by hot embossing and UV nanoimprinting

    Science.gov (United States)

    Hong, Sung-Hoon; Hwang, Jaeyeon; Lee, Heon

    2009-09-01

    The hydrophobicity of the cicada wing originates from its naturally occurring, surface nano-structure. The nano-structure of the cicada wing consists of an array of nano-sized pillars, 100 nm in diameter and 300 nm in height. In this study, the nano-structure of the cicada wing was successfully duplicated by using hot embossing lithography and UV nanoimprint lithography (NIL). The diameter and pitch of replication were the same as those of the original cicada wing and the height was a little smaller than that of the original master. The transmittance of the hot embossed PVC film was increased by 2-6% compared with that of the bare PVC film. The hydrophobicity was measured by water contact angle measurements. The water contact angle of the replica, made of UV cured polymer, was 132° ± 2°, which was slightly lower than that of the original cicada wing (138° ± 2°), but much higher than that of the UV cured polymer surface without any nano-sized pillars (86°).

  18. Three-dimensional distribution of cortical synapses: a replicated point pattern-based analysis

    Science.gov (United States)

    Anton-Sanchez, Laura; Bielza, Concha; Merchán-Pérez, Angel; Rodríguez, José-Rodrigo; DeFelipe, Javier; Larrañaga, Pedro

    2014-01-01

    The biggest problem when analyzing the brain is that its synaptic connections are extremely complex. Generally, the billions of neurons making up the brain exchange information through two types of highly specialized structures: chemical synapses (the vast majority) and so-called gap junctions (a substrate of one class of electrical synapse). Here we are interested in exploring the three-dimensional spatial distribution of chemical synapses in the cerebral cortex. Recent research has showed that the three-dimensional spatial distribution of synapses in layer III of the neocortex can be modeled by a random sequential adsorption (RSA) point process, i.e., synapses are distributed in space almost randomly, with the only constraint that they cannot overlap. In this study we hypothesize that RSA processes can also explain the distribution of synapses in all cortical layers. We also investigate whether there are differences in both the synaptic density and spatial distribution of synapses between layers. Using combined focused ion beam milling and scanning electron microscopy (FIB/SEM), we obtained three-dimensional samples from the six layers of the rat somatosensory cortex and identified and reconstructed the synaptic junctions. A total volume of tissue of approximately 4500μm3 and around 4000 synapses from three different animals were analyzed. Different samples, layers and/or animals were aggregated and compared using RSA replicated spatial point processes. The results showed no significant differences in the synaptic distribution across the different rats used in the study. We found that RSA processes described the spatial distribution of synapses in all samples of each layer. We also found that the synaptic distribution in layers II to VI conforms to a common underlying RSA process with different densities per layer. Interestingly, the results showed that synapses in layer I had a slightly different spatial distribution from the other layers. PMID:25206325

  19. Investigations for modelling hardness of biomedical implant during replication of FDM-based patterns by vacuum moulding

    Indian Academy of Sciences (India)

    RUPINDER SINGH; GURINDER SINGH

    2017-03-01

    In the present work, effort has been made for modelling the microhardness of biomedical implant prepared by combining fused deposition modelling, vacuum moulding and stir casting (SC) process. A dynamic condylar screw (DCS) plate was selected as a real ‘3D’ biomedical implant for this case study. The DCS plate,made of acrylonitrile butadiene styrene material, was fabricated as a master pattern by fused deposition modelling. After preparation of the master pattern, the mould cavity was fabricated by the vacuum moulding process.Finally a metal–matrix composite of Al and Al2O3 prepared by SC process has been poured in the vacuum mould for fabrication of DCS plate. This study outlines the replication procedure of DCS plate in detail from the master pattern to final product. The contribution of the paper is towards finding out the effect and optimumvalues of three different process parameters (namely: percentage composition of Al and Al2O3, vacuum pressure and grain size of silica) towards microhardness of the DCS plate manufactured by the combined process.

  20. A D-Shaped Bileaflet Bioprosthesis which Replicates Physiological Left Ventricular Flow Patterns.

    Directory of Open Access Journals (Sweden)

    Sean Guo-Dong Tan

    Full Text Available Prior studies have shown that in a healthy heart, there exist a large asymmetric vortex structure that aids in establishing a steady flow field in the left ventricle. However, the implantation of existing artificial heart valves at the mitral position is found to have a negative effect on this physiological flow pattern. In light of this, a novel D-shaped bileaflet porcine bioprosthesis (GD valve has been designed based on the native geometry mitral valve, with the hypothesis that biomimicry in valve design can restore physiological left ventricle flow patterns after valve implantation. An in-vitro experiment using two dimensional particle velocimetry imaging was carried out to determine the hemodynamic performance of the new bileaflet design and then compared to that of the well-established St. Jude Epic valve which functioned as a control in the experiment. Although both valves were found to have similar Reynolds shear stress and Turbulent Kinetic Energy levels, the novel D-shape valve was found to have lower turbulence intensity and greater mean kinetic energy conservation.

  1. Useful Pattern Mining on Time Series

    DEFF Research Database (Denmark)

    Goumatianos, Nikitas; Christou, Ioannis T; Lindgren, Peter

    2013-01-01

    We present the architecture of a “useful pattern” mining system that is capable of detecting thousands of different candlestick sequence patterns at the tick or any higher granularity levels. The system architecture is highly distributed and performs most of its highly compute-intensive aggregation...

  2. DnaA and the timing of chromosome replication in Es-cherichia coli as a function of growth rate

    Directory of Open Access Journals (Sweden)

    Grant Matthew AA

    2011-12-01

    Full Text Available Abstract Background In Escherichia coli, overlapping rounds of DNA replication allow the bacteria to double in faster times than the time required to copy the genome. The precise timing of initiation of DNA replication is determined by a regulatory circuit that depends on the binding of a critical number of ATP-bound DnaA proteins at the origin of replication, resulting in the melting of the DNA and the assembly of the replication complex. The synthesis of DnaA in the cell is controlled by a growth-rate dependent, negatively autoregulated gene found near the origin of replication. Both the regulatory and initiation activity of DnaA depend on its nucleotide bound state and its availability. Results In order to investigate the contributions of the different regulatory processes to the timing of initiation of DNA replication at varying growth rates, we formulate a minimal quantitative model of the initiator circuit that includes the key ingredients known to regulate the activity of the DnaA protein. This model describes the average-cell oscillations in DnaA-ATP/DNA during the cell cycle, for varying growth rates. We evaluate the conditions under which this ratio attains the same threshold value at the time of initiation, independently of the growth rate. Conclusions We find that a quantitative description of replication initiation by DnaA must rely on the dependency of the basic parameters on growth rate, in order to account for the timing of initiation of DNA replication at different cell doubling times. We isolate two main possible scenarios for this, depending on the roles of DnaA autoregulation and DnaA ATP-hydrolysis regulatory process. One possibility is that the basal rate of regulatory inactivation by ATP hydrolysis must vary with growth rate. Alternatively, some parameters defining promoter activity need to be a function of the growth rate. In either case, the basal rate of gene expression needs to increase with the growth rate, in

  3. A reminder on millisecond timing accuracy and potential replication failure in computer-based psychology experiments: An open letter.

    Science.gov (United States)

    Plant, Richard R

    2016-03-01

    There is an ongoing 'replication crisis' across the field of psychology in which researchers, funders, and members of the public are questioning the results of some scientific studies and the validity of the data they are based upon. However, few have considered that a growing proportion of research in modern psychology is conducted using a computer. Could it simply be that the hardware and software, or experiment generator, being used to run the experiment itself be a cause of millisecond timing error and subsequent replication failure? This article serves as a reminder that millisecond timing accuracy in psychology studies remains an important issue and that care needs to be taken to ensure that studies can be replicated on current computer hardware and software.

  4. Greedy scheduling of cellular self-replication leads to optimal doubling times with a log-Frechet distribution.

    Science.gov (United States)

    Pugatch, Rami

    2015-02-24

    Bacterial self-replication is a complex process composed of many de novo synthesis steps catalyzed by a myriad of molecular processing units, e.g., the transcription-translation machinery, metabolic enzymes, and the replisome. Successful completion of all production tasks requires a schedule-a temporal assignment of each of the production tasks to its respective processing units that respects ordering and resource constraints. Most intracellular growth processes are well characterized. However, the manner in which they are coordinated under the control of a scheduling policy is not well understood. When fast replication is favored, a schedule that minimizes the completion time is desirable. However, if resources are scarce, it is typically computationally hard to find such a schedule, in the worst case. Here, we show that optimal scheduling naturally emerges in cellular self-replication. Optimal doubling time is obtained by maintaining a sufficiently large inventory of intermediate metabolites and processing units required for self-replication and additionally requiring that these processing units be "greedy," i.e., not idle if they can perform a production task. We calculate the distribution of doubling times of such optimally scheduled self-replicating factories, and find it has a universal form-log-Frechet, not sensitive to many microscopic details. Analyzing two recent datasets of Escherichia coli growing in a stationary medium, we find excellent agreement between the observed doubling-time distribution and the predicted universal distribution, suggesting E. coli is optimally scheduling its replication. Greedy scheduling appears as a simple generic route to optimal scheduling when speed is the optimization criterion. Other criteria such as efficiency require more elaborate scheduling policies and tighter regulation.

  5. Polycomb Mediated Epigenetic Silencing and Replication Timing at the INK4a/ARF Locus during Senescence

    Science.gov (United States)

    Verthuy, Christophe; Chasson, Lionel; Serrano, Manuel; Djabali, Malek

    2009-01-01

    Background The INK4/ARF locus encodes three tumor suppressor genes (p15Ink4b, Arf and p16Ink4a) and is frequently inactivated in a large number of human cancers. Mechanisms regulating INK4/ARF expression are not fully characterized. Principal Findings Here we show that in young proliferating embryonic fibroblasts (MEFs) the Polycomb Repressive Complex 2 (PRC2) member EZH2 together with PRC1 members BMI1 and M33 are strongly expressed and localized at the INK4/ARF regulatory domain (RD) identified as a DNA replication origin. When cells enter senescence the binding to RD of both PRC1 and PRC2 complexes is lost leading to a decreased level of histone H3K27 trimethylation (H3K27me3). This loss is accompanied with an increased expression of the histone demethylase Jmjd3 and with the recruitment of the MLL1 protein, and correlates with the expression of the Ink4a/Arf genes. Moreover, we show that the Polycomb protein BMI1 interacts with CDC6, an essential regulator of DNA replication in eukaryotic cells. Finally, we demonstrate that Polycomb proteins and associated epigenetic marks are crucial for the control of the replication timing of the INK4a/ARF locus during senescence. Conclusions We identified the replication licencing factor CDC6 as a new partner of the Polycomb group member BMI1. Our results suggest that in young cells Polycomb proteins are recruited to the INK4/ARF locus through CDC6 and the resulting silent locus is replicated during late S-phase. Upon senescence, Jmjd3 is overexpressed and the MLL1 protein is recruited to the locus provoking the dissociation of Polycomb from the INK4/ARF locus, its transcriptional activation and its replication during early S-phase. Together, these results provide a unified model that integrates replication, transcription and epigenetics at the INK4/ARF locus. PMID:19462008

  6. Polycomb mediated epigenetic silencing and replication timing at the INK4a/ARF locus during senescence.

    Directory of Open Access Journals (Sweden)

    Hanane Agherbi

    Full Text Available BACKGROUND: The INK4/ARF locus encodes three tumor suppressor genes (p15(Ink4b, Arf and p16(Ink4a and is frequently inactivated in a large number of human cancers. Mechanisms regulating INK4/ARF expression are not fully characterized. PRINCIPAL FINDINGS: Here we show that in young proliferating embryonic fibroblasts (MEFs the Polycomb Repressive Complex 2 (PRC2 member EZH2 together with PRC1 members BMI1 and M33 are strongly expressed and localized at the INK4/ARF regulatory domain (RD identified as a DNA replication origin. When cells enter senescence the binding to RD of both PRC1 and PRC2 complexes is lost leading to a decreased level of histone H3K27 trimethylation (H3K27me3. This loss is accompanied with an increased expression of the histone demethylase Jmjd3 and with the recruitment of the MLL1 protein, and correlates with the expression of the Ink4a/Arf genes. Moreover, we show that the Polycomb protein BMI1 interacts with CDC6, an essential regulator of DNA replication in eukaryotic cells. Finally, we demonstrate that Polycomb proteins and associated epigenetic marks are crucial for the control of the replication timing of the INK4a/ARF locus during senescence. CONCLUSIONS: We identified the replication licencing factor CDC6 as a new partner of the Polycomb group member BMI1. Our results suggest that in young cells Polycomb proteins are recruited to the INK4/ARF locus through CDC6 and the resulting silent locus is replicated during late S-phase. Upon senescence, Jmjd3 is overexpressed and the MLL1 protein is recruited to the locus provoking the dissociation of Polycomb from the INK4/ARF locus, its transcriptional activation and its replication during early S-phase. Together, these results provide a unified model that integrates replication, transcription and epigenetics at the INK4/ARF locus.

  7. High Power Picosecond Laser Surface Micro-texturing of H13 Tool Steel and Pattern Replication onto ABS Plastics via Injection Moulding

    Science.gov (United States)

    Otanocha, Omonigho B.; Li, Lin; Zhong, Shan; Liu, Zhu

    2016-03-01

    H13 tool steels are often used as dies and moulds for injection moulding of plastic components. Certain injection moulded components require micro-patterns on their surfaces in order to modify the physical properties of the components or for better mould release to reduce mould contamination. With these applications it is necessary to study micro-patterning to moulds and to ensure effective pattern transfer and replication onto the plastic component during moulding. In this paper, we report an investigation into high average powered (100 W) picosecond laser interactions with H13 tool steel during surface micro-patterning (texturing) and the subsequent pattern replication on ABS plastic material through injection moulding. Design of experiments and statistical modelling were used to understand the influences of laser pulse repetition rate, laser fluence, scanning velocity, and number of scans on the depth of cut, kerf width and heat affected zones (HAZ) size. The characteristics of the surface patterns are analysed. The process parameter interactions and significance of process parameters on the processing quality and efficiency are characterised. An optimum operating window is recommended. The transferred geometry is compared with the patterns generated on the dies. A discussion is made to explain the characteristics of laser texturing and pattern replication on plastics.

  8. Design Optimization of Time- and Cost-Constrained Fault-Tolerant Embedded Systems with Checkpointing and Replication

    DEFF Research Database (Denmark)

    Pop, Paul; Izosimov, Viacheslav; Eles, Petru;

    2009-01-01

    We present an approach to the synthesis of fault-tolerant hard real-time systems for safety-critical applications. We use checkpointing with rollback recovery and active replication for tolerating transient faults. Processes and communications are statically scheduled. Our synthesis approach deci...

  9. Therapeutic Assessment for Preadolescent Boys with Oppositional Defiant Disorder: A Replicated Single-Case Time-Series Design

    Science.gov (United States)

    Smith, Justin D.; Handler, Leonard; Nash, Michael R.

    2010-01-01

    The Therapeutic Assessment (TA) model is a relatively new treatment approach that fuses assessment and psychotherapy. The study examines the efficacy of this model with preadolescent boys with oppositional defiant disorder and their families. A replicated single-case time-series design with daily measures is used to assess the effects of TA and to…

  10. YAP controls retinal stem cell DNA replication timing and genomic stability.

    Science.gov (United States)

    Cabochette, Pauline; Vega-Lopez, Guillermo; Bitard, Juliette; Parain, Karine; Chemouny, Romain; Masson, Christel; Borday, Caroline; Hedderich, Marie; Henningfeld, Kristine A; Locker, Morgane; Bronchain, Odile; Perron, Muriel

    2015-09-22

    The adult frog retina retains a reservoir of active neural stem cells that contribute to continuous eye growth throughout life. We found that Yap, a downstream effector of the Hippo pathway, is specifically expressed in these stem cells. Yap knock-down leads to an accelerated S-phase and an abnormal progression of DNA replication, a phenotype likely mediated by upregulation of c-Myc. This is associated with an increased occurrence of DNA damage and eventually p53-p21 pathway-mediated cell death. Finally, we identified PKNOX1, a transcription factor involved in the maintenance of genomic stability, as a functional and physical interactant of YAP. Altogether, we propose that YAP is required in adult retinal stem cells to regulate the temporal firing of replication origins and quality control of replicated DNA. Our data reinforce the view that specific mechanisms dedicated to S-phase control are at work in stem cells to protect them from genomic instability.

  11. Understanding human activity patterns based on space-time-semantics

    Science.gov (United States)

    Huang, Wei; Li, Songnian

    2016-11-01

    Understanding human activity patterns plays a key role in various applications in an urban environment, such as transportation planning and traffic forecasting, urban planning, public health and safety, and emergency response. Most existing studies in modeling human activity patterns mainly focus on spatiotemporal dimensions, which lacks consideration of underlying semantic context. In fact, what people do and discuss at some places, inferring what is happening at the places, cannot be simple neglected because it is the root of human mobility patterns. We believe that the geo-tagged semantic context, representing what individuals do and discuss at a place and a specific time, drives a formation of specific human activity pattern. In this paper, we aim to model human activity patterns not only based on space and time but also with consideration of associated semantics, and attempt to prove a hypothesis that similar mobility patterns may have different motivations. We develop a spatiotemporal-semantic model to quantitatively express human activity patterns based on topic models, leading to an analysis of space, time and semantics. A case study is conducted using Twitter data in Toronto based on our model. Through computing the similarities between users in terms of spatiotemporal pattern, semantic pattern and spatiotemporal-semantic pattern, we find that only a small number of users (2.72%) have very similar activity patterns, while the majority (87.14%) show different activity patterns (i.e., similar spatiotemporal patterns and different semantic patterns, similar semantic patterns and different spatiotemporal patterns, or different in both). The population of users that has very similar activity patterns is decreased by 56.41% after incorporating semantic information in the corresponding spatiotemporal patterns, which can quantitatively prove the hypothesis.

  12. Transcription-replication conflicts at chromosomal fragile sites—consequences in M phase and beyond

    DEFF Research Database (Denmark)

    Østergaard, Vibe Hallundbæk; Lisby, Michael

    2017-01-01

    transcription and replication patterns. At the same time, these chromosomal fragile sites engage in aberrant DNA structures in mitosis. Here, we discuss the mechanistic details of transcription–replication conflicts including putative scenarios for R-loop-induced replication inhibition to understand how...... transcription–replication conflicts transition from S phase into various aberrant DNA structures in mitosis....

  13. On the interpretation of time-resolved anisotropic diffraction patterns

    DEFF Research Database (Denmark)

    Lorenz, Ulf; Møller, Klaus Braagaard; Henriksen, Niels Engholm

    2010-01-01

    In this paper, we review existing systematic treatments for the interpretation of anisotropic diffraction patterns from partially aligned symmetric top molecules. Such patterns arise in the context of time-resolved diffraction experiments. We calculate diffraction patterns for ground-state NaI ex......I excited with an ultraviolet laser. The results are interpreted with the help of a qualitative analytic model, and general recommendations on the analysis and interpretation of anisotropic diffraction patterns are given....

  14. Motor control by precisely timed spike patterns

    DEFF Research Database (Denmark)

    Srivastava, Kyle H; Holmes, Caroline M; Vellema, Michiel

    2017-01-01

    A fundamental problem in neuroscience is understanding how sequences of action potentials ("spikes") encode information about sensory signals and motor outputs. Although traditional theories assume that this information is conveyed by the total number of spikes fired within a specified time...

  15. Turning the hands of time again: a purely confirmatory replication study and a Bayesian analysis

    NARCIS (Netherlands)

    E.-J. Wagenmakers; T.F. Beek; M. Rotteveel; A. Gierholz; D. Matzke; H. Steingroever; A. Ly; J. Verhagen; R. Selker; A. Sasiadek; Q.F. Gronau; J. Love; Y. Pinto

    2015-01-01

    In a series of four experiments, Topolinski and Sparenberg (2012) found support for the conjecture that clockwise movements induce psychological states of temporal progression and an orientation toward the future and novelty. Here we report the results of a preregistered replication attempt of Exper

  16. Analysis of time-varying psoriasis lesion image patterns

    DEFF Research Database (Denmark)

    Maletti, Gabriela Mariel; Ersbøll, Bjarne Kjær; Nielsen, Allan Aasbjerg

    2004-01-01

    The multivariate alteration detection transform is applied to pairs of within and between time varying registered psoriasis image patterns. Color band contribution to the variates explaining maximal change is analyzed.......The multivariate alteration detection transform is applied to pairs of within and between time varying registered psoriasis image patterns. Color band contribution to the variates explaining maximal change is analyzed....

  17. Fractal patterns in Stock Intertrading Times

    Science.gov (United States)

    White, Ainslie; Lee, Youngki; Ivanov, Plamen Ch.

    2003-03-01

    We study intertrades times (ITT) of stock trades of a range of companies included in the New York Stock Exchange's Trades and Quotes (TAQ) database. The time between transactions is an indicator of the dynamics of the market, and in the field of econometrics, intertrade durations play a key role in the understanding of the market activity and microstructure. Previous work has mainly focused on the properties of price changes of individual company stocks as well as global financial indices (e.g. SP500, DJ etc.). We hypothesize that there is a relation between the dynamics of price change and the trading activity. To investigate this relation we first study the statistical features of ITT data. The TAQ database covers all transactions on the NSE, AMEX, NASDAQ and the US regional exchanges. We have performed a preliminary analysis of 100 company stocks from a range of industries of the US economy selecting predominantly those companies which have large market capitalisations (MC). We focus on companies with large MC, since the dynamics of the price change and trading activity of stocks of such companies has a considerable impact on the market behaviour.

  18. Inferring Patterns in Network Traffic: Time Scales and Variations

    Science.gov (United States)

    2014-10-21

    2014 Carnegie Mellon University Inferring Patterns in Network Traffic : Time Scales and Variation Soumyo Moitra smoitra@sei.cmu.edu...number. 1. REPORT DATE 21 OCT 2014 2. REPORT TYPE N/A 3. DATES COVERED 4. TITLE AND SUBTITLE Inferring Patterns in Network Traffic : Time...method and metrics for Situational Awareness • SA  Monitoring trends and changes in traffic • Analysis over timeTime series data analysis • Metrics

  19. Laser-induced heating integrated with a microfluidic platform for real-time DNA replication and detection

    Science.gov (United States)

    Hung, Min-Sheng; Ho, Chia-Chin; Chen, Chih-Pin

    2016-08-01

    This study developed a microfluidic platform for replicating and detecting DNA in real time by integrating a laser and a microfluidic device composed of polydimethylsiloxane. The design of the microchannels consisted of a laser-heating area and a detection area. An infrared laser was used as the heating source for DNA replication, and the laser power was adjusted to heat the solutions directly. In addition, strong biotin-avidin binding was used to capture and detect the replicated products. The biotin on one end was bound to avidin and anchored to the surface of the microchannels, whereas the biotin on the other end was bound to the quantum dots (Qdots). The results showed that the fluorescent intensity of the Qdots bound to the replicated products in the detection area increased with the number of thermal cycles created by the laser. When the number of thermal cycles was ≥10, the fluorescent intensity of the Qdots was directly detectable on the surface of the microchannels. The proposed method is more sensitive than detection methods entailing gel electrophoresis.

  20. Gambler's fallacy, hot hand belief, and the time of patterns

    Directory of Open Access Journals (Sweden)

    Hongbin Wang

    2010-04-01

    Full Text Available The gambler's fallacy and the hot hand belief have been classified as two exemplars of human misperceptions of random sequential events. This article examines the times of pattern occurrences where a fair or biased coin is tossed repeatedly. We demonstrate that, due to different pattern composition, two different statistics (mean time and waiting time can arise from the same independent Bernoulli trials. When the coin is fair, the mean time is equal for all patterns of the same length but the waiting time is the longest for streak patterns. When the coin is biased, both mean time and waiting time change more rapidly with the probability of heads for a streak pattern than for a non-streak pattern. These facts might provide a new insight for understanding why people view streak patterns as rare and remarkable. The statistics of waiting time may not justify the prediction by the gambler's fallacy, but paying attention to streaks in the hot hand belief appears to be meaningful in detecting the changes in the underlying process.

  1. The pattern of cognitive symptoms predicts time to dementia onset.

    NARCIS (Netherlands)

    Sacuiu, S.; Gustafson, D.; Johansson, B.; Thorvaldsson, V.; Berg, S.; Sjogren, J.M.C.; Guo, X.; Ostling, S.; Skoog, I.

    2009-01-01

    BACKGROUND: Few studies have examined whether cognitive symptom patterns differ by age and length of time before dementia onset. Our objective was to investigate whether different patterns of cognitive symptoms at ages 70, 75, and 79 years predict short-term (< or =5 years) and long-term (>5 y

  2. The pattern of cognitive symptoms predicts time to dementia onset.

    NARCIS (Netherlands)

    Sacuiu, S.; Gustafson, D.; Johansson, B.; Thorvaldsson, V.; Berg, S.; Sjogren, J.M.C.; Guo, X.; Ostling, S.; Skoog, I.

    2009-01-01

    BACKGROUND: Few studies have examined whether cognitive symptom patterns differ by age and length of time before dementia onset. Our objective was to investigate whether different patterns of cognitive symptoms at ages 70, 75, and 79 years predict short-term (< or =5 years) and long-term (>5 y

  3. The pattern of cognitive symptoms predicts time to dementia onset.

    NARCIS (Netherlands)

    Sacuiu, S.; Gustafson, D.; Johansson, B.; Thorvaldsson, V.; Berg, S.; Sjogren, J.M.C.; Guo, X.; Ostling, S.; Skoog, I.

    2009-01-01

    BACKGROUND: Few studies have examined whether cognitive symptom patterns differ by age and length of time before dementia onset. Our objective was to investigate whether different patterns of cognitive symptoms at ages 70, 75, and 79 years predict short-term (< or =5 years) and long-term (>5

  4. Temporal metastates are associated with differential patterns of time-resolved connectivity, network topology, and attention.

    Science.gov (United States)

    Shine, James M; Koyejo, Oluwasanmi; Poldrack, Russell A

    2016-08-30

    Little is currently known about the coordination of neural activity over longitudinal timescales and how these changes relate to behavior. To investigate this issue, we used resting-state fMRI data from a single individual to identify the presence of two distinct temporal states that fluctuated over the course of 18 mo. These temporal states were associated with distinct patterns of time-resolved blood oxygen level dependent (BOLD) connectivity within individual scanning sessions and also related to significant alterations in global efficiency of brain connectivity as well as differences in self-reported attention. These patterns were replicated in a separate longitudinal dataset, providing additional supportive evidence for the presence of fluctuations in functional network topology over time. Together, our results underscore the importance of longitudinal phenotyping in cognitive neuroscience.

  5. Relating movement recurrence and expressive timing patterns in music performances.

    Science.gov (United States)

    Teixeira, Euler C F; Yehia, Hani C; Loureiro, Mauricio A

    2015-09-01

    In this study the movement patterns of ten expert musicians are quantitatively related to expressive timing patterns and the music structure during performances. The hypothesis is that ancillary gestures recurrently employed are closely related to expressive intentions, and that the expressive content imposed in key musical passages is thus reflected in the patterns of gestural recurrence. A movement and an audio analysis of 30 clarinet performances of a Brahms' excerpt are compared. Results show direct correlations between the recurrence pattern of clarinetists' ancillary movements and expressive bar duration manipulations employed by them, associated with melodic phrasing and harmonic transitions.

  6. High Performance Embedded System for Real-Time Pattern Matching

    CERN Document Server

    Sotiropoulou, Calliope Louisa; The ATLAS collaboration; Gkaitatzis, Stamatios; Citraro, Saverio; Giannetti, Paola; Dell'Orso, Mauro

    2016-01-01

    In this paper we present an innovative and high performance embedded system for real-time pattern matching. This system is based on the evolution of hardware and algorithms developed for the field of High Energy Physics (HEP) and more specifically for the execution of extremely fast pattern matching for tracking of particles produced by proton-proton collisions in hadron collider experiments. A miniaturised version of this complex system is being developed for pattern matching in generic image processing applications. The system works as a contour identifier able to extract the salient features of an image. It is based on the principles of cognitive image processing, which means that it executes fast pattern matching and data reduction mimicking the operation of the human brain. The pattern matching can be executed by a custom designed Associative Memory (AM) chip. The reference patterns are chosen by a complex training algorithm implemented on an FPGA device. Post processing algorithms (e.g. pixel clustering...

  7. Time activity patterns: a case of south Durban, South Africa

    CSIR Research Space (South Africa)

    Matooane, M

    2010-08-01

    Full Text Available be insufficient to adequately represent the time-activity patterns of the south Durban population. Particular factors include, among others, the amount of time spent in varying microenvironments and the drivers for time spent in these microenvironments. Therefore...

  8. Response time patterns in a stated choice experiment

    DEFF Research Database (Denmark)

    Börjesson, Maria; Fosgerau, Mogens

    2015-01-01

    This paper studies how response times vary between unlabelled binary choice occasions in a stated choice (SC) experiment, with alternatives differing with respect to in-vehicle travel time and travel cost. The pattern of response times is interpreted as an indicator of the cognitive processes emp...

  9. Scene Context Dependency of Pattern Constancy of Time Series Imagery

    Science.gov (United States)

    Woodell, Glenn A.; Jobson, Daniel J.; Rahman, Zia-ur

    2008-01-01

    A fundamental element of future generic pattern recognition technology is the ability to extract similar patterns for the same scene despite wide ranging extraneous variables, including lighting, turbidity, sensor exposure variations, and signal noise. In the process of demonstrating pattern constancy of this kind for retinex/visual servo (RVS) image enhancement processing, we found that the pattern constancy performance depended somewhat on scene content. Most notably, the scene topography and, in particular, the scale and extent of the topography in an image, affects the pattern constancy the most. This paper will explore these effects in more depth and present experimental data from several time series tests. These results further quantify the impact of topography on pattern constancy. Despite this residual inconstancy, the results of overall pattern constancy testing support the idea that RVS image processing can be a universal front-end for generic visual pattern recognition. While the effects on pattern constancy were significant, the RVS processing still does achieve a high degree of pattern constancy over a wide spectrum of scene content diversity, and wide ranging extraneousness variations in lighting, turbidity, and sensor exposure.

  10. Patterns across multiple memories are identified over time.

    Science.gov (United States)

    Richards, Blake A; Xia, Frances; Santoro, Adam; Husse, Jana; Woodin, Melanie A; Josselyn, Sheena A; Frankland, Paul W

    2014-07-01

    Memories are not static but continue to be processed after encoding. This is thought to allow the integration of related episodes via the identification of patterns. Although this idea lies at the heart of contemporary theories of systems consolidation, it has yet to be demonstrated experimentally. Using a modified water-maze paradigm in which platforms are drawn stochastically from a spatial distribution, we found that mice were better at matching platform distributions 30 d compared to 1 d after training. Post-training time-dependent improvements in pattern matching were associated with increased sensitivity to new platforms that conflicted with the pattern. Increased sensitivity to pattern conflict was reduced by pharmacogenetic inhibition of the medial prefrontal cortex (mPFC). These results indicate that pattern identification occurs over time, which can lead to conflicts between new information and existing knowledge that must be resolved, in part, by computations carried out in the mPFC.

  11. List and Text Recall Differ in Their Predictors: Replication Over Samples and Time

    Science.gov (United States)

    Lewis, Kayan L.

    2010-01-01

    This study tested the hypothesis that latent list and text recall invoke somewhat different processes. A bivariate outcome path model of latent list and text recall evaluated the effects of age, latent speed, working memory, and vocabulary as their predictors. Independent of age, working memory reliably predicted both recall variables, whereas speed reliably predicted list recall only. The relationship between vocabulary and recall was mediated by age, working memory, and speed. The generalizability of this model, based on data from the 1994 testing of the Long Beach Longitudinal Study, was evaluated across samples by testing its invariance on baseline data from an additional panel and for eventual attrition at baseline and at a subsequent testing of retested participants and dropouts. Results showed that the model was invariant over all groups, supporting a replicable distinction between list and text recall. PMID:20498454

  12. High Performance Embedded System for Real-Time Pattern Matching

    CERN Document Server

    Sotiropoulou, Calliope Louisa; The ATLAS collaboration; Gkaitatzis, Stamatios; Citraro, Saverio; Giannetti, Paola; Dell'Orso, Mauro

    2016-01-01

    We present an innovative and high performance embedded system for real-time pattern matching. This system is based on the evolution of hardware and algorithms developed for the field of High Energy Physics (HEP) and more specifically for the execution of extremely fast pattern matching for tracking of particles produced by proton-proton collisions in hadron collider experiments. A miniaturized version of this complex system is being developed for pattern matching in generic image processing applications. The design uses the flexibility of Field Programmable Gate Arrays (FPGAs) and the powerful Associative Memory Chip (ASIC) to achieve real-time performance. The system works as a contour identifier able to extract the salient features of an image. It is based on the principles of cognitive image processing, which means that it executes fast pattern matching and data reduction mimicking the operation of the human brain.

  13. The impact of sampling, PCR, and sequencing replication on discerning changes in drinking water bacterial community over diurnal time-scales.

    Science.gov (United States)

    Bautista-de Los Santos, Quyen Melina; Schroeder, Joanna L; Blakemore, Oliver; Moses, Jonathan; Haffey, Mark; Sloan, William; Pinto, Ameet J

    2016-03-01

    High-throughput and deep DNA sequencing, particularly amplicon sequencing, is being increasingly utilized to reveal spatial and temporal dynamics of bacterial communities in drinking water systems. Whilst the sampling and methodological biases associated with PCR and sequencing have been studied in other environments, they have not been quantified for drinking water. These biases are likely to have the greatest effect on the ability to characterize subtle spatio-temporal patterns influenced by process/environmental conditions. In such cases, intra-sample variability may swamp any underlying small, systematic variation. To evaluate this, we undertook a study with replication at multiple levels including sampling sites, sample collection, PCR amplification, and high throughput sequencing of 16S rRNA amplicons. The variability inherent to the PCR amplification and sequencing steps is significant enough to mask differences between bacterial communities from replicate samples. This was largely driven by greater variability in detection of rare bacteria (relative abundance water use. This suggests hydraulic changes (driven by changes in water demand) contribute to shaping the bacterial community in bulk drinking water over diurnal time-scales.

  14. Real-Time Design Patterns for LVC Simulation

    Science.gov (United States)

    2009-01-15

    Possible. (But Must Get Done at Some Point) MVC Pattern (Tailored for LVC) MVC Pattern  Model is the Application’s Domain Logic  It’s the Simulation...View is the Application’s Graphical Displays  Controller Connects Model to View(s) Adapted MVC Pattern  Asynchronous Execution of Simulated System...Graphics and Network I/O  Architecture Maps to Real-time Design Paradigms  Good “Fit” for LVC Requirements  Leverages Multi-CPU & Multi-core

  15. High performance embedded system for real-time pattern matching

    Science.gov (United States)

    Sotiropoulou, C.-L.; Luciano, P.; Gkaitatzis, S.; Citraro, S.; Giannetti, P.; Dell'Orso, M.

    2017-02-01

    In this paper we present an innovative and high performance embedded system for real-time pattern matching. This system is based on the evolution of hardware and algorithms developed for the field of High Energy Physics and more specifically for the execution of extremely fast pattern matching for tracking of particles produced by proton-proton collisions in hadron collider experiments. A miniaturized version of this complex system is being developed for pattern matching in generic image processing applications. The system works as a contour identifier able to extract the salient features of an image. It is based on the principles of cognitive image processing, which means that it executes fast pattern matching and data reduction mimicking the operation of the human brain. The pattern matching can be executed by a custom designed Associative Memory chip. The reference patterns are chosen by a complex training algorithm implemented on an FPGA device. Post processing algorithms (e.g. pixel clustering) are also implemented on the FPGA. The pattern matching can be executed on a 2D or 3D space, on black and white or grayscale images, depending on the application and thus increasing exponentially the processing requirements of the system. We present the firmware implementation of the training and pattern matching algorithm, performance and results on a latest generation Xilinx Kintex Ultrascale FPGA device.

  16. Chromatin replication and epigenome maintenance

    DEFF Research Database (Denmark)

    Alabert, Constance; Groth, Anja

    2012-01-01

    initiates, whereas the replication process itself disrupts chromatin and challenges established patterns of genome regulation. Specialized replication-coupled mechanisms assemble new DNA into chromatin, but epigenome maintenance is a continuous process taking place throughout the cell cycle. If DNA...

  17. Chromatin replication and epigenome maintenance

    DEFF Research Database (Denmark)

    Alabert, Constance; Groth, Anja

    2012-01-01

    initiates, whereas the replication process itself disrupts chromatin and challenges established patterns of genome regulation. Specialized replication-coupled mechanisms assemble new DNA into chromatin, but epigenome maintenance is a continuous process taking place throughout the cell cycle. If DNA...

  18. Nonlinear effects on Turing patterns: Time oscillations and chaos

    KAUST Repository

    Aragón, J. L.

    2012-08-08

    We show that a model reaction-diffusion system with two species in a monostable regime and over a large region of parameter space produces Turing patterns coexisting with a limit cycle which cannot be discerned from the linear analysis. As a consequence, the patterns oscillate in time. When varying a single parameter, a series of bifurcations leads to period doubling, quasiperiodic, and chaotic oscillations without modifying the underlying Turing pattern. A Ruelle-Takens-Newhouse route to chaos is identified. We also examine the Turing conditions for obtaining a diffusion-driven instability and show that the patterns obtained are not necessarily stationary for certain values of the diffusion coefficients. These results demonstrate the limitations of the linear analysis for reaction-diffusion systems. © 2012 American Physical Society.

  19. Space-Time Analysis of Crime Patterns in Central London

    Science.gov (United States)

    Cheng, T.; Williams, D.

    2012-07-01

    Crime continues to cast a shadow over citizen well-being in big cities today, while also imposing huge economic and social costs. Timely understanding of how criminality emerges and how crime patterns evolve is crucial to anticipating crime, dealing with it when it occurs and developing public confidence in the police service. Every day, about 10,000 crime incidents are reported by citizens, recorded and geo-referenced in the London Metropolitan Police Service Computer Aided Dispatch (CAD) database. The unique nature of this dataset allows the patterns to be explored at particularly fine temporal granularity and at multiple spatial resolutions. This study provides a framework for the exploratory spatio-temporal analysis of crime patterns that combines visual inquiry tools (interactive animations, space-time cubes and map matrices) with cluster analysis (spatial-temporal scan statistics and the self-organizing map). This framework is tested on the CAD dataset for the London Borough of Camden in March 2010. Patterns of crime through space and time are discovered and the clustering methods were evaluated on their ability to facilitate the discovery and interpretation of these patterns.

  20. Time frequency analysis of Jovian and Saturnian radio spectral patterns

    Science.gov (United States)

    Boudjada, Mohammed Y.; Galopeau, Patrick H. M.; Al-Haddad, Emad; Lammer, Helmut

    2016-04-01

    Prominent radio spectral patterns were observed by the Cassini Radio and Plasma Wave Science experiment (RPWS) principally at Jupiter and Saturn. The spectral shapes are displayed in the usual dynamic spectra showing the flux density versus the time and the frequency. Those patterns exhibit well-organized shapes in the time-frequency plane connected with the rotation of the planet. We consider in this analysis the auroral emissions which occurred in the frequency range between 10 kHz and approximately 3 MHz. It concerns the Jovian hectometric emission (HOM) and the Saturnian kilometric radiation (SKR). We show in the case of Jupiter's HOM that the spectral patterns are well-arranged arc structures with curvatures depending on the Jovian rotation. Regarding the SKR emission, the spectral shapes exhibit generally complex patterns, and only sometimes arc structures are observed. We emphasize the curve alterations from vertex-early to vertex-late arcs (and vice versa) and we study their dependences, or not, on the planetary rotations. We also discuss the common physical process at the origin of the HOM and SKR emissions, specifically the spectral patterns created by the interaction between planetary satellites (e.g. Io or Dione) and the Jovian and Saturnian magnetospheres.

  1. DNA replication timing is maintained genome-wide in primary human myoblasts independent of D4Z4 contraction in FSH muscular dystrophy.

    Directory of Open Access Journals (Sweden)

    Benjamin D Pope

    Full Text Available Facioscapulohumeral muscular dystrophy (FSHD is linked to contraction of an array of tandem 3.3-kb repeats (D4Z4 at 4q35.2 from 11-100 copies to 1-10 copies. The extent to which D4Z4 contraction at 4q35.2 affects overall 4q35.2 chromatin organization remains unclear. Because DNA replication timing is highly predictive of long-range chromatin interactions, we generated genome-wide replication-timing profiles for FSHD and control myogenic precursor cells. We compared non-immortalized myoblasts from four FSHD patients and three control individuals to each other and to a variety of other human cell types. This study also represents the first genome-wide comparison of replication timing profiles in non-immortalized human cell cultures. Myoblasts from both control and FSHD individuals all shared a myoblast-specific replication profile. In contrast, male and female individuals were readily distinguished by monoallelic differences in replication timing at DXZ4 and other regions across the X chromosome affected by X inactivation. We conclude that replication timing is a robust cell-type specific feature that is unaffected by FSHD-related D4Z4 contraction.

  2. The sense, landscape and image. How the tourist destination is replicated in postmodernist times

    Directory of Open Access Journals (Sweden)

    Maximiliano E. Korstanje

    2013-07-01

    Full Text Available Policy makers, practitioners and analysts have focused on the psychology to induce consumers to new products. These new eye-catching packaging products in tourism and hospitality industries and beyond are commercialized to thousands of home thanks to the media. We are living in times, digital times where organic image plays a pivotal role in arousing emotions and experiences, although these experiences were not authentic. Following this discussion, initialized some time ago by D. Maccannell and other sociologists, the present paper explores the philosophical roots of image to expand the current understanding about our ocular-centrism. At time, tourists select a destination, they are moved by “the wish of majority”, but once destination is maturated, its attractiveness declines. What seems to be interesting to discuss here is the connection between perceived safety (risk and attraction (organic image. Following I. Kant’s contributions, we present a conceptual model to understand how the dilemma of safety leads consumers to visual pollution.

  3. The sense, landscape and image. How the tourist destination is replicated in postmodernist times

    Directory of Open Access Journals (Sweden)

    Maximiliano E. Korstanje

    2013-01-01

    Full Text Available Policy makers, practitioners and analysts have focused on the psychology to induce consumers to new products. These new eye-catching packaging products in tourism and hospitality industries and beyond are commercialized to thousands of home thanks to the media. We are living in times, digital times where organic image plays a pivotal role in arousing emotions and experiences, although these experiences were not authentic. Following this discussion, initialized some time ago by D. Maccannell and other sociologists, the present paper explores the philosophical roots of image to expand the current understanding about our ocular-centrism. At time, tourists select a destination, they are moved by “the wish of majority”, but once destination is maturated, its attractiveness declines. What seems to be inter- esting to discuss here is the connection between perceived safety (risk and attraction (organic image. Following I. Kant’s contributions, we present a conceptual model to understand how the dilemma of safety leads consumers to visual pollution.

  4. Negative Correlates of Part-Time Employment during Adolescence: Replication and Elaboration.

    Science.gov (United States)

    Steinberg, Laurence; Dornbusch, Sanford M.

    This study examined the relation between part-time employment and adolescent behavior and development in a multi-ethnic, multi-class sample of approximately 4,000 15- through 18-year-olds. The results indicated that long work hours during the school year were associated with diminished investment in schooling and lowered school performance,…

  5. Diversity and dynamics of dominant and rare bacterial taxa in replicate sequencing batch reactors operated under different solids retention time

    KAUST Repository

    Bagchi, Samik

    2014-10-19

    In this study, 16S rRNA gene pyrosequencing was applied in order to provide a better insight on the diversity and dynamics of total, dominant, and rare bacterial taxa in replicate lab-scale sequencing batch reactors (SBRs) operated at different solids retention time (SRT). Rank-abundance curves showed few dominant operational taxonomic units (OTUs) and a long tail of rare OTUs in all reactors. Results revealed that there was no detectable effect of SRT (2 vs. 10 days) on Shannon diversity index and OTU richness of both dominant and rare taxa. Nonmetric multidimensional scaling analysis showed that the total, dominant, and rare bacterial taxa were highly dynamic during the entire period of stable reactor performance. Also, the rare taxa were more dynamic than the dominant taxa despite expected low invasion rates because of the use of sterile synthetic media.

  6. Time Curves: Folding Time to Visualize Patterns of Temporal Evolution in Data.

    Science.gov (United States)

    Bach, Benjamin; Shi, Conglei; Heulot, Nicolas; Madhyastha, Tara; Grabowski, Tom; Dragicevic, Pierre

    2016-01-01

    We introduce time curves as a general approach for visualizing patterns of evolution in temporal data. Examples of such patterns include slow and regular progressions, large sudden changes, and reversals to previous states. These patterns can be of interest in a range of domains, such as collaborative document editing, dynamic network analysis, and video analysis. Time curves employ the metaphor of folding a timeline visualization into itself so as to bring similar time points close to each other. This metaphor can be applied to any dataset where a similarity metric between temporal snapshots can be defined, thus it is largely datatype-agnostic. We illustrate how time curves can visually reveal informative patterns in a range of different datasets.

  7. Substrate size rather than heterogeneity controls downstream travel time distributions in replicate small streams

    Science.gov (United States)

    Aubeneau, A. F.; Hanrahan, B.; Tank, J. L.; Bolster, D.

    2013-12-01

    Dissolved solutes are exported from watersheds with water flow and fluxes are therefore influenced by advection, that carries them further, but also retention processes, that delay their travel. It is especially important to understand the factors controlling network solute retention for biogeoreactive species that can be processed if afforded extended residence. In alluvial systems, substrate characteristics play a crucial role in slowing downstream transport. The roughness size (i.e., grain size relative to water depth) is associated with the distortion of the velocity profile and therefore is related to short term delays from additional dispersion. Surface and subsurface water also continually turn over, creating longer delays in the slow-flowing hyporheic region below the water/sediment interface. Sediment structure could also control transport, as pockets of slower hydraulic conductivity may influence the longest travel times. We present results from multiple solute injection experiments testing the influence of sediment size (pea gravel vs. coarse gravel) and heterogeneity (alternating sections vs. well mixed) on solute transport dynamics in four experimental streams located at the Notre Dame Linked Experimental Ecosystem Facility (ND-LEEF). We show that the stream with homogeneously coarse gravel induced more short-term delays but less long-term retention than the stream with smaller pea gravel. Inverse modeling suggested that the short-term delays were exponentially distributed while the long-term retention followed a truncated power-law behavior. Even though transport in all four streams was anomalous, the scaling truncation time was influenced by sediment size, with the smaller pea gravel exhibiting scaling longer than the coarse gravel. Streams with heterogeneous substrate had an intermediate cut-off. These results uniquely associate transport scaling in fluvial systems and substrate characteristics. The streams revealed truncation timescales that had

  8. Mining approximate periodic pattern in hydrological time series

    Science.gov (United States)

    Zhu, Y. L.; Li, S. J.; Bao, N. N.; Wan, D. S.

    2012-04-01

    There is a lot of information about the hidden laws of nature evolution and the influences of human beings activities on the earth surface in long sequence of hydrological time series. Data mining technology can help find those hidden laws, such as flood frequency and abrupt change, which is useful for the decision support of hydrological prediction and flood control scheduling. The periodic nature of hydrological time series is important for trend forecasting of drought and flood and hydraulic engineering planning. In Hydrology, the full period analysis of hydrological time series has attracted a lot of attention, such as the discrete periodogram, simple partial wave method, Fourier analysis method, and maximum entropy spectral analysis method and wavelet analysis. In fact, the hydrological process is influenced both by deterministic factors and stochastic ones. For example, the tidal level is also affected by moon circling the Earth, in addition to the Earth revolution and its rotation. Hence, there is some kind of approximate period hidden in the hydrological time series, sometimes which is also called the cryptic period. Recently, partial period mining originated from the data mining domain can be a remedy for the traditional period analysis methods in hydrology, which has a loose request of the data integrity and continuity. They can find some partial period in the time series. This paper is focused on the partial period mining in the hydrological time series. Based on asynchronous periodic pattern and partial period mining with suffix tree, this paper proposes to mine multi-event asynchronous periodic pattern based on modified suffix tree representation and traversal, and invent a dynamic candidate period intervals adjusting method, which can avoids period omissions or waste of time and space. The experimental results on synthetic data and real water level data of the Yangtze River at Nanjing station indicate that this algorithm can discover hydrological

  9. Demand Flexibility Time Intervals for Aggregate Residential Load Patterns

    OpenAIRE

    Sajjad, Intisar A.; CHICCO Gianfranco; Napoli, Roberto

    2015-01-01

    This paper deals with the definition of demand flexibility time intervals. These intervals are extracted from the binomial probability model of load variation patterns with the two possible categories of increase and non-increase in demand. These intervals along with the information on the coefficient of variation of the aggregate demand are used to assess the potential of demand flexibility exhibited by the aggregate residential demand in different periods of the day. The results of the prop...

  10. Understanding the timing and magnitude of advertising spending patterns.

    OpenAIRE

    Gijsenberg, Maarten; van Heerde, Harald J.; Dekimpe, Marnik; Jan-Benedict E M Steenkamp; Nijs, Vincent R.

    2009-01-01

    Notwithstanding the fact that advertising is one of the most used marketing tools, little is known about what is driving (i) the timing and (ii) the magnitude of advertising actions. Building on normative theory, the authors develop a parsimonious model that captures this dual investment process. They explain advertising spending patterns as observed in the market, and investigate the impact of company, competitive, and category-related factors on these decisions, thereby introducing the nove...

  11. Time-dependent scaling patterns in high frequency financial data

    Science.gov (United States)

    Nava, Noemi; Di Matteo, Tiziana; Aste, Tomaso

    2016-10-01

    We measure the influence of different time-scales on the intraday dynamics of financial markets. This is obtained by decomposing financial time series into simple oscillations associated with distinct time-scales. We propose two new time-varying measures of complexity: 1) an amplitude scaling exponent and 2) an entropy-like measure. We apply these measures to intraday, 30-second sampled prices of various stock market indices. Our results reveal intraday trends where different time-horizons contribute with variable relative amplitudes over the course of the trading day. Our findings indicate that the time series we analysed have a non-stationary multifractal nature with predominantly persistent behaviour at the middle of the trading session and anti-persistent behaviour at the opening and at the closing of the session. We demonstrate that these patterns are statistically significant, robust, reproducible and characteristic of each stock market. We argue that any modelling, analytics or trading strategy must take into account these non-stationary intraday scaling patterns.

  12. A personal reflection on the replicon theory: from R1 plasmid to replication timing regulation in human cells.

    Science.gov (United States)

    Masai, Hisao

    2013-11-29

    Fifty years after the Replicon Theory was originally presented, detailed mechanistic insight into prokaryotic replicons has been obtained and rapid progress is being made to elucidate the more complex regulatory mechanisms of replicon regulation in eukaryotic cells. Here, I present my personal perspectives on how studies of model replicons have contributed to our understanding of the basic mechanisms of DNA replication as well as the evolution of replication regulation in human cells. I will also discuss how replication regulation contributes to the stable maintenance of the genome and how disruption of replication regulation leads to human diseases.

  13. Temporal patterns in adult salmon migration timing across southeast Alaska

    Science.gov (United States)

    Kovach, Ryan P.; Ellison, Stephen; Pyare, Sanjay; Tallmon, David

    2015-01-01

    Pacific salmon migration timing can drive population productivity, ecosystem dynamics, and human harvest. Nevertheless, little is known about long-term variation in salmon migration timing for multiple species across broad regions. We used long-term data for five Pacific salmon species throughout rapidly warming southeast Alaska to describe long-term changes in salmon migration timing, interannual phenological synchrony, relationships between climatic variation and migratory timing, and to test whether long-term changes in migration timing are related to glaciation in headwater streams. Temporal changes in the median date of salmon migration timing varied widely across species. Most sockeye populations are migrating later over time (11 of 14), but pink, chum, and especially coho populations are migrating earlier than they did historically (16 of 19 combined). Temporal trends in duration and interannual variation in migration timing were highly variable across species and populations. The greatest temporal shifts in the median date of migration timing were correlated with decreases in the duration of migration timing, suggestive of a loss of phenotypic variation due to natural selection. Pairwise interannual correlations in migration timing varied widely but were generally positive, providing evidence for weak region-wide phenological synchrony. This synchrony is likely a function of climatic variation, as interannual variation in migration timing was related to climatic phenomenon operating at large- (Pacific decadal oscillation), moderate- (sea surface temperature), and local-scales (precipitation). Surprisingly, the presence or the absence of glaciers within a watershed was unrelated to long-term shifts in phenology. Overall, there was extensive heterogeneity in long-term patterns of migration timing throughout this climatically and geographically complex region, highlighting that future climatic change will likely have widely divergent impacts on salmon

  14. Microenvironmental time-activity patterns in Chongqing, China

    Institute of Scientific and Technical Information of China (English)

    Yu ZHAO; Shuxiao WANG; Gangcai CHEN; Fei WANG; Kristin AUNAN; Jiming HAO

    2009-01-01

    An investigation using recall questionnaires was conducted in winter and autumn 2006 to evaluate the time-activity patterns in Chongqing, China. The average time spent in seven microenvironments (MEs) including outdoors, transit, living room, bedroom, kitchen, classroom/office, and other indoors were found to be about 3.5,1.1, 2.5, 9.7, 1.4, 4.2, and 1.7 h per day, respectively.According to the results of a nonparametric test, the sampling period and day of week were significant for the variation of the time spent in all MEs except for transit and outdoors. The time budget was analyzed using a general linear model (GLM), which exhibited significant variability by demographic factors such as gender, age,residence, education, and household income.

  15. Spatial patterns of ecosystem carbon residence time in Chinese forests

    Institute of Scientific and Technical Information of China (English)

    2010-01-01

    Capacity of carbon sequestration in forest ecosystem largely depends on the trend of net primary production (NPP) and the length of ecosystem carbon residence time. Retrieving spatial patterns of ecosystem carbon residence time is important and necessary for accurately predicting regional carbon cycles in the future. In this study, a data-model fusion method that combined a process-based regional carbon model (TECO-R) with various ground-based ecosystem observations (NPP, biomass, and soil organic carbon) and auxiliary data sets (NDVI, meteorological data, and maps of vegetation and soil texture) was applied to estimate spatial patterns of ecosystem carbon residence time in Chinese forests at steady state. In the data-model fusion, the genetic algorithm was used to estimate the optimal model parameters related with the ecosystem carbon residence time by minimizing total deviation between modeled and observed values. The results indicated that data-model fusion technology could effectively retrieve model parameters and simulate carbon cycling processes for Chinese forest ecosystems. The estimated carbon residence times were highly heterogenous over China, with most of regions having values between 24 and 70 years. The deciduous needleleaf forest and the evergreen needleleaf forest had the highest averaged carbon residence times (73.8 and 71.3 years, respectively), the mixed forest and the deciduous broadleaf forest had moderate values (38.1 and 37.3 years, respectively), and the evergreen broadleaf forest had the lowest value (31.7 years). The averaged carbon residence time of forest ecosystems in China was 57.8 years.

  16. Initiation of adenovirus DNA replication.

    OpenAIRE

    Reiter, T; Fütterer, J; Weingärtner, B; Winnacker, E L

    1980-01-01

    In an attempt to study the mechanism of initiation of adenovirus DNA replication, an assay was developed to investigate the pattern of DNA synthesis in early replicative intermediates of adenovirus DNA. By using wild-type virus-infected cells, it was possible to place the origin of adenovirus type 2 DNA replication within the terminal 350 to 500 base pairs from either of the two molecular termini. In addition, a variety of parameters characteristic of adenovirus DNA replication were compared ...

  17. Chromatin replication and epigenome maintenance

    DEFF Research Database (Denmark)

    Alabert, Constance; Groth, Anja

    2012-01-01

    Stability and function of eukaryotic genomes are closely linked to chromatin structure and organization. During cell division the entire genome must be accurately replicated and the chromatin landscape reproduced on new DNA. Chromatin and nuclear structure influence where and when DNA replication...... initiates, whereas the replication process itself disrupts chromatin and challenges established patterns of genome regulation. Specialized replication-coupled mechanisms assemble new DNA into chromatin, but epigenome maintenance is a continuous process taking place throughout the cell cycle. If DNA...

  18. Temperature and solids retention time control microbial population dynamics and volatile fatty acid production in replicated anaerobic digesters

    Science.gov (United States)

    Vanwonterghem, Inka; Jensen, Paul D.; Rabaey, Korneel; Tyson, Gene W.

    2015-02-01

    Anaerobic digestion is a widely used technology for waste stabilization and generation of biogas, and has recently emerged as a potentially important process for the production of high value volatile fatty acids (VFAs) and alcohols. Here, three reactors were seeded with inoculum from a stably performing methanogenic digester, and selective operating conditions (37°C and 55°C 12 day and 4 day solids retention time) were applied to restrict methanogenesis while maintaining hydrolysis and fermentation. Replicated experiments performed at each set of operating conditions led to reproducible VFA production profiles which could be correlated with specific changes in microbial community composition. The mesophilic reactor at short solids retention time showed accumulation of propionate and acetate (42 +/- 2% and 15 +/- 6% of CODhydrolyzed, respectively), and dominance of Fibrobacter and Bacteroidales. Acetate accumulation (>50% of CODhydrolyzed) was also observed in the thermophilic reactors, which were dominated by Clostridium. Under all tested conditions, there was a shift from acetoclastic to hydrogenotrophic methanogenesis, and a reduction in methane production by >50% of CODhydrolyzed. Our results demonstrate that shortening the SRT and increasing the temperature are effective strategies for driving microbial communities towards controlled production of high levels of specific volatile fatty acids.

  19. Common scaling patterns in intertrade times of U. S. stocks.

    Science.gov (United States)

    Ivanov, Plamen Ch; Yuen, Ainslie; Podobnik, Boris; Lee, Youngki

    2004-05-01

    We analyze the sequence of time intervals between consecutive stock trades of thirty companies representing eight sectors of the U.S. economy over a period of 4 yrs. For all companies we find that: (i) the probability density function of intertrade times may be fit by a Weibull distribution, (ii) when appropriately rescaled the probability densities of all companies collapse onto a single curve implying a universal functional form, (iii) the intertrade times exhibit power-law correlated behavior within a trading day and a consistently greater degree of correlation over larger time scales, in agreement with the correlation behavior of the absolute price returns for the corresponding company, and (iv) the magnitude series of intertrade time increments is characterized by long-range power-law correlations suggesting the presence of nonlinear features in the trading dynamics, while the sign series is anticorrelated at small scales. Our results suggest that independent of industry sector, market capitalization and average level of trading activity, the series of intertrade times exhibit possibly universal scaling patterns, which may relate to a common mechanism underlying the trading dynamics of diverse companies. Further, our observation of long-range power-law correlations and a parallel with the crossover in the scaling of absolute price returns for each individual stock, support the hypothesis that the dynamics of transaction times may play a role in the process of price formation.

  20. Food pattern analysis over time: unhealthful eating trajectories predict obesity.

    Science.gov (United States)

    Pachucki, M A

    2012-05-01

    Analysis of dietary patterns is prominent in nutrition literatures, yet few studies have taken advantage of multiple repeated measurements to understand the nature of individual-level changes over time in food choice, or the relation between these changes and body mass index (BMI). To investigate changes in eating patterns at the individual level across three exam periods, and to prospectively examine the relation of eating trajectories to BMI at the cohort level. The study included 3418 participants at baseline. Clinically measured BMI and dietary intake were assessed during three exam periods between 1991 and 2001 using a validated food frequency questionnaire. An individual's eating trajectory across exam periods was analyzed using sequence analysis, and then used to estimate outcomes of continuous BMI and categorical obesity status. Ordinary least squares regression models with robust standard errors were adjusted for socio-economic and demographic confounders, baseline BMI and baseline eating. A total of 66.2% (n=1614) of participants change their diet pattern during the study period, 33.8% (n=823) remain stable. After accounting for potential confounders, an unhealthful trajectory is significantly associated with a 0.42 kg m(-2) increase in BMI (confidence interval (CI): 0.1, 0.7). Those with an unhealthful trajectory are 1.79 times more likely to be overweight (relative risk ratio, 95% CI: 1.1, 2.8) and 2.4 times more likely to be obese (relative risk ratio, 95% CI: 1.3, 4.4). Moreover, a number of specific diet transitions between exams are predictive of weight gain or loss. Contextualizing an individual's current eating behaviors with an eye towards diet history may be an important boon in the reduction of obesity. Although it may not be realistic for many people to shift from the least to most healthful diet, results from this study suggest that consistent movement in an overall healthier direction is associated with less weight gain.

  1. DNA sequence, products, and transcriptional pattern of the genes involved in production of the DNA replication inhibitor microcin B17.

    Science.gov (United States)

    Genilloud, O; Moreno, F; Kolter, R

    1989-02-01

    The 3.8-kilobase segment of plasmid DNA that contains the genes required for production of the DNA replication inhibitor microcin B17 was sequenced. The sequence contains four open reading frames which were shown to be translated in vivo by the construction of fusions to lacZ. The location of these open reading frames fits well with the location of the four microcin B17 production genes, mcbABCD, identified previously through genetic complementation. The products of the four genes have been identified, and the observed molecular weights of the proteins agree with those predicted from the nucleotide sequence. The transcription of these genes was studied by using fusions to lacZ and physical mapping of mRNA start sites. Three promoters were identified in this region. The major promoter for all the genes is a growth phase-regulated OmpR-dependent promoter located upstream of mcbA. A second promoter is located within mcbC and is responsible for a low-level basal expression of mcbD. A third promoter, located within mcbD, promotes transcription in the reverse direction starting within mcbD and extending through mcbC. The resulting mRNA appears to be an untranslated antisense transcript that could play a regulatory role in the expression of these genes.

  2. Classification of time series patterns from complex dynamic systems

    Energy Technology Data Exchange (ETDEWEB)

    Schryver, J.C.; Rao, N.

    1998-07-01

    An increasing availability of high-performance computing and data storage media at decreasing cost is making possible the proliferation of large-scale numerical databases and data warehouses. Numeric warehousing enterprises on the order of hundreds of gigabytes to terabytes are a reality in many fields such as finance, retail sales, process systems monitoring, biomedical monitoring, surveillance and transportation. Large-scale databases are becoming more accessible to larger user communities through the internet, web-based applications and database connectivity. Consequently, most researchers now have access to a variety of massive datasets. This trend will probably only continue to grow over the next several years. Unfortunately, the availability of integrated tools to explore, analyze and understand the data warehoused in these archives is lagging far behind the ability to gain access to the same data. In particular, locating and identifying patterns of interest in numerical time series data is an increasingly important problem for which there are few available techniques. Temporal pattern recognition poses many interesting problems in classification, segmentation, prediction, diagnosis and anomaly detection. This research focuses on the problem of classification or characterization of numerical time series data. Highway vehicles and their drivers are examples of complex dynamic systems (CDS) which are being used by transportation agencies for field testing to generate large-scale time series datasets. Tools for effective analysis of numerical time series in databases generated by highway vehicle systems are not yet available, or have not been adapted to the target problem domain. However, analysis tools from similar domains may be adapted to the problem of classification of numerical time series data.

  3. Spatial patterns in timing of the diurnal temperature cycle

    Directory of Open Access Journals (Sweden)

    T. R. H. Holmes

    2013-10-01

    Full Text Available This paper investigates the structural difference in timing of the diurnal temperature cycle (DTC over land resulting from choice of measuring device or model framework. It is shown that the timing can be reliably estimated from temporally sparse observations acquired from a constellation of low Earth-orbiting satellites given record lengths of at least three months. Based on a year of data, the spatial patterns of mean DTC timing are compared between temperature estimates from microwave Ka-band, geostationary thermal infrared (TIR, and numerical weather prediction model output from the Global Modeling and Assimilation Office (GMAO. It is found that the spatial patterns can be explained by vegetation effects, sensing depth differences and more speculatively the orientation of orographic relief features. In absolute terms, the GMAO model puts the peak of the DTC on average at 12:50 local solar time, 23 min before TIR with a peak temperature at 13:13 (both averaged over Africa and Europe. Since TIR is the shallowest observation of the land surface, this small difference represents a structural error that possibly affects the model's ability to assimilate observations that are closely tied to the DTC. The equivalent average timing for Ka-band is 13:44, which is influenced by the effect of increased sensing depth in desert areas. For non-desert areas, the Ka-band observations lag the TIR observations by only 15 min, which is in agreement with their respective theoretical sensing depth. The results of this comparison provide insights into the structural differences between temperature measurements and models, and can be used as a first step to account for these differences in a coherent way.

  4. Transmission of linear regression patterns between time series: from relationship in time series to complex networks.

    Science.gov (United States)

    Gao, Xiangyun; An, Haizhong; Fang, Wei; Huang, Xuan; Li, Huajiao; Zhong, Weiqiong; Ding, Yinghui

    2014-07-01

    The linear regression parameters between two time series can be different under different lengths of observation period. If we study the whole period by the sliding window of a short period, the change of the linear regression parameters is a process of dynamic transmission over time. We tackle fundamental research that presents a simple and efficient computational scheme: a linear regression patterns transmission algorithm, which transforms linear regression patterns into directed and weighted networks. The linear regression patterns (nodes) are defined by the combination of intervals of the linear regression parameters and the results of the significance testing under different sizes of the sliding window. The transmissions between adjacent patterns are defined as edges, and the weights of the edges are the frequency of the transmissions. The major patterns, the distance, and the medium in the process of the transmission can be captured. The statistical results of weighted out-degree and betweenness centrality are mapped on timelines, which shows the features of the distribution of the results. Many measurements in different areas that involve two related time series variables could take advantage of this algorithm to characterize the dynamic relationships between the time series from a new perspective.

  5. The role of time and species identities in spatial patterns of species richness and conservation.

    Science.gov (United States)

    Hewitt, Judi E; Thrush, Simon F; Ellingsen, Kari E

    2016-10-01

    Many conservation actions are justified on the basis of managing biodiversity. Biodiversity, in terms of species richness, is largely the product of rare species. This is problematic because the intensity of sampling needed to characterize communities and patterns of rarity or to justify the use of surrogates has biased sampling in favor of space over time. However, environmental fluctuations interacting with community dynamics lead to temporal variations in where and when species occur, potentially affecting conservation planning by generating uncertainty about results of species distribution modeling (including range determinations), selection of surrogates for biodiversity, and the proportion of biodiversity composed of rare species. To have confidence in the evidence base for conservation actions, one must consider whether temporal replication is necessary to produce broad inferences. Using approximately 20 years of macrofaunal data from tidal flats in 2 harbors, we explored variation in the identity of rare, common, restricted range, and widespread species over time and space. Over time, rare taxa were more likely to increase in abundance or occurrence than to remain rare or disappear and to exhibit temporal patterns in their occurrence. Space-time congruency in ranges (i.e., spatially widespread taxa were also temporally widespread) was observed only where samples were collected across an environmental gradient. Fifteen percent of the taxa in both harbors changed over time from having spatially restricted ranges to having widespread ranges. Our findings suggest that rare species can provide stability against environmental change, because the majority of species were not random transients, but that selection of biodiversity surrogates requires temporal validation. Rarity needs to be considered both spatially and temporally, as species that occur randomly over time are likely to play a different role in ecosystem functioning than those exhibiting temporal

  6. Simple Patterns in Fluctuations of Time Series of Economic Interest

    Science.gov (United States)

    Fanchiotti, H.; García Canal, C. A.; García Zúñiga, H.

    Time series corresponding to nominal exchange rates between the US dollar and Argentina, Brazil and European Economic Community currencies; different financial indexes as the Industrial Dow Jones, the British Footsie, the German DAX Composite, the Australian Share Price and the Nikkei Cash and also different Argentine local tax revenues, are analyzed looking for the appearance of simple patterns and the possible definition of forecast evaluators. In every case, the statistical fractal dimensions are obtained from the behavior of the corresponding variance of increments at a given lag. The detrended fluctuation analysis of the data in terms of the corresponding exponent in the resulting power law is carried out. Finally, the frequency power spectra of all the time series considered are computed and compared

  7. Visualization of feline calicivirus replication in real-time with recombinant viruses engineered to express fluorescent reporter proteins.

    Science.gov (United States)

    Abente, Eugenio J; Sosnovtsev, Stanislav V; Bok, Karin; Green, Kim Y

    2010-04-25

    Caliciviruses are non-enveloped, icosahedral viruses with a single-stranded, positive sense RNA genome. Transposon-mediated insertional mutagenesis was used to insert a transprimer sequence into random sites of an infectious full-length cDNA clone of the feline calicivirus (FCV) genome. A site in the LC gene (encoding the capsid leader protein) of the FCV genome was identified that could tolerate foreign insertions, and two viable recombinant FCV variants expressing LC fused either to AcGFP, or DsRedFP were recovered. The effects of the insertions on LC processing, RNA replication, and stability of the viral genome were analyzed, and the progression of a calicivirus single infection and co-infection were captured by real-time imaging fluorescent microscopy. The ability to engineer viable recombinant caliciviruses expressing foreign markers enables new approaches to investigate virus and host cell interactions, as well as studies of viral recombination, one of the driving forces of calicivirus evolution. Published by Elsevier Inc.

  8. Spatial patterns in timing of the diurnal temperature cycle

    Directory of Open Access Journals (Sweden)

    T. R. H. Holmes

    2013-05-01

    Full Text Available This paper investigates the structural difference in timing of the diurnal temperature cycle (DTC over land resulting from choice of measuring device or model framework. It is shown that the timing can be reliably estimated from temporally sparse observations acquired from a constellation of low Earth orbiting satellites given record lengths of at least three months. Based on a year of data, the spatial patterns of mean DTC timing are compared between Ka-band temperature estimates, geostationary thermal infrared (TIR temperature estimates and numerical weather prediction model output from the Global Modeling and Assimilation Office (GMAO. It is found that the spatial patterns can be explained by vegetation effects, sensing depth differences and more speculatively the orientation of orographic relief features. In absolute terms, the GMAO model puts the peak of the DTC on average at 12:50 local solar time, 23 min before TIR with a peak temperature at 13:13. Since TIR is the shallowest observation of the land surface, this small difference represents a structural error that possibly affects the models ability to assimilate observations that are closely tied to the DTC. For non-desert areas, the Ka-band observations have only a small delay of about 15 min with the TIR observations which is in agreement with their respective theoretical sensing depth. The results of this comparison provide insights into the structural differences between temperature measurements and models, and can be used as a first step to account for these differences in a coherent way.

  9. Time rescaling and pattern formation in biological evolution.

    Science.gov (United States)

    Igamberdiev, Abir U

    2014-09-01

    Biological evolution is analyzed as a process of continuous measurement in which biosystems interpret themselves in the environment resulting in changes of both. This leads to rescaling of internal time (heterochrony) followed by spatial reconstructions of morphology (heterotopy). The logical precondition of evolution is the incompleteness of biosystem's internal description, while the physical precondition is the uncertainty of quantum measurement. The process of evolution is based on perpetual changes in interpretation of information in the changing world. In this interpretation the external biospheric gradients are used for establishment of new features of organization. It is concluded that biological evolution involves the anticipatory epigenetic changes in the interpretation of genetic symbolism which cannot generally be forecasted but can provide canalization of structural transformations defined by the existing organization and leading to predictable patterns of form generation.

  10. Pattern recognition computation using action potential timing for stimulus representation

    Science.gov (United States)

    Hopfield, J. J.

    1995-07-01

    A computational model is described in which the sizes of variables are represented by the explicit times at which action potentials occur, rather than by the more usual 'firing rate' of neurons. The comparison of patterns over sets of analogue variables is done by a network using different delays for different information paths. This mode of computation explains how one scheme of neuroarchitecture can be used for very different sensory modalities and seemingly different computations. The oscillations and anatomy of the mammalian olfactory systems have a simple interpretation in terms of this representation, and relate to processing in the auditory system. Single-electrode recording would not detect such neural computing. Recognition 'units' in this style respond more like radial basis function units than elementary sigmoid units.

  11. 连续时间动态复制定理的推广与证明%Extension and Proof of the Continuous-Time Dynamic Replication Theorem

    Institute of Scientific and Technical Information of China (English)

    刘海龙; 吴冲锋

    2002-01-01

    This paper extends the continuous-time dynamic replication theorem for incomplete Markets, which is proposed by Bertsimas, Kogan and Lo (1997)[1]. Then this extended dynamic replication theorem is proved using the theory of the stochastic optimal control.%推广了由Bertsimas,Kogan andLo(1997)[1]提出的非完全市场中的连续时间动态复制定理,然后,我们运用随机最优控制理论证明了这个定理.

  12. Database Replication

    CERN Document Server

    Kemme, Bettina

    2010-01-01

    Database replication is widely used for fault-tolerance, scalability and performance. The failure of one database replica does not stop the system from working as available replicas can take over the tasks of the failed replica. Scalability can be achieved by distributing the load across all replicas, and adding new replicas should the load increase. Finally, database replication can provide fast local access, even if clients are geographically distributed clients, if data copies are located close to clients. Despite its advantages, replication is not a straightforward technique to apply, and

  13. Searching for Contracting Patterns over Time: Do Prime Contractor and Subcontractor Relations Follow Similar Patterns for Professional Services Provision?

    Science.gov (United States)

    Ponomariov, Branco; Kingsley, Gordon; Boardman, Craig

    2011-01-01

    This paper compares over a 12-year period (1) patterns of contracting between a state transportation agency and its prime contractors providing engineering design services with (2) patterns between these prime contractors and their subcontractors. We find evidence of different contracting patterns at each level that emerge over time and coexist in…

  14. The Ctf18 RFC-like complex positions yeast telomeres but does not specify their replication time.

    Science.gov (United States)

    Hiraga, Shin-ichiro; Robertson, E Douglas; Donaldson, Anne D

    2006-04-05

    Chromosome ends in Saccharomyces cerevisiae are positioned in clusters at the nuclear rim. We report that Ctf18, Ctf8, and Dcc1, the subunits of a Replication Factor C (RFC)-like complex, are essential for the perinuclear positioning of telomeres. In both yeast and mammalian cells, peripheral nuclear positioning of chromatin during G1 phase correlates with late DNA replication. We find that the mislocalized telomeres of ctf18 cells still replicate late, showing that late DNA replication does not require peripheral positioning during G1. The Ku and Sir complexes have been shown to act through separate pathways to position telomeres, but in the absence of Ctf18 neither pathway can act fully to maintain telomere position. Surprisingly CTF18 is not required for Ku or Sir4-mediated peripheral tethering of a nontelomeric chromosome locus. Our results suggest that the Ctf18 RFC-like complex modifies telomeric chromatin to make it competent for normal localization to the nuclear periphery.

  15. Effects of solution chemistry and aging time on prion protein adsorption and replication of soil-bound prions.

    Directory of Open Access Journals (Sweden)

    Samuel E Saunders

    Full Text Available Prion interactions with soil may play an important role in the transmission of chronic wasting disease (CWD and scrapie. Prions are known to bind to a wide range of soil surfaces, but the effects of adsorption solution chemistry and long-term soil binding on prion fate and transmission risk are unknown. We investigated HY TME prion protein (PrP(Sc adsorption to soil minerals in aqueous solutions of phosphate buffered saline (PBS, sodium chloride, calcium chloride, and deionized water using western blotting. The replication efficiency of bound prions following adsorption in these solutions was also evaluated by protein misfolding cyclic amplification (PMCA. Aging studies investigated PrP(Sc desorption and replication efficiency up to one year following adsorption in PBS or DI water. Results indicate that adsorption solution chemistry can affect subsequent prion replication or desorption ability, especially after incubation periods of 30 d or longer. Observed effects were minor over the short-term (7 d or less. Results of long-term aging experiments demonstrate that unbound prions or prions bound to a diverse range of soil surfaces can readily replicate after one year. Our results suggest that while prion-soil interactions can vary with solution chemistry, prions bound to soil could remain a risk for transmitting prion diseases after months in the environment.

  16. The breeding pattern and variations in timing and reproductive ...

    African Journals Online (AJOL)

    that breeding patterns on the equator will be continuous and less synchronized between sexes. Peak spawning ..... could be the differences in the light regime where this species ... with several studies reporting spawning at the full moon ...

  17. Chlamydia psittaci reference genes for normalisation of expression data differ depending on the culture conditions and selected time points during the chlamydial replication cycle

    Directory of Open Access Journals (Sweden)

    Van Lent Sarah

    2016-12-01

    Full Text Available Introduction: Chlamydia psittaci is a gram-negative obligate intracellular pathogen of birds. Poultry infections lead to economic losses and can be transmitted to humans. No vaccine is available and the bacterium-host cell interaction is not completely understood. Replicating bacteria cause pneumonia, but C. psittaci can also be non-replicating and persistent inside the cytoplasm of avian cells. RT-qPCR provides insight into the molecular pathogenesis of both active replicating and persistent Chlamydia psittaci in birds, but requires identification of stably expressed reference genes to avoid biases. Material and Methods: We investigated the expression stability of 10 C. psittaci candidate reference genes for gene expression analysis during normal growth and penicillin-induced persistence. C. psittaci Cal10 was cultured in HeLa229 and RNA was extracted. The expression level of each candidate was examined by RT-qPCR and Cq values were analysed using geNorm. Results: The genes tyrS, gidA, radA, and 16S rRNA ranked among the most stably expressed. The final selected reference genes differed according to the bacterial growth status (normal growth versus persistent status, and the time points selected during the duration of the normal chlamydial developmental cycle. Conclusion: The study data show the importance of systematic validation of reference genes to confirm their stability within the strains and under the conditions selected.

  18. Time: The Biggest Pattern in Natural History Research

    Science.gov (United States)

    Gontier, Nathalie

    2016-10-01

    We distinguish between four cosmological transitions in the history of Western intellectual thought, and focus on how these cosmologies differentially define matter, space and time. We demonstrate that how time is conceptualized significantly impacts a cosmology's notion on causality, and hone in on how time is conceptualized differentially in modern physics and evolutionary biology. The former conflates time with space into a single space-time continuum and focuses instead on the movement of matter, while the evolutionary sciences have a tradition to understand time as a given when they cartography how organisms change across generations over or in time, thereby proving the phenomenon of evolution. The gap becomes more fundamental when we take into account that phenomena studied by chrono-biologists demonstrate that numerous organisms, including humans, have evolved a "sense" of time. And micro-evolutionary/genetic, meso-evolutionary/developmental and macro-evolutionary phenomena including speciation and extinction not only occur by different evolutionary modes and at different rates, they are also timely phenomena that follow different periodicities. This article focusses on delineating the problem by finding its historical roots. We conclude that though time might be an obsolete concept for the physical sciences, it is crucial for the evolutionary sciences where evolution is defined as the change that biological individuals undergo in/over or through time.

  19. Storm blueprints patterns for distributed real-time computation

    CERN Document Server

    Goetz, P Taylor

    2014-01-01

    A blueprints book with 10 different projects built in 10 different chapters which demonstrate the various use cases of storm for both beginner and intermediate users, grounded in real-world example applications.Although the book focuses primarily on Java development with Storm, the patterns are more broadly applicable and the tips, techniques, and approaches described in the book apply to architects, developers, and operations.Additionally, the book should provoke and inspire applications of distributed computing to other industries and domains. Hadoop enthusiasts will also find this book a go

  20. Ventilation and respiratory pattern and timing in resting awake cats.

    Science.gov (United States)

    Jennings, D B; Szlyk, P C

    1985-02-01

    The purpose of this study was to characterize the variability and patterns of spontaneous respiratory behaviour in awake cats. Respiration was measured in six cats over 80 or 90 min by the plethysmographic technique. In three cats, arterial blood gases were measured. Breath frequency (f) and tidal volume (VT) varied considerably breath-to-breath, although on average, these measurements as well as average ventilation remained relatively constant. The incidence of breath ventilation (VT X 60/TTOT) and VT were distributed unimodally but the incidence of breath f had a bimodal distribution. In the low f range, average f was 22.5 breaths/min, and in the high f range, average f was 41.6 breaths/min. The latter range appeared to be associated with purring. Inspiratory duration (TI) was less than expiratory duration (TE) at low f but exceeded TE at high f. For a given breath ventilation there was a predictable f and VT. At shorter TI (higher f) mean inspiratory flow, an index of central respiratory drive, increased but VT decreased. This study indicates that "normal" control respiratory behaviour in awake cats is better described by the range and pattern of breathing than by average values.

  1. Real-time pose invariant logo and pattern detection

    Science.gov (United States)

    Sidla, Oliver; Kottmann, Michal; Benesova, Wanda

    2011-01-01

    The detection of pose invariant planar patterns has many practical applications in computer vision and surveillance systems. The recognition of company logos is used in market studies to examine the visibility and frequency of logos in advertisement. Danger signs on vehicles could be detected to trigger warning systems in tunnels, or brand detection on transport vehicles can be used to count company-specific traffic. We present the results of a study on planar pattern detection which is based on keypoint detection and matching of distortion invariant 2d feature descriptors. Specifically we look at the keypoint detectors of type: i) Lowe's DoG approximation from the SURF algorithm, ii) the Harris Corner Detector, iii) the FAST Corner Detector and iv) Lepetit's keypoint detector. Our study then compares the feature descriptors SURF and compact signatures based on Random Ferns: we use 3 sets of sample images to detect and match 3 logos of different structure to find out which combinations of keypoint detector/feature descriptors work well. A real-world test tries to detect vehicles with a distinctive logo in an outdoor environment under realistic lighting and weather conditions: a camera was mounted on a suitable location for observing the entrance to a parking area so that incoming vehicles could be monitored. In this 2 hour long recording we can successfully detect a specific company logo without false positives.

  2. Discovering Patterns in Time-Varying Graphs: A Triclustering Approach

    CERN Document Server

    Guigourès, Romain; Rossi, Fabrice

    2016-01-01

    This paper introduces a novel technique to track structures in time varying graphs. The method uses a maximum a posteriori approach for adjusting a three-dimensional co-clustering of the source vertices, the destination vertices and the time, to the data under study, in a way that does not require any hyper-parameter tuning. The three dimensions are simultaneously segmented in order to build clusters of source vertices, destination vertices and time segments where the edge distributions across clusters of vertices follow the same evolution over the time segments. The main novelty of this approach lies in that the time segments are directly inferred from the evolution of the edge distribution between the vertices, thus not requiring the user to make any a priori quantization. Experiments conducted on artificial data illustrate the good behavior of the technique, and a study of a real-life data set shows the potential of the proposed approach for exploratory data analysis.

  3. Modeling inhomogeneous DNA replication kinetics.

    Directory of Open Access Journals (Sweden)

    Michel G Gauthier

    Full Text Available In eukaryotic organisms, DNA replication is initiated at a series of chromosomal locations called origins, where replication forks are assembled proceeding bidirectionally to replicate the genome. The distribution and firing rate of these origins, in conjunction with the velocity at which forks progress, dictate the program of the replication process. Previous attempts at modeling DNA replication in eukaryotes have focused on cases where the firing rate and the velocity of replication forks are homogeneous, or uniform, across the genome. However, it is now known that there are large variations in origin activity along the genome and variations in fork velocities can also take place. Here, we generalize previous approaches to modeling replication, to allow for arbitrary spatial variation of initiation rates and fork velocities. We derive rate equations for left- and right-moving forks and for replication probability over time that can be solved numerically to obtain the mean-field replication program. This method accurately reproduces the results of DNA replication simulation. We also successfully adapted our approach to the inverse problem of fitting measurements of DNA replication performed on single DNA molecules. Since such measurements are performed on specified portion of the genome, the examined DNA molecules may be replicated by forks that originate either within the studied molecule or outside of it. This problem was solved by using an effective flux of incoming replication forks at the model boundaries to represent the origin activity outside the studied region. Using this approach, we show that reliable inferences can be made about the replication of specific portions of the genome even if the amount of data that can be obtained from single-molecule experiments is generally limited.

  4. A Rough Sets Partitioning Model for Mining Sequential Patterns with Time Constraint

    CERN Document Server

    Bisaria, Jigyasa; Pardasani, K R

    2009-01-01

    Now a days, data mining and knowledge discovery methods are applied to a variety of enterprise and engineering disciplines to uncover interesting patterns from databases. The study of Sequential patterns is an important data mining problem due to its wide applications to real world time dependent databases. Sequential patterns are inter-event patterns ordered over a time-period associated with specific objects under study. Analysis and discovery of frequent sequential patterns over a predetermined time-period are interesting data mining results, and can aid in decision support in many enterprise applications. The problem of sequential pattern mining poses computational challenges as a long frequent sequence contains enormous number of frequent subsequences. Also useful results depend on the right choice of event window. In this paper, we have studied the problem of sequential pattern mining through two perspectives, one the computational aspect of the problem and the other is incorporation and adjustability o...

  5. Hospitalisation patterns change over time in patients with atrial fibrillation

    DEFF Research Database (Denmark)

    Fristrup Qvist, Janne; Høgh Sørensen, Pernille; Dixen, Ulrik

    2014-01-01

    INTRODUCTION: Atrial fibrillation (AF) is a cardiac epidemic. In this study, we aimed to describe the causes of hospital-isation in an AF population over time and to study how different AF treatment strategies affected hospitalization. MATERIAL AND METHODS: This was an observational study in which...

  6. The timing and spatiotemporal patterning of Neanderthal disappearance.

    Science.gov (United States)

    Higham, Tom; Douka, Katerina; Wood, Rachel; Ramsey, Christopher Bronk; Brock, Fiona; Basell, Laura; Camps, Marta; Arrizabalaga, Alvaro; Baena, Javier; Barroso-Ruíz, Cecillio; Bergman, Christopher; Boitard, Coralie; Boscato, Paolo; Caparrós, Miguel; Conard, Nicholas J; Draily, Christelle; Froment, Alain; Galván, Bertila; Gambassini, Paolo; Garcia-Moreno, Alejandro; Grimaldi, Stefano; Haesaerts, Paul; Holt, Brigitte; Iriarte-Chiapusso, Maria-Jose; Jelinek, Arthur; Jordá Pardo, Jesús F; Maíllo-Fernández, José-Manuel; Marom, Anat; Maroto, Julià; Menéndez, Mario; Metz, Laure; Morin, Eugène; Moroni, Adriana; Negrino, Fabio; Panagopoulou, Eleni; Peresani, Marco; Pirson, Stéphane; de la Rasilla, Marco; Riel-Salvatore, Julien; Ronchitelli, Annamaria; Santamaria, David; Semal, Patrick; Slimak, Ludovic; Soler, Joaquim; Soler, Narcís; Villaluenga, Aritza; Pinhasi, Ron; Jacobi, Roger

    2014-08-21

    The timing of Neanderthal disappearance and the extent to which they overlapped with the earliest incoming anatomically modern humans (AMHs) in Eurasia are key questions in palaeoanthropology. Determining the spatiotemporal relationship between the two populations is crucial if we are to understand the processes, timing and reasons leading to the disappearance of Neanderthals and the likelihood of cultural and genetic exchange. Serious technical challenges, however, have hindered reliable dating of the period, as the radiocarbon method reaches its limit at ∼50,000 years ago. Here we apply improved accelerator mass spectrometry (14)C techniques to construct robust chronologies from 40 key Mousterian and Neanderthal archaeological sites, ranging from Russia to Spain. Bayesian age modelling was used to generate probability distribution functions to determine the latest appearance date. We show that the Mousterian ended by 41,030-39,260 calibrated years bp (at 95.4% probability) across Europe. We also demonstrate that succeeding 'transitional' archaeological industries, one of which has been linked with Neanderthals (Châtelperronian), end at a similar time. Our data indicate that the disappearance of Neanderthals occurred at different times in different regions. Comparing the data with results obtained from the earliest dated AMH sites in Europe, associated with the Uluzzian technocomplex, allows us to quantify the temporal overlap between the two human groups. The results reveal a significant overlap of 2,600-5,400 years (at 95.4% probability). This has important implications for models seeking to explain the cultural, technological and biological elements involved in the replacement of Neanderthals by AMHs. A mosaic of populations in Europe during the Middle to Upper Palaeolithic transition suggests that there was ample time for the transmission of cultural and symbolic behaviours, as well as possible genetic exchanges, between the two groups.

  7. Replication-Fork Dynamics

    NARCIS (Netherlands)

    Duderstadt, Karl E.; Reyes-Lamothe, Rodrigo; van Oijen, Antoine M.; Sherratt, David J.

    2014-01-01

    The proliferation of all organisms depends on the coordination of enzymatic events within large multiprotein replisomes that duplicate chromosomes. Whereas the structure and function of many core replisome components have been clarified, the timing and order of molecular events during replication re

  8. Hepatitis B virus replication

    Institute of Scientific and Technical Information of China (English)

    2007-01-01

    Hepadnaviruses, including human hepatitis B virus (HBV), replicate through reverse transcription of an RNA intermediate, the pregenomic RNA (pgRNA). Despite this kinship to retroviruses, there are fundamental differences beyond the fact that hepadnavirions contain DNA instead of RNA. Most peculiar is the initiation of reverse transcription: it occurs by protein-priming, is strictly committed to using an RNA hairpin on the pgRNA,ε, as template, and depends on cellular chaperones;moreover, proper replication can apparently occur only in the specialized environment of intact nucleocapsids.This complexity has hampered an in-depth mechanistic understanding. The recent successful reconstitution in the test tube of active replication initiation complexes from purified components, for duck HBV (DHBV),now allows for the analysis of the biochemistry of hepadnaviral replication at the molecular level. Here we review the current state of knowledge at all steps of the hepadnaviral genome replication cycle, with emphasis on new insights that turned up by the use of such cellfree systems. At this time, they can, unfortunately,not be complemented by three-dimensional structural information on the involved components. However, at least for the s RNA element such information is emerging,raising expectations that combining biophysics with biochemistry and genetics will soon provide a powerful integrated approach for solving the many outstanding questions. The ultimate, though most challenging goal,will be to visualize the hepadnaviral reverse transcriptase in the act of synthesizing DNA, which will also have strong implications for drug development.

  9. Hospitalisation patterns change over time in patients with atrial fibrillation

    DEFF Research Database (Denmark)

    Fristrup Qvist, Janne; Høgh Sørensen, Pernille; Dixen, Ulrik

    2014-01-01

    INTRODUCTION: Atrial fibrillation (AF) is a cardiac epidemic. In this study, we aimed to describe the causes of hospital-isation in an AF population over time and to study how different AF treatment strategies affected hospitalization. MATERIAL AND METHODS: This was an observational study in which...... long-term follow-up data were collected from hospital records, discharge papers and diagnostic codes. The study population (n = 156) was observed over a total period of ten years which was divided into two successive observation periods (OP), OP1 and OP2. Fourteen endpoints of cardiovascular...... hospitalisations were evaluated. RESULTS: The causes of hospitalisation shifted over time. We observed a lower proportion of admissions due to AF in OP2 (63%) than in OP1 (87%) and a higher proportion of admissions due to congestive heart failure (16% versus 3%) and of days of inpatient care due to ischaemic...

  10. Homelessness, mental illness, and criminal activity: examining patterns over time.

    Science.gov (United States)

    Fischer, Sean N; Shinn, Marybeth; Shrout, Patrick; Tsemberis, Sam

    2008-12-01

    This study examined whether street homelessness, sheltered homelessness, and the severity of psychological symptoms predicted non-violent and violent crime among 207 mentally ill participants who were homeless at baseline. Participants were interviewed at 9 time points over 4 years. Hierarchical linear modeling (HLM) was used to examine whether changes in homelessness status and symptom severity predicted changes in criminal activity over time. Results indicated that homelessness both on the streets and in shelters and psychological symptom severity predicted increases in non-violent crime. Sheltered homelessness and symptom severity predicted increases in violent crime, although street homelessness did not. A separate mediational analysis with 181 participants showed that the relationship between diagnosis of a psychotic disorder and both non-violent and violent criminal activity was partially mediated through the severity of psychotic symptoms. Implications for research and intervention are discussed.

  11. Influence of time and pressure of forming a pattern on mechanical properties

    Directory of Open Access Journals (Sweden)

    T. Pacyniak

    2011-07-01

    Full Text Available In this paper, the technology of forming patterns on a research station equipped with an autoclave A-600 of Polish company GROM is presented. This study was conducted to determine the influence of pressure and time of forming a pattern on the bending strength. Analysis of the results confirmed that bending strength increases with increasing the pressure. The time of forming a pattern has a similar effect.

  12. Experimental stabilisation of 2D vortex patterns using time-dependent forcing

    NARCIS (Netherlands)

    Lauret, M.; Kamp, L. P. J.; van Heijst, G. J. F.; M.R. de Baar,; Nijmeijer, H.

    2013-01-01

    Experimental results of the effect of time-periodic and “chirped” (electro-magnetic) forcing on vortex patterns in shallow-water-layer flows are presented. Analogously to vibrational control, the use of a time-periodic forcing results in stabilisation of otherwise unstable vortex patterns. Chirped f

  13. Time evolution of the diffraction pattern of an ultrashort laser pulse.

    Science.gov (United States)

    Lefrancois, M; Pereira, S

    2003-05-19

    An analytical expression for the time evolution of the diffraction pattern of an ultrashort laser pulse passing through a circular aperture is obtained in the Fresnel regime. The diffraction is not constant in time as the pulse travels through the aperture. This may have implications in experiments involving fast dynamics. Examples of the evolution of the diffraction pattern are given.

  14. Dynamics of Escherichia coli chromosome segregation during multifork replication.

    Science.gov (United States)

    Nielsen, Henrik J; Youngren, Brenda; Hansen, Flemming G; Austin, Stuart

    2007-12-01

    Slowly growing Escherichia coli cells have a simple cell cycle, with replication and progressive segregation of the chromosome completed before cell division. In rapidly growing cells, initiation of replication occurs before the previous replication rounds are complete. At cell division, the chromosomes contain multiple replication forks and must be segregated while this complex pattern of replication is still ongoing. Here, we show that replication and segregation continue in step, starting at the origin and progressing to the replication terminus. Thus, early-replicated markers on the multiple-branched chromosomes continue to separate soon after replication to form separate protonucleoids, even though they are not segregated into different daughter cells until later generations. The segregation pattern follows the pattern of chromosome replication and does not follow the cell division cycle. No extensive cohesion of sister DNA regions was seen at any growth rate. We conclude that segregation is driven by the progression of the replication forks.

  15. Can post-error dynamics explain sequential reaction time patterns?

    Directory of Open Access Journals (Sweden)

    Stephanie eGoldfarb

    2012-07-01

    Full Text Available We investigate human error dynamics in sequential two-alternative choice tasks. When subjects repeatedly discriminate between two stimuli, their error rates and mean reaction times (RTs systematically depend on prior sequences of stimuli. We analyze these sequential effects on RTs, separating error and correct responses, and identify a sequential RT tradeoff: a sequence of stimuli which yields a relatively fast RT on error trials will produce a relatively slow RT on correct trials and vice versa. We reanalyze previous data and acquire and analyze new data in a choice task with stimulus sequences generated by a first-order Markov process having unequal probabilities of repetitions and alternations. We then show that relationships among these stimulus sequences and the corresponding RTs for correct trials, error trials, and averaged over all trials are significantly influenced by the probability of alternations; these relationships have not been captured by previous models. Finally, we show that simple, sequential updates to the initial condition and thresholds of a pure drift diffusion model can account for the trends in RT for correct and error trials. Our results suggest that error-based parameter adjustments are critical to modeling sequential effects.

  16. Permutation approach, high frequency trading and variety of micro patterns in financial time series

    Science.gov (United States)

    Aghamohammadi, Cina; Ebrahimian, Mehran; Tahmooresi, Hamed

    2014-11-01

    Permutation approach is suggested as a method to investigate financial time series in micro scales. The method is used to see how high frequency trading in recent years has affected the micro patterns which may be seen in financial time series. Tick to tick exchange rates are considered as examples. It is seen that variety of patterns evolve through time; and that the scale over which the target markets have no dominant patterns, have decreased steadily over time with the emergence of higher frequency trading.

  17. R and D on a New Technology of Micro-pattern Gaseous Detectors Fast Timing Micro-pattern Detector

    CERN Document Server

    Salva Diblen, Sinem

    2016-01-01

    After the upgrades of the Large Hadron Collider (LHC) planned for the second and the third Long Shutdown (LS), the LHC luminosity will approach very high values. Such conditions will affect the performance of the CMS muon system, especially in the very forward region, due to the harsh expected background environment and high pile-up conditions. The CMS collaboration considers upgrading the muon forward region to take advantage of the pixel tracking coverage extension a new detector, ME0 station, possibly behind the new forward calorimeter. New resistive micro-pattern gaseous detectors that are able to handle the very demanding spatial, time resolution and rate capability, are being considered. In this contribution we introduce a new type of MPGD technology the Fast Timing Micro-pattern (FTM) detector, utilizing a fully resistive WELL structure. It consists of a stack of several coupled layers where drift and WELL multiplication stages alternate in the structure, yielding a significant improvement in timing p...

  18. Turing patterns and long-time behavior in a three-species food-chain model

    KAUST Repository

    Parshad, Rana D.

    2014-08-01

    We consider a spatially explicit three-species food chain model, describing generalist top predator-specialist middle predator-prey dynamics. We investigate the long-time dynamics of the model and show the existence of a finite dimensional global attractor in the product space, L2(Ω). We perform linear stability analysis and show that the model exhibits the phenomenon of Turing instability, as well as diffusion induced chaos. Various Turing patterns such as stripe patterns, mesh patterns, spot patterns, labyrinth patterns and weaving patterns are obtained, via numerical simulations in 1d as well as in 2d. The Turing and non-Turing space, in terms of model parameters, is also explored. Finally, we use methods from nonlinear time series analysis to reconstruct a low dimensional chaotic attractor of the model, and estimate its fractal dimension. This provides a lower bound, for the fractal dimension of the attractor, of the spatially explicit model. © 2014 Elsevier Inc.

  19. Patterns of Human Immunodeficiency Virus type 1 recombination ex vivo provide evidence for coadaptation of distant sites, resulting in purifying selection for intersubtype recombinants during replication

    DEFF Research Database (Denmark)

    Galli, Andrea; Kearney, Mary; Nikolaitchik, Olga A

    2010-01-01

    High-frequency recombination is a hallmark of HIV-1 replication. Recombination can occur between two members of the same subtype or between viruses from two different subtypes, generating intra- or intersubtype recombinants, respectively. Many intersubtype recombinants have been shown to circulate....../B) and between viruses with pol genes from subtype B or F (B/F). Recombination events generated during a single cycle of infection without selection pressure on pol gene function were analyzed by single-genome sequencing. We found that recombination occurred slightly ( approximately 30%) less frequently in B...... subtypes; these sites may be segregated by recombination events, causing the newly generated intersubtype recombinants to undergo purifying selection. Therefore, the ability of the recombinants to replicate is the major barrier for many of these viruses....

  20. DATABASE REPLICATION IN HETEROGENOUS PLATFORM

    Directory of Open Access Journals (Sweden)

    Hendro Nindito

    2014-01-01

    Full Text Available The application of diverse database technologies in enterprises today is increasingly a common practice. To provide high availability and survavibality of real-time information, a database replication technology that has capability to replicate databases under heterogenous platforms is required. The purpose of this research is to find the technology with such capability. In this research, the data source is stored in MSSQL database server running on Windows. The data will be replicated to MySQL running on Linux as the destination. The method applied in this research is prototyping in which the processes of development and testing can be done interactively and repeatedly. The key result of this research is that the replication technology applied, which is called Oracle GoldenGate, can successfully manage to do its task in replicating data in real-time and heterogeneous platforms.

  1. Replication domains are self-interacting structural chromatin units of human chromosomes

    Science.gov (United States)

    Arneodo, Alain

    2011-03-01

    In higher eukaryotes, the absence of specific sequence motifs marking the origins of replication has been a serious hindrance to the understanding of the mechanisms that regulate the initiation and the maintenance of the replication program in different cell types. In silico analysis of nucleotide compositional skew has predicted the existence, in the germline, of replication N-domains bordered by putative replication origins and where the skew decreases rather linearly as the signature of a progressive inversion of the average fork polarity. Here, from the demonstration that the average fork polarity can be directly extracted from the derivative of replication timing profiles, we develop a wavelet-based pattern recognition methodology to delineate replication U-domains where the replication timing profile is shaped as a U and its derivative as a N. Replication U-domains are robustly found in seven cell lines as covering a significant portion (40-50%) of the human genome where the replication timing data actually displays some plasticity between cell lines. The early replication initiation zones at U-domains borders are found to be hypersensitive to DNase I cleavage, to be associated with transcriptional activity and to present a significant enrichment in insular-binding proteins CTCF, the hallmark of an open chromatin structure. A comparative analysis of genome-wide chromatin interaction (HiC) data shows that replication-U domains correspond to self-interacting structural high order chromatin units of megabase characteristic size. Taken together, these findings provide evidence that the epigenetic compartmentalization of the human genome into autonomous replication U-domains comes along with an extensive remodelling of the threedimensional chromosome architecture during development or in specific diseases. The observed cell specific conservation of the replication timing between the human and mouse genomes strongly suggests that this chromosome organization into

  2. SHAPE-BASED TIME SERIES SIMILARITY MEASURE AND PATTERN DISCOVERY ALGORITHM

    Institute of Scientific and Technical Information of China (English)

    Zeng Fanzi; Qiu Zhengding; Li Dongsheng; Yue Jianhai

    2005-01-01

    Pattern discovery from time series is of fundamental importance. Most of the algorithms of pattern discovery in time series capture the values of time series based on some kinds of similarity measures. Affected by the scale and baseline, value-based methods bring about problem when the objective is to capture the shape. Thus, a similarity measure based on shape, Sh measure, is originally proposed, andthe properties of this similarity and corresponding proofs are given. Then a time series shape pattern discovery algorithm based on Sh measure is put forward. The proposed algorithm is terminated in finite iteration with given computational and storage complexity. Finally the experiments on synthetic datasets and sunspot datasets demonstrate that the time series shape pattern algorithm is valid.

  3. Arabidopsis thaliana chromosome 4 replicates in two phases that correlate with chromatin state.

    Science.gov (United States)

    Lee, Tae-Jin; Pascuzzi, Pete E; Settlage, Sharon B; Shultz, Randall W; Tanurdzic, Milos; Rabinowicz, Pablo D; Menges, Margit; Zheng, Ping; Main, Dorrie; Murray, James A H; Sosinski, Bryon; Allen, George C; Martienssen, Robert A; Hanley-Bowdoin, Linda; Vaughn, Matthew W; Thompson, William F

    2010-06-10

    DNA replication programs have been studied extensively in yeast and animal systems, where they have been shown to correlate with gene expression and certain epigenetic modifications. Despite the conservation of core DNA replication proteins, little is known about replication programs in plants. We used flow cytometry and tiling microarrays to profile DNA replication of Arabidopsis thaliana chromosome 4 (chr4) during early, mid, and late S phase. Replication profiles for early and mid S phase were similar and encompassed the majority of the euchromatin. Late S phase exhibited a distinctly different profile that includes the remaining euchromatin and essentially all of the heterochromatin. Termination zones were consistent between experiments, allowing us to define 163 putative replicons on chr4 that clustered into larger domains of predominately early or late replication. Early-replicating sequences, especially the initiation zones of early replicons, displayed a pattern of epigenetic modifications specifying an open chromatin conformation. Late replicons, and the termination zones of early replicons, showed an opposite pattern. Histone H3 acetylated on lysine 56 (H3K56ac) was enriched in early replicons, as well as the initiation zones of both early and late replicons. H3K56ac was also associated with expressed genes, but this effect was local whereas replication time correlated with H3K56ac over broad regions. The similarity of the replication profiles for early and mid S phase cells indicates that replication origin activation in euchromatin is stochastic. Replicon organization in Arabidopsis is strongly influenced by epigenetic modifications to histones and DNA. The domain organization of Arabidopsis is more similar to that in Drosophila than that in mammals, which may reflect genome size and complexity. The distinct patterns of association of H3K56ac with gene expression and early replication provide evidence that H3K56ac may be associated with initiation zones

  4. Arabidopsis thaliana chromosome 4 replicates in two phases that correlate with chromatin state.

    Directory of Open Access Journals (Sweden)

    Tae-Jin Lee

    2010-06-01

    Full Text Available DNA replication programs have been studied extensively in yeast and animal systems, where they have been shown to correlate with gene expression and certain epigenetic modifications. Despite the conservation of core DNA replication proteins, little is known about replication programs in plants. We used flow cytometry and tiling microarrays to profile DNA replication of Arabidopsis thaliana chromosome 4 (chr4 during early, mid, and late S phase. Replication profiles for early and mid S phase were similar and encompassed the majority of the euchromatin. Late S phase exhibited a distinctly different profile that includes the remaining euchromatin and essentially all of the heterochromatin. Termination zones were consistent between experiments, allowing us to define 163 putative replicons on chr4 that clustered into larger domains of predominately early or late replication. Early-replicating sequences, especially the initiation zones of early replicons, displayed a pattern of epigenetic modifications specifying an open chromatin conformation. Late replicons, and the termination zones of early replicons, showed an opposite pattern. Histone H3 acetylated on lysine 56 (H3K56ac was enriched in early replicons, as well as the initiation zones of both early and late replicons. H3K56ac was also associated with expressed genes, but this effect was local whereas replication time correlated with H3K56ac over broad regions. The similarity of the replication profiles for early and mid S phase cells indicates that replication origin activation in euchromatin is stochastic. Replicon organization in Arabidopsis is strongly influenced by epigenetic modifications to histones and DNA. The domain organization of Arabidopsis is more similar to that in Drosophila than that in mammals, which may reflect genome size and complexity. The distinct patterns of association of H3K56ac with gene expression and early replication provide evidence that H3K56ac may be associated

  5. Spatial change analysis of paddy cropping pattern using MODIS time series imagery in Central Java

    Science.gov (United States)

    Arif Fatoni, Muhammad; Dwi Nugroho, Kreshna; Fatikhunnada, Alvin; Liyantono; Setiawan, Yudi

    2017-01-01

    Central Java had the diverse paddy field cropping patterns and it was influenced by several factors such as water availability, land condition, paddy fields ownership, and local culture. This research was aimed to analyze dynamic changes of paddy cropping pattern using MODIS imagery (MOD13Q1 16-day composite from 2001 to 2015). This research used k-means clustering algorithm for classified cropping pattern in Central Java based on similarity pattern of annual data from vegetation index. The result of this research classified cropping pattern become a main class and produced 15 maps of distribution cropping patterns (from 2001 to 2015). The result also divided Central Java’s paddy fields become 2 section (constant and change) based on cropping pattern that majority was caused by water availability. This research got the better accuracy (77.67%) of cropping pattern than long time series analysis from previous research. Although some classes successfully obtained upon annual time series analysis, MODIS still difficult to detect mixed crop pattern.

  6. Pause Time Patterns in Writing Narrative and Expository Texts by Children and Adults

    NARCIS (Netherlands)

    Hell, J.G. van; Verhoeven, L.T.W.; Beijsterveldt, E.M. van

    2008-01-01

    How do beginning and skilled writers compose a text in the course of time? To gain insight into the temporal aspects of planning and translating activities during writing, this article examined writing in real time and analyzed pause time patterns in writing in relation to linguistic characteristics

  7. Bayesian Procedures for Identifying Aberrant Response-Time Patterns in Adaptive Testing

    NARCIS (Netherlands)

    van der Linden, Willem J.; Guo, Fanmin

    In order to identify aberrant response-time patterns on educational and psychological tests, it is important to be able to separate the speed at which the test taker operates from the time the items require. A lognormal model for response times with this feature was used to derive a Bayesian

  8. Bayesian Procedures for Identifying Aberrant Response-Time Patterns in Adaptive Testing

    NARCIS (Netherlands)

    Linden, van der Wim J.; Guo, Fanmin

    2008-01-01

    In order to identify aberrant response-time patterns on educational and psychological tests, it is important to be able to separate the speed at which the test taker operates from the time the items require. A lognormal model for response times with this feature was used to derive a Bayesian procedu

  9. Time Use Patterns between Maintenance, Subsistence and Leisure Activities: A Case Study in China

    Science.gov (United States)

    Hui-fen, Zhou; Zhen-shan, Li; Dong-qian, Xue; Yang, Lei

    2012-01-01

    The Chinese government conducted its first time use survey of the activities of Chinese individuals in 2008. Activities were classified into three broad types, maintenance activities, subsistence activities and leisure activities. Time use patterns were defined by an individuals' time spent on maintenance, subsistence and leisure activities each…

  10. Bayesian Procedures for Identifying Aberrant Response-Time Patterns in Adaptive Testing

    NARCIS (Netherlands)

    van der Linden, Willem J.; Guo, Fanmin

    2008-01-01

    In order to identify aberrant response-time patterns on educational and psychological tests, it is important to be able to separate the speed at which the test taker operates from the time the items require. A lognormal model for response times with this feature was used to derive a Bayesian procedu

  11. Archaeal DNA replication.

    Science.gov (United States)

    Kelman, Lori M; Kelman, Zvi

    2014-01-01

    DNA replication is essential for all life forms. Although the process is fundamentally conserved in the three domains of life, bioinformatic, biochemical, structural, and genetic studies have demonstrated that the process and the proteins involved in archaeal DNA replication are more similar to those in eukaryal DNA replication than in bacterial DNA replication, but have some archaeal-specific features. The archaeal replication system, however, is not monolithic, and there are some differences in the replication process between different species. In this review, the current knowledge of the mechanisms governing DNA replication in Archaea is summarized. The general features of the replication process as well as some of the differences are discussed.

  12. Object Individuation or Object Movement as Attractor? A Replication of the Wide-Screen/Narrow-Screen Study by Means of (a Standard Looking Time Methodology and (b Eye Tracking

    Directory of Open Access Journals (Sweden)

    Peter Krøjgaard

    2013-01-01

    Full Text Available We report a replication experiment of a mechanized version of the seminal wide-screen/narrow-screen design of Wilcox and Baillargeon (1998 with 9.5-month-old infants (N=80. Two different methodologies were employed simultaneously: (a the standard looking time paradigm and (b eye tracking. Across conditions with three different screen sizes, the results from both methodologies revealed a clear and interesting pattern: the looking times increased as a significantly linear function of reduced screen sizes, that is, independently of the number of different objects involved. There was no indication in the data that the infants made use of the featural differences between the different-looking objects involved. The results suggest a simple, novel, and thought-provoking interpretation of the infants’ looking behavior in the wide-screen/narrow-screen design: moving objects are attractors, and the more space left for visible object movement in the visual field, the longer are infants’ looks. Consequently, no cognitive interpretation may be needed.

  13. Impact of different discharge patterns on bed occupancy rate and bed waiting time: a simulation approach.

    Science.gov (United States)

    Zhu, Zhecheng

    2011-01-01

    Beds are one of the most important resources in a healthcare system. How to manage beds efficiently is an important indicator of the efficiency of the healthcare system. Bed management is challenging to many healthcare service providers in many aspects. In recent years, population growth and aging society impose extra pressure on bed requirement. There are usually two key performance indicators of a bed management system: bed occupancy rate and bed waiting time. In this paper, different discharge patterns and their impacts on the bed occupancy rate and bed waiting time are studied. A discrete event simulation model is constructed to evaluate the existing discharge pattern in a Singapore regional hospital using actual hospital admission and discharge transaction data. Then different discharge patterns are tested in the same context. Simulation results show that a proper discharge pattern significantly smoothes the fluctuation of bed occupancy rate and reduce the bed waiting time.

  14. The Time Is Up: Compression of Visual Time Interval Estimations of Bimodal Aperiodic Patterns

    Directory of Open Access Journals (Sweden)

    Fabiola Duarte

    2017-08-01

    Full Text Available The ability to estimate time intervals subserves many of our behaviors and perceptual experiences. However, it is not clear how aperiodic (AP stimuli affect our perception of time intervals across sensory modalities. To address this question, we evaluated the human capacity to discriminate between two acoustic (A, visual (V or audiovisual (AV time intervals of trains of scattered pulses. We first measured the periodicity of those stimuli and then sought for correlations with the accuracy and reaction times (RTs of the subjects. We found that, for all time intervals tested in our experiment, the visual system consistently perceived AP stimuli as being shorter than the periodic (P ones. In contrast, such a compression phenomenon was not apparent during auditory trials. Our conclusions are: first, the subjects exposed to P stimuli are more likely to measure their durations accurately. Second, perceptual time compression occurs for AP visual stimuli. Lastly, AV discriminations are determined by A dominance rather than by AV enhancement.

  15. Developing register-based measures for assessment of working time patterns for epidemiologic studies.

    Science.gov (United States)

    Härmä, Mikko; Ropponen, Annina; Hakola, Tarja; Koskinen, Aki; Vanttola, Päivi; Puttonen, Sampsa; Sallinen, Mikael; Salo, Paula; Oksanen, Tuula; Pentti, Jaana; Vahtera, Jussi; Kivimäki, Mika

    2015-05-01

    Epidemiological studies suggest that long working hours and shift work may increase the risk of chronic diseases, but the "toxic" elements remain unclear due to crude assessment of working time patterns based on self-reports. In this methodological paper, we present and evaluate objective register-based algorithms for assessment of working time patterns and validate a method to retrieve standard payroll data on working hours from the employer electronic records. Detailed working hour records from employers' registers were obtained for 12 391 nurses and physicians, a total 14.5 million separate work shifts from 2008-2013. We examined the quality and validity of the obtained register data and designed 29 algorithms characterizing four potentially health-relevant working time patterns: (i) length of the working hours; (ii) time of the day; (iii) shift intensity; and (iv) social aspects of the working hours. The collection of the company-based register data was feasible and the retrieved data matched with the originally published shift plans. The transferred working time records included working time patterns, generated for each year, were stable across the follow-up (year-to-year correlation coefficients from r=0.7-0.9 for 23 variables), their distributions were as expected, and correlations of the variables within the four main dimensions of working hours were plausible. The developed method and algorithms allow a detailed characterization of four main dimensions of working time patterns potentially relevant for health. We recommend this method for future large-scale epidemiological studies.

  16. Method for diagnostics of characteristic patterns of observable time series and its real-time experimental implementation for neurophysiological signals

    NARCIS (Netherlands)

    Ovchinnikov, A.; Hramov, A.E.; Luttjohann, A.K.; Koronovskii, A.A.; Luijtelaar, E.L.J.M. van

    2011-01-01

    A method is proposed for analysis and automatic diagnostics of characteristic oscillatory patterns of the electric activity of the brain in real time on the basis of a continuous wavelet transformation. The results of experimental investigation of automatic recognition of epileptic activity episodes

  17. Principal Time Management Skills: Explaining Patterns in Principals' Time Use, Job Stress, and Perceived Effectiveness

    Science.gov (United States)

    Grissom, Jason A.; Loeb, Susanna; Mitani, Hajime

    2015-01-01

    Purpose: Time demands faced by school principals make principals' work increasingly difficult. Research outside education suggests that effective time management skills may help principals meet job demands, reduce job stress, and improve their performance. The purpose of this paper is to investigate these hypotheses. Design/methodology/approach:…

  18. Principal Time Management Skills: Explaining Patterns in Principals' Time Use, Job Stress, and Perceived Effectiveness

    Science.gov (United States)

    Grissom, Jason A.; Loeb, Susanna; Mitani, Hajime

    2015-01-01

    Purpose: Time demands faced by school principals make principals' work increasingly difficult. Research outside education suggests that effective time management skills may help principals meet job demands, reduce job stress, and improve their performance. The purpose of this paper is to investigate these hypotheses. Design/methodology/approach:…

  19. A quantitative model of DNA replication in Xenopus embryos: reliable replication despite stochasticity

    Science.gov (United States)

    Cheng-Hsin Yang, Scott; Bechhoefer, John

    2008-03-01

    DNA synthesis in Xenopus frog embryos initiates stochastically in time at many sites (origins) along the chromosome. Stochastic initiation implies fluctuations in the replication time and may lead to cell death if replication takes longer than the cell cycle time (˜ 25 min.). Surprisingly, although the typical replication time is about 20 min., in vivo experiments show that replication fails to complete only about 1 in 250 times. How is replication timing accurately controlled despite the stochasticity? Biologists have proposed two mechanisms: the first uses a regular spatial distribution of origins, while the second uses randomly located origins but increases their probability of initiation as the cell cycle proceeds. Here, we show that both mechanisms yield similar end-time distributions, implying that regular origin spacing is not needed for control of replication time. Moreover, we show that the experimentally inferred time-dependent initiation rate satisfies the observed low failure probability and nearly optimizes the use of replicative proteins.

  20. Determining patterns of variability in ecological communities: time lag analysis revisited

    NARCIS (Netherlands)

    Kampichler, C.; Van der Jeugd, H.P.

    2013-01-01

    All ecological communities experience change over time. One method to quantify temporal variation in the patterns of relative abundance of communities is time lag analysis (TLA). It uses a distance-based approach to study temporal community dynamics by regressing community dissimilarity over increas

  1. Time-Use Patterns and Sustainable Urban Form: A Case Study to Explore Potential Links

    Directory of Open Access Journals (Sweden)

    Edeltraud Haselsteiner

    2015-06-01

    Full Text Available Linking time use of the inhabitants of a city with their energy consumption and urban form is an approach which allows integration of the social dimension into research on sustainable urban development. While much has been written about the planning of cities and its implications for human social life, the question of the relationship between time-use patterns and urban form remains underexplored. This is all the more astonishing as time-use statistics offer a unique tool for analysing socio-economic changes regarding family and household structures, gender relations, working hours, recreational behaviour and consumption patterns. Furthermore, spatial planning plays a significant role in establishing time structures. With this paper we aim to explore the possibility of using the time-use data of an urban population to find links between individual time-use patterns and urban form. We describe a case study in Vienna where we addressed time use and mobility of citizens in a participatory approach to jointly develop an integrated socio-ecological model of urban time-use patterns and energy consumption.

  2. Common Spatio-Time-Frequency Patterns for Motor Imagery-Based Brain Machine Interfaces

    Directory of Open Access Journals (Sweden)

    Hiroshi Higashi

    2013-01-01

    Full Text Available For efficient decoding of brain activities in analyzing brain function with an application to brain machine interfacing (BMI, we address a problem of how to determine spatial weights (spatial patterns, bandpass filters (frequency patterns, and time windows (time patterns by utilizing electroencephalogram (EEG recordings. To find these parameters, we develop a data-driven criterion that is a natural extension of the so-called common spatial patterns (CSP that are known to be effective features in BMI. We show that the proposed criterion can be optimized by an alternating procedure to achieve fast convergence. Experiments demonstrate that the proposed method can effectively extract discriminative features for a motor imagery-based BMI.

  3. Disease activity patterns over time in patients with SLE: analysis of the Hopkins Lupus Cohort

    Science.gov (United States)

    Györi, Noémi; Giannakou, Ioanna; Chatzidionysiou, Katerina; Magder, Laurence; van Vollenhoven, Ronald F; Petri, Michelle

    2017-01-01

    Objective To describe SLE disease activity patterns in the Hopkins Lupus Cohort. Methods Disease activity was studied in 1886 patients followed-up for 1–28 years. Disease activity patterns were defined using (1) Physician Global Assessment (PGA) and (2) modified SLE Disease Activity Index (M-SLEDAI) as follows: long quiescent (LQ), M-SLEDAI=0/PGA=0 at all visits; relapsing-remitting (RR), periods of activity (M-SLEDAI>0/PGA>0) interspersed with inactivity (M-SLEDAI=0/PGA=0); chronic active (CA), M-SLEDAI>0/PGA>0 at all visits. The pattern of first 3 consecutive follow-up years was determined in 916 patients as: persistent LQ (pLQ), persistent RR (pRR) and persistent CA (pCA), LQ, RR and CA pattern in each of the 3 years, respectively; mixed, at least two different pattern types were identified. Results The RR pattern accounted for the greatest proportion of follow-up time both by M-SLEDAI and PGA, representing 53.8% and 49.9% of total patient-years, respectively. The second most frequent pattern was LQ based on M-SLEDAI (30.7%) and CA based on PGA (40.4%). For the first 3-year intervals, the mixed pattern type was the most common (56.6%). The pRR was the second most frequent (M-SLEDAI 33.3%, PGA 26.5%), while pLQ (M-SLEDAI 6.4%, PGA 0.7%) and pCA were less frequent (M-SLEDAI 3.7%, PGA 16.3%). Conclusions The RR pattern was the most prevalent pattern. LQ was achieved in a subset of patients, using the M-SLEDAI. However, the PGA captured mild activity missed on the M-SLEDAI in these patients. Over a 3-year perspective, less than half of patients maintained their original pattern. PMID:28243457

  4. Pattern Formation in a Predator-Prey Model with Both Cross Diffusion and Time Delay

    Directory of Open Access Journals (Sweden)

    Boli Xie

    2014-01-01

    Full Text Available A predator-prey model with both cross diffusion and time delay is considered. We give the conditions for emerging Turing instability in detail. Furthermore, we illustrate the spatial patterns via numerical simulations, which show that the model dynamics exhibits a delay and diffusion controlled formation growth not only of spots and stripe-like patterns, but also of the two coexist. The obtained results show that this system has rich dynamics; these patterns show that it is useful for the diffusive predation model with a delay effect to reveal the spatial dynamics in the real model.

  5. Investigation of Time Series Representations and Similarity Measures for Structural Damage Pattern Recognition

    Science.gov (United States)

    Swartz, R. Andrew

    2013-01-01

    This paper investigates the time series representation methods and similarity measures for sensor data feature extraction and structural damage pattern recognition. Both model-based time series representation and dimensionality reduction methods are studied to compare the effectiveness of feature extraction for damage pattern recognition. The evaluation of feature extraction methods is performed by examining the separation of feature vectors among different damage patterns and the pattern recognition success rate. In addition, the impact of similarity measures on the pattern recognition success rate and the metrics for damage localization are also investigated. The test data used in this study are from the System Identification to Monitor Civil Engineering Structures (SIMCES) Z24 Bridge damage detection tests, a rigorous instrumentation campaign that recorded the dynamic performance of a concrete box-girder bridge under progressively increasing damage scenarios. A number of progressive damage test case datasets and damage test data with different damage modalities are used. The simulation results show that both time series representation methods and similarity measures have significant impact on the pattern recognition success rate. PMID:24191136

  6. Investigation of time series representations and similarity measures for structural damage pattern recognition.

    Science.gov (United States)

    Liu, Wenjia; Chen, Bo; Swartz, R Andrew

    2013-01-01

    This paper investigates the time series representation methods and similarity measures for sensor data feature extraction and structural damage pattern recognition. Both model-based time series representation and dimensionality reduction methods are studied to compare the effectiveness of feature extraction for damage pattern recognition. The evaluation of feature extraction methods is performed by examining the separation of feature vectors among different damage patterns and the pattern recognition success rate. In addition, the impact of similarity measures on the pattern recognition success rate and the metrics for damage localization are also investigated. The test data used in this study are from the System Identification to Monitor Civil Engineering Structures (SIMCES) Z24 Bridge damage detection tests, a rigorous instrumentation campaign that recorded the dynamic performance of a concrete box-girder bridge under progressively increasing damage scenarios. A number of progressive damage test case datasets and damage test data with different damage modalities are used. The simulation results show that both time series representation methods and similarity measures have significant impact on the pattern recognition success rate.

  7. Accelerating the discovery of space-time patterns of infectious diseases using parallel computing.

    Science.gov (United States)

    Hohl, Alexander; Delmelle, Eric; Tang, Wenwu; Casas, Irene

    2016-11-01

    Infectious diseases have complex transmission cycles, and effective public health responses require the ability to monitor outbreaks in a timely manner. Space-time statistics facilitate the discovery of disease dynamics including rate of spread and seasonal cyclic patterns, but are computationally demanding, especially for datasets of increasing size, diversity and availability. High-performance computing reduces the effort required to identify these patterns, however heterogeneity in the data must be accounted for. We develop an adaptive space-time domain decomposition approach for parallel computation of the space-time kernel density. We apply our methodology to individual reported dengue cases from 2010 to 2011 in the city of Cali, Colombia. The parallel implementation reaches significant speedup compared to sequential counterparts. Density values are visualized in an interactive 3D environment, which facilitates the identification and communication of uneven space-time distribution of disease events. Our framework has the potential to enhance the timely monitoring of infectious diseases.

  8. The Trade-offs with Space Time Cube Representation of Spatiotemporal Patterns

    CERN Document Server

    Kristensson, Per Ola; Anundi, Daniel; Bjornstad, Marius; Gillberg, Hanna; Haraldsson, Jonas; Martensson, Ingrid; Nordvall, Matttias; Stahl, Josefin

    2007-01-01

    Space time cube representation is an information visualization technique where spatiotemporal data points are mapped into a cube. Fast and correct analysis of such information is important in for instance geospatial and social visualization applications. Information visualization researchers have previously argued that space time cube representation is beneficial in revealing complex spatiotemporal patterns in a dataset to users. The argument is based on the fact that both time and spatial information are displayed simultaneously to users, an effect difficult to achieve in other representations. However, to our knowledge the actual usefulness of space time cube representation in conveying complex spatiotemporal patterns to users has not been empirically validated. To fill this gap we report on a between-subjects experiment comparing novice users error rates and response times when answering a set of questions using either space time cube or a baseline 2D representation. For some simple questions the error rat...

  9. Time-lapse ultrashort pulse microscopy of infection in three-dimensional versus two-dimensional culture environments reveals enhanced extra-chromosomal virus replication compartment formation

    Science.gov (United States)

    Gibbs, Holly C.; Sing, Garwin; Armas, Juan Carlos González; Campbell, Colin J.; Ghazal, Peter; Yeh, Alvin T.

    2013-03-01

    The mechanisms that enable viruses to harness cellular machinery for their own survival are primarily studied in cell lines cultured in two-dimensional (2-D) environments. However, there are increasing reports of biological differences between cells cultured in 2-D versus three-dimensional (3-D) environments. Here we report differences in host-virus interactions based on differences in culture environment. Using ultrashort pulse microscopy (UPM), a form of two-photon microscopy that utilizes sub-10-fs pulses to efficiently excite fluorophores, we have shown that de novo development of extra-chromosomal virus replication compartments (VRCs) upon murine cytomegalovirus (mCMV) infection is markedly enhanced when host cells are cultured in 3-D collagen gels versus 2-D monolayers. In addition, time-lapse imaging revealed that mCMV-induced VRCs have the capacity to grow by coalescence. This work supports the future potential of 3-D culture as a useful bridge between traditional monolayer cultures and animal models to study host-virus interactions in a more physiologically relevant environment for the development of effective anti-viral therapeutics. These advances will require broader adoption of modalities, such as UPM, to image deep within scattering tissues.

  10. Perceptually related analysis of time-frequency patterns via a hearing model (Sottek), a pattern-measurement algorithm (``relative approach'') and a window-deconvolution algorithm

    Science.gov (United States)

    Bray, Wade

    2004-05-01

    The presence of patterns (time structure and/or tonal structure) in sound situations elicits a different analytic process by the human hearing system than when sound situations are without pattern. In the presence of pattern, two issues can interfere with the effectiveness of conventional measurement methods: the human hearing is not acting as an absolute magnitude measurer so conventional measurements may not, or only poorly, resolve the important criteria; and pattern information that is subjectively highly significant is frequently of low magnitude amid general high-level structure that is not a direct part of the subjective pattern-response problem yet carries significance. Several automotive sound quality and information technology time-data recordings involving various patterns, of different strengths, were analyzed using conventional, psychoacoustic, and specialized pattern-sensitive techniques. In general, the advanced perception-related methods proved superior in quantifying ``patterned'' sound situations according to subjective impression.

  11. Underwater Acoustic Communication Based on Pattern Time Delay Shift Coding Scheme

    Institute of Scientific and Technical Information of China (English)

    YIN Jing-wei; HUI Jun-ying; HUI Juan; YAO Zhi-xiang; WANG Yi-lin

    2006-01-01

    Underwater acoustic communication based on Pattern Time Delay Shift Coding (PDS) communication scheme is studied. The time delay shift values of the pattern are used to encode the digital information in the PDS scheme, which belongs to the Pulse Position Modulation (PPM). The duty cycle of the PDS scheme is small, so it can economize the power for communication. By use of different patterns for code division and different frequencies for channel division, the communication system is capable of mitigating the inter-symbol interference (ISI) caused by the multipath channel. The data rate of communication is 1000 bits/s at 8 kHz bandwidth. The receiver separates the channels by means of band-pass filters, and performs decoding by 4 copy-correlators to estimate the time delay shift value. Based on the theoretical analysis and numerical simulations, the PDS scheme is shown to be a robust and effective approach for underwater acoustic communication.

  12. Concept mediation in trilingual translation: evidence from response time and repetition priming patterns.

    Science.gov (United States)

    Francis, Wendy S; Gallard, Sabrina L K

    2005-12-01

    Translation responses to individual words were elicited from 48 English-Spanish-French trilinguals, who translated in six directions at study and two directions at test. Patterns of translation response times and error rates at study reflected the relative proficiency of the trilinguals in comprehension and production of their three languages. At test, repeated items were translated more quickly than new items, with the strongest priming effects occurring for identical repetitions. Repetition priming was also substantial when only the stimulus language or only the response language matched from study to test, implying that repeated comprehension and production processes contribute to priming in translation. Patterns of response times and repetition priming indicate that translation in all directions involved conceptual access. Additive patterns in response time asymmetries and repetition priming were consistent with the treatment of word comprehension and production processes of translation as independent.

  13. Neural code alterations and abnormal time patterns in Parkinson’s disease

    Science.gov (United States)

    Andres, Daniela Sabrina; Cerquetti, Daniel; Merello, Marcelo

    2015-04-01

    Objective. The neural code used by the basal ganglia is a current question in neuroscience, relevant for the understanding of the pathophysiology of Parkinson’s disease. While a rate code is known to participate in the communication between the basal ganglia and the motor thalamus/cortex, different lines of evidence have also favored the presence of complex time patterns in the discharge of the basal ganglia. To gain insight into the way the basal ganglia code information, we studied the activity of the globus pallidus pars interna (GPi), an output node of the circuit. Approach. We implemented the 6-hydroxydopamine model of Parkinsonism in Sprague-Dawley rats, and recorded the spontaneous discharge of single GPi neurons, in head-restrained conditions at full alertness. Analyzing the temporal structure function, we looked for characteristic scales in the neuronal discharge of the GPi. Main results. At a low-scale, we observed the presence of dynamic processes, which allow the transmission of time patterns. Conversely, at a middle-scale, stochastic processes force the use of a rate code. Regarding the time patterns transmitted, we measured the word length and found that it is increased in Parkinson’s disease. Furthermore, it showed a positive correlation with the frequency of discharge, indicating that an exacerbation of this abnormal time pattern length can be expected, as the dopamine depletion progresses. Significance. We conclude that a rate code and a time pattern code can co-exist in the basal ganglia at different temporal scales. However, their normal balance is progressively altered and replaced by pathological time patterns in Parkinson’s disease.

  14. PAMELA: Pattern Matching Engine with Limited-Time Update for NIDS/NIPS

    Science.gov (United States)

    Thinh, Tran Ngoc; Kittitornkun, Surin; Tomiyama, Shigenori

    Several hardware-based pattern matching engines for network intrusion/prevention detection systems (NIDS/NIPSs) can achieve high throughput with less hardware resources. However, their flexibility to update new patterns is limited and still challenging. This paper describes a PAttern Matching Engine with Limited-time updAte (PAMELA) engine using a recently proposed hashing algorithm called Cuckoo Hashing. PAMELA features on-the-fly pattern updates without reconfiguration, more efficient hardware utilization, and higher performance compared with other works. First, we implement the improved parallel exact pattern matching with arbitrary length based on Cuckoo Hashing and linked-list technique. Second, while PAMELA is being updated with new attack patterns, both stack and FIFO are utilized to bound insertion time due to the drawback of Cuckoo Hashing and to avoid interruption of input data stream. Third, we extend the system for multi-character processing to achieve higher throughput. Our engine can accommodate the latest Snort rule-set, an open source NIDS/NIPS, and achieve the throughput up to 8.8 Gigabit per second while consuming the lowest amount of hardware. Compared to other approaches, ours is far more efficient than any other implemented on Xilinx FPGA architectures.

  15. Temporal Patterns in Fine Particulate Matter Time Series in Beijing: A Calendar View

    Science.gov (United States)

    Liu, Jianzheng; Li, Jie; Li, Weifeng

    2016-08-01

    Extremely high fine particulate matter (PM2.5) concentration has become synonymous to Beijing, the capital of China, posing critical challenges to its sustainable development and leading to major public health concerns. In order to formulate mitigation measures and policies, knowledge on PM2.5 variation patterns should be obtained. While previous studies are limited either because of availability of data, or because of problematic a priori assumptions that PM2.5 concentration follows subjective seasonal, monthly, or weekly patterns, our study aims to reveal the data on a daily basis through visualization rather than imposing subjective periodic patterns upon the data. To achieve this, we conduct two time-series cluster analyses on full-year PM2.5 data in Beijing in 2014, and provide an innovative calendar visualization of PM2.5 measurements throughout the year. Insights from the analysis on temporal variation of PM2.5 concentration show that there are three diurnal patterns and no weekly patterns; seasonal patterns exist but they do not follow a strict temporal division. These findings advance current understanding on temporal patterns in PM2.5 data and offer a different perspective which can help with policy formulation on PM2.5 mitigation.

  16. Spatial Patterns of a Predator-Prey System of Leslie Type with Time Delay

    Science.gov (United States)

    Wang, Caiyun; Chang, Lili; Liu, Huifeng

    2016-01-01

    Time delay due to maturation time, capturing time or other reasons widely exists in biological systems. In this paper, a predator-prey system of Leslie type with diffusion and time delay is studied based on mathematical analysis and numerical simulations. Conditions for both delay induced and diffusion induced Turing instability are obtained by using bifurcation theory. Furthermore, a series of numerical simulations are performed to illustrate the spatial patterns, which reveal the information of density changes of both prey and predator populations. The obtained results show that the interaction between diffusion and time delay may give rise to rich dynamics in ecosystems. PMID:26930573

  17. Spatial Patterns of a Predator-Prey System of Leslie Type with Time Delay.

    Science.gov (United States)

    Wang, Caiyun; Chang, Lili; Liu, Huifeng

    2016-01-01

    Time delay due to maturation time, capturing time or other reasons widely exists in biological systems. In this paper, a predator-prey system of Leslie type with diffusion and time delay is studied based on mathematical analysis and numerical simulations. Conditions for both delay induced and diffusion induced Turing instability are obtained by using bifurcation theory. Furthermore, a series of numerical simulations are performed to illustrate the spatial patterns, which reveal the information of density changes of both prey and predator populations. The obtained results show that the interaction between diffusion and time delay may give rise to rich dynamics in ecosystems.

  18. Spatial Patterns of a Predator-Prey System of Leslie Type with Time Delay.

    Directory of Open Access Journals (Sweden)

    Caiyun Wang

    Full Text Available Time delay due to maturation time, capturing time or other reasons widely exists in biological systems. In this paper, a predator-prey system of Leslie type with diffusion and time delay is studied based on mathematical analysis and numerical simulations. Conditions for both delay induced and diffusion induced Turing instability are obtained by using bifurcation theory. Furthermore, a series of numerical simulations are performed to illustrate the spatial patterns, which reveal the information of density changes of both prey and predator populations. The obtained results show that the interaction between diffusion and time delay may give rise to rich dynamics in ecosystems.

  19. Order Patterns Networks (orpan – a method toestimate time-evolving functional connectivity frommultivariate time series

    Directory of Open Access Journals (Sweden)

    Stefan eSchinkel

    2012-11-01

    Full Text Available Complex networks provide an excellent framework for studying the functionof the human brain activity. Yet estimating functional networks from mea-sured signals is not trivial, especially if the data is non-stationary and noisyas it is often the case with physiological recordings. In this article we proposea method that uses the local rank structure of the data to define functionallinks in terms of identical rank structures. The method yields temporal se-quences of networks which permits to trace the evolution of the functionalconnectivity during the time course of the observation. We demonstrate thepotentials of this approach with model data as well as with experimentaldata from an electrophysiological study on language processing.

  20. Development of new punch shape to replicate scale-up issues in laboratory tablet press II: a new design of punch head to emulate consolidation and dwell times in commercial tablet press.

    Science.gov (United States)

    Aoki, Shigeru; Uchiyama, Jumpei; Ito, Manabu

    2014-06-01

    Differences between laboratory and commercial tablet presses are frequently observed during scale-up of tableting process. These scale-up issues result from the differences in total compression time that is the sum of consolidation and dwell times. When a lubricated blend is compressed into tablets, the tablet thickness produced by the commercial tablet press is often thicker than that by a laboratory tablet press. A new punch shape design, designated as shape adjusted for scale-up (SAS), was developed and used to demonstrate the ability to replicate scale-up issues in commercial-scale tableting processes. It was found that the consolidation time can be slightly shortened by changing the vertical curvature of the conventional punch head rim. However, this approach is not enough to replicate the consolidation time. A secondary two-stage SAS punch design and an embossed punch head was designed to replicate the consolidation and dwell times on a laboratory tablet press to match those of a commercial tablet press. The resulting tablet thickness using this second SAS punch on a laboratory tablet press was thicker than when using a conventional punch in the same laboratory tablet press. The secondary SAS punches are more useful tools for replicating and understanding potential scale-up issues. © 2014 Wiley Periodicals, Inc. and the American Pharmacists Association J Pharm Sci. © 2014 Wiley Periodicals, Inc. and the American Pharmacists Association.

  1. Time-Location Patterns of a Population Living in an Air Pollution Hotspot

    Directory of Open Access Journals (Sweden)

    Xiangmei (May Wu

    2010-01-01

    Full Text Available This study characterized the time-location pattern of 107 residents living in air pollution hotspots, the Waterfront South and Copewood/Davis Streets communities in Camden, NJ. Most residents in the two communities are minority and impoverished individuals. Results showed that employment status played the fundamental role in determining time-location patterns of this study population, and the variations of time-location pattern by season and by day-type were partially attributed to employment status. Compared to the National Human Activity Pattern Survey, the Camden cohort spent significantly more time outdoors (3.8 hours versus 1.8 hours and less time indoors (19.4 hours versus 20.9 hours than the general US population, indicating a higher risk of exposure to ambient air pollution for the Camden cohort. The findings of the study are important for understanding exposure routes and sources for the socioeconomically disadvantaged subgroup and ultimately help develop effective strategies to reduce community exposure to ambient air pollution in “hotspots”.

  2. Spatiotemporal Mining of Time-Series Remote Sensing Images Based on Sequential Pattern Mining

    Science.gov (United States)

    Liu, H. C.; He, G. J.; Zhang, X. M.; Jiang, W.; Ling, S. G.

    2015-07-01

    With the continuous development of satellite techniques, it is now possible to acquire a regular series of images concerning a given geographical zone with both high accuracy and low cost. Research on how best to effectively process huge volumes of observational data obtained on different dates for a specific geographical zone, and to exploit the valuable information regarding land cover contained in these images has received increasing interest from the remote sensing community. In contrast to traditional land cover change measures using pair-wise comparisons that emphasize the compositional or configurational changes between dates, this research focuses on the analysis of the temporal sequence of land cover dynamics, which refers to the succession of land cover types for a given area over more than two observational periods. Using a time series of classified Landsat images, ranging from 2006 to 2011, a sequential pattern mining method was extended to this spatiotemporal context to extract sets of connected pixels sharing similar temporal evolutions. The resultant sequential patterns could be selected (or not) based on the range of support values. These selected patterns were used to explore the spatial compositions and temporal evolutions of land cover change within the study region. Experimental results showed that continuous patterns that represent consistent land cover over time appeared as quite homogeneous zones, which agreed with our domain knowledge. Discontinuous patterns that represent land cover change trajectories were dominated by the transition from vegetation to bare land, especially during 2009-2010. This approach quantified land cover changes in terms of the percentage area affected and mapped the spatial distribution of these changes. Sequential pattern mining has been used for string mining or itemset mining in transactions analysis. The expected novel significance of this study is the generalization of the application of the sequential pattern

  3. Using Model Replication to Improve the Reliability of Agent-Based Models

    Science.gov (United States)

    Zhong, Wei; Kim, Yushim

    The basic presupposition of model replication activities for a computational model such as an agent-based model (ABM) is that, as a robust and reliable tool, it must be replicable in other computing settings. This assumption has recently gained attention in the community of artificial society and simulation due to the challenges of model verification and validation. Illustrating the replication of an ABM representing fraudulent behavior in a public service delivery system originally developed in the Java-based MASON toolkit for NetLogo by a different author, this paper exemplifies how model replication exercises provide unique opportunities for model verification and validation process. At the same time, it helps accumulate best practices and patterns of model replication and contributes to the agenda of developing a standard methodological protocol for agent-based social simulation.

  4. Replication of prions in differentiated muscle cells.

    Science.gov (United States)

    Herbst, Allen; Aiken, Judd M; McKenzie, Debbie

    2014-01-01

    We have demonstrated that prions accumulate to high levels in non-proliferative C2C12 myotubes. C2C12 cells replicate as myoblasts but can be differentiated into myotubes. Earlier studies indicated that C2C12 myoblasts are not competent for prion replication. (1) We confirmed that observation and demonstrated, for the first time, that while replicative myoblasts do not accumulate PrP(Sc), differentiated post-mitotic myotube cultures replicate prions robustly. Here we extend our observations and describe the implication and utility of this system for replicating prions.

  5. Characterization of space-time rainfall patterns over Switzerland based on high-resolution radar images

    Science.gov (United States)

    Benoit, Lionel; Mariethoz, Gregoire; Vrac, Mathieu

    2017-04-01

    Rainfall is generated by diverse and complex processes that produce rain fields with a large variability of patterns. High-resolution measurements of rainfall, provided for instance by networks of terrestrial weather radars, allow observing the spatial variability of rainfall patterns and its temporal evolution. The characterization of these space-time rainfall patterns is important for both the understanding of rain generation processes and the study of environmental impacts of rainfall on hydrology, erosion or plants growth, among others. Here we propose to study rainfall patterns using image processing methods on high-resolution radar images (1km x 1km x 1min) over Switzerland. The time series of radar images is first segmented in rain events. Then, the spatial structure of each rain event is characterized by computing statistics over several geometrical indices extracted from radar images, by adapting to the context of mid-latitude rainfalls the indices proposed by Aghakouchak, Nasrollahi et al. (2011) and Zick and Matyas (2016) for tropical rainfall characterization. Finally, the dynamics of rainfall patterns is characterized by estimating rain advection through image correlation, and by quantifying the temporal morphing of spatial patterns in a Lagrangian reference frame, where radar images are re-projected to cancel out rain advection. Two years of data (2015 - 2016) are used to investigate the variability of rainfall patterns over Switzerland. Typical values of the indicators measuring rainfall patterns and their dynamics are extracted for different areas, namely the Jura Mountain, the Swiss Plateau and the Alps. These measures of rainfall variability could be subsequently used to parameterize local weather generators or to investigate the relationships between rainfall patterns and atmospheric synoptic conditions. References: Aghakouchak, A., N. Nasrollahi, J. Li, B. Imam and S. Sorooshian (2011). "Geometrical Characterization of Precipitation Patterns

  6. Improvement of replication fidelity in injection moulding of nano structures using an induction heating system

    DEFF Research Database (Denmark)

    Menotti, Stefano; Hansen, Hans Nørgaard; Bissacco, Giuliano

    2014-01-01

    In today’s industry, applications involving surface pattering with sub-μm scale structures have shown a high interest. The replication of these structures by injection molding leads to special requirements for the mold in order to ensure proper replication and an acceptable cycle time. A tool...... quantitatively characterized by atomic force microscopy comparing the measurement in the nickel insert with the corresponding polymer nano-features. The experimental results show that the use of the induction heating system is an efficient way to improve the pattern replication....

  7. Improvement of replication fidelity in injection moulding of nano structures using an induction heating system

    DEFF Research Database (Denmark)

    Menotti, Stefano; Hansen, Hans Nørgaard; Bissacco, Giuliano

    2014-01-01

    In today’s industry, applications involving surface pattering with sub-μm scale structures have shown a high interest. The replication of these structures by injection molding leads to special requirements for the mold in order to ensure proper replication and an acceptable cycle time. A tool ins...... quantitatively characterized by atomic force microscopy comparing the measurement in the nickel insert with the corresponding polymer nano-features. The experimental results show that the use of the induction heating system is an efficient way to improve the pattern replication....

  8. Gait Patterns in Twins with Cerebral Palsy: Similarities and Development over Time after Multilevel Surgery

    Science.gov (United States)

    van Drongelen, Stefan; Dreher, Thomas; Heitzmann, Daniel W. W.; Wolf, Sebastian I.

    2013-01-01

    To examine gait patterns and gait quality, 7 twins with cerebral palsy were measured preoperatively and after surgical intervention. The aim was to study differences and/or similarities in gait between twins, the influence of personal characteristics and birth conditions, and to describe the development of gait over time after single event…

  9. Location, Timing, and Social Structure Patterns Related to Physical Activity Participation in Weight Loss Programs

    Science.gov (United States)

    Gay, Jennifer L.; Trevarthen, Grace

    2013-01-01

    Less than half of the adults in the United States meet national guidelines for physical activity. Physical activity programs can induce short-term improvements in physical activity. To develop effective interventions, researchers and practitioners should consider the timing, location, and social structure patterns of participants. Using a pretest,…

  10. Acoustic Analyses and Intelligibility Assessments of Timing Patterns among Chinese English Learners with Different Dialect Backgrounds

    Science.gov (United States)

    Chen, Hsueh Chu

    2015-01-01

    This paper includes two interrelated studies. The first production study investigates the timing patterns of English as spoken by Chinese learners with different dialect backgrounds. The second comprehension study explores native and non-native speakers' assessments of the intelligibility of Chinese-accented English, and examines the effects of…

  11. Location, Timing, and Social Structure Patterns Related to Physical Activity Participation in Weight Loss Programs

    Science.gov (United States)

    Gay, Jennifer L.; Trevarthen, Grace

    2013-01-01

    Less than half of the adults in the United States meet national guidelines for physical activity. Physical activity programs can induce short-term improvements in physical activity. To develop effective interventions, researchers and practitioners should consider the timing, location, and social structure patterns of participants. Using a pretest,…

  12. Cumulative Advantage and Success-Breeds-Success: The Value of Time Pattern Analysis.

    Science.gov (United States)

    Huber, John C.

    1998-01-01

    For the case of the distribution of papers across authors, the Success-Breeds-Success or Cumulative Advantage model is a popular candidate for informetrics. The method of time pattern of publication for individual authors can be used to discriminate between Cumulative Advantage and non-uniform giftedness models. The non-uniform giftedness model is…

  13. Sharing Time and the Poetic Patterning of Caribbean Independence: The Narrative Architecture of Voice

    Science.gov (United States)

    Van der Aa, Jef

    2013-01-01

    This article discusses the narrative architecture and interactional uptake of a school child's story about independence in Barbados during sharing time. It is found that an institutional focus on standard resources impacts both teachers' and children's sociolinguistic behavior. Ethnopoetic analysis brings out the child's patterned use of narrative…

  14. Gait Patterns in Twins with Cerebral Palsy: Similarities and Development over Time after Multilevel Surgery

    Science.gov (United States)

    van Drongelen, Stefan; Dreher, Thomas; Heitzmann, Daniel W. W.; Wolf, Sebastian I.

    2013-01-01

    To examine gait patterns and gait quality, 7 twins with cerebral palsy were measured preoperatively and after surgical intervention. The aim was to study differences and/or similarities in gait between twins, the influence of personal characteristics and birth conditions, and to describe the development of gait over time after single event…

  15. Opportunities, constraints and constrained opportunities - A study on mothers' working time patterns in 22 European countries

    OpenAIRE

    Milla Salin

    2014-01-01

    The aim of this study was to analyze mothers’ working time patters across 22 European countries. The focu was on three questions: how much mothers prefer to work, how much they actually work, and to what degree their preferred and actual working times are (in)consistent with each other. The focus was on cross-national differences in mothers’ working time patterns, comparison of mothers’ working times to that of childless women and fathers, as well as on individual- and country-level factors t...

  16. Self-timed vertacolor dichromatic vision sensor for low power pattern detection

    OpenAIRE

    2008-01-01

    This paper proposes a simple focal plane pattern detector architecture using a novel pixel sensor based on the dichromatic vertacolor structure. Additionally, the sensor transfers dichromatic intensity values using a self-timed time-to- first-spike scheme, which provides high dynamic range imaging. The intensity information is transmitted using the address event representation protocol. The spectral information is sampled automatically at each intensity reading in a ratioed way that maintains...

  17. Real-time 3D shape inspection system of automotive parts based on structured light pattern

    Science.gov (United States)

    Xu, Jing; Xi, Ning; Zhang, Chi; Shi, Quan; Gregory, John

    2011-02-01

    The non-contact 3D area sensor technology has achieved many successes in a variety of offline measurements. However, it has not been implemented for online measurement in the automotive production lines. The biggest challenge is the capability of simultaneously satisfying the efficiency, reliability, and accuracy requirements. For this purpose, a real-time 3D area sensor based on structured light pattern is proposed. To satisfy the requirement of online measurement, a one-shot pattern using monochromatic light is proposed. Compared with the previous patterns, this pattern is more robust because it can avoid the influence of the ambient light and the inspected part reflective property. Moreover, the requirement of the accuracy performance is achieved by the pattern primitive which is similar to the corner of the checkerboard since it can provide high accuracy performance even when the occlusion occurs; also, the pixel-to-pixel calibration strategy is utilized to increase the accuracy of the inspection system. Such a real-time shape measurement system has been successfully developed in our laboratory. Last, the evaluation experiments are conducted. The experiment results demonstrate the robustness and accuracy of the approach on automotive parts with different surface properties.

  18. Real-Time Classification of Complex Patterns Using Spike-Based Learning in Neuromorphic VLSI.

    Science.gov (United States)

    Mitra, S; Fusi, S; Indiveri, G

    2009-02-01

    Real-time classification of patterns of spike trains is a difficult computational problem that both natural and artificial networks of spiking neurons are confronted with. The solution to this problem not only could contribute to understanding the fundamental mechanisms of computation used in the biological brain, but could also lead to efficient hardware implementations of a wide range of applications ranging from autonomous sensory-motor systems to brain-machine interfaces. Here we demonstrate real-time classification of complex patterns of mean firing rates, using a VLSI network of spiking neurons and dynamic synapses which implement a robust spike-driven plasticity mechanism. The learning rule implemented is a supervised one: a teacher signal provides the output neuron with an extra input spike-train during training, in parallel to the spike-trains that represent the input pattern. The teacher signal simply indicates if the neuron should respond to the input pattern with a high rate or with a low one. The learning mechanism modifies the synaptic weights only as long as the current generated by all the stimulated plastic synapses does not match the output desired by the teacher, as in the perceptron learning rule. We describe the implementation of this learning mechanism and present experimental data that demonstrate how the VLSI neural network can learn to classify patterns of neural activities, also in the case in which they are highly correlated.

  19. Quantifying Landscape-Scale Patterns of Temperate Forests over Time by Means of Neutral Simulation Models

    Directory of Open Access Journals (Sweden)

    Maria Laura Carranza

    2013-03-01

    Full Text Available Several studies attempt to describe changes in the spatial patterns of forests over time, resorting to the comparison of landscape pattern indices (LPI, but new methods for quantifying landscape differences in a statistical context are necessary. In this paper, we quantified and assessed the statistical significance of the forests pattern changes, which have occurred since the end of WWII in Central Italy (Isernia. To do this; based on the proportion of forest cover (pi and contagion (H of three land cover maps (1954–1981–2006; we generated 100 forest maps with predictable results through the midpoint displacement algorithm. Then, for both observed and simulated maps, we computed a set of LPI (number of patches, cohesion, largest forest patch index and area weighted mean shape index and we derived their empirical distributions; finally, we compared the empirical distributions using the non-parametric Kruskal-Wallis test. Our results show significant changes in the spatial pattern of forests and underline the process of natural forest re-growth, which, in the area, is constrained by “remnants” of traditional activities. The adopted approach could be extended to a large ensemble of landscapes and spatial scales and could become a standard procedure when comparing patterns in time.

  20. Epigenetically-inherited centromere and neocentromere DNA replicates earliest in S-phase.

    Directory of Open Access Journals (Sweden)

    Amnon Koren

    2010-08-01

    Full Text Available Eukaryotic centromeres are maintained at specific chromosomal sites over many generations. In the budding yeast Saccharomyces cerevisiae, centromeres are genetic elements defined by a DNA sequence that is both necessary and sufficient for function; whereas, in most other eukaryotes, centromeres are maintained by poorly characterized epigenetic mechanisms in which DNA has a less definitive role. Here we use the pathogenic yeast Candida albicans as a model organism to study the DNA replication properties of centromeric DNA. By determining the genome-wide replication timing program of the C. albicans genome, we discovered that each centromere is associated with a replication origin that is the first to fire on its respective chromosome. Importantly, epigenetic formation of new ectopic centromeres (neocentromeres was accompanied by shifts in replication timing, such that a neocentromere became the first to replicate and became associated with origin recognition complex (ORC components. Furthermore, changing the level of the centromere-specific histone H3 isoform led to a concomitant change in levels of ORC association with centromere regions, further supporting the idea that centromere proteins determine origin activity. Finally, analysis of centromere-associated DNA revealed a replication-dependent sequence pattern characteristic of constitutively active replication origins. This strand-biased pattern is conserved, together with centromere position, among related strains and species, in a manner independent of primary DNA sequence. Thus, inheritance of centromere position is correlated with a constitutively active origin of replication that fires at a distinct early time. We suggest a model in which the distinct timing of DNA replication serves as an epigenetic mechanism for the inheritance of centromere position.

  1. Real-time star identification using synthetic radial pattern and its hardware implementation

    Science.gov (United States)

    Zhao, Yang; Wei, Xinguo; Wang, Gangyi; Li, Jian

    2017-02-01

    Star identification algorithm has always been the core strategy of star sensors. For the time being, the identification speed is becoming the bottleneck of satisfying real-time requirements (e.g. high-speed maneuvering applications, power breakdown and so on) on the premise of the robustness. To solve this problem, this paper proposes a novel lost-in-space star identification algorithm based on the synthetic radial pattern, which is dedicated to the pipelined parallel architecture of FPGAs (Field Programmable Gate Arrays). The synthetic radial pattern consists of two single radial patterns connected by their two respective polestars. In the algorithm, the polestar-pair is firstly matched and optimum identification results can be obtained after the follow-up radial pattern filtering. Then, the number of spurious matches can be reduced to a much less level and a mathematical model is also developed to demonstrate the efficiency compared with conventional radial algorithms. Simulations show that the approach is very robust towards various noise conditions and the quantified identification time is less than 1 ms at a low resource cost when it is implemented on FPGA platforms.

  2. Replication Restart in Bacteria.

    Science.gov (United States)

    Michel, Bénédicte; Sandler, Steven J

    2017-07-01

    In bacteria, replication forks assembled at a replication origin travel to the terminus, often a few megabases away. They may encounter obstacles that trigger replisome disassembly, rendering replication restart from abandoned forks crucial for cell viability. During the past 25 years, the genes that encode replication restart proteins have been identified and genetically characterized. In parallel, the enzymes were purified and analyzed in vitro, where they can catalyze replication initiation in a sequence-independent manner from fork-like DNA structures. This work also revealed a close link between replication and homologous recombination, as replication restart from recombination intermediates is an essential step of DNA double-strand break repair in bacteria and, conversely, arrested replication forks can be acted upon by recombination proteins and converted into various recombination substrates. In this review, we summarize this intense period of research that led to the characterization of the ubiquitous replication restart protein PriA and its partners, to the definition of several replication restart pathways in vivo, and to the description of tight links between replication and homologous recombination, responsible for the importance of replication restart in the maintenance of genome stability. Copyright © 2017 American Society for Microbiology.

  3. Distributed Real-Time Emulation of Formally-Defined Patterns for Safe Medical Device Control

    CERN Document Server

    Sun, Mu; 10.4204/EPTCS.36.9

    2010-01-01

    Safety of medical devices and of their interoperation is an unresolved issue causing severe and sometimes deadly accidents for patients with shocking frequency. Formal methods, particularly in support of highly reusable and provably safe patterns which can be instantiated to many device instances can help in this regard. However, this still leaves open the issue of how to pass from their formal specifications in logical time to executable emulations that can interoperate in physical time with other devices and with simulations of patient and/or doctor behaviors. This work presents a specification-based methodology in which virtual emulation environments can be easily developed from formal specifications in Real-Time Maude, and can support interactions with other real devices and with simulation models. This general methodology is explained in detail and is illustrated with two concrete scenarios which are both instances of a common safe formal pattern: one scenario involves the interaction of a provably safe ...

  4. Parallel streams versus integrated timing in multilimb pattern generation: A test of Korte's Third Law.

    Science.gov (United States)

    Jagacinski, Richard J; Rizzi, Emanuele; Kim, Tae Hoon; Lavender, Steven A; Speller, Lassiter F; Klapp, Stuart T

    2016-11-01

    Skilled drummers performed a 4:3:2 polyrhythm with 2 hands and 1 foot. For each pair of limbs patterns of temporal covariation were used to infer relatively independent parallel streams versus integrated timing relationships. Parallel timing was more prevalent between hand and foot than between the 2 hands, and parallel timing generally increased with tapping rate. Different combinations of integrated and parallel timing were found among the 3 limbs. A second experiment used a wider range of tapping rates and explored 3:2 tapping with 2 hands, 2 feet, or hand and foot. The latter 2 limb pairs resulted in greater prevalence of parallel timing. These results can be interpreted in terms of a Gestalt principle of grouping known as Korte's Third Law, which can be extended from the perceptual domain to the perceptual-motor domain. This principle indicates that perceived velocity is a key factor in determining whether a sequence of events is represented as a single integrated pattern or as multiple parallel patterns. The present results put disparate previous findings on bimanual polyrhythmic tapping and rhythmic aspects of the golf swing under a common theoretical perspective. (PsycINFO Database Record

  5. Lethal body concentrations and accumulation patterns determine time-dependent toxicity of cadmium in soil arthropods

    Energy Technology Data Exchange (ETDEWEB)

    Crommentuijn, T.; Doodeman, C.J.A.M.; Doornekamp, A.; Pol, J.J.C. van der; Bedaux, J.J.M.; Gestel, C.A.M. van (Vrije Univ., Amsterdam (Netherlands))

    1994-11-01

    Time-dependent toxicity in bioassays is usually explained in terms of uptake and elimination kinetics of the toxicant. By comparing different species with essentially different accumulation kinetics, a firm test of this concept may be made. This article compares the sensitivity of six soil arthropods, the collembolans Orchesella cincta and Tomocerus minor, the oribatid mite Platynothrus peltifer, the isopods Porcellio scaber and Oniscus asellus, and the diplopod Cylindroiulus britannicus, when exposed to cadmium in the food. Survival was determined at various time intervals; accumulation of cadmium in the animals was measured at one time interval. Kinetic-based toxicity models were fitted to the data, and estimates were obtained for lethal body concentration, uptake rate constant, elimination rate constant, and ultimate LC50. Two different accumulation patterns could be discerned; these were correlated with time-survival relationships. One, species that have the possibility to eliminate cadmium will reach an equilibrium for the internal concentration and also an ultimate LC50. Two, species that are unable to eliminate cadmium but store it in the body will have an ultimate LC50 equal to zero. For these species the time in which the lethal body concentration is reached is more important. Taxonomically related species appeared to have comparable accumulation patterns, but lethal body concentrations differed. It is concluded that knowledge of the accumulation pattern is indispensable for the evaluation of species' sensitivities to toxicants.

  6. Emerging Patterns Of Bangsa Malaysia In Anthony Burgess’ Time For A Tiger

    Directory of Open Access Journals (Sweden)

    Farahanna Abd Razak

    2016-01-01

    Full Text Available Time for a Tiger (1956, a novel by Anthony Burgess, is believed to have been overlooked in the Malaysian literary context. Existing scholarship has maintained that the central themes of Time for a Tiger are colliding cultures, clashes of religion and racial conflicts but, in spite of these themes, this paper attempts to argue that there are in fact emerging patterns of Bangsa Malaysia in Time for a Tiger, which in turn reflect the elements of unity among the rich mixture of multi-ethnic characters. Bangsa Malaysia is not only the first of the nine challenges listed in Vision 2020 as conceptualised by Dr. Mahathir Mohamad (1991, but also marks the first time the Malaysian government is officially putting forward a clear vision in building a nation, launched to create a oneness atmosphere among the ethnic groups, in hopes it will reduce, if not erase, the tension among them. This study reveals that there are indeed emerging patterns of Bangsa Malaysia depicted through a mixture of characters from various ethnicities, namely the Malays, the Chinese and the Indians, through the implementation of government policies, education, a change of mindset and personal judgement, patriotism and the unifying role of the monarchy. Additionally, the patterns do support the earlier stage of the formation of Bangsa Malaysia, namely tolerance. Keywords: Bangsa Malaysia, Anthony Burgess, Time for a Tiger, Malayans, tolerance, unity

  7. Integrating real-time CD corrections into a laser pattern generator

    Science.gov (United States)

    Haddleton, Steven; Ivansen, Lars; Simecek, Michal; Schnitker, Uwe; Stiblert, Lars; Enzinger, Manfred; Roessl, Wolfgang; Sundqvist, Mats; Kalus, Christian K.

    2002-07-01

    Controlling the critical dimension is central in mask manufacturing, and with the ever-shrinking design rule - and hence the increasing requirements on the mask fidelity - new and visionary ways of pushing the envelope of the critical dimension (CD), becomes essential. Research tools and off-line solutions for sizing, proximity correction and other CD compensations have been pursued for some time, but making efficient use of such technologies have been limited by ease-of-use, fracturing and computational time and data volumes associated. Here, we present techniques to deal with these challenges by taking the approach to integrate the solutions into a modern, real-time pattern generator datapath. The solution is based on hierarchical treatment of the patterns in the real-time data path of the pattern generator. By placing it in the real-time domain, we avoid the problem with exploding stream data volumes, and can exploit the parallel architecture and raw computational power of the data path engine.

  8. Extracting information in spike time patterns with wavelets and information theory.

    Science.gov (United States)

    Lopes-dos-Santos, Vítor; Panzeri, Stefano; Kayser, Christoph; Diamond, Mathew E; Quian Quiroga, Rodrigo

    2015-02-01

    We present a new method to assess the information carried by temporal patterns in spike trains. The method first performs a wavelet decomposition of the spike trains, then uses Shannon information to select a subset of coefficients carrying information, and finally assesses timing information in terms of decoding performance: the ability to identify the presented stimuli from spike train patterns. We show that the method allows: 1) a robust assessment of the information carried by spike time patterns even when this is distributed across multiple time scales and time points; 2) an effective denoising of the raster plots that improves the estimate of stimulus tuning of spike trains; and 3) an assessment of the information carried by temporally coordinated spikes across neurons. Using simulated data, we demonstrate that the Wavelet-Information (WI) method performs better and is more robust to spike time-jitter, background noise, and sample size than well-established approaches, such as principal component analysis, direct estimates of information from digitized spike trains, or a metric-based method. Furthermore, when applied to real spike trains from monkey auditory cortex and from rat barrel cortex, the WI method allows extracting larger amounts of spike timing information. Importantly, the fact that the WI method incorporates multiple time scales makes it robust to the choice of partly arbitrary parameters such as temporal resolution, response window length, number of response features considered, and the number of available trials. These results highlight the potential of the proposed method for accurate and objective assessments of how spike timing encodes information. Copyright © 2015 the American Physiological Society.

  9. Compaction and transport properties of newly replicated Caulobacter crescentus DNA.

    Science.gov (United States)

    Hong, Sun-Hae; McAdams, Harley H

    2011-12-01

    Upon initiating replication of the Caulobacter chromosome, one copy of the parS centromere remains at the stalked pole; the other moves to the distal pole. We identified the segregation dynamics and compaction characteristics of newly replicated Caulobacter DNA during transport (highly variable from cell to cell) using time-lapse fluorescence microscopy. The parS centromere and a length (also highly variable) of parS proximal DNA on each arm of the chromosome are segregated with the same relatively slow transport pattern as the parS locus. Newly replicated DNA further than about 100 kb from parS segregates with a different and faster pattern, while loci at 48 kb from parS segregate with the slow pattern in some cells and the fast pattern in others. The observed parS-proximal DNA compaction characteristics have scaling properties that suggest the DNA is branched. HU2-deletion strains exhibited a reduced compaction phenotype except near the parS site where only the ΔHU1ΔHU2 double mutant had a compaction phenotype. The chromosome shows speed-dependent extension during translocation suggesting the DNA polymer is under tension. While DNA segregation is highly reliable and succeeds in virtually all wild-type cells, the high degree of cell to cell variation in the segregation process is noteworthy.

  10. Cross-Sectional Analysis of Levels and Patterns of Objectively Measured Sedentary Time in Adolescent Females

    LENUS (Irish Health Repository)

    Harrington, Deirdre M.

    2011-10-28

    Abstract Background Adolescent females have been highlighted as a particularly sedentary population and the possible negative effects of a sedentary lifestyle are being uncovered. However, much of the past sedentary research is based on self-report or uses indirect methods to quantity sedentary time. Total time spent sedentary and the possible intricate sedentary patterns of adolescent females have not been described using objective and direct measure of body inclination. The objectives of this article are to examine the sedentary levels and patterns of a group of adolescent females using the ActivPAL™ and to highlight possible differences in sedentary levels and patterns across the week and within the school day. A full methodological description of how the data was analyzed is also presented. Methods One hundred and eleven adolescent females, age 15-18 yrs, were recruited from urban and rural areas in the Republic of Ireland. Participants wore an ActivPAL physical activity monitor for a 7.5 day period. The ActivPAL directly reports total time spent sitting\\/lying every 15 seconds and accumulation (frequency and duration) of sedentary activity was examined using a customized MATLAB ® computer software programme. Results While no significant difference was found in the total time spent sitting\\/lying over the full 24 hour day between weekday and weekend day (18.8 vs. 18.9 hours; p = .911), significantly more sedentary bouts of 1 to 5 minutes and 21 to 40 minutes in duration were accumulated on weekdays compared to weekend days (p < .001). The mean length of each sedentary bout was also longer (9.8 vs. 8.8 minutes; p < .001). When school hours (9 am-3 pm) and after school hours (4 pm-10 pm) were compared, there was no difference in total time spent sedentary (3.9 hours; p = .796) but the pattern of accumulation of the sedentary time differed. There were a greater number of bouts of > 20 minutes duration during school hours than after school hours (4.7 vs. 3

  11. Metadata Control Agent approach for Replication in Grid Environments

    Directory of Open Access Journals (Sweden)

    P. SunilGavaskar

    2013-10-01

    Full Text Available since grid environment is dynamic, network latency and user requests may change. In order to provide better communication, access time and fault tolerant in decentralized systems, the replication is a technique to reduce access time, storage space. The objective of the work is to propose an agent control approach for Heterogeneous environments using the Agents for storing objects as replicas in decentralized environments. Our idea minimizes the more replicas (i.e. causes overhead on response time and update cost, therefore maintaining suitable number of replicas is important. Fixed replicas provides file access structure to identify the esteem files and gives optimal replication location, which minimize replication issues like access time and update cost by assuming a given traffic pattern. In this context we present the Agents as replicas to maintain a suitable scalable architecture. The solution uses fewer replicas, which lead to fewer agents as a result of that frequent updating is possible. Our tests show that the proposed strategy outperforms previous solutions in terms of replication issues.

  12. Real-time intelligent pattern recognition algorithm for surface EMG signals

    Directory of Open Access Journals (Sweden)

    Jahed Mehran

    2007-12-01

    Full Text Available Abstract Background Electromyography (EMG is the study of muscle function through the inquiry of electrical signals that the muscles emanate. EMG signals collected from the surface of the skin (Surface Electromyogram: sEMG can be used in different applications such as recognizing musculoskeletal neural based patterns intercepted for hand prosthesis movements. Current systems designed for controlling the prosthetic hands either have limited functions or can only be used to perform simple movements or use excessive amount of electrodes in order to achieve acceptable results. In an attempt to overcome these problems we have proposed an intelligent system to recognize hand movements and have provided a user assessment routine to evaluate the correctness of executed movements. Methods We propose to use an intelligent approach based on adaptive neuro-fuzzy inference system (ANFIS integrated with a real-time learning scheme to identify hand motion commands. For this purpose and to consider the effect of user evaluation on recognizing hand movements, vision feedback is applied to increase the capability of our system. By using this scheme the user may assess the correctness of the performed hand movement. In this work a hybrid method for training fuzzy system, consisting of back-propagation (BP and least mean square (LMS is utilized. Also in order to optimize the number of fuzzy rules, a subtractive clustering algorithm has been developed. To design an effective system, we consider a conventional scheme of EMG pattern recognition system. To design this system we propose to use two different sets of EMG features, namely time domain (TD and time-frequency representation (TFR. Also in order to decrease the undesirable effects of the dimension of these feature sets, principle component analysis (PCA is utilized. Results In this study, the myoelectric signals considered for classification consists of six unique hand movements. Features chosen for EMG signal

  13. Real-Time Digitization of Metabolomics Patterns from a Living System Using Mass Spectrometry

    Science.gov (United States)

    Heinemann, Joshua; Noon, Brigit; Mohigmi, Mohammad J.; Mazurie, Aurélien; Dickensheets, David L.; Bothner, Brian

    2014-10-01

    The real-time quantification of changes in intracellular metabolic activities has the potential to vastly improve upon traditional transcriptomics and metabolomics assays for the prediction of current and future cellular phenotypes. This is in part because intracellular processes reveal themselves as specific temporal patterns of variation in metabolite abundance that can be detected with existing signal processing algorithms. Although metabolite abundance levels can be quantified by mass spectrometry (MS), large-scale real-time monitoring of metabolite abundance has yet to be realized because of technological limitations for fast extraction of metabolites from cells and biological fluids. To address this issue, we have designed a microfluidic-based inline small molecule extraction system, which allows for continuous metabolomic analysis of living systems using MS. The system requires minimal supervision, and has been successful at real-time monitoring of bacteria and blood. Feature-based pattern analysis of Escherichia coli growth and stress revealed cyclic patterns and forecastable metabolic trajectories. Using these trajectories, future phenotypes could be inferred as they exhibit predictable transitions in both growth and stress related changes. Herein, we describe an interface for tracking metabolic changes directly from blood or cell suspension in real-time.

  14. Extracting biologically significant patterns from short time series gene expression data

    Directory of Open Access Journals (Sweden)

    McGinnis Thomas

    2009-08-01

    Full Text Available Abstract Background Time series gene expression data analysis is used widely to study the dynamics of various cell processes. Most of the time series data available today consist of few time points only, thus making the application of standard clustering techniques difficult. Results We developed two new algorithms that are capable of extracting biological patterns from short time point series gene expression data. The two algorithms, ASTRO and MiMeSR, are inspired by the rank order preserving framework and the minimum mean squared residue approach, respectively. However, ASTRO and MiMeSR differ from previous approaches in that they take advantage of the relatively few number of time points in order to reduce the problem from NP-hard to linear. Tested on well-defined short time expression data, we found that our approaches are robust to noise, as well as to random patterns, and that they can correctly detect the temporal expression profile of relevant functional categories. Evaluation of our methods was performed using Gene Ontology (GO annotations and chromatin immunoprecipitation (ChIP-chip data. Conclusion Our approaches generally outperform both standard clustering algorithms and algorithms designed specifically for clustering of short time series gene expression data. Both algorithms are available at http://www.benoslab.pitt.edu/astro/.

  15. Diversity of eukaryotic DNA replication origins revealed by genome-wide analysis of chromatin structure.

    Directory of Open Access Journals (Sweden)

    Nicolas M Berbenetz

    2010-09-01

    Full Text Available Eukaryotic DNA replication origins differ both in their efficiency and in the characteristic time during S phase when they become active. The biological basis for these differences remains unknown, but they could be a consequence of chromatin structure. The availability of genome-wide maps of nucleosome positions has led to an explosion of information about how nucleosomes are assembled at transcription start sites, but no similar maps exist for DNA replication origins. Here we combine high-resolution genome-wide nucleosome maps with comprehensive annotations of DNA replication origins to identify patterns of nucleosome occupancy at eukaryotic replication origins. On average, replication origins contain a nucleosome depleted region centered next to the ACS element, flanked on both sides by arrays of well-positioned nucleosomes. Our analysis identified DNA sequence properties that correlate with nucleosome occupancy at replication origins genome-wide and that are correlated with the nucleosome-depleted region. Clustering analysis of all annotated replication origins revealed a surprising diversity of nucleosome occupancy patterns. We provide evidence that the origin recognition complex, which binds to the origin, acts as a barrier element to position and phase nucleosomes on both sides of the origin. Finally, analysis of chromatin reconstituted in vitro reveals that origins are inherently nucleosome depleted. Together our data provide a comprehensive, genome-wide view of chromatin structure at replication origins and suggest a model of nucleosome positioning at replication origins in which the underlying sequence occludes nucleosomes to permit binding of the origin recognition complex, which then (likely in concert with nucleosome modifiers and remodelers positions nucleosomes adjacent to the origin to promote replication origin function.

  16. Relating interesting quantitative time series patterns with text events and text features

    Science.gov (United States)

    Wanner, Franz; Schreck, Tobias; Jentner, Wolfgang; Sharalieva, Lyubka; Keim, Daniel A.

    2013-12-01

    In many application areas, the key to successful data analysis is the integrated analysis of heterogeneous data. One example is the financial domain, where time-dependent and highly frequent quantitative data (e.g., trading volume and price information) and textual data (e.g., economic and political news reports) need to be considered jointly. Data analysis tools need to support an integrated analysis, which allows studying the relationships between textual news documents and quantitative properties of the stock market price series. In this paper, we describe a workflow and tool that allows a flexible formation of hypotheses about text features and their combinations, which reflect quantitative phenomena observed in stock data. To support such an analysis, we combine the analysis steps of frequent quantitative and text-oriented data using an existing a-priori method. First, based on heuristics we extract interesting intervals and patterns in large time series data. The visual analysis supports the analyst in exploring parameter combinations and their results. The identified time series patterns are then input for the second analysis step, in which all identified intervals of interest are analyzed for frequent patterns co-occurring with financial news. An a-priori method supports the discovery of such sequential temporal patterns. Then, various text features like the degree of sentence nesting, noun phrase complexity, the vocabulary richness, etc. are extracted from the news to obtain meta patterns. Meta patterns are defined by a specific combination of text features which significantly differ from the text features of the remaining news data. Our approach combines a portfolio of visualization and analysis techniques, including time-, cluster- and sequence visualization and analysis functionality. We provide two case studies, showing the effectiveness of our combined quantitative and textual analysis work flow. The workflow can also be generalized to other

  17. Using missing ordinal patterns to detect nonlinearity in time series data

    Science.gov (United States)

    Kulp, Christopher W.; Zunino, Luciano; Osborne, Thomas; Zawadzki, Brianna

    2017-08-01

    The number of missing ordinal patterns (NMP) is the number of ordinal patterns that do not appear in a series after it has been symbolized using the Bandt and Pompe methodology. In this paper, the NMP is demonstrated as a test for nonlinearity using a surrogate framework in order to see if the NMP for a series is statistically different from the NMP of iterative amplitude adjusted Fourier transform (IAAFT) surrogates. It is found that the NMP works well as a test statistic for nonlinearity, even in the cases of very short time series. Both model and experimental time series are used to demonstrate the efficacy of the NMP as a test for nonlinearity.

  18. Constructing and predicting solitary pattern solutions for nonlinear time-fractional dispersive partial differential equations

    Science.gov (United States)

    Arqub, Omar Abu; El-Ajou, Ahmad; Momani, Shaher

    2015-07-01

    Building fractional mathematical models for specific phenomena and developing numerical or analytical solutions for these fractional mathematical models are crucial issues in mathematics, physics, and engineering. In this work, a new analytical technique for constructing and predicting solitary pattern solutions of time-fractional dispersive partial differential equations is proposed based on the generalized Taylor series formula and residual error function. The new approach provides solutions in the form of a rapidly convergent series with easily computable components using symbolic computation software. For method evaluation and validation, the proposed technique was applied to three different models and compared with some of the well-known methods. The resultant simulations clearly demonstrate the superiority and potentiality of the proposed technique in terms of the quality performance and accuracy of substructure preservation in the construct, as well as the prediction of solitary pattern solutions for time-fractional dispersive partial differential equations.

  19. First-passage times for pattern formation in nonlocal partial differential equations

    Science.gov (United States)

    Cáceres, Manuel O.; Fuentes, Miguel A.

    2015-10-01

    We describe the lifetimes associated with the stochastic evolution from an unstable uniform state to a patterned one when the time evolution of the field is controlled by a nonlocal Fisher equation. A small noise is added to the evolution equation to define the lifetimes and to calculate the mean first-passage time of the stochastic field through a given threshold value, before the patterned steady state is reached. In order to obtain analytical results we introduce a stochastic multiscale perturbation expansion. This multiscale expansion can also be used to tackle multiplicative stochastic partial differential equations. A critical slowing down is predicted for the marginal case when the Fourier phase of the unstable initial condition is null. We carry out Monte Carlo simulations to show the agreement with our theoretical predictions. Analytic results for the bifurcation point and asymptotic analysis of traveling wave-front solutions are included to get insight into the noise-induced transition phenomena mediated by invading fronts.

  20. Population declines lead to replicate patterns of internal range structure at the tips of the distribution of the California red-legged frog (Rana draytonii)

    Science.gov (United States)

    Richmond, Jonathan Q.; Backlin, Adam R.; Tatarian, Patricia J.; Solvesky, Ben G.; Fisher, Robert N.

    2014-01-01

    Demographic declines and increased isolation of peripheral populations of the threatened California red-legged frog (Rana draytonii) have led to the formation of internal range boundaries at opposite ends of the species’ distribution. While the population genetics of the southern internal boundary has been studied in some detail, similar information is lacking for the northern part of the range. In this study, we used microsatellite and mtDNA data to examine the genetic structuring and diversity of some of the last remaining R. draytonii populations in the northern Sierra Nevada, which collectively form the northern external range boundary. We compared these data to coastal populations in the San Francisco Bay Area, where the species is notably more abundant and still exists throughout much of its historic range. We show that ‘external’ Sierra Nevada populations have lower genetic diversity and are more differentiated from one another than their ‘internal’ Bay Area counterparts. This same pattern was mirrored across the distribution in California, where Sierra Nevada and Bay Area populations had lower allelic variability compared to those previously studied in coastal southern California. This genetic signature of northward range expansion was mirrored in the phylogeography of mtDNA haplotypes; northern Sierra Nevada haplotypes showed greater similarity to haplotypes from the south Coast Ranges than to the more geographically proximate populations in the Bay Area. These data cast new light on the geographic origins of Sierra Nevada R. draytonii populations and highlight the importance of distinguishing the genetic effects of contemporary demographic declines from underlying signatures of historic range expansion when addressing the most immediate threats to population persistence. Because there is no evidence of contemporary gene flow between any of the Sierra Nevada R. draytonii populations, we suggest that management activities should focus on

  1. CLINICAL FEATURES AND PATTERN OF FRACTURES AT THE TIME OF DIAGNOSIS OF OSTEOGENESIS IMPERFECTA IN CHILDREN

    OpenAIRE

    Brizola,Evelise; Zambrano,Marina Bauer; Pinheiro,Bruna de Souza; Vanz, Ana Paula; F?lix, T?mis Maria

    2017-01-01

    ABSTRACT Objective: To characterize the fracture pattern and the clinical history at the time of diagnosis of osteogenesis imperfecta. Methods: In this retrospective study, all patients with osteogenesis imperfecta, of both genders, aged 0-18 years, who were treated between 2002 and 2014 were included. Medical records were assessed to collect clinical data, including the presence of blue sclerae, dentinogenesis imperfecta, positive familial history of osteogenesis imperfecta, and the site of ...

  2. Pattern recognition of surface electromyography signals for real-time control of wrist exoskeletons

    OpenAIRE

    Khokhar, Zeeshan Omer

    2010-01-01

    Surface electromyography (sEMG) signals have been used in numerous studies for the classification of hand gestures and successfully implemented in the position control of different prosthetic hands. An estimation of the intended torque of the user could also provide sufficient information for an effective force control of hand prosthesis or an assistive device. This thesis presents the use of pattern recognition to estimate the torque applied by a human wrist and its real-time implementation ...

  3. Observed variations in U.S. frost timing linked to atmospheric circulation patterns

    Science.gov (United States)

    Strong, Courtenay; McCabe, Gregory J.

    2017-01-01

    Several studies document lengthening of the frost-free season within the conterminous United States (U.S.) over the past century, and report trends in spring and fall frost timing that could stem from hemispheric warming. In the absence of warming, theory and case studies link anomalous frost timing to atmospheric circulation anomalies. However, recent efforts to relate a century of observed changes in U.S. frost timing to various atmospheric circulations yielded only modest correlations, leaving the relative importance of circulation and warming unclear. Here, we objectively partition the U.S. into four regions and uncover atmospheric circulations that account for 25–48% of spring and fall-frost timing. These circulations appear responsive to historical warming, and they consistently account for more frost timing variability than hemispheric or regional temperature indices. Reliable projections of future variations in growing season length depend on the fidelity of these circulation patterns in global climate models.

  4. 3D Pattern Synthesis of Time-Modulated Conformal Arrays with a Multiobjective Optimization Approach

    Directory of Open Access Journals (Sweden)

    Wentao Li

    2014-01-01

    Full Text Available This paper addresses the synthesis of the three-dimensional (3D radiation patterns of the time-modulated conformal arrays. Due to the nature of periodic time modulation, harmonic radiation patterns are generated at the multiples of the modulation frequency in time-modulated arrays. Thus, the optimization goal of the time-modulated conformal array includes the optimization of the sidelobe level at the operating frequency and the sideband levels (SBLs at the harmonic frequency, and the design can be regarded as a multiobjective problem. The multiobjective particle swarm optimization (MOPSO is applied to optimize the switch-on instants and pulse durations of the time-modulated conformal array. To significantly reduce the optimization variables, the modified Bernstein polynomial is employed in the synthesis process. Furthermore, dual polarized patch antenna is designed as radiator to achieve low cross-polarization level during the beam scanning. A 12 × 13 (156-element conical conformal microstrip array is simulated to demonstrate the proposed synthesis mechanism, and good results reveal the promising ability of the proposed algorithm in solving the synthesis of the time-modulated conformal arrays problem.

  5. Active dynamics of colloidal particles in time-varying laser speckle patterns

    Science.gov (United States)

    Bianchi, Silvio; Pruner, Riccardo; Vizsnyiczai, Gaszton; Maggi, Claudio; di Leonardo, Roberto

    2016-06-01

    Colloidal particles immersed in a dynamic speckle pattern experience an optical force that fluctuates both in space and time. The resulting dynamics presents many interesting analogies with a broad class of non-equilibrium systems like: active colloids, self propelled microorganisms, transport in dynamical intracellular environments. Here we show that the use of a spatial light modulator allows to generate light fields that fluctuate with controllable space and time correlations and a prescribed average intensity profile. In particular we generate ring-shaped random patterns that can confine a colloidal particle over a quasi one-dimensional random energy landscape. We find a mean square displacement that is diffusive at both short and long times, while a superdiffusive or subdiffusive behavior is observed at intermediate times depending on the value of the speckles correlation time. We propose two alternative models for the mean square displacement in the two limiting cases of a short or long speckles correlation time. A simple interpolation formula is shown to account for the full phenomenology observed in the mean square displacement across the entire range from fast to slow fluctuating speckles.

  6. Replication program of active and inactive multigene families in mammalian cells

    Energy Technology Data Exchange (ETDEWEB)

    Hatton, K.S.; Dhar, V.; Brown, E.H.; Iqbal, M.A.; Stuart, S.; Didamo, V.T.; Schildkraut, C.L.

    1988-05-01

    In a comprehensive study, the temporal replication of tissue-specific genes and flanking sequences was compared in nine cells lines exhibiting different tissue-specific functions. Some of the rules the authors determined for the replication of these tissue specific genes include the following. (i) Actively transcribed genes usually replicate during the first quarter of the S phase. (ii) Some immunoglobulin genes replicate during the first half of S phase even when no transcriptional activity is detected but appear to replicate even earlier in cell lines where they are transcribed. (iii) Nontranscribed genes can replicate during any interval of S phase. (iv) Multigene families arranged in clusters of 250 kilobases or less define a temporal compartment comprising approximately one-quarter of S phase. While these rules, and others that are discussed, apply to the tissue-specific genes studied here, all tissue-specific genes may not follow this pattern. In addition, housekeeping genes did not follow some of these rules. These results provide the first molecular evidence that the coordinate timing of replication of contiguous sequences within a multigene family is a general property of the mammalian genome. The relationship between replication very early during S phase and the transcriptional activity within a chromosomal domain is discussed.

  7. The mortality rates and the space-time patterns of John Snow's cholera epidemic map.

    Science.gov (United States)

    Shiode, Narushige; Shiode, Shino; Rod-Thatcher, Elodie; Rana, Sanjay; Vinten-Johansen, Peter

    2015-06-17

    Snow's work on the Broad Street map is widely known as a pioneering example of spatial epidemiology. It lacks, however, two significant attributes required in contemporary analyses of disease incidence: population at risk and the progression of the epidemic over time. Despite this has been repeatedly suggested in the literature, no systematic investigation of these two aspects was previously carried out. Using a series of historical documents, this study constructs own data to revisit Snow's study to examine the mortality rate at each street location and the space-time pattern of the cholera outbreak. This study brings together records from a series of historical documents, and prepares own data on the estimated number of residents at each house location as well as the space-time data of the victims, and these are processed in GIS to facilitate the spatial-temporal analysis. Mortality rates and the space-time pattern in the victims' records are explored using Kernel Density Estimation and network-based Scan Statistic, a recently developed method that detects significant concentrations of records such as the date and place of victims with respect to their distance from others along the street network. The results are visualised in a map form using a GIS platform. Data on mortality rates and space-time distribution of the victims were collected from various sources and were successfully merged and digitised, thus allowing the production of new map outputs and new interpretation of the 1854 cholera outbreak in London, covering more cases than Snow's original report and also adding new insights into their space-time distribution. They confirmed that areas in the immediate vicinity of the Broad Street pump indeed suffered from excessively high mortality rates, which has been suspected for the past 160 years but remained unconfirmed. No distinctive pattern was found in the space-time distribution of victims' locations. The high mortality rates identified around the

  8. CO2 time series patterns in contrasting headwater streams of North America

    Science.gov (United States)

    Crawford, John T.; Stanley, Emily H.; Dornblaser, Mark M.; Striegl, Rob

    2017-01-01

    We explored the underlying patterns of temporal stream CO2 partial pressure (pCO2) variability using highfrequency sensors in seven disparate headwater streams distributed across the northern hemisphere. We also compared this dataset of [40,000 pCO2 records with other published records from lotic systems. Individual stream sites exhibited relatively distinct pCO2 patterns over time with few consistent traits across sites. Some sites showed strong diel variability, some exhibited increasing pCO2 with increasing discharge, whereas other streams had reduced pCO2 with increasing discharge or no clear response to changes in flow. The only ‘‘universal’’ signature observed in headwater streams was a late summer pCO2 maxima that was likely driven by greatest rates of organic matter respiration due to highest annual temperatures. However, we did not observe this seasonal pattern in a southern hardwood forest site, likely because the region was transitioning from a severe drought. This work clearly illustrates the heterogeneous nature of headwater streams, and highlights the idiosyncratic nature of a non-conservative solute that is jointly influenced by physics, hydrology, and biology. We suggest that future researchers carefully select sensor locations (within and among streams) and provide additional contextual information when attempting to explain pCO2 patterns.

  9. Fluid flow pattern and water residence time in waste stabilisation ponds.

    Science.gov (United States)

    Badrot-Nico, F; Guinot, V; Brissaud, F

    2009-01-01

    As treatment processes are kinetic-dependent, a consistent description of water residence times is essential to the prediction of waste stabilization ponds performance. A physically-based 3D transient CFD model simulating the water velocity, temperature and concentration fields as a function of all influent meteorological factors--wind speed and direction, solar radiation, air temperature and relative humidity--was used to identify the relationships between the meteorological conditions and the hydrodynamic patterns and water residence times distributions in a polishing pond. The required meteorological data were recorded on site and water temperatures recorded at 10 sampling sites for 141 days. Stratification events appear on very calm days for wind speeds lower than 3 m s(-1) and on sunny days for wind speeds lower than 5 m s(-1). De-stratification is related to two mixing processes: nightly convection cells and global mixing patterns. Numerical tracer experiments show that the results of the flow patterns can be evaluated using the dispersed flow regime approximation and, for wind speeds exceeding 6 m s(-1), the completely stirred tank reactor assumption.

  10. Regulation of beta cell replication

    DEFF Research Database (Denmark)

    Lee, Ying C; Nielsen, Jens Høiriis

    2008-01-01

    Beta cell mass, at any given time, is governed by cell differentiation, neogenesis, increased or decreased cell size (cell hypertrophy or atrophy), cell death (apoptosis), and beta cell proliferation. Nutrients, hormones and growth factors coupled with their signalling intermediates have been...... suggested to play a role in beta cell mass regulation. In addition, genetic mouse model studies have indicated that cyclins and cyclin-dependent kinases that determine cell cycle progression are involved in beta cell replication, and more recently, menin in association with cyclin-dependent kinase...... inhibitors has been demonstrated to be important in beta cell growth. In this review, we consider and highlight some aspects of cell cycle regulation in relation to beta cell replication. The role of cell cycle regulation in beta cell replication is mostly from studies in rodent models, but whether...

  11. Pattern and Variation in the Timing of Aksak Meter: Commentary on Goldberg

    Directory of Open Access Journals (Sweden)

    Rainer Polak

    2016-01-01

    Full Text Available Daniel Goldberg (2015, this issue explores relations between timing variations, grouping structure, and musical form in the percussive accompaniment of Balkan folk dance music. A chronometric re-analysis of one of the target article’s two audio samples finds a regular metric timing pattern to consistently underlie the variations Goldberg uncovered. Read together, the target article and this commentary demonstrate the complex interplay of a regular timing pattern with several levels of nuanced variation to be performed with fluency, flexibility, and accuracy. This might appear commonplace, but here it is observed in the context of an asymmetric rhythmic mode, non-isochronous beat sequence, and asymmetric metric hierarchy. This context evidently does not represent a constraint of any sort in respect to the rhythmic timing performance, which casts doubts on the deep-seated assumption that metric regularity depends on iso-periodicity and vertical symmetry. This assumption is sometimes explicitly and often implicitly taken as universal; this comment suggests that, on the contrary, it might well be culturally biased.

  12. Time pattern locking scheme for secure multimedia contents in human-centric device.

    Science.gov (United States)

    Kim, Hyun-Woo; Kim, Jun-Ho; Park, Jong Hyuk; Jeong, Young-Sik

    2014-01-01

    Among the various smart multimedia devices, multimedia smartphones have become the most widespread due to their convenient portability and real-time information sharing, as well as various other built-in features. Accordingly, since personal and business activities can be carried out using multimedia smartphones without restrictions based on time and location, people have more leisure time and convenience than ever. However, problems such as loss, theft, and information leakage because of convenient portability have also increased proportionally. As a result, most multimedia smartphones are equipped with various built-in locking features. Pattern lock, personal identification numbers, and passwords are the most used locking features on current smartphones, but these are vulnerable to shoulder surfing and smudge attacks, allowing malicious users to bypass the security feature easily. In particular, the smudge attack technique is a convenient way to unlock multimedia smartphones after they have been stolen. In this paper, we propose the secure locking screen using time pattern (SLSTP) focusing on improved security and convenience for users to support human-centric multimedia device completely. The SLSTP can provide a simple interface to users and reduce the risk factors pertaining to security leakage to malicious third parties.

  13. Hybrid model for forecasting time series with trend, seasonal and salendar variation patterns

    Science.gov (United States)

    Suhartono; Rahayu, S. P.; Prastyo, D. D.; Wijayanti, D. G. P.; Juliyanto

    2017-09-01

    Most of the monthly time series data in economics and business in Indonesia and other Moslem countries not only contain trend and seasonal, but also affected by two types of calendar variation effects, i.e. the effect of the number of working days or trading and holiday effects. The purpose of this research is to develop a hybrid model or a combination of several forecasting models to predict time series that contain trend, seasonal and calendar variation patterns. This hybrid model is a combination of classical models (namely time series regression and ARIMA model) and/or modern methods (artificial intelligence method, i.e. Artificial Neural Networks). A simulation study was used to show that the proposed procedure for building the hybrid model could work well for forecasting time series with trend, seasonal and calendar variation patterns. Furthermore, the proposed hybrid model is applied for forecasting real data, i.e. monthly data about inflow and outflow of currency at Bank Indonesia. The results show that the hybrid model tend to provide more accurate forecasts than individual forecasting models. Moreover, this result is also in line with the third results of the M3 competition, i.e. the hybrid model on average provides a more accurate forecast than the individual model.

  14. Spatial regulation and organization of DNA replication within the nucleus

    OpenAIRE

    2009-01-01

    Duplication of chromosomal DNA is a temporally and spatially regulated process. The timing of DNA replication initiation at various origins is highly coordinated; some origins fire early and others late during S phase. Moreover, inside the nuclei, the bulk of DNA replication is physically organized in replication factories, consisting of DNA polymerases and other replication proteins. In this review article, we discuss how DNA replication is organized and regulated spatially within the nucleu...

  15. Measuring information interactions on the ordinal pattern of stock time series.

    Science.gov (United States)

    Zhao, Xiaojun; Shang, Pengjian; Wang, Jing

    2013-02-01

    The interactions among time series as individual components of complex systems can be quantified by measuring to what extent they exchange information among each other. In many applications, one focuses not on the original series but on its ordinal pattern. In such cases, trivial noises appear more likely to be filtered and the abrupt influence of extreme values can be weakened. Cross-sample entropy and inner composition alignment have been introduced as prominent methods to estimate the information interactions of complex systems. In this paper, we modify both methods to detect the interactions among the ordinal pattern of stock return and volatility series, and we try to uncover the information exchanges across sectors in Chinese stock markets.

  16. Spatial regulation and organization of DNA replication within the nucleus.

    Science.gov (United States)

    Natsume, Toyoaki; Tanaka, Tomoyuki U

    2010-01-01

    Duplication of chromosomal DNA is a temporally and spatially regulated process. The timing of DNA replication initiation at various origins is highly coordinated; some origins fire early and others late during S phase. Moreover, inside the nuclei, the bulk of DNA replication is physically organized in replication factories, consisting of DNA polymerases and other replication proteins. In this review article, we discuss how DNA replication is organized and regulated spatially within the nucleus and how this spatial organization is linked to temporal regulation. We focus on DNA replication in budding yeast and fission yeast and, where applicable, compare yeast DNA replication with that in bacteria and metazoans.

  17. DNA replication and cancer

    DEFF Research Database (Denmark)

    Boyer, Anne-Sophie; Walter, David; Sørensen, Claus Storgaard

    2016-01-01

    A dividing cell has to duplicate its DNA precisely once during the cell cycle to preserve genome integrity avoiding the accumulation of genetic aberrations that promote diseases such as cancer. A large number of endogenous impacts can challenge DNA replication and cells harbor a battery of pathways...... causing DNA replication stress and genome instability. Further, we describe cellular and systemic responses to these insults with a focus on DNA replication restart pathways. Finally, we discuss the therapeutic potential of exploiting intrinsic replicative stress in cancer cells for targeted therapy....

  18. Chromosome replication and segregation in bacteria.

    Science.gov (United States)

    Reyes-Lamothe, Rodrigo; Nicolas, Emilien; Sherratt, David J

    2012-01-01

    In dividing cells, chromosome duplication once per generation must be coordinated with faithful segregation of newly replicated chromosomes and with cell growth and division. Many of the mechanistic details of bacterial replication elongation are well established. However, an understanding of the complexities of how replication initiation is controlled and coordinated with other cellular processes is emerging only slowly. In contrast to eukaryotes, in which replication and segregation are separate in time, the segregation of most newly replicated bacterial genetic loci occurs sequentially soon after replication. We compare the strategies used by chromosomes and plasmids to ensure their accurate duplication and segregation and discuss how these processes are coordinated spatially and temporally with growth and cell division. We also describe what is known about the three conserved families of ATP-binding proteins that contribute to chromosome segregation and discuss their inter-relationships in a range of disparate bacteria.

  19. Interaction patterns of brain activity across space, time and frequency. Part I: methods

    CERN Document Server

    Pascual-Marqui, Roberto D

    2011-01-01

    We consider exploratory methods for the discovery of cortical functional connectivity. Typically, data for the i-th subject (i=1...NS) is represented as an NVxNT matrix Xi, corresponding to brain activity sampled at NT moments in time from NV cortical voxels. A widely used method of analysis first concatenates all subjects along the temporal dimension, and then performs an independent component analysis (ICA) for estimating the common cortical patterns of functional connectivity. There exist many other interesting variations of this technique, as reviewed in [Calhoun et al. 2009 Neuroimage 45: S163-172]. We present methods for the more general problem of discovering functional connectivity occurring at all possible time lags. For this purpose, brain activity is viewed as a function of space and time, which allows the use of the relatively new techniques of functional data analysis [Ramsay & Silverman 2005: Functional data analysis. New York: Springer]. In essence, our method first vectorizes the data from...

  20. Developmental patterns and parental correlates of youth leisure-time physical activity.

    Science.gov (United States)

    Lam, Chun Bun; McHale, Susan M

    2015-02-01

    This study examined the developmental patterns and parental correlates of youth leisure-time physical activity from middle childhood through adolescence. On 5 occasions across 7 years, fathers, mothers, and children who were first- and second born from 201 European American, working- and middle-class families participated in home and multiple nightly phone interviews. Multilevel modeling revealed that, controlling for family socioeconomic status, neighborhood characteristics, and youth overweight status and physical health, leisure-time physical activity increased during middle childhood and declined across adolescence, and the decline was more pronounced for girls than for boys. Moreover, controlling for time-varying, parental work hours and youth interest in sports and outdoor activities, on occasions when fathers and mothers spent proportionally more time on these activities with youth than usual, youth also spent more total time on these activities than usual. The within-person association between mother-youth joint involvement and youth's total involvement in leisure-time physical activity reached statistical significance at the transition to adolescence, and became stronger over time. Findings highlight the importance of maintaining adolescents', especially girls', physical activity levels and targeting both fathers' and mothers' involvement to promote youth's physical activity.

  1. Food preparation patterns in German family households. An econometric approach with time budget data.

    Science.gov (United States)

    Möser, Anke

    2010-08-01

    In Germany, the rising importance of out-of-home consumption, increasing usage of convenience products and decreasing knowledge of younger individuals how to prepare traditional dishes can be seen as obvious indicators for shifting patterns in food preparation. In this paper, econometric analyses are used to shed more light on the factors which may influence the time spent on food preparation in two-parent family households with children. Two time budget surveys, carried out 1991/92 and 2001/02 through the German National Statistical Office, provide the necessary data. Time budget data analyses reveal that over the last ten years the time spent on food preparation in Germany has decreased. The results point out that time resources of a household, for example gainful employment of the parents, significantly affect the amount of time spent on food preparation. The analysis confirms further that there is a more equal allocation of time spent on cooking, baking or laying the table between women and men in the last ten years. Due to changing attitudes and conceivably adaption of economic conditions, differences in time devoted to food preparation seem to have vanished between Eastern and Western Germany. Greater time spent on eating out in Germany as well as decreasing time spent on food preparation at home reveal that the food provisioning of families is no longer a primarily private task of the households themselves but needs more public attention and institutional offers and help. Among other points, the possibility of addressing mothers' lack of time as well as growing "food illiteracy" of children and young adults are discussed.

  2. Demonstration of real-time pattern correction for high-throughput maskless lithography

    Science.gov (United States)

    Hakkennes, E. A.; Wiersma, A. D.; Hoving, M.; Venema, N.; Woutersen, S.; van de Peut, T.; Sanderse, M.; Wieland, M. J.

    2011-04-01

    MAPPER Lithography is developing a maskless lithography technology based on massively-parallel electron-beam writing with high speed optical data transport for switching the electron beams. In this way electron optical columns can be made with a throughput of 10 wafers per hour. The amount of data for each 26mm x 33mm field is 8 Tbyte. The data rate is approximately 3 Tbyte per second. In order to realize overlay the patterns for different fields on the wafer need to be slightly adjusted. Additionally it is beneficial for the electron optics design to be able to correct a number of tool parameters on the data. For this it is desirable to be able to correct the pattern data in real time. By implementing the correction algorithms on an FPGA test board it has been demonstrated that it is possible to perform the corrections on the exposed data real time. By using a pixel size of 3.5nm, a CDu and overlay contribution of smaller than 1nm 3s is obtained. A datapath for 10wph based on an FPGA implementation that stores the switching data uncompressed in DRAM fits in 4 racks of 2 meters high, with a footprint of 600mm x 700mm each. By replacing the FPGA by an ASIC implementation, and by using real time decompression, the footprint can be reduced in a later stage.

  3. Sphingoid Base Metabolism in Yeast: Mapping Gene Expression Patterns Into Qualitative Metabolite Time Course Predictions

    OpenAIRE

    Tomas Radivoyevitch

    2001-01-01

    Can qualitative metabolite time course predictions be inferred from measured mRNA expression patterns? Speaking against this possibility is the large number of ‘decoupling’ control points that lie between these variables, i.e. translation, protein degradation, enzyme inhibition and enzyme activation. Speaking for it is the notion that these control points might be coordinately regulated such that action exerted on the mRNA level is informative of action exerted on the protein and me...

  4. Morbidity pattern and time trends of filaria cases at a PHC in Dakshina Kannada District.

    Science.gov (United States)

    Ravikiran, E; Sajjan, B S; Vijaya, K; Kumar, S; Ramkrishna, V A; Dev, A V; Jegan, D P

    2005-01-01

    A study on morbity pattern and time trends of filaria cases was carried out in a PHC of Dakshin Kannada District during November 2000 to January 2001. The age and sex distribution of all 416 filaria cases recorded revealed that 235 (56.49%) were females and maximum concentration of 263 (63.21%) was in the age group of 16-45 years. The seasonal distribution revealed that rainy season accounted the highest number of cases 197 (47.35%). The prevalence was highest, 1.96/1000 population in the year 1993 and lowest, 0.71/1000 population in the year 1995.

  5. Exploiting the Time-Reversal Operator for Adaptative Optics, Selective Focusing and Scattering Pattern Analysis

    CERN Document Server

    Popoff, Sébastien Michel; Lerosey, Geoffroy; Fink, Mathias; Boccara, Albert-Claude; Gigan, Sylvain

    2011-01-01

    We report on the experimental measurement of the backscattering matrix of a weakly scattering medium in optics, composed of a few dispersed gold nanobeads. The DORT method (Decomposition of the Time Reversal Operator) is applied to this matrix and we demonstrate selective and efficient focusing on individual scatterers, even through an aberrating layer. Moreover, we show that this approach provides the decomposition of the scattering pattern of a single nanoparticle. These results open important perspectives for optical imaging, characterization and selective excitation of nanoparticles.

  6. Predictable patterns in planetary transit timing variations and transit duration variations due to exomoons

    CERN Document Server

    Heller, René; Placek, Ben; Angerhausen, Daniel; Agol, Eric

    2016-01-01

    We present new ways to identify single and multiple moons around extrasolar planets using planetary transit timing variations (TTVs) and transit duration variations (TDVs). For planets with one moon, measurements from successive transits exhibit a hitherto undescribed pattern in the TTV-TDV diagram, originating from the stroboscopic sampling of the planet's orbit around the planet-moon barycenter. This pattern is fully determined and analytically predictable after three consecutive transits. The more measurements become available, the more the TTV-TDV diagram approaches an ellipse. For planets with multiple moons in orbital mean motion resonance (MMR), like the Galilean moons, the pattern is much more complex and addressed numerically in this report. Exomoons in MMR can also form closed, predictable TTV-TDV figures if the drift of the moons' pericenters is sufficiently slow. We find that MMR exomoons produce loops in the TTV-TDV diagram and that the number of these loops is equal to the order of the MMR, or t...

  7. Replicating animal mitochondrial DNA

    Directory of Open Access Journals (Sweden)

    Emily A. McKinney

    2013-01-01

    Full Text Available The field of mitochondrial DNA (mtDNA replication has been experiencing incredible progress in recent years, and yet little is certain about the mechanism(s used by animal cells to replicate this plasmid-like genome. The long-standing strand-displacement model of mammalian mtDNA replication (for which single-stranded DNA intermediates are a hallmark has been intensively challenged by a new set of data, which suggests that replication proceeds via coupled leading-and lagging-strand synthesis (resembling bacterial genome replication and/or via long stretches of RNA intermediates laid on the mtDNA lagging-strand (the so called RITOLS. The set of proteins required for mtDNA replication is small and includes the catalytic and accessory subunits of DNA polymerase y, the mtDNA helicase Twinkle, the mitochondrial single-stranded DNA-binding protein, and the mitochondrial RNA polymerase (which most likely functions as the mtDNA primase. Mutations in the genes coding for the first three proteins are associated with human diseases and premature aging, justifying the research interest in the genetic, biochemical and structural properties of the mtDNA replication machinery. Here we summarize these properties and discuss the current models of mtDNA replication in animal cells.

  8. Replicating Cardiovascular Condition-Birth Month Associations

    Science.gov (United States)

    Li, Li; Boland, Mary Regina; Miotto, Riccardo; Tatonetti, Nicholas P.; Dudley, Joel T.

    2016-01-01

    Independent replication is vital for study findings drawn from Electronic Health Records (EHR). This replication study evaluates the relationship between seasonal effects at birth and lifetime cardiovascular condition risk. We performed a Season-wide Association Study on 1,169,599 patients from Mount Sinai Hospital (MSH) to compute phenome-wide associations between birth month and CVD. We then evaluated if seasonal patterns found at MSH matched those reported at Columbia University Medical Center. Coronary arteriosclerosis, essential hypertension, angina, and pre-infarction syndrome passed phenome-wide significance and their seasonal patterns matched those previously reported. Atrial fibrillation, cardiomyopathy, and chronic myocardial ischemia had consistent patterns but were not phenome-wide significant. We confirm that CVD risk peaks for those born in the late winter/early spring among the evaluated patient populations. The replication findings bolster evidence for a seasonal birth month effect in CVD. Further study is required to identify the environmental and developmental mechanisms. PMID:27624541

  9. Towards limb position invariant myoelectric pattern recognition using time-dependent spectral features.

    Science.gov (United States)

    Khushaba, Rami N; Takruri, Maen; Miro, Jaime Valls; Kodagoda, Sarath

    2014-07-01

    Recent studies in Electromyogram (EMG) pattern recognition reveal a gap between research findings and a viable clinical implementation of myoelectric control strategies. One of the important factors contributing to the limited performance of such controllers in practice is the variation in the limb position associated with normal use as it results in different EMG patterns for the same movements when carried out at different positions. However, the end goal of the myoelectric control scheme is to allow amputees to control their prosthetics in an intuitive and accurate manner regardless of the limb position at which the movement is initiated. In an attempt to reduce the impact of limb position on EMG pattern recognition, this paper proposes a new feature extraction method that extracts a set of power spectrum characteristics directly from the time-domain. The end goal is to form a set of features invariant to limb position. Specifically, the proposed method estimates the spectral moments, spectral sparsity, spectral flux, irregularity factor, and signals power spectrum correlation. This is achieved through using Fourier transform properties to form invariants to amplification, translation and signal scaling, providing an efficient and accurate representation of the underlying EMG activity. Additionally, due to the inherent temporal structure of the EMG signal, the proposed method is applied on the global segments of EMG data as well as the sliced segments using multiple overlapped windows. The performance of the proposed features is tested on EMG data collected from eleven subjects, while implementing eight classes of movements, each at five different limb positions. Practical results indicate that the proposed feature set can achieve significant reduction in classification error rates, in comparison to other methods, with ≈8% error on average across all subjects and limb positions. A real-time implementation and demonstration is also provided and made available

  10. Replication and characterization of the compound eye of a fruit fly for imaging purpose

    Energy Technology Data Exchange (ETDEWEB)

    Li, Hefu [State Key Laboratory of Applied Optics, Changchun Institute of Optics, Fine Mechanics and Physics, Chinese Academy of Sciences, No. 3888, Dongnanhu Road, Changchun, Jilin (China); University of Chinese Academy of Sciences, Beijing 10039 (China); Gong, Xianwei; Ni, Qiliang; Zhao, Jingli; Zhang, Hongsheng; Wang, Taisheng [State Key Laboratory of Applied Optics, Changchun Institute of Optics, Fine Mechanics and Physics, Chinese Academy of Sciences, No. 3888, Dongnanhu Road, Changchun, Jilin (China); Yu, Weixing, E-mail: yuwx@szu.edu.cn [Insititue of Micro and Nano Optics, College of Optoelectronic Engineering, Shenzhen University, Shenzhen 518060 (China)

    2014-10-06

    In this work, we report the replication and characterization of the compound eye of a fruit fly for imaging purpose. In the replication, soft lithography method was employed to replicate the compound eye of a fruit fly into a UV-curable polymer. The method was demonstrated to be effective and the compound eye is replicated into the polymer (NOA78) where each ommatidium has a diameter of about 30 μm and a sag height of about 7 μm. To characterize its optical property, the point spread function of the compound eye was tested and a NA of 0.386 has been obtained for the replicated polymeric ommatidium. Comparing with the NA of a real fruit fly ommatidium which was measured to be about 0.212, the replicated polymeric ommatidium has a much larger NA due to the refractive index of NOA78 is much higher than that of the material used to form the real fruit fly ommatidium. Furthermore, the replicated compound eye was used to image a photomask patterned with grating structures to test its imaging property. It is shown that the grating with a line width of 20 μm can be clearly imaged. The image of the grating formed by the replicated compound eye was shrunk by about 10 times and therefore a line width of about 2.2 μm in the image plane has been obtained, which is close to the diffraction limited resolution calculated through the measured NA. In summary, the replication method demonstrated is effective and the replicated compound eye has the great potential in optical imaging.

  11. Replication and characterization of the compound eye of a fruit fly for imaging purpose

    Science.gov (United States)

    Li, Hefu; Gong, Xianwei; Ni, Qiliang; Zhao, Jingli; Zhang, Hongsheng; Wang, Taisheng; Yu, Weixing

    2014-10-01

    In this work, we report the replication and characterization of the compound eye of a fruit fly for imaging purpose. In the replication, soft lithography method was employed to replicate the compound eye of a fruit fly into a UV-curable polymer. The method was demonstrated to be effective and the compound eye is replicated into the polymer (NOA78) where each ommatidium has a diameter of about 30 μm and a sag height of about 7 μm. To characterize its optical property, the point spread function of the compound eye was tested and a NA of 0.386 has been obtained for the replicated polymeric ommatidium. Comparing with the NA of a real fruit fly ommatidium which was measured to be about 0.212, the replicated polymeric ommatidium has a much larger NA due to the refractive index of NOA78 is much higher than that of the material used to form the real fruit fly ommatidium. Furthermore, the replicated compound eye was used to image a photomask patterned with grating structures to test its imaging property. It is shown that the grating with a line width of 20 μm can be clearly imaged. The image of the grating formed by the replicated compound eye was shrunk by about 10 times and therefore a line width of about 2.2 μm in the image plane has been obtained, which is close to the diffraction limited resolution calculated through the measured NA. In summary, the replication method demonstrated is effective and the replicated compound eye has the great potential in optical imaging.

  12. REPLICATION TOOL AND METHOD OF PROVIDING A REPLICATION TOOL

    DEFF Research Database (Denmark)

    2016-01-01

    structured master surface (3a, 3b, 3c, 3d) having a lateral master pattern and a vertical master profile. The microscale structured master surface (3a, 3b, 3c, 3d) has been provided by localized pulsed laser treatment to generate microscale phase explosions. A method for producing a part with microscale......The invention relates to a replication tool (1, 1a, 1b) for producing a part (4) with a microscale textured replica surface (5a, 5b, 5c, 5d). The replication tool (1, 1a, 1b) comprises a tool surface (2a, 2b) defining a general shape of the item. The tool surface (2a, 2b) comprises a microscale...... energy directors on flange portions thereof uses the replication tool (1, 1a, 1b) to form an item (4) with a general shape as defined by the tool surface (2a, 2b). The formed item (4) comprises a microscale textured replica surface (5a, 5b, 5c, 5d) with a lateral arrangement of polydisperse microscale...

  13. Focal-plane CMOS wavelet feature extraction for real-time pattern recognition

    Science.gov (United States)

    Olyaei, Ashkan; Genov, Roman

    2005-09-01

    Kernel-based pattern recognition paradigms such as support vector machines (SVM) require computationally intensive feature extraction methods for high-performance real-time object detection in video. The CMOS sensory parallel processor architecture presented here computes delta-sigma (ΔΣ)-modulated Haar wavelet transform on the focal plane in real time. The active pixel array is integrated with a bank of column-parallel first-order incremental oversampling analog-to-digital converters (ADCs). Each ADC performs distributed spatial focal-plane sampling and concurrent weighted average quantization. The architecture is benchmarked in SVM face detection on the MIT CBCL data set. At 90% detection rate, first-level Haar wavelet feature extraction yields a 7.9% reduction in the number of false positives when compared to classification with no feature extraction. The architecture yields 1.4 GMACS simulated computational throughput at SVGA imager resolution at 8-bit output depth.

  14. Pattern of Refractive Correction and Timing of Stage II IOL Implantation after Congenital Cataract Extraction

    Institute of Scientific and Technical Information of China (English)

    Yan Li; Haotian Lin

    2014-01-01

    Congenital cataract occurs during infancy when the axial length and corneal and visual function are in the sensitive stages of rapid development..Inappropriate surgical interven-tion not only fails to restore visual function,.but also causes irreversible serious influences upon eyeball development in children diagnosed with congenital cataract. At present, the uncertainty of selection of intraocular lens (IOL) degrees dur-ing the eyeball development period is averted by using a main treatment of congenital cataract that includes two -stage surgery:.stage I cataract extraction and stage II IOL implanta-tion. However, the accurate selection of a refractive correction method and the timing of IOL implantation during stage II surgery for aphakic eyes remains controversial following stage I cataract extraction..This review retrospectively summarizes the current progress and existing problems indicated by related recent studies focusing on refractive correction pattern and IOL implantation timing.

  15. Pattern of refractive correction and timing of stage II IOL implantation after congenital cataract extraction.

    Science.gov (United States)

    Li, Yan; Lin, Haotian

    2014-12-01

    Congenital cataract occurs during infancy when the axial length and corneal and visual function are in the sensitive stages of rapid development. Inappropriate surgical intervention not only fails to restore visual function, but also causes irreversible serious influences upon eyeball development in children diagnosed with congenital cataract. At present, the uncertainty of selection of intraocular lens (IOL) degrees during the eyeball development period is averted by using a main treatment of congenital cataract that includes two-stage surgery: stage I cataract extraction and stage II IOL implantation. However, the accurate selection of a refractive correction method and the timing of IOL implantation during stage II surgery for aphakic eyes remains controversial following stage I cataract extraction. This review retrospectively summarizes the current progress and existing problems indicated by related recent studies focusing on refractive correction pattern and IOL implantation timing.

  16. Spike timing dependent plasticity finds the start of repeating patterns in continuous spike trains.

    Directory of Open Access Journals (Sweden)

    Timothée Masquelier

    Full Text Available Experimental studies have observed Long Term synaptic Potentiation (LTP when a presynaptic neuron fires shortly before a postsynaptic neuron, and Long Term Depression (LTD when the presynaptic neuron fires shortly after, a phenomenon known as Spike Timing Dependent Plasticity (STDP. When a neuron is presented successively with discrete volleys of input spikes STDP has been shown to learn 'early spike patterns', that is to concentrate synaptic weights on afferents that consistently fire early, with the result that the postsynaptic spike latency decreases, until it reaches a minimal and stable value. Here, we show that these results still stand in a continuous regime where afferents fire continuously with a constant population rate. As such, STDP is able to solve a very difficult computational problem: to localize a repeating spatio-temporal spike pattern embedded in equally dense 'distractor' spike trains. STDP thus enables some form of temporal coding, even in the absence of an explicit time reference. Given that the mechanism exposed here is simple and cheap it is hard to believe that the brain did not evolve to use it.

  17. Multivariate pattern analysis of MEG and EEG: A comparison of representational structure in time and space.

    Science.gov (United States)

    Cichy, Radoslaw Martin; Pantazis, Dimitrios

    2017-07-14

    Multivariate pattern analysis of magnetoencephalography (MEG) and electroencephalography (EEG) data can reveal the rapid neural dynamics underlying cognition. However, MEG and EEG have systematic differences in sampling neural activity. This poses the question to which degree such measurement differences consistently bias the results of multivariate analysis applied to MEG and EEG activation patterns. To investigate, we conducted a concurrent MEG/EEG study while participants viewed images of everyday objects. We applied multivariate classification analyses to MEG and EEG data, and compared the resulting time courses to each other, and to fMRI data for an independent evaluation in space. We found that both MEG and EEG revealed the millisecond spatio-temporal dynamics of visual processing with largely equivalent results. Beyond yielding convergent results, we found that MEG and EEG also captured partly unique aspects of visual representations. Those unique components emerged earlier in time for MEG than for EEG. Identifying the sources of those unique components with fMRI, we found the locus for both MEG and EEG in high-level visual cortex, and in addition for MEG in low-level visual cortex. Together, our results show that multivariate analyses of MEG and EEG data offer a convergent and complimentary view on neural processing, and motivate the wider adoption of these methods in both MEG and EEG research. Copyright © 2017 Elsevier Inc. All rights reserved.

  18. Patient characteristics and patterns of intoxication: one-time and repeated use of emergency ambulance services.

    Science.gov (United States)

    Holzer, Barbara M; Minder, Christoph E; Rosset, Nina; Schaetti, Gabriela; Battegay, Edouard; Mueller, Stefan; Zimmerli, Lukas

    2013-05-01

    The aim of this study was to investigate the utilization of ambulance services that resulted from alcohol and drug intoxication over a period of 1 year in a metropolitan area, with an emphasis on characteristic differences between patients with one-time versus repeated use. All ambulance-service report forms filed in 2010 were systematically screened for utilizations in which alcohol intoxication or intoxication resulting from consumption of illicit or legal drugs other than alcohol was the chief complaint (N = 2,341 patients; 65% male). Repeat users differed from persons with one-time use in their characteristics and patterns of intoxication. On average, patients with repeated ambulance use were almost 8 years older and had a different pattern of ambulance use over the course of the week with no clear peak on any specific day. The mean number of ambulance services in patients with repeated use was 2.8 (SD = 1.517) in the 1-year study period. Repeat users were less likely to be injured than patients with one-time ambulance-service use and more often showed aggression or uncooperative behavior toward paramedics. All cases of death associated with intoxication involved patients with one-time ambulance use. The ambulance-service users' generally slight impairment of consciousness and the high proportion of intoxicated patients without any injuries raise the question of how many of these patients could be adequately cared for in a sobering center. Sobering centers might relieve hospital emergency departments of patients not requiring acute emergency care and, in addition, could provide intervention services to prevent relapses.

  19. The pre-states, the time precision and the response pattern of oscillatory neurons

    Science.gov (United States)

    Pei, Xing

    1998-03-01

    Rate and temporal codes are two main strategies for encoding neural information. The temporal code contains more information but requires substantial timing precision of the spike discharges. Cortical neurons can respond to stimulation with good time precision. However, action potential responses depend not only upon the stimulus but also upon the history of a neuron. We have studied this problem with an oscillatory system: the primary afferent cells that innervate the ampullary electroreceptors in the paddlefish. The endogenous discharges represent a noisy oscillator. We demonstrate how the pre-state of a neuron affects the response timing precision to an applied stimulus, by re-ordering the data according to the time between the last endogenous spike and the delivery of the stimulus. Raster plots of discharges show clear striped patterns for the re-ordered data. In contrast, plots of the original data show random distributions or broadened stripes. We confirm this phenomenon by numerical simulation using a noisy Hodgkin-Huxley model with and without an endogenous oscillator. This technique can also be applied to other systems, e.g. cortical neurons, where oscillations are thought to be important. Oscillatory neurons demonstrate that the pre-state of the system is crucial in determining the post stimulus spike timing and precision.

  20. What can neuromorphic event-driven precise timing add to spike-based pattern recognition?

    Science.gov (United States)

    Akolkar, Himanshu; Meyer, Cedric; Clady, Zavier; Marre, Olivier; Bartolozzi, Chiara; Panzeri, Stefano; Benosman, Ryad

    2015-03-01

    This letter introduces a study to precisely measure what an increase in spike timing precision can add to spike-driven pattern recognition algorithms. The concept of generating spikes from images by converting gray levels into spike timings is currently at the basis of almost every spike-based modeling of biological visual systems. The use of images naturally leads to generating incorrect artificial and redundant spike timings and, more important, also contradicts biological findings indicating that visual processing is massively parallel, asynchronous with high temporal resolution. A new concept for acquiring visual information through pixel-individual asynchronous level-crossing sampling has been proposed in a recent generation of asynchronous neuromorphic visual sensors. Unlike conventional cameras, these sensors acquire data not at fixed points in time for the entire array but at fixed amplitude changes of their input, resulting optimally sparse in space and time-pixel individually and precisely timed only if new, (previously unknown) information is available (event based). This letter uses the high temporal resolution spiking output of neuromorphic event-based visual sensors to show that lowering time precision degrades performance on several recognition tasks specifically when reaching the conventional range of machine vision acquisition frequencies (30-60 Hz). The use of information theory to characterize separability between classes for each temporal resolution shows that high temporal acquisition provides up to 70% more information that conventional spikes generated from frame-based acquisition as used in standard artificial vision, thus drastically increasing the separability between classes of objects. Experiments on real data show that the amount of information loss is correlated with temporal precision. Our information-theoretic study highlights the potentials of neuromorphic asynchronous visual sensors for both practical applications and theoretical

  1. Discovering temporal patterns in water quality time series, focusing on floods with the LDA method

    Science.gov (United States)

    Hélène Aubert, Alice; Tavenard, Romain; Emonet, Rémi; Malinowski, Simon; Guyet, Thomas; Quiniou, René; Odobez, Jean-Marc; Gascuel-Odoux, Chantal

    2013-04-01

    Studying floods has been a major issue in hydrological research for years. It is often done in terms of water quantity but it is also of interest in terms of water quality. Stream chemistry is a mix of solutes. They originate from various sources in the catchment, reach the stream by various flow pathways and are transformed by biogeochemical reactions at different locations. Therefore, we hypothesized that reaction of the stream chemistry to a rainfall event is not unique but varies according to the season (1), and the global meteorological conditions of the year (2). Identifying a typology of temporal chemical patterns of reaction to a rainfall event is a way to better understand catchment processes at the flood time scale. To answer this issue, we applied a probabilistic model (Latent Dirichlet Allocation or LDA (3)) mining recurrent sequential patterns to a dataset of floods. The dataset is 12 years long and daily recorded. It gathers a broad range of parameters from which we selected rainfall, discharge, water table depth, temperature as well as nitrate, dissolved organic carbon, sulphate and chloride concentrations. It comes from a long-term hydrological observatory (AgrHys, western France) located at Kervidy-Naizin. A set of 472 floods was automatically extracted (4). From each flood, a document has been generated that is made of a set of "hydrological words". Each hydrological word corresponds to a measurement: it is a triplet made of the considered variable, the time at which the measurement is made (relative to the beginning of the flood), and its magnitude (that can be low, medium or high). The documents are used as input data to the LDA algorithm. LDA relies on spotting co-occurrences (as an alternative to the more traditional study of correlation) between words that appear within the flood documents. It has two nice properties that are its ability to easily deal with missing data and its additive property that allows a document to be seen as a mixture

  2. Replication intermediate analysis confirms that chromosomal replication origin initiates from an unusual intergenic region in Caulobacter crescentus.

    Science.gov (United States)

    Brassinga, A K; Marczynski, G T

    2001-11-01

    The alpha-proteobacterium Caulobacter crescentus possesses a developmental cell cycle that restricts chromosome replication to a stalked cell type. The proposed C.crescentus chromosome replication origin (Cori) lies between hemE and RP001, an unusual intergenic region not previously associated with bacterial replication origins, although a similar genomic arrangement is also present at the putative replication origin in the related bacterium Rickettsia prowazekii. The cloned Cori supports autonomous plasmid replication selectively in the stalked cell type implying that replication of the entire chromosome also initiates between hemE and RP001. To confirm this location, we applied the 2-D (N/N) agarose gel electrophoresis technique to resolve and identify chromosome replication intermediates throughout a 30 kb region spanning Cori. Replication initiation in Cori was uniquely characterized by an 'origin bubble and Y-arc' pattern and this observation was supported by simple replication fork 'Y-arc' patterns that characterized the regions flanking Cori. These replication forks originated bi-directionally from within Cori as determined by the fork direction assay. Therefore, chromosomal replication initiates from the unusual hemE/RP001 intergenic region that we propose represents a new class of replication origins.

  3. Vector projectile imaging: time-resolved dynamic visualization of complex flow patterns.

    Science.gov (United States)

    Yiu, Billy Y S; Lai, Simon S M; Yu, Alfred C H

    2014-09-01

    Achieving non-invasive, accurate and time-resolved imaging of vascular flow with spatiotemporal fluctuations is well acknowledged to be an ongoing challenge. In this article, we present a new ultrasound-based framework called vector projectile imaging (VPI) that can dynamically render complex flow patterns over an imaging view at millisecond time resolution. VPI is founded on three principles: (i) high-frame-rate broad-view data acquisition (based on steered plane wave firings); (ii) flow vector estimation derived from multi-angle Doppler analysis (coupled with data regularization and least-squares fitting); (iii) dynamic visualization of color-encoded vector projectiles (with flow speckles displayed as adjunct). Calibration results indicated that by using three transmit angles and three receive angles (-10°, 0°, +10° for both), VPI can consistently compute flow vectors in a multi-vessel phantom with three tubes positioned at different depths (1.5, 4, 6 cm), oriented at different angles (-10°, 0°, +10°) and of different sizes (dilated diameter: 2.2, 4.4 and 6.3 mm; steady flow rate: 2.5 mL/s). The practical merit of VPI was further illustrated through an anthropomorphic flow phantom investigation that considered both healthy and stenosed carotid bifurcation geometries. For the healthy bifurcation with 1.2-Hz carotid flow pulses, VPI was able to render multi-directional and spatiotemporally varying flow patterns (using a nominal frame rate of 416 fps or 2.4-ms time resolution). In the case of stenosed bifurcations (50% eccentric narrowing), VPI enabled dynamic visualization of flow jet and recirculation zones. These findings suggest that VPI holds promise as a new tool for complex flow analysis.

  4. Predicting decisions in human social interactions using real-time fMRI and pattern classification.

    Directory of Open Access Journals (Sweden)

    Maurice Hollmann

    Full Text Available Negotiation and trade typically require a mutual interaction while simultaneously resting in uncertainty which decision the partner ultimately will make at the end of the process. Assessing already during the negotiation in which direction one's counterpart tends would provide a tremendous advantage. Recently, neuroimaging techniques combined with multivariate pattern classification of the acquired data have made it possible to discriminate subjective states of mind on the basis of their neuronal activation signature. However, to enable an online-assessment of the participant's mind state both approaches need to be extended to a real-time technique. By combining real-time functional magnetic resonance imaging (fMRI and online pattern classification techniques, we show that it is possible to predict human behavior during social interaction before the interacting partner communicates a specific decision. Average accuracy reached approximately 70% when we predicted online the decisions of volunteers playing the ultimatum game, a well-known paradigm in economic game theory. Our results demonstrate the successful online analysis of complex emotional and cognitive states using real-time fMRI, which will enable a major breakthrough for social fMRI by providing information about mental states of partners already during the mutual interaction. Interestingly, an additional whole brain classification across subjects confirmed the online results: anterior insula, ventral striatum, and lateral orbitofrontal cortex, known to act in emotional self-regulation and reward processing for adjustment of behavior, appeared to be strong determinants of later overt behavior in the ultimatum game. Using whole brain classification we were also able to discriminate between brain processes related to subjective emotional and motivational states and brain processes related to the evaluation of objective financial incentives.

  5. The Replication Recipe: What makes for a convincing replication?

    NARCIS (Netherlands)

    Brandt, M.J.; IJzerman, H.; Dijksterhuis, A.J.; Farach, F.J.; Geller, J.; Giner-Sorolla, R.; Grange, J.A.; Perugini, M.; Spies, J.R.; Veer, A. van 't

    2014-01-01

    Psychological scientists have recently started to reconsider the importance of close replications in building a cumulative knowledge base; however, there is no consensus about what constitutes a convincing close replication study. To facilitate convincing close replication attempts we have developed

  6. How frog embryos replicate their DNA reliably

    Science.gov (United States)

    Bechhoefer, John; Marshall, Brandon

    2007-03-01

    Frog embryos contain three billion base pairs of DNA. In early embryos (cycles 2-12), DNA replication is extremely rapid, about 20 min., and the entire cell cycle lasts only 25 min., meaning that mitosis (cell division) takes place in about 5 min. In this stripped-down cell cycle, there are no efficient checkpoints to prevent the cell from dividing before its DNA has finished replication - a disastrous scenario. Even worse, the many origins of replication are laid down stochastically and are also initiated stochastically throughout the replication process. Despite the very tight time constraints and despite the randomness introduced by origin stochasticity, replication is extremely reliable, with cell division failing no more than once in 10,000 tries. We discuss a recent model of DNA replication that is drawn from condensed-matter theories of 1d nucleation and growth. Using our model, we discuss different strategies of replication: should one initiate all origins as early as possible, or is it better to hold back and initiate some later on? Using concepts from extreme-value statistics, we derive the distribution of replication times given a particular scenario for the initiation of origins. We show that the experimentally observed initiation strategy for frog embryos meets the reliability constraint and is close to the one that requires the fewest resources of a cell.

  7. Real-time Walking Pattern Generation for a Biped Robot with Hybrid CPG-ZMP Algorithm

    Directory of Open Access Journals (Sweden)

    Bin He

    2014-10-01

    Full Text Available Biped robots have better mobility than conventional wheeled robots. The bio-inspired method based on a central pattern generator (CPG can be used to control biped robot walking in a manner like human beings. However, to achieve stable locomotion, it is difficult to modulate the parameters for the neural networks to coordinate every degree of freedom of the walking robot. The zero moment point (ZMP method is very popular for the stability control of biped robot walking. However, the reference trajectories have low energy efficiency, lack naturalness and need significant offline calculation. This paper presents a new method for biped real-time walking generation using a hybrid CPG-ZMP control algorithm. The method can realize a stable walking pattern by combining the ZMP criterion with rhythmic motion control. The CPG component is designed to generate the desired motion for each robot joint, which is modulated by phase resetting according to foot contact information. By introducing the ZMP location, the activity of the CPG output signal is adjusted to coordinate the limbs’ motion and allow the robot to maintain balance during the process of locomotion. The numerical simulation results show that, compared with the CPG method, the new hybrid CPG-ZMP algorithm can enhance the robustness of the CPG parameters and improve the stability of the robot. In addition, the proposed algorithm is more energy efficient than the ZMP method. The results also demonstrate that the control system can generate an adaptive walking pattern through interactions between the robot, the CPG and the environment.

  8. Predictable patterns in planetary transit timing variations and transit duration variations due to exomoons

    Science.gov (United States)

    Heller, René; Hippke, Michael; Placek, Ben; Angerhausen, Daniel; Agol, Eric

    2016-06-01

    We present new ways to identify single and multiple moons around extrasolar planets using planetary transit timing variations (TTVs) and transit duration variations (TDVs). For planets with one moon, measurements from successive transits exhibit a hitherto undescribed pattern in the TTV-TDV diagram, originating from the stroboscopic sampling of the planet's orbit around the planet-moon barycenter. This pattern is fully determined and analytically predictable after three consecutive transits. The more measurements become available, the more the TTV-TDV diagram approaches an ellipse. For planets with multiple moons in orbital mean motion resonance (MMR), like the Galilean moon system, the pattern is much more complex and addressed numerically in this report. Exomoons in MMR can also form closed, predictable TTV-TDV figures, as long as the drift of the moons' pericenters is sufficiently slow. We find that MMR exomoons produce loops in the TTV-TDV diagram and that the number of these loops is equal to the order of the MMR, or the largest integer in the MMR ratio. We use a Bayesian model and Monte Carlo simulations to test the discoverability of exomoons using TTV-TDV diagrams with current and near-future technology. In a blind test, two of us (BP, DA) successfully retrieved a large moon from simulated TTV-TDV by co-authors MH and RH, which resembled data from a known Kepler planet candidate. Single exomoons with a 10% moon-to-planet mass ratio, like to Pluto-Charon binary, can be detectable in the archival data of the Kepler primary mission. Multi-exomoon systems, however, require either larger telescopes or brighter target stars. Complementary detection methods invoking a moon's own photometric transit or its orbital sampling effect can be used for validation or falsification. A combination of TESS, CHEOPS, and PLATO data would offer a compelling opportunity for an exomoon discovery around a bright star.

  9. A generic probability based algorithm to derive regional patterns of crops in time and space

    Science.gov (United States)

    Wattenbach, Martin; Oijen, Marcel v.; Leip, Adrian; Hutchings, Nick; Balkovic, Juraj; Smith, Pete

    2013-04-01

    Croplands are not only the key to human food supply, they also change the biophysical and biogeochemical properties of the land surface leading to changes in the water cycle, energy partitioning, influence soil erosion and substantially contribute to the amount of greenhouse gases entering the atmosphere. The effects of croplands on the environment depend on the type of crop and the associated management which both are related to the site conditions, economic boundary settings as well as preferences of individual farmers. However, at a given point of time the pattern of crops in a landscape is not only determined by environmental and socioeconomic conditions but also by the compatibility to the crops which had been grown in the years before at the current field and its surrounding cropping area. The crop compatibility is driven by factors like pests and diseases, crop driven changes in soil structure and timing of cultivation steps. Given these effects of crops on the biochemical cycle and their interdependence with the mentioned boundary conditions, there is a demand in the regional and global modelling community to account for these regional patterns. Here we present a Bayesian crop distribution generator algorithm that is used to calculate the combined and conditional probability for a crop to appear in time and space using sparse and disparate information. The input information to define the most probable crop per year and grid cell is based on combined probabilities derived from the a crop transition matrix representing good agricultural practice, crop specific soil suitability derived from the European soil database and statistical information about harvested area from the Eurostat database. The reported Eurostat crop area also provides the target proportion to be matched by the algorithm on the level of administrative units (Nomenclature des Unités Territoriales Statistiques - NUTS). The algorithm is applied for the EU27 to derive regional spatial and

  10. The Influence of Gene Expression Time Delays on Gierer–Meinhardt Pattern Formation Systems

    KAUST Repository

    Seirin Lee, S.

    2010-03-23

    There are numerous examples of morphogen gradients controlling long range signalling in developmental and cellular systems. The prospect of two such interacting morphogens instigating long range self-organisation in biological systems via a Turing bifurcation has been explored, postulated, or implicated in the context of numerous developmental processes. However, modelling investigations of cellular systems typically neglect the influence of gene expression on such dynamics, even though transcription and translation are observed to be important in morphogenetic systems. In particular, the influence of gene expression on a large class of Turing bifurcation models, namely those with pure kinetics such as the Gierer-Meinhardt system, is unexplored. Our investigations demonstrate that the behaviour of the Gierer-Meinhardt model profoundly changes on the inclusion of gene expression dynamics and is sensitive to the sub-cellular details of gene expression. Features such as concentration blow up, morphogen oscillations and radical sensitivities to the duration of gene expression are observed and, at best, severely restrict the possible parameter spaces for feasible biological behaviour. These results also indicate that the behaviour of Turing pattern formation systems on the inclusion of gene expression time delays may provide a means of distinguishing between possible forms of interaction kinetics. Finally, this study also emphasises that sub-cellular and gene expression dynamics should not be simply neglected in models of long range biological pattern formation via morphogens. © 2010 Society for Mathematical Biology.

  11. Real-Time Control of an Exoskeleton Hand Robot with Myoelectric Pattern Recognition.

    Science.gov (United States)

    Lu, Zhiyuan; Chen, Xiang; Zhang, Xu; Tong, Kay-Yu; Zhou, Ping

    2017-08-01

    Robot-assisted training provides an effective approach to neurological injury rehabilitation. To meet the challenge of hand rehabilitation after neurological injuries, this study presents an advanced myoelectric pattern recognition scheme for real-time intention-driven control of a hand exoskeleton. The developed scheme detects and recognizes user's intention of six different hand motions using four channels of surface electromyography (EMG) signals acquired from the forearm and hand muscles, and then drives the exoskeleton to assist the user accomplish the intended motion. The system was tested with eight neurologically intact subjects and two individuals with spinal cord injury (SCI). The overall control accuracy was [Formula: see text] for the neurologically intact subjects and [Formula: see text] for the SCI subjects. The total lag of the system was approximately 250[Formula: see text]ms including data acquisition, transmission and processing. One SCI subject also participated in training sessions in his second and third visits. Both the control accuracy and efficiency tended to improve. These results show great potential for applying the advanced myoelectric pattern recognition control of the wearable robotic hand system toward improving hand function after neurological injuries.

  12. Control of chromosome replication in caulobacter crescentus.

    Science.gov (United States)

    Marczynski, Gregory T; Shapiro, Lucy

    2002-01-01

    Caulobacter crescentus permits detailed analysis of chromosome replication control during a developmental cell cycle. Its chromosome replication origin (Cori) may be prototypical of the large and diverse class of alpha-proteobacteria. Cori has features that both affiliate and distinguish it from the Escherichia coli chromosome replication origin. For example, requirements for DnaA protein and RNA transcription affiliate both origins. However, Cori is distinguished by several features, and especially by five binding sites for the CtrA response regulator protein. To selectively repress and limit chromosome replication, CtrA receives both protein degradation and protein phosphorylation signals. The signal mediators, proteases, response regulators, and kinases, as well as Cori DNA and the replisome, all show distinct patterns of temporal and spatial organization during cell cycle progression. Future studies should integrate our knowledge of biochemical activities at Cori with our emerging understanding of cytological dynamics in C. crescentus and other bacteria.

  13. Modeling DNA Replication.

    Science.gov (United States)

    Bennett, Joan

    1998-01-01

    Recommends the use of a model of DNA made out of Velcro to help students visualize the steps of DNA replication. Includes a materials list, construction directions, and details of the demonstration using the model parts. (DDR)

  14. Eukaryotic DNA Replication Fork.

    Science.gov (United States)

    Burgers, Peter M J; Kunkel, Thomas A

    2017-06-20

    This review focuses on the biogenesis and composition of the eukaryotic DNA replication fork, with an emphasis on the enzymes that synthesize DNA and repair discontinuities on the lagging strand of the replication fork. Physical and genetic methodologies aimed at understanding these processes are discussed. The preponderance of evidence supports a model in which DNA polymerase ε (Pol ε) carries out the bulk of leading strand DNA synthesis at an undisturbed replication fork. DNA polymerases α and δ carry out the initiation of Okazaki fragment synthesis and its elongation and maturation, respectively. This review also discusses alternative proposals, including cellular processes during which alternative forks may be utilized, and new biochemical studies with purified proteins that are aimed at reconstituting leading and lagging strand DNA synthesis separately and as an integrated replication fork.

  15. Abiotic self-replication.

    Science.gov (United States)

    Meyer, Adam J; Ellefson, Jared W; Ellington, Andrew D

    2012-12-18

    The key to the origins of life is the replication of information. Linear polymers such as nucleic acids that both carry information and can be replicated are currently what we consider to be the basis of living systems. However, these two properties are not necessarily coupled. The ability to mutate in a discrete or quantized way, without frequent reversion, may be an additional requirement for Darwinian evolution, in which case the notion that Darwinian evolution defines life may be less of a tautology than previously thought. In this Account, we examine a variety of in vitro systems of increasing complexity, from simple chemical replicators up to complex systems based on in vitro transcription and translation. Comparing and contrasting these systems provides an interesting window onto the molecular origins of life. For nucleic acids, the story likely begins with simple chemical replication, perhaps of the form A + B → T, in which T serves as a template for the joining of A and B. Molecular variants capable of faster replication would come to dominate a population, and the development of cycles in which templates could foster one another's replication would have led to increasingly complex replicators and from thence to the initial genomes. The initial genomes may have been propagated by RNA replicases, ribozymes capable of joining oligonucleotides and eventually polymerizing mononucleotide substrates. As ribozymes were added to the genome to fill gaps in the chemistry necessary for replication, the backbone of a putative RNA world would have emerged. It is likely that such replicators would have been plagued by molecular parasites, which would have been passively replicated by the RNA world machinery without contributing to it. These molecular parasites would have been a major driver for the development of compartmentalization/cellularization, as more robust compartments could have outcompeted parasite-ridden compartments. The eventual outsourcing of metabolic

  16. A cyclic time-dependent Markov process to model daily patterns in wind turbine power production

    CERN Document Server

    Scholz, Teresa; Estanqueiro, Ana

    2013-01-01

    Wind energy is becoming a top contributor to the renewable energy mix, which raises potential reliability issues for the grid due to the fluctuating nature of its source. To achieve adequate reserve commitment and to promote market participation, it is necessary to provide models that can capture daily patterns in wind power production. This paper presents a cyclic inhomogeneous Markov process, which is based on a three-dimensional state-space (wind power, speed and direction). Each time-dependent transition probability is expressed as a Bernstein polynomial. The model parameters are estimated by solving a constrained optimization problem: The objective function combines two maximum likelihood estimators, one to ensure that the Markov process long-term behavior reproduces the data accurately and another to capture daily fluctuations. A convex formulation for the overall optimization problem is presented and its applicability demonstrated through the analysis of a case-study. The proposed model is capable of r...

  17. Predicting the Location and Time of Mobile Phone Users by Using Sequential Pattern Mining Techniques

    DEFF Research Database (Denmark)

    Ozer, Mert; Keles, Ilkcan; Toroslu, Hakki

    2016-01-01

    In recent years, using cell phone log data to model human mobility patterns became an active research area. This problem is a challenging data mining problem due to huge size and non-uniformity of the log data, which introduces several granularity levels for the specification of temporal...... and spatial dimensions. This paper focuses on the prediction of the location of the next activity of the mobile phone users. There are several versions of this problem. In this work, we have concentrated on the following three problems: predicting the location and the time of the next user activity...... the success of these methods with real data obtained from one of the largest mobile phone operators in Turkey. Our results are very encouraging, since we were able to obtain quite high accuracy results under small prediction sets....

  18. Numerical Studies on Time Resolution of Micro-Pattern Gaseous Detectors

    CERN Document Server

    Bhattacharya, Purba; Mukhopadhyay, Supratik; Bhattacharya, Sudeb

    2016-01-01

    The Micro-Pattern Gaseous Detectors offer excellent spatial and temporal resolution in harsh radiation environments of high-luminosity colliders. In this work, an attempt has been made to establish an algorithm for estimating the time resolution of different MPGDs. It has been estimated numerically on the basis of two aspects, statistics and distribution of primary electrons and their diffusion in gas medium, while ignoring their multiplication. The effect of detector design parameters, field configuration and the composition of gas mixture on the resolution have also been investigated. Finally, a modification in the numerical approach considering the threshold limit of detecting the signal has been done and tested for the RPC detector for its future implementation in case of MPGDs.

  19. Acoustic Analyses and Intelligibility Assessments of Timing Patterns Among Chinese English Learners with Different Dialect Backgrounds.

    Science.gov (United States)

    Chen, Hsueh Chu

    2015-12-01

    This paper includes two interrelated studies. The first production study investigates the timing patterns of English as spoken by Chinese learners with different dialect backgrounds. The second comprehension study explores native and non-native speakers' assessments of the intelligibility of Chinese-accented English, and examines the effects of the listeners' language backgrounds on their perceptions of Chinese-accented English. The results showed that the Hong Kong (HK) group performed better in unstressed syllable duration compared with the Taiwan (TW) and Beijing (BJ) groups. The results also revealed that all six listener groups achieved at least 78% intelligibility, with the native speaker accent achieving the highest rating, followed by the HK, TW, and BJ accents. A shared first language (L1) background may have little or no impact on intelligibility. The speech properties might prevail over the shared L1 effect. All listeners perceived inappropriate word-stress shift and consonant cluster simplifications to be the most unintelligible features.

  20. Time-resolved measurements with streaked diffraction patterns from electrons generated in laser plasma wakefield

    Science.gov (United States)

    He, Zhaohan; Nees, John; Hou, Bixue; Krushelnick, Karl; Thomas, Alec; Beaurepaire, Benoît; Malka, Victor; Faure, Jérôme

    2013-10-01

    Femtosecond bunches of electrons with relativistic to ultra-relativistic energies can be robustly produced in laser plasma wakefield accelerators (LWFA). Scaling the electron energy down to sub-relativistic and MeV level using a millijoule laser system will make such electron source a promising candidate for ultrafast electron diffraction (UED) applications due to the intrinsic short bunch duration and perfect synchronization with the optical pump. Recent results of electron diffraction from a single crystal gold foil, using LWFA electrons driven by 8-mJ, 35-fs laser pulses at 500 Hz, will be presented. The accelerated electrons were collimated with a solenoid magnetic lens. By applying a small-angle tilt to the magnetic lens, the diffraction pattern can be streaked such that the temporal evolution is separated spatially on the detector screen after propagation. The observable time window and achievable temporal resolution are studied in pump-probe measurements of photo-induced heating on the gold foil.

  1. Efficiency and internal noise for detection of suprathreshold patterns measured using simple reaction time.

    Science.gov (United States)

    Simpson, William A; Findlay, Kellyanne; Manahilov, Velitchko

    2003-05-01

    Studies of the detection of simple visual patterns at threshold contrast have found that human performance is limited by the addition of internal noise and by the sub-optimal sampling efficiency of the visual system. Many common visual tasks require the detection of a signal having a contrast well above threshold, and we sought to measure the internal noise and sampling efficiency for such signals using simple reaction time (RT). Observers were presented with suprathreshold Gabors in dynamic Gaussian white noise and were required to hit a button as soon as each was detected. By comparing the RT variances from humans to those of an ideal observer, visuomotor internal noise and sampling efficiency were measured. The internal noise remains constant and the sampling efficiency increases as the signal contrast increases.

  2. Adenovirus DNA Replication

    OpenAIRE

    Hoeben, Rob C.; Uil, Taco G.

    2013-01-01

    Adenoviruses have attracted much attention as probes to study biological processes such as DNA replication, transcription, splicing, and cellular transformation. More recently these viruses have been used as gene-transfer vectors and oncolytic agents. On the other hand, adenoviruses are notorious pathogens in people with compromised immune functions. This article will briefly summarize the basic replication strategy of adenoviruses and the key proteins involved and will deal with the new deve...

  3. Semaphorin 3A controls timing and patterning of the dental pulp innervation.

    Science.gov (United States)

    Moe, Kyaw; Sijaona, Angelina; Shrestha, Anjana; Kettunen, Paivi; Taniguchi, Masahiko; Luukko, Keijo

    2012-12-01

    Timing and patterning of dental pulp innervation are strictly spatio-temporally regulated but it is still not known how they are controlled at molecular level. We analyzed postnatal innervation of the dental pulp in the mandibular first molar of mice deficient for Semaphorin 3A (Sema3A) axon repellant molecule. Immunohistochemical localization of nerve fibers on serial sections covering the whole tooth germs using anti-peripherin antibody revealed that nerve fibers were prematurely present within the preodontoblast layer next to the inner enamel epithelium already at PN0 in Sema3A(-/-) mice. In contrast, in the wild-type (Sema3A(+/+)) mice nerve fibers were seen in the pulp only after enamel formation at PN3. The nerves in Sema3A(-/-) pulp were notably defasciculated and thinner compared to that of Sema3A(+/+) mice. A premature formation of an abnormal, enlarged nerve plexus with a high number of arborizations was apparent in the pulp-dentin border target area in Sema3A(-/-) already at PN2 whereas in the wild-type mice the first sign of plexus formation was seen at PN7. The expression of mRNAs for Ngf, Gdnf and Ncam neuroregulatory molecules in mandibular molar as well as receptors for neurotrophic factors and class 3 semaphorins including Sema3A (TrkA, p75, TrkB, TrkC, Ret, Npn1, Npn2, PlxA4) in trigeminal ganglia were not altered in the Sema3A(-/-) mice. Collectively, this data show that Sema3A serves an essential role in molar tooth pulp innervation controlling the timing of nerve fiber penetration into the pulp, their patterning and the formation of nerve plexus at pulp-dentin border area, and provide further support for the hypothesis that tooth innervation is regulated by the coordinated activity of locally expressed neuroregulatory molecules exerting positive and negative influences on growing dental nerve fibers.

  4. Timing and patterns of diversification in the Neotropical bat genus Pteronotus (Mormoopidae).

    Science.gov (United States)

    Pavan, Ana C; Marroig, Gabriel

    2017-03-01

    We investigate the biogeographic processes related to the origin and current patterns of distribution of the extant species of the genus Pteronotus. This clade of insectivorous bats is widely distributed in the Neotropical Region and has recently gone through a taxonomic update which increased more than twice its diversity. Using six molecular markers of 15 Pteronotus lineages ranging from Mexico to Central Brazil, we reconstruct a time-calibrated tree and infer molecular evolutionary rates for this bat genus. In addition, estimates of range evolution across phylogeny were obtained through statistical model testing among six different biogeographic models. The origin of the genus Pteronotus occurred approximately 16million years ago (Ma), with initial cladogenesis events being evenly distributed across the phylogeny. Divergence between most closely related species is recent, falling in the Pleistocene period less than 2.6Ma. Mainland lineages present congruent patterns of north versus south continent splitting while insular clades differ in their time of arrival in the Caribbean Islands. Temporal and geographic range estimates for early nodes of Pteronotus phylogeny suggest a central role of Neogene tectonic reorganizations of Central America in the group diversification process. Also, South American colonization by Pteronotus occurred early in the genus history. Founder-event speciation was an important mode of lineage splitting in Pteronotus, with two independent dispersal jumps having occurred to the Greater Antilles. Finally, Pleistocenic sea-level variation and climatic oscillations are possibly associated with divergence between sister-species and recent ages of MRCA for Pteronotus species. Copyright © 2017 Elsevier Inc. All rights reserved.

  5. Time-Use Patterns and Sustainable Urban Form: A Case Study to Explore Potential Links[dagger

    National Research Council Canada - National Science Library

    Edeltraud Haselsteiner; Barbara Smetschka; Alexander Remesch; Veronika Gaube

    2015-01-01

    .... While much has been written about the planning of cities and its implications for human social life, the question of the relationship between time-use patterns and urban form remains underexplored...

  6. An Image Pattern Tracking Algorithm for Time-resolved Measurement of Mini- and Micro-scale Motion of Complex Object

    Directory of Open Access Journals (Sweden)

    John M. Seiner

    2009-03-01

    Full Text Available An image pattern tracking algorithm is described in this paper for time-resolved measurements of mini- and micro-scale movements of complex objects. This algorithm works with a high-speed digital imaging system, which records thousands of successive image frames in a short time period. The image pattern of the observed object is tracked among successively recorded image frames with a correlation-based algorithm, so that the time histories of the position and displacement of the investigated object in the camera focus plane are determined with high accuracy. The speed, acceleration and harmonic content of the investigated motion are obtained by post processing the position and displacement time histories. The described image pattern tracking algorithm is tested with synthetic image patterns and verified with tests on live insects.

  7. IN VITRO IRON AVAILABILITY AND ADSORPTION PATTERN ON COMBINATION OF ACIDITY AND LENGTH OF BOILING TIME ON YARD LONG BEAN

    Directory of Open Access Journals (Sweden)

    Leny Yuanita

    2010-06-01

    Full Text Available The aim of the study is to find iron availability and binding pattern by dietary fiber macromolecule on combination of acidity and length of boiling time, through Kads and Keff, boiling procees at the level of pH 4 and 7 with boiling time at 0 (raw, 5, 15, and 25 minutes. Iron availability and adsorption pattern were analyzed through Miller's in-vitro and Langmuir-Scatchard graph methods. The results of the study showed: (1 the highest iron availability occurs at raw-pH4 treatment; (2 decreasing pH and increasing boiling time decrease Kads,Keff, percent iron bound, and increase iron availability; (3 iron binding pattern by dietary fiber macromolecules through formation of complex compound was more prominent than physical adsorption, involving two types of specific binding sites, one of which showed a higher affinity.   Keywords: iron availability, adsorption pattern, dietary fiber, acidity (pH, boiling time

  8. A transcription and translation-coupled DNA replication system using rolling-circle replication.

    Science.gov (United States)

    Sakatani, Yoshihiro; Ichihashi, Norikazu; Kazuta, Yasuaki; Yomo, Tetsuya

    2015-05-27

    All living organisms have a genome replication system in which genomic DNA is replicated by a DNA polymerase translated from mRNA transcribed from the genome. The artificial reconstitution of this genome replication system is a great challenge in in vitro synthetic biology. In this study, we attempted to construct a transcription- and translation-coupled DNA replication (TTcDR) system using circular genomic DNA encoding phi29 DNA polymerase and a reconstituted transcription and translation system. In this system, phi29 DNA polymerase was translated from the genome and replicated the genome in a rolling-circle manner. When using a traditional translation system composition, almost no DNA replication was observed, because the tRNA and nucleoside triphosphates included in the translation system significantly inhibited DNA replication. To minimize these inhibitory effects, we optimized the composition of the TTcDR system and improved replication by approximately 100-fold. Using our system, genomic DNA was replicated up to 10 times in 12 hours at 30 °C. This system provides a step toward the in vitro construction of an artificial genome replication system, which is a prerequisite for the construction of an artificial cell.

  9. Completion of DNA replication in Escherichia coli.

    Science.gov (United States)

    Wendel, Brian M; Courcelle, Charmain T; Courcelle, Justin

    2014-11-18

    The mechanism by which cells recognize and complete replicated regions at their precise doubling point must be remarkably efficient, occurring thousands of times per cell division along the chromosomes of humans. However, this process remains poorly understood. Here we show that, in Escherichia coli, the completion of replication involves an enzymatic system that effectively counts pairs and limits cellular replication to its doubling point by allowing converging replication forks to transiently continue through the doubling point before the excess, over-replicated regions are incised, resected, and joined. Completion requires RecBCD and involves several proteins associated with repairing double-strand breaks including, ExoI, SbcDC, and RecG. However, unlike double-strand break repair, completion occurs independently of homologous recombination and RecA. In some bacterial viruses, the completion mechanism is specifically targeted for inactivation to allow over-replication to occur during lytic replication. The results suggest that a primary cause of genomic instabilities in many double-strand-break-repair mutants arises from an impaired ability to complete replication, independent from DNA damage.

  10. Tissue and time specific expression pattern of interferon regulated genes in the chicken.

    Science.gov (United States)

    Röll, Susanne; Härtle, Stefan; Lütteke, Thomas; Kaspers, Bernd; Härtle, Sonja

    2017-03-28

    Type I interferons are major players against viral infections and mediate their function by the induction of Interferon regulated genes (IRGs). Recently, it became obvious that these cytokines have a multitude of additional functions. Due to the unique features of the chickens' immune system, available data from mouse models are not easily transferable; hence we performed an extensive analysis of chicken IRGs. A broad database search for homologues to described mammalian IRGs (common IRGs, cIRGs) was combined with a transcriptome analysis of spleen and lung at different time points after application of IFNα. To apply physiological amounts of IFN, half-life of IFN in the chicken was determined. Interestingly, the calculated 36 min are considerably shorter than the ones obtained for human and mouse. Microarray analysis revealed many additional IRGs (newly identified IRGs; nIRGs) and network analysis for selected IRGs showed a broad interaction of nIRGs among each other and with cIRGs. We found that IRGs exhibit a highly tissue and time specific expression pattern as expression quality and quantity differed strongly between spleen and lung and over time. While in the spleen for many affected genes changes in RNA abundance peaked already after 3 h, an increasing or plateau-like regulation after 3, 6 and 9 h was observed in the lung. The induction or suppression of IRGs in chickens is both tissue and time specific and beside known antiviral mechanisms type I IFN induces many additional cellular functions. We confirmed many known IRGs and established a multitude of so far undescribed ones, thus providing a large database for future research on antiviral mechanisms and additional IFN functions in non-mammalian species.

  11. Minichromosome replication in vitro: inhibition of re-replication by replicatively assembled nucleosomes.

    Science.gov (United States)

    Krude, T; Knippers, R

    1994-08-19

    Single-stranded circular DNA, containing the SV40 origin sequence, was used as a template for complementary DNA strand synthesis in cytosolic extracts from HeLa cells. In the presence of the replication-dependent chromatin assembly factor CAF-1, defined numbers of nucleosomes were assembled during complementary DNA strand synthesis. These minichromosomes were then induced to semiconservatively replicate by the addition of the SV40 initiator protein T antigen (re-replication). The results indicate that re-replication of minichromosomes appears to be inhibited by two independent mechanisms. One acts at the initiation of minichromosome re-replication, and the other affects replicative chain elongation. To directly demonstrate the inhibitory effect of replicatively assembled nucleosomes, two types of minichromosomes were prepared: (i) post-replicative minichromosomes were assembled in a reaction coupled to replication as above; (ii) pre-replicative minichromosomes were assembled independently of replication on double-stranded DNA. Both types of minichromosomes were used as templates for DNA replication under identical conditions. Replicative fork movement was found to be impeded only on post-replicative minichromosome templates. In contrast, pre-replicative minichromosomes allowed one unconstrained replication cycle, but re-replication was inhibited due to a block in fork movement. Thus, replicatively assembled chromatin may have a profound influence on the re-replication of DNA.

  12. Refinement and Pattern Formation in Neural Circuits by the Interaction of Traveling Waves with Spike-Timing Dependent Plasticity

    Science.gov (United States)

    Bennett, James E. M.; Bair, Wyeth

    2015-01-01

    Traveling waves in the developing brain are a prominent source of highly correlated spiking activity that may instruct the refinement of neural circuits. A candidate mechanism for mediating such refinement is spike-timing dependent plasticity (STDP), which translates correlated activity patterns into changes in synaptic strength. To assess the potential of these phenomena to build useful structure in developing neural circuits, we examined the interaction of wave activity with STDP rules in simple, biologically plausible models of spiking neurons. We derive an expression for the synaptic strength dynamics showing that, by mapping the time dependence of STDP into spatial interactions, traveling waves can build periodic synaptic connectivity patterns into feedforward circuits with a broad class of experimentally observed STDP rules. The spatial scale of the connectivity patterns increases with wave speed and STDP time constants. We verify these results with simulations and demonstrate their robustness to likely sources of noise. We show how this pattern formation ability, which is analogous to solutions of reaction-diffusion systems that have been widely applied to biological pattern formation, can be harnessed to instruct the refinement of postsynaptic receptive fields. Our results hold for rich, complex wave patterns in two dimensions and over several orders of magnitude in wave speeds and STDP time constants, and they provide predictions that can be tested under existing experimental paradigms. Our model generalizes across brain areas and STDP rules, allowing broad application to the ubiquitous occurrence of traveling waves and to wave-like activity patterns induced by moving stimuli. PMID:26308406

  13. Mechanism of chromosomal DNA replication initiation and replication fork stabilization in eukaryotes.

    Science.gov (United States)

    Wu, LiHong; Liu, Yang; Kong, DaoChun

    2014-05-01

    Chromosomal DNA replication is one of the central biological events occurring inside cells. Due to its large size, the replication of genomic DNA in eukaryotes initiates at hundreds to tens of thousands of sites called DNA origins so that the replication could be completed in a limited time. Further, eukaryotic DNA replication is sophisticatedly regulated, and this regulation guarantees that each origin fires once per S phase and each segment of DNA gets duplication also once per cell cycle. The first step of replication initiation is the assembly of pre-replication complex (pre-RC). Since 1973, four proteins, Cdc6/Cdc18, MCM, ORC and Cdt1, have been extensively studied and proved to be pre-RC components. Recently, a novel pre-RC component called Sap1/Girdin was identified. Sap1/Girdin is required for loading Cdc18/Cdc6 to origins for pre-RC assembly in the fission yeast and human cells, respectively. At the transition of G1 to S phase, pre-RC is activated by the two kinases, cyclindependent kinase (CDK) and Dbf4-dependent kinase (DDK), and subsequently, RPA, primase-polα, PCNA, topoisomerase, Cdc45, polδ, and polɛ are recruited to DNA origins for creating two bi-directional replication forks and initiating DNA replication. As replication forks move along chromatin DNA, they frequently stall due to the presence of a great number of replication barriers on chromatin DNA, such as secondary DNA structures, protein/DNA complexes, DNA lesions, gene transcription. Stalled forks must require checkpoint regulation for their stabilization. Otherwise, stalled forks will collapse, which results in incomplete DNA replication and genomic instability. This short review gives a concise introduction regarding the current understanding of replication initiation and replication fork stabilization.

  14. Time markers for Drosophila morphogenesis based on cell-pattern topology.

    Science.gov (United States)

    Zallen, Richard; Zallen, Jennifer A.

    2007-03-01

    Recent work on convergent extension in Drosophila has shown that the accumulation of actin-myosin networks at specific cell interfaces initiates planar polarity and the formation of multicellular rosette structures that contribute to elongation of the body axis [1]. This cell-rearrangement process takes place within a one-cell-thick layer, and the changing two-dimensional cell pattern can be characterized using topological measures such as cell-shape statistics [2]. We find that the timeline for the process contains a well-defined marker corresponding to a sharp increase in the slope of the time dependence of the variance of the cell-shape (number-of-sides) distribution. A rosette in this context is a cluster of cells enclosing high-order vertices at which 4 or 5 or more cells meet. While the cell-shape variance climbs steadily during axis elongation, the frequency of high-order vertices and large rosettes plateaus after 10 and 13 minutes, respectively. These time markers calibrate the conventional timeline descriptors referred to as stages 7 and 8 of embryonic development [3]. [1] J.T. Blankenship et al., Developmental Cell 11, 459 (2006); [2] J.A. Zallen and R. Zallen, J. Phys.: Condensed Matter 16, S5073 (2004); [3] J.A. Campos-Ortega and V. Hartenstein, The embryonic development of Drosophila melanogaster (1985).

  15. Tests of Micro-Pattern Gaseous Detectors for active target time projection chambers in nuclear physics

    Energy Technology Data Exchange (ETDEWEB)

    Pancin, J., E-mail: pancin@ganil.fr [GANIL, CEA/DSM-CNRS/IN2P3, Bvd H. Becquerel, Caen (France); Damoy, S.; Perez Loureiro, D. [GANIL, CEA/DSM-CNRS/IN2P3, Bvd H. Becquerel, Caen (France); Chambert, V.; Dorangeville, F. [IPNO, CNRS/IN2P3, Orsay (France); Druillole, F. [CEA, DSM/Irfu/SEDI, Gif-Sur-Yvette (France); Grinyer, G.F. [GANIL, CEA/DSM-CNRS/IN2P3, Bvd H. Becquerel, Caen (France); Lermitage, A.; Maroni, A.; Noël, G. [IPNO, CNRS/IN2P3, Orsay (France); Porte, C.; Roger, T. [GANIL, CEA/DSM-CNRS/IN2P3, Bvd H. Becquerel, Caen (France); Rosier, P. [IPNO, CNRS/IN2P3, Orsay (France); Suen, L. [GANIL, CEA/DSM-CNRS/IN2P3, Bvd H. Becquerel, Caen (France)

    2014-01-21

    Active target detection systems, where the gas used as the detection medium is also a target for nuclear reactions, have been used for a wide variety of nuclear physics applications since the eighties. Improvements in Micro-Pattern Gaseous Detectors (MPGDs) and in micro-electronics achieved in the last decade permit the development of a new generation of active targets with higher granularity pad planes that allow spatial and time information to be determined with unprecedented accuracy. A novel active target and time projection chamber (ACTAR TPC), that will be used to study reactions and decays of exotic nuclei at facilities such as SPIRAL2, is presently under development and will be based on MPGD technology. Several MPGDs (Micromegas and Thick GEM) coupled to a 2×2 mm{sup 2} pixelated pad plane have been tested and their performances have been determined with different gases over a wide range of pressures. Of particular interest for nuclear physics experiments are the angular and energy resolutions. The angular resolution has been determined to be better than 1° FWHM for short traces of about 4 cm in length and the energy resolution deduced from the particle range was found to be better than 5% for 5.5 MeV α particles. These performances have been compared to Geant4 simulations. These experimental results validate the use of these detectors for several applications in nuclear physics.

  16. Sleep patterns in Spanish adolescents: associations with TV watching and leisure-time physical activity.

    Science.gov (United States)

    Ortega, Francisco B; Chillón, Palma; Ruiz, Jonatan R; Delgado, Manuel; Albers, Ulrike; Alvarez-Granda, Jesús L; Marcos, Ascensión; Moreno, Luis A; Castillo, Manuel J

    2010-10-01

    We aimed to describe the sleep patterns in Spanish adolescents and to examine the relationships of sleep duration and morning tiredness with participation in leisure-time physical-sporting activities (LT-PA) and television (TV) watching. Sleep duration, morning tiredness, participation in LT-PA and time spent on watching TV were reported by 2,179 (1,139 females) Spanish adolescents (AVENA study). Data were analyzed by binary logistic regression. One-fifth of the adolescents reported insufficient night sleep (sleep as long as adolescents from central Europe, and longer than those from other Mediterranean countries, South Africa, Asia and North America. Insufficient sleep duration doubled the odds of excessive TV watching (≥3 h/day) in males, regardless of morning tiredness (OR 2.15, 95% CI 1.42-3.27). Morning tiredness reduced the odds of participating in any LT-PA in both males and females (0.49, 0.34-0.70 and 0.49, 0.35-0.69, respectively), and increased the odds of excessive TV watching in females, regardless of sleep duration (2.49, 1.64-3.79). We conclude that non-participation in LT-PA is associated with morning tiredness in male and female adolescents, while excessive TV watching is more associated with short sleep or morning tiredness depending on gender.

  17. Uniform approach to linear and nonlinear interrelation patterns in multivariate time series

    Science.gov (United States)

    Rummel, Christian; Abela, Eugenio; Müller, Markus; Hauf, Martinus; Scheidegger, Olivier; Wiest, Roland; Schindler, Kaspar

    2011-06-01

    Currently, a variety of linear and nonlinear measures is in use to investigate spatiotemporal interrelation patterns of multivariate time series. Whereas the former are by definition insensitive to nonlinear effects, the latter detect both nonlinear and linear interrelation. In the present contribution we employ a uniform surrogate-based approach, which is capable of disentangling interrelations that significantly exceed random effects and interrelations that significantly exceed linear correlation. The bivariate version of the proposed framework is explored using a simple model allowing for separate tuning of coupling and nonlinearity of interrelation. To demonstrate applicability of the approach to multivariate real-world time series we investigate resting state functional magnetic resonance imaging (rsfMRI) data of two healthy subjects as well as intracranial electroencephalograms (iEEG) of two epilepsy patients with focal onset seizures. The main findings are that for our rsfMRI data interrelations can be described by linear cross-correlation. Rejection of the null hypothesis of linear iEEG interrelation occurs predominantly for epileptogenic tissue as well as during epileptic seizures.

  18. Range verification of passively scattered proton beams based on prompt gamma time patterns

    Science.gov (United States)

    Testa, Mauro; Min, Chul Hee; Verburg, Joost M.; Schümann, Jan; Lu, Hsiao-Ming; Paganetti, Harald

    2014-07-01

    We propose a proton range verification technique for passive scattering proton therapy systems where spread out Bragg peak (SOBP) fields are produced with rotating range modulator wheels. The technique is based on the correlation of time patterns of the prompt gamma ray emission with the range of protons delivering the SOBP. The main feature of the technique is the ability to verify the proton range with a single point of measurement and a simple detector configuration. We performed four-dimensional (time-dependent) Monte Carlo simulations using TOPAS to show the validity and accuracy of the technique. First, we validated the hadronic models used in TOPAS by comparing simulations and prompt gamma spectrometry measurements published in the literature. Second, prompt gamma simulations for proton range verification were performed for the case of a water phantom and a prostate cancer patient. In the water phantom, the proton range was determined with 2 mm accuracy with a full ring detector configuration for a dose of ~2.5 cGy. For the prostate cancer patient, 4 mm accuracy on range determination was achieved for a dose of ~15 cGy. The results presented in this paper are encouraging in view of a potential clinical application of the technique.

  19. A tool for exploring space-time patterns : an animation user research

    Directory of Open Access Journals (Sweden)

    Ogao Patrick J

    2006-08-01

    Full Text Available Abstract Background Ever since Dr. John Snow (1813–1854 used a case map to identify water well as the source of a cholera outbreak in London in the 1800s, the use of spatio-temporal maps have become vital tools in a wide range of disease mapping and control initiatives. The increasing use of spatio-temporal maps in these life-threatening sectors warrants that they are accurate, and easy to interpret to enable prompt decision making by health experts. Similar spatio-temporal maps are observed in urban growth and census mapping – all critical aspects a of a country's socio-economic development. In this paper, a user test research was carried out to determine the effectiveness of spatio-temporal maps (animation in exploring geospatial structures encompassing disease, urban and census mapping. Results Three types of animation were used, namely; passive, interactive and inference-based animation, with the key differences between them being on the level of interactivity and complementary domain knowledge that each offers to the user. Passive animation maintains the view only status. The user has no control over its contents and dynamic variables. Interactive animation provides users with the basic media player controls, navigation and orientation tools. Inference-based animation incorporates these interactive capabilities together with a complementary automated intelligent view that alerts users to interesting patterns, trends or anomalies that may be inherent in the data sets. The test focussed on the role of animation passive and interactive capabilities in exploring space-time patterns by engaging test-subjects in thinking aloud evaluation protocol. The test subjects were selected from a geoinformatics (map reading, interpretation and analysis abilities background. Every test-subject used each of the three types of animation and their performances for each session assessed. The results show that interactivity in animation is a preferred

  20. Lethal pedestrian--passenger car collisions in Berlin. Changed injury patterns in two different time intervals.

    Science.gov (United States)

    Ehrlich, Edwin; Tischer, Anja; Maxeiner, H

    2009-04-01

    To expand the passive safety of automobiles protecting traffic participants technological innovations were done in the last decades. Objective of our retrospective analysis was to examine if these technical modifications led to a clearly changed pattern of injuries of pedestrians whose death was caused by the accidents. Another reduction concerns the exclusion of injured car passengers--only pedestrians walking or standing at the moment of collision were included. We selected time intervals 1975-1985 and 1991-2004 (=years of construction of the involved passenger cars). The cars were classified depending on their frontal construction in types as presented by Schindler et al. [Schindler V, Kühn M, Weber S, Siegler H, Heinrich T. Verletzungsmechanismen und Wirkabschätzungen der Fahrzegfrontgestaltung bei Pkw-Fussgänger-Kollisionen. Abschlussbericht im Auftrag der Deutschen Versicherungswirtschaft e.V. TU-Berlin Fachgebiet Kraftfahrzeuge (GDV) 2004:36-40]. In both periods more than 90% of all cars were from the usual types small/medium/large class. Hundred and thirty-four autopsy records of such cases from Department of Forensic Medicine (Charité Berlin) data were analysed. The data included technical information of the accidents and vehicles and the external and internal injuries of the victims. The comparison of the two periods showed a decrease of serious head injuries and femoral fractures but an increase of chest-, abdominal and pelvic injuries. This situation could be explained by an increased occurrence of soft-face-constructions and changed front design of modern passenger cars, resulting in a favourable effects concerning head impact to the car during accident. Otherwise the same kinetic energy was transferred to the (complete) victim - but because of a displacement of main focus of impact the pattern of injuries modified (went distally).

  1. Schmallenberg virus circulation in culicoides in Belgium in 2012: field validation of a real time RT-PCR approach to assess virus replication and dissemination in midges.

    Directory of Open Access Journals (Sweden)

    Nick De Regge

    Full Text Available Indigenous Culicoides biting midges are suggested to be putative vectors for the recently emerged Schmallenberg virus (SBV based on SBV RNA detection in field-caught midges. Furthermore, SBV replication and dissemination has been evidenced in C. sonorensis under laboratory conditions. After SBV had been detected in Culicoides biting midges from Belgium in August 2011, it spread all over the country by the end of 2011, as evidenced by very high between-herd seroprevalence rates in sheep and cattle. This study investigated if a renewed SBV circulation in midges occurred in 2012 in the context of high seroprevalence in the animal host population and evaluated if a recently proposed realtime RT-PCR approach that is meant to allow assessing the vector competence of Culicoides for SBV and bluetongue virus under laboratory conditions was applicable to field-caught midges. Therefore midges caught with 12 OVI traps in four different regions in Belgium between May and November 2012, were morphologically identified, age graded, pooled and tested for the presence of SBV RNA by realtime RT-PCR. The results demonstrate that although no SBV could be detected in nulliparous midges caught in May 2012, a renewed but short lived circulation of SBV in parous midges belonging to the subgenus Avaritia occured in August 2012 at all four regions. The infection prevalence reached up to 2.86% in the south of Belgium, the region where a lower seroprevalence was found at the end of 2011 than in the rest of the country. Furthermore, a frequency analysis of the Ct values obtained for 31 SBV-S segment positive pools of Avaritia midges showed a clear bimodal distribution with peaks of Ct values between 21-24 and 33-36. This closely resembles the laboratory results obtained for SBV infection of C. sonorensis and implicates indigenous midges belonging to the subgenus Avaritia as competent vectors for SBV.

  2. Schmallenberg virus circulation in culicoides in Belgium in 2012: field validation of a real time RT-PCR approach to assess virus replication and dissemination in midges.

    Science.gov (United States)

    De Regge, Nick; Madder, Maxime; Deblauwe, Isra; Losson, Bertrand; Fassotte, Christiane; Demeulemeester, Julie; Smeets, François; Tomme, Marie; Cay, Ann Brigitte

    2014-01-01

    Indigenous Culicoides biting midges are suggested to be putative vectors for the recently emerged Schmallenberg virus (SBV) based on SBV RNA detection in field-caught midges. Furthermore, SBV replication and dissemination has been evidenced in C. sonorensis under laboratory conditions. After SBV had been detected in Culicoides biting midges from Belgium in August 2011, it spread all over the country by the end of 2011, as evidenced by very high between-herd seroprevalence rates in sheep and cattle. This study investigated if a renewed SBV circulation in midges occurred in 2012 in the context of high seroprevalence in the animal host population and evaluated if a recently proposed realtime RT-PCR approach that is meant to allow assessing the vector competence of Culicoides for SBV and bluetongue virus under laboratory conditions was applicable to field-caught midges. Therefore midges caught with 12 OVI traps in four different regions in Belgium between May and November 2012, were morphologically identified, age graded, pooled and tested for the presence of SBV RNA by realtime RT-PCR. The results demonstrate that although no SBV could be detected in nulliparous midges caught in May 2012, a renewed but short lived circulation of SBV in parous midges belonging to the subgenus Avaritia occured in August 2012 at all four regions. The infection prevalence reached up to 2.86% in the south of Belgium, the region where a lower seroprevalence was found at the end of 2011 than in the rest of the country. Furthermore, a frequency analysis of the Ct values obtained for 31 SBV-S segment positive pools of Avaritia midges showed a clear bimodal distribution with peaks of Ct values between 21-24 and 33-36. This closely resembles the laboratory results obtained for SBV infection of C. sonorensis and implicates indigenous midges belonging to the subgenus Avaritia as competent vectors for SBV.

  3. Dynamic replication of Web contents

    Institute of Scientific and Technical Information of China (English)

    2007-01-01

    The phenomenal growth of the World Wide Web has brought huge increase in the traffic to the popular web sites.Long delays and denial of service experienced by the end-users,especially during the peak hours,continues to be the common problem while accessing popular sites.Replicating some of the objects at multiple sites in a distributed web-server environment is one of the possible solutions to improve the response time/Iatency. The decision of what and where to replicate requires solving a constraint optimization problem,which is NP-complete in general.In this paper, we consider the problem of placing copies of objects in a distributed web server system to minimize the cost of serving read and write requests when the web servers have Iimited storage capacity.We formulate the problem as a 0-1 optimization problem and present a polynomial time greedy algorithm with backtracking to dynamically replicate objects at the appropriate sites to minimize a cost function.To reduce the solution search space,we present necessary condi tions for a site to have a replica of an object jn order to minimize the cost function We present simulation resuIts for a variety of problems to illustrate the accuracy and efficiency of the proposed algorithms and compare them with those of some well-known algorithms.The simulation resuIts demonstrate the superiority of the proposed algorithms.

  4. A maize root tip system to study DNA replication programmes in somatic and endocycling nuclei during plant development.

    Science.gov (United States)

    Bass, Hank W; Wear, Emily E; Lee, Tae-Jin; Hoffman, Gregg G; Gumber, Hardeep K; Allen, George C; Thompson, William F; Hanley-Bowdoin, Linda

    2014-06-01

    The progress of nuclear DNA replication is complex in both time and space, and may reflect several levels of chromatin structure and 3-dimensional organization within the nucleus. To understand the relationship between DNA replication and developmental programmes, it is important to examine replication and nuclear substructure in different developmental contexts including natural cell-cycle progressions in situ. Plant meristems offer an ideal opportunity to analyse such processes in the context of normal growth of an organism. Our current understanding of large-scale chromosomal DNA replication has been limited by the lack of appropriate tools to visualize DNA replication with high resolution at defined points within S phase. In this perspective, we discuss a promising new system that can be used to visualize DNA replication in isolated maize (Zea mays L.) root tip nuclei after in planta pulse labelling with the thymidine analogue, 5-ethynyl-2'-deoxyuridine (EdU). Mixed populations of EdU-labelled nuclei are then separated by flow cytometry into sequential stages of S phase and examined directly using 3-dimensional deconvolution microscopy to characterize spatial patterns of plant DNA replication. Combining spatiotemporal analyses with studies of replication and epigenetic inheritance at the molecular level enables an integrated experimental approach to problems of mitotic inheritance and cellular differentiation.

  5. Investigating variation in replicability: A "Many Labs" replication project

    NARCIS (Netherlands)

    Klein, R.A.; Ratliff, K.A.; Vianello, M.; Adams, R.B.; Bahnik, S.; Bernstein, M.J.; Bocian, K.; Brandt, M.J.; Brooks, B.; Brumbaugh, C.C.; Cemalcilar, Z.; Chandler, J.; Cheong, W.; Davis, W.E.; Devos, T.; Eisner, M.; Frankowska, N.; Furrow, D.; Galliani, E.M.; Hasselman, F.W.; Hicks, J.A.; Hovermale, J.F.; Hunt, S.J.; Huntsinger, J.R.; IJzerman, H.; John, M.S.; Joy-Gaba, J.A.; Kappes, H.B.; Krueger, L.E.; Kurtz, J.; Levitan, C.A.; Mallett, R.K.; Morris, W.L.; Nelson, A.J.; Nier, J.A.; Packard, G.; Pilati, R.; Rutchick, A.M.; Schmidt, K.; Skorinko, J.L.M.; Smith, R.; Steiner, T.G.; Storbeck, J.; Van Swol, L.M.; Thompson, D.; Veer, A.E. van 't; Vaughn, L.A.; Vranka, M.; Wichman, A.L.; Woodzicka, J.A.; Nosek, B.A.

    2014-01-01

    Although replication is a central tenet of science, direct replications are rare in psychology. This research tested variation in the replicability of 13 classic and contemporary effects across 36 independent samples totaling 6,344 participants. In the aggregate, 10 effects replicated consistently.

  6. Visualizing Single-molecule DNA Replication with Fluorescence Microscopy

    NARCIS (Netherlands)

    Tanner, Nathan A.; Loparo, Joseph J.; Oijen, Antoine M. van

    2009-01-01

    We describe a simple fluorescence microscopy-based real-time method for observing DNA replication at the single-molecule level. A circular, forked DNA template is attached to a functionalized glass coverslip and replicated extensively after introduction of replication proteins and nucleotides. The

  7. Visualizing Single-molecule DNA Replication with Fluorescence Microscopy

    NARCIS (Netherlands)

    Tanner, Nathan A.; Loparo, Joseph J.; Oijen, Antoine M. van

    2009-01-01

    We describe a simple fluorescence microscopy-based real-time method for observing DNA replication at the single-molecule level. A circular, forked DNA template is attached to a functionalized glass coverslip and replicated extensively after introduction of replication proteins and nucleotides. The g

  8. Understanding the residual patterns of timing solutions of radio pulsars with a model of magnetic field oscillation

    Science.gov (United States)

    Gao, Xu-Dong; Zhang, Shuang-Nan; Yi, Shu-Xu; Xie, Yi; Fu, Jian-Ning

    2016-06-01

    We explain some phenomena existing generally in the timing residuals: amplitude and sign of the second derivative of a pulsar's spin-frequency (ddot{ν }), some sophisticated residual patterns, which also change with the time span of data segments. The sample is taken from Hobbs et al., in which the pulsar's spin-frequency and its first derivative have been subtracted from the timing solution fitting. We first classify the timing residual patterns into different types based on the sign of ddot{ν }. Then we use the magnetic field oscillation model developed in our group to fit successfully the different kinds of timing residuals with the Markov Chain Monte Carlo method. Finally, we simulate the spin evolution over 20 years for a pulsar with typical parameters and analyse the data with the conventional timing solution fitting. By choosing different segments of the simulated data, we find that most of the observed residual patterns can be reproduced successfully. This is the first time that the observed residual patterns are fitted by a model and reproduced by simulations with very few parameters. From the distribution of the different residual patterns in the P-dot{P} diagram, we argue that (1) a single magnetic field oscillation mode exists commonly in all pulsars throughout their lifetimes; (2) there may be a transition period over the lifetimes of pulsars, in which multiple magnetic field oscillation modes exist.

  9. Complex patterns in a space- and time-discrete predator-prey model with Beddington-DeAngelis functional response

    Science.gov (United States)

    Huang, Tousheng; Zhang, Huayong; Yang, Hongju; Wang, Ning; Zhang, Feifan

    2017-02-01

    The spatial pattern formation of predator-prey systems is an important issue widely concerned. In this research, we address this issue by developing a new space- and time-discrete predator-prey model, with predation relationship described by Beddington-DeAngelis functional response. The discrete model is given by a coupled map lattice, taking a nonlinear relationship between predator-prey "reaction" stage and dispersal stage. Through analysis of Turing instability and Hopf instability for the discrete model, the parametric conditions for pattern formation are determined. Numerical simulations reveal a surprising variety of spatiotemporal patterns, including regular and irregular patterns of spots, stripes, labyrinth, gaps, mosaics, spirals, circles, and many intermediate patterns in-between. These patterns cover a majority of predator-prey pattern types recorded in literature. Besides, the discrete model predicts the occurrence of spatiotemporal chaos, which is responsible for the formation of irregular patterns. This research demonstrates that the nonlinear mechanisms of the discrete model better capture the complexity of pattern formation of predator-prey systems.

  10. Models of mixed irradiation with a 'reciprocal-time' pattern of the repair function

    Energy Technology Data Exchange (ETDEWEB)

    Suzuki, Shozo; Miura, Yuri; Mizuno, Shoichi [Tokyo Metropolitan Inst. of Gerontology (Japan); Furusawa, Yoshiya [National Inst. of Radiological Sciences, Chiba (Japan)

    2002-09-01

    Suzuki presented models for mixed irradiation with two and multiple types of radiation by extending the Zaider and Rossi model, which is based on the theory of dual radiation action. In these models, the repair function was simply assumed to be semi-logarithmically linear (i.e., monoexponential), or a first-order process, which has been experimentally contradicted. Fowler, however, suggested that the repair of radiation damage might be largely a second-order process rather than a first-order one, and presented data in support of this hypothesis. In addition, a second-order repair function is preferred to an n-exponential repair function for the reason that only one parameter is used in the former instead of 2n-1 parameters for the latter, although both repair functions show a good fit to the experimental data. However, according to a second-order repair function, the repair rate depends on the dose, which is incompatible with the experimental data. We, therefore, revised the models for mixed irradiation by Zaider and Rossi and by Suzuki, by substituting a 'reciprocal-time' pattern of the repair function, which is derived from the assumption that the repair rate is independent of the dose in a second-order repair function, for a first-order one in reduction and interaction factors of the models, although the underlying mechanism for this assumption cannot be well-explained. The reduction factor, which reduces the contribution of the square of a dose to cell killing in the linear-quadratic model and its derivatives, and the interaction factor, which also reduces the contribution of the interaction of two or more doses of different types of radiation, were formulated by using a 'reciprocal-time' patterns of the repair function. Cell survivals calculated from the older and the newly modified models were compared in terms of the dose-rate by assuming various types of single and mixed irradiation. The result implies that the newly modified models for

  11. Mathematical Framework for A Novel Database Replication Algorithm

    Directory of Open Access Journals (Sweden)

    Divakar Singh Yadav

    2013-10-01

    Full Text Available In this paper, the detailed overview of the database replication is presented. Thereafter, PDDRA (Pre-fetching based dynamic data replication algorithm algorithm as recently published is detailed. In this algorithm, further, modifications are suggested to minimize the delay in data replication. Finally a mathematical framework is presented to evaluate mean waiting time before a data can be replicated on the requested site.

  12. A New Replication Norm for Psychology

    Directory of Open Access Journals (Sweden)

    Etienne P LeBel

    2015-10-01

    Full Text Available In recent years, there has been a growing concern regarding the replicability of findings in psychology, including a mounting number of prominent findings that have failed to replicate via high-powered independent replication attempts. In the face of this replicability “crisis of confidence”, several initiatives have been implemented to increase the reliability of empirical findings. In the current article, I propose a new replication norm that aims to further boost the dependability of findings in psychology. Paralleling the extant social norm that researchers should peer review about three times as many articles that they themselves publish per year, the new replication norm states that researchers should aim to independently replicate important findings in their own research areas in proportion to the number of original studies they themselves publish per year (e.g., a 4:1 original-to-replication studies ratio. I argue this simple approach could significantly advance our science by increasing the reliability and cumulative nature of our empirical knowledge base, accelerating our theoretical understanding of psychological phenomena, instilling a focus on quality rather than quantity, and by facilitating our transformation toward a research culture where executing and reporting independent direct replications is viewed as an ordinary part of the research process. To help promote the new norm, I delineate (1 how each of the major constituencies of the research process (i.e., funders, journals, professional societies, departments, and individual researchers can incentivize replications and promote the new norm and (2 any obstacles each constituency faces in supporting the new norm.

  13. A sensitive real-time PCR based assay to estimate the impact of amino acid substitutions on the competitive replication fitness of human immunodeficiency virus type 1 in cell culture.

    Science.gov (United States)

    Liu, Yi; Holte, Sarah; Rao, Ushnal; McClure, Jan; Konopa, Philip; Swain, J Victor; Lanxon-Cookson, Erinn; Kim, Moon; Chen, Lennie; Mullins, James I

    2013-04-01

    Fixation of mutations in human immunodeficiency virus type 1 (HIV-1), such as those conferring drug resistance and immune escape, can result in a change in replication fitness. To assess these changes, a real-time TaqMan PCR detection assay and statistical methods for data analysis were developed to estimate sensitively relative viral fitness in competitive viral replication experiments in cell culture. Chimeric viruses with the gene of interest in an HIV-1NL4-3 backbone were constructed in two forms, vifA (native vif gene in NL4-3) and vifB (vif gene with six synonymous nucleotide differences from vifA). Subsequently, mutations of interest were introduced into the chimeric viruses in NL4-3VifA backbones, and the mutants were competed against the chimera with the isogenic viral sequence in the NL4-3VifB backbone in cell culture. In order to assess subtle fitness differences, culture supernatants were sampled longitudinally, and the viruses differentially quantified using vifA- and vifB-specific primers in real-time PCR assays. Based on an exponential net growth model, the growth rate of each virus was determined and the fitness cost of the mutation(s) distinguishing the two viruses represented as the net growth rate difference between the mutant and the native variants. Using this assay, the fitness impact of eight amino acid substitutions was quantitated at highly conserved sites in HIV-1 Gag and Env.

  14. Psychology, replication & beyond.

    Science.gov (United States)

    Laws, Keith R

    2016-06-01

    Modern psychology is apparently in crisis and the prevailing view is that this partly reflects an inability to replicate past findings. If a crisis does exists, then it is some kind of 'chronic' crisis, as psychologists have been censuring themselves over replicability for decades. While the debate in psychology is not new, the lack of progress across the decades is disappointing. Recently though, we have seen a veritable surfeit of debate alongside multiple orchestrated and well-publicised replication initiatives. The spotlight is being shone on certain areas and although not everyone agrees on how we should interpret the outcomes, the debate is happening and impassioned. The issue of reproducibility occupies a central place in our whig history of psychology.

  15. Commercial Building Partnerships Replication and Diffusion

    Energy Technology Data Exchange (ETDEWEB)

    Antonopoulos, Chrissi A.; Dillon, Heather E.; Baechler, Michael C.

    2013-09-16

    This study presents findings from survey and interview data investigating replication efforts of Commercial Building Partnership (CBP) partners that worked directly with the Pacific Northwest National Laboratory (PNNL). PNNL partnered directly with 12 organizations on new and retrofit construction projects, which represented approximately 28 percent of the entire U.S. Department of Energy (DOE) CBP program. Through a feedback survey mechanism, along with personal interviews, PNNL gathered quantitative and qualitative data relating to replication efforts by each organization. These data were analyzed to provide insight into two primary research areas: 1) CBP partners’ replication efforts of technologies and approaches used in the CBP project to the rest of the organization’s building portfolio (including replication verification), and, 2) the market potential for technology diffusion into the total U.S. commercial building stock, as a direct result of the CBP program. The first area of this research focused specifically on replication efforts underway or planned by each CBP program participant. Factors that impact replication include motivation, organizational structure and objectives firms have for implementation of energy efficient technologies. Comparing these factors between different CBP partners revealed patterns in motivation for constructing energy efficient buildings, along with better insight into market trends for green building practices. The second area of this research develops a diffusion of innovations model to analyze potential broad market impacts of the CBP program on the commercial building industry in the United States.

  16. The pattern of time management in college students of Kerman University of Medical Sciences in the year 2006

    OpenAIRE

    Ali Ravari; Fatemeh Alhani; Monireh Anoosheh; Tayebeh Mirzaie-Khalilabadi

    2008-01-01

    Background: One potential coping strategy frequently offered by university counseling services is time management for studying. Besides stress relief, time management skills will positively influence key outcomes such as academic performance, problem-solving ability, and health. Thus, it is necessary to investigate how college students manage their timing for studying. The aim of the present study was to assess the pattern of college students' time management in Kerman University of Medical S...

  17. Switching Dynamics Between Two Movement Patterns Varies According to Time Interval

    Science.gov (United States)

    Hirakawa, Takehito; Suzuki, Hiroo; Okumura, Motoki; Gohara, Kazutoshi; Yamamoto, Yuji

    This study investigated the regularity that characterizes the behavior of dissipative dynamical systems excited by external temporal inputs for pointing movements. Right-handed healthy male participants were asked to continuously point their right index finger at two light-emitting diodes (LEDs) located in the oblique left and right directions in front of them. These movements were performed under two conditions: one in which the direction was repeated and one in which the directions were switched on a stochastic basis. These conditions consisted of 12 tempos (30, 36, 42, 48, 51, 54, 57, 60, 63, 66, 69, and 72 beats per minute). Data from the conditions under which the input pattern was repeated revealed two different trajectories in hyper-cylindrical state space ℳ, whereas the conditions under which the inputs were switched induced transitions between the two trajectories, which were considered to be excited attractors. The transitions between the two excited attractors were characterized by a self-similar structure. Moreover, the correlation dimensions increased as the tempos increased. These results suggest a relationship of D ∝ 1/T (T is the switching-time length; i.e. the condition) between temporal input and pointing behavior and that continuous pointing movements are regular rather than random noise.

  18. Switched pattern laser projection for real-time depth extraction and visualization through endoscopes

    Science.gov (United States)

    Keller, Kurtis; Ackerman, Jeremy D.; Fuchs, Henry

    2002-09-01

    Gathering depth information through an endoscope or laparoscope during surgical or other procedures is quite difficult. There are stereo laparoscopes but generating three-dimensional models with them is very difficult. Accurate real-time generation of three-dimensional models through a laparoscope is a needed technology to enable a wide range of surgical applications. We have designed a miniature laparoscopic optical system consisting of a single laser whose pattern is modulated and uses the laparoscope as the optical display path into the body. Two cameras, one sensitive to the laser light and the other for full color imaging share this same tube as the laser projector but use the light from the opposite direction. The images gathered by the laser sensitive camera are used to generate a three dimensional map, and the color image is used to acquire the corresponding texture map. High-speed image processing hardware is used to generate 3D information using a structured light technique. The user can then re-render the acquired scene in 3D. The optical system is divided into a removable upper half consisting of the cameras, laser, digital light switches and combining optics. The lower half is the laparoscope or endocope that can be sterilized. There can be several variations in the configuration of the laparoscope optical half that tailor to different procedures.

  19. Time-series studies of drainage pattern and morphological features along the Leitha river (Eastern Austria)

    Science.gov (United States)

    Zámolyi, A.; Draganits, E.; Doneus, M.; Fera, M.; Griebl, M.

    2009-04-01

    Geomorphologic mapping and drainage network analysis was conducted in the Southern Vienna Basin on the Leitha and Fischa rivers. The study area belongs to an active pull-apart basin between the Eastern Alps and the Carpathians that started to subside in Karpatian times (~ 17 Ma), but with still active faults, proven by fault scarps and earth quakes. The investigated rivers are important tributaries to the Danube river and run through a region that has been subject to settlement since Neoltihic times. Thus, interaction between land use, settlement pattern and river dynamics can be studied. Several datasets are integrated to perform a comprehensive overview of geomorphological, as well as river dynamic changes in the landscape. During an earlier stage of this investigation a map of paleochannel distribution including the location and shape of the paleochannels was extracted from color-infrared and RGB digital orthophotos. Based on this map the location, character and shape of palaeomeanders is studied on different georeferenced historic maps (Timár et al., 2006; Biszak et al., 2007) in order to derive a time-series study. The paleochannels extracted from the digital orthophotos show a good coincidence with the depicted rivers on the historic maps. This partly allows quite well constrained age estimates of the paleochannel sections. The investigated maps are the Walter maps, the First, Second and Third Military Survey of the Habsburg/Austro-Hungarian Empire. Mapping of the Walter maps was conducted 1754-56 (Ulbrich, 1952), the First, Second and Third Military Surveys were mapped in this area in the time-span of 1782-1785, 1819-1869, and 1872-1873, respectively (Kretschmer et al., 2004). This sequence of georeferenced historical maps allows to study only a very short time-span (1755 - 1873) compared to the geological time scale. However, the characteristics of river dynamics special for the study area can be derived and, considering certain assumptions, extrapolated

  20. Real-time biomimetic Central Pattern Generators in an FPGA for hybrid experiments.

    Science.gov (United States)

    Ambroise, Matthieu; Levi, Timothée; Joucla, Sébastien; Yvert, Blaise; Saïghi, Sylvain

    2013-01-01

    This investigation of the leech heartbeat neural network system led to the development of a low resources, real-time, biomimetic digital hardware for use in hybrid experiments. The leech heartbeat neural network is one of the simplest central pattern generators (CPG). In biology, CPG provide the rhythmic bursts of spikes that form the basis for all muscle contraction orders (heartbeat) and locomotion (walking, running, etc.). The leech neural network system was previously investigated and this CPG formalized in the Hodgkin-Huxley neural model (HH), the most complex devised to date. However, the resources required for a neural model are proportional to its complexity. In response to this issue, this article describes a biomimetic implementation of a network of 240 CPGs in an FPGA (Field Programmable Gate Array), using a simple model (Izhikevich) and proposes a new synapse model: activity-dependent depression synapse. The network implementation architecture operates on a single computation core. This digital system works in real-time, requires few resources, and has the same bursting activity behavior as the complex model. The implementation of this CPG was initially validated by comparing it with a simulation of the complex model. Its activity was then matched with pharmacological data from the rat spinal cord activity. This digital system opens the way for future hybrid experiments and represents an important step toward hybridization of biological tissue and artificial neural networks. This CPG network is also likely to be useful for mimicking the locomotion activity of various animals and developing hybrid experiments for neuroprosthesis development.

  1. CLINICAL FEATURES AND PATTERN OF FRACTURES AT THE TIME OF DIAGNOSIS OF OSTEOGENESIS IMPERFECTA IN CHILDREN

    Science.gov (United States)

    Brizola, Evelise; Zambrano, Marina Bauer; Pinheiro, Bruna de Souza; Vanz, Ana Paula; Félix, Têmis Maria

    2017-01-01

    ABSTRACT Objective: To characterize the fracture pattern and the clinical history at the time of diagnosis of osteogenesis imperfecta. Methods: In this retrospective study, all patients with osteogenesis imperfecta, of both genders, aged 0-18 years, who were treated between 2002 and 2014 were included. Medical records were assessed to collect clinical data, including the presence of blue sclerae, dentinogenesis imperfecta, positive familial history of osteogenesis imperfecta, and the site of the fractures. In addition, radiographic findings at the time of the diagnosis were reviewed. Results: Seventy-six patients (42 females) were included in the study. Individuals’ age ranged from 0 to 114 months, with a median (interquartile range) age of 38 (6-96) months. Blue sclerae were present in 93.4% of patients, dentinogenesis imperfecta was observed in 27.6% of patients, and wormian bones in 29.4% of them. The number of fractures at diagnosis ranged from 0 to 17, with a median of 3 (2-8) fractures. Forty (57%) patients had fractures of the upper and lower extremities, and 9 patients also had spinal fractures. The diagnosis was performed at birth in 85.7% of patients with type 3, and 39.3% of those with type 4/5 of the disorder. Conclusions: Osteogenesis imperfecta is a genetic disorder with distinctive clinical features such as bone fragility, recurrent fractures, blue sclerae, and dentinogenesis imperfecta. It is important to know how to identify these characteristics in order to facilitate the diagnosis, optimize the treatment, and differentiate osteogenesis imperfecta from other disorders that also can lead to fractures. PMID:28977334

  2. Real-time biomimetic Central Pattern Generators into FPGA for hybrid experiments

    Directory of Open Access Journals (Sweden)

    Matthieu eAmbroise

    2013-11-01

    Full Text Available This article investigates the neural network system in the leech heartbeat and develops a real-time biomimetic digital hardware using few-resource implementation for hybrid experiments. The leech heartbeat neural network is one of the most simple central pattern generators (CPG. In biology, CPG provide for rhythmic bursts of spikes and is the basis for all muscles contractions orders (heartbeat and locomotion (walking, running….. The leech neural network system was already investigated and this CPG has been already formalized with Hodgkin-Huxley neural model (HH that is the most complex neuron model. However, the resources needed for a neural model is proportional to its complexity. To answer to this issue, this article describes a biomimetic implementation into FPGA (Field Programmable Gate Array of a network of 240 CPGs using a simple model (Izhikevich model and by proposing a new synapse model: activity dependent depression synapse. The architecture of the network implementation allows working on a single computation core. This digital system works in real-time, needs few resources and has the same bursting activity behavior than complex model. To validate our implementation of this CPG, we compare it firstly with a simulation of the complex model. Then we match its activity with the pharmacological data of the activity of the rat’s spinal cord. This digital system allows future hybrid experiments and will be a great step towards hybridation between biological tissue and artificial neural network. This network of CPG could be also useful for mimic the activity of a different animal locomotion or developing hybrid experiments for neuroprosthesis development.

  3. CLINICAL FEATURES AND PATTERN OF FRACTURES AT THE TIME OF DIAGNOSIS OF OSTEOGENESIS IMPERFECTA IN CHILDREN.

    Science.gov (United States)

    Brizola, Evelise; Zambrano, Marina Bauer; Pinheiro, Bruna de Souza; Vanz, Ana Paula; Félix, Têmis Maria

    2017-01-01

    To characterize the fracture pattern and the clinical history at the time of diagnosis of osteogenesis imperfecta. In this retrospective study, all patients with osteogenesis imperfecta, of both genders, aged 0-18 years, who were treated between 2002 and 2014 were included. Medical records were assessed to collect clinical data, including the presence of blue sclerae, dentinogenesis imperfecta, positive familial history of osteogenesis imperfecta, and the site of the fractures. In addition, radiographic findings at the time of the diagnosis were reviewed. Seventy-six patients (42 females) were included in the study. Individuals' age ranged from 0 to 114 months, with a median (interquartile range) age of 38 (6-96) months. Blue sclerae were present in 93.4% of patients, dentinogenesis imperfecta was observed in 27.6% of patients, and wormian bones in 29.4% of them. The number of fractures at diagnosis ranged from 0 to 17, with a median of 3 (2-8) fractures. Forty (57%) patients had fractures of the upper and lower extremities, and 9 patients also had spinal fractures. The diagnosis was performed at birth in 85.7% of patients with type 3, and 39.3% of those with type 4/5 of the disorder. Osteogenesis imperfecta is a genetic disorder with distinctive clinical features such as bone fragility, recurrent fractures, blue sclerae, and dentinogenesis imperfecta. It is important to know how to identify these characteristics in order to facilitate the diagnosis, optimize the treatment, and differentiate osteogenesis imperfecta from other disorders that also can lead to fractures.

  4. Assessment of Saturation Patterns on Agricultural Land Using Time-lapse Photography

    Science.gov (United States)

    Silasari, R.; Bloeschl, G.

    2015-12-01

    Agricultural land generates overland flow differently from natural environment due to features from anthropogenic activities such as cultivated soil layer and tile drain pipe. During rainfall events, the formation of overland flow may happen from infiltration excess and/or saturation excess according to the threshold processes which are influenced by rainfall characteristics and soil hydraulic parameters. The dynamics of threshold processes in varying rainfall and soil hydraulic conditions will affect the surface runoff response which can be inversely analyzed by visually observing the generated saturation patterns. This study aims to explore the use of time-lapse photographs of saturated plot during rainfall events to observe and understand the threshold processes of overland flow generation. The observation was conducted at Hydrological Open Air Laboratory (HOAL) in Lower Austria with a 2 megapixels surveillance camera overlooking a 1.8 ha tile-drained agricultural field situated on a hillslope. The main tile drain pipe extends from the higher ground into the riparian area - creating a depression line which generates the main saturation track. The time-lapse photographs are able to capture the spatial and temporal dynamics of 0.1 ha saturated plot (117 m long and 10 m wide in average) during three big rainfall events in 2014 which produced measurable overland flow. The photographs also manage to capture the behavior of overland flow on tractor tracks which were generated faster than on the main saturated plot - due to the more compacted soil - and contribute significantly to the overall overland flow discharge and movements. Comparison of the photographs with on-field manual plotting shows good accuracy of the captured saturation plot and the possibility of calculating the plot area digitally. This method gives opportunity to observe overland flow generation on visual basis as a complement of the customary discharge measurements.

  5. Exponential growth and selection in self-replicating materials from DNA origami rafts

    Science.gov (United States)

    He, Xiaojin; Sha, Ruojie; Zhuo, Rebecca; Mi, Yongli; Chaikin, Paul M.; Seeman, Nadrian C.

    2017-10-01

    Self-replication and evolution under selective pressure are inherent phenomena in life, and but few artificial systems exhibit these phenomena. We have designed a system of DNA origami rafts that exponentially replicates a seed pattern, doubling the copies in each diurnal-like cycle of temperature and ultraviolet illumination, producing more than 7 million copies in 24 cycles. We demonstrate environmental selection in growing populations by incorporating pH-sensitive binding in two subpopulations. In one species, pH-sensitive triplex DNA bonds enable parent-daughter templating, while in the second species, triplex binding inhibits the formation of duplex DNA templating. At pH 5.3, the replication rate of species I is ~1.3-1.4 times faster than that of species II. At pH 7.8, the replication rates are reversed. When mixed together in the same vial, the progeny of species I replicate preferentially at pH 7.8 similarly at pH 5.3, the progeny of species II take over the system. This addressable selectivity should be adaptable to the selection and evolution of multi-component self-replicating materials in the nanoscopic-to-microscopic size range.

  6. Patterns of Physical Activity Outside of School Time among Japanese Junior High School Students

    Science.gov (United States)

    He, Li; Ishii, Kaori; Shibata, Ai; Adachi, Minoru; Nonoue, Keiko; Oka, Koichiro

    2013-01-01

    Background: Physical activity is beneficial for adolescent health. The physical activity patterns of Japanese adolescents are relatively unknown. Therefore, this study aimed to describe the current patterns of physical activity and to identify sex and grade differences among them. Methods: The participants comprised 714 Japanese adolescents aged…

  7. DNA replication origins in archaea

    OpenAIRE

    Zhenfang eWu; Jingfang eLiu; Haibo eYang; Hua eXiang

    2014-01-01

    DNA replication initiation, which starts at specific chromosomal site (known as replication origins), is the key regulatory stage of chromosome replication. Archaea, the third domain of life, use a single or multiple origin(s) to initiate replication of their circular chromosomes. The basic structure of replication origins is conserved among archaea, typically including an AT-rich unwinding region flanked by several conserved repeats (origin recognition box, ORB) that are located adjacent to ...

  8. Replicative intermediates of maize streak virus found during leaf development.

    Science.gov (United States)

    Erdmann, Julia B; Shepherd, Dionne N; Martin, Darren P; Varsani, Arvind; Rybicki, Edward P; Jeske, Holger

    2010-04-01

    Geminiviruses of the genera Begomovirus and Curtovirus utilize three replication modes: complementary-strand replication (CSR), rolling-circle replication (RCR) and recombination-dependent replication (RDR). Using two-dimensional gel electrophoresis, we now show for the first time that maize streak virus (MSV), the type member of the most divergent geminivirus genus, Mastrevirus, does the same. Although mastreviruses have fewer regulatory genes than other geminiviruses and uniquely express their replication-associated protein (Rep) from a spliced transcript, the replicative intermediates of CSR, RCR and RDR could be detected unequivocally within infected maize tissues. All replicative intermediates accumulated early and, to varying degrees, were already present in the shoot apex and leaves at different maturation stages. Relative to other replicative intermediates, those associated with RCR increased in prevalence during leaf maturation. Interestingly, in addition to RCR-associated DNA forms seen in other geminiviruses, MSV also apparently uses dimeric open circular DNA as a template for RCR.

  9. Replication studies in longevity

    DEFF Research Database (Denmark)

    Varcasia, O; Garasto, S; Rizza, T

    2001-01-01

    In Danes we replicated the 3'APOB-VNTR gene/longevity association study previously carried out in Italians, by which the Small alleles (less than 35 repeats) had been identified as frailty alleles for longevity. In Danes, neither genotype nor allele frequencies differed between centenarians and 20...

  10. Coronavirus Attachment and Replication

    Science.gov (United States)

    1988-03-28

    synthesis during RNA replication of vesicular stomatitis virus. J. Virol. 49:303-309. Pedersen, N.C. 1976a. Feline infectious peritonitis: Something old...receptors on intestinal brush border membranes from normal host species were developed for canine (CCV), feline (FIPV), porcine (TGEV), human (HCV...gastroenteritis receptor on pig BBMs ...... ................. ... 114 Feline infectious peritonitis virus receptor on cat BBMs ... .............. 117 Human

  11. Surface EMG pattern recognition for real-time control of a wrist exoskeleton

    Directory of Open Access Journals (Sweden)

    Khokhar Zeeshan O

    2010-08-01

    Full Text Available Abstract Background Surface electromyography (sEMG signals have been used in numerous studies for the classification of hand gestures and movements and successfully implemented in the position control of different prosthetic hands for amputees. sEMG could also potentially be used for controlling wearable devices which could assist persons with reduced muscle mass, such as those suffering from sarcopenia. While using sEMG for position control, estimation of the intended torque of the user could also provide sufficient information for an effective force control of the hand prosthesis or assistive device. This paper presents the use of pattern recognition to estimate the torque applied by a human wrist and its real-time implementation to control a novel two degree of freedom wrist exoskeleton prototype (WEP, which was specifically developed for this work. Methods Both sEMG data from four muscles of the forearm and wrist torque were collected from eight volunteers by using a custom-made testing rig. The features that were extracted from the sEMG signals included root mean square (rms EMG amplitude, autoregressive (AR model coefficients and waveform length. Support Vector Machines (SVM was employed to extract classes of different force intensity from the sEMG signals. After assessing the off-line performance of the used classification technique, the WEP was used to validate in real-time the proposed classification scheme. Results The data gathered from the volunteers were divided into two sets, one with nineteen classes and the second with thirteen classes. Each set of data was further divided into training and testing data. It was observed that the average testing accuracy in the case of nineteen classes was about 88% whereas the average accuracy in the case of thirteen classes reached about 96%. Classification and control algorithm implemented in the WEP was executed in less than 125 ms. Conclusions The results of this study showed that

  12. Gender and Age Differences in Hourly and Daily Patterns of Sedentary Time in Older Adults Living in Retirement Communities.

    Directory of Open Access Journals (Sweden)

    John Bellettiere

    Full Text Available Total sedentary time varies across population groups with important health consequences. Patterns of sedentary time accumulation may vary and have differential health risks. The purpose of this study is to describe sedentary patterns of older adults living in retirement communities and illustrate gender and age differences in those patterns.Baseline accelerometer data from 307 men and women (mean age = 84±6 years who wore ActiGraph GT3X+ accelerometers for ≥ 4 days as part of a physical activity intervention were classified into bouts of sedentary time (<100 counts per minute. Linear mixed models were used to account for intra-person and site-level clustering. Daily and hourly summaries were examined in mutually non-exclusive bouts of sedentary time that were 1+, 5+, 10+, 20+, 30+, 40+, 50+, 60+, 90+ and 120+ minutes in duration. Variations by time of day, age and gender were explored.Men accumulated more sedentary time than women in 1+, 5+, 10+, 20+, 30+, 40+, 50+ and 60+ minute bouts; the largest gender-differences were observed in 10+ and 20+ minute bouts. Age was positively associated with sedentary time, but only in bouts of 10+, 20+, 30+, and 40+ minutes. Women had more daily 1+ minute sedentary bouts than men (71.8 vs. 65.2, indicating they break up sedentary time more often. For men and women, a greater proportion of time was spent being sedentary during later hours of the day than earlier. Gender differences in intra-day sedentary time were observed during morning hours with women accumulating less sedentary time overall and having more 1+ minute bouts.Patterns identified using bouts of sedentary time revealed gender and age differences in the way in which sedentary time was accumulated by older adults in retirement communities. Awareness of these patterns can help interventionists better target sedentary time and may aid in the identification of health risks associated with sedentary behavior. Future studies should investigate the

  13. Leisure-time physical activity patterns and correlates among pregnant women in Ontario, Canada.

    Science.gov (United States)

    Gaston, Anca; Vamos, Cheryl A

    2013-04-01

    Physical activity significantly impacts public health as it reduces the risk of chronic diseases and provides numerous protective factors during pregnancy. Although Canadian guidelines recommend regular physical activity for healthy pregnant women, little is known about their leisure-time physical activity patterns. This study compared the physical activity levels of pregnant and non-pregnant women and examined socio-demographic and health correlates of physical activity during pregnancy. Canadian Community Health Survey data (2005-2008) from 623 pregnant women and 20,392 non-pregnant women aged 15-49 years in Ontario, Canada were examined. The prevalence of regular physical activity (15 or more minutes on at least 3 days of the week) was 58.3 % [95 % CI 52.9, 63.4], among pregnant women and 66.9 % [95 % CI 65.8, 68.0] among non-pregnant women. However, the prevalence of meeting Canadian guidelines for physical activity during pregnancy (30 or more minutes on at least 4 days of the week) was only 23.3 %, [95 % CI 19.4, 27.7] among pregnant women and 33.6 % [95 % CI 32.7, 34.6] among non-pregnant women. Pregnant women were less likely to be meeting guidelines if they were single, divorced, separated or widowed, a visible minority, had a household income between $20,000 and $79,999, and reported being in good or fair/poor health; when it came to education, women who had completed high school were more likely to be meeting guidelines. Few pregnant women in Ontario are meeting guidelines for physical activity during pregnancy. Results indicate that promoting physical activity during pregnancy should remain a public health priority.

  14. A time and motion study of junior doctor work patterns on the weekend: a potential contributor to the weekend effect?

    Science.gov (United States)

    Richardson, L C; Lehnbom, E C; Baysari, M T; Walter, S R; Day, R O; Westbrook, J I

    2016-07-01

    Patients admitted to hospital on weekends have a greater risk of mortality compared to patients admitted on weekdays. Junior medical officers (JMO) make up the majority of medical staff on weekends. No previous study has quantified JMO work patterns on weekends. To describe and quantify JMO work patterns on weekends and compare them with patterns previously observed during the week. Observational time and motion study of JMO working weekends using the Work Observation Method by Activity Timing (WOMBAT; Australian Institute of Health Innovation, Macquarie University, Sydney, NSW, Australia) software. Descriptive statistics were used to determine the proportion of total observed time spent in tasks. Weekend JMO predominately spent time in indirect care (32.0%), direct care (23.0%) and professional communication (22.1%). JMO spent 20.9% of time multitasking and were interrupted, on average, every 9 min. Weekend JMO spent significantly more time in direct care compared with weekdays (13.0%; P pattern of JMO work could be a potential contributing factor to the weekend effect in terms of JMO abilities to respond safely and adequately to care demands. © 2016 Royal Australasian College of Physicians.

  15. Algorithm for real-time detection of signal patterns using phase synchrony: an application to an electrode array

    Science.gov (United States)

    Sadeghi, Saman; MacKay, William A.; van Dam, R. Michael; Thompson, Michael

    2011-02-01

    Real-time analysis of multi-channel spatio-temporal sensor data presents a considerable technical challenge for a number of applications. For example, in brain-computer interfaces, signal patterns originating on a time-dependent basis from an array of electrodes on the scalp (i.e. electroencephalography) must be analyzed in real time to recognize mental states and translate these to commands which control operations in a machine. In this paper we describe a new technique for recognition of spatio-temporal patterns based on performing online discrimination of time-resolved events through the use of correlation of phase dynamics between various channels in a multi-channel system. The algorithm extracts unique sensor signature patterns associated with each event during a training period and ranks importance of sensor pairs in order to distinguish between time-resolved stimuli to which the system may be exposed during real-time operation. We apply the algorithm to electroencephalographic signals obtained from subjects tested in the neurophysiology laboratories at the University of Toronto. The extension of this algorithm for rapid detection of patterns in other sensing applications, including chemical identification via chemical or bio-chemical sensor arrays, is also discussed.

  16. Monitoring Agricultural Cropping Patterns in the Great Lakes Basin Using MODIS-NDVI Time Series Data

    Science.gov (United States)

    This research examined changes in agricultural cropping patterns across the Great Lakes Basin (GLB) using the Moderate Resolution Imaging Spectroradiometer (MODIS) Normalized Difference Vegetation Index (NDVI) data. Specific research objectives were to characterize the distribut...

  17. [The effects of TorR protein on initiation of DNA replication in Escherichia coli].

    Science.gov (United States)

    Yuan, Yao; Jiaxin, Qiao; Jing, Li; Hui, Li; Morigen, Morigen

    2015-03-01

    The two-component systems, which could sense and respond to environmental changes, widely exist in bacteria as a signal transduction pathway. The bacterial CckA/CtrA, ArcA/ArcB and PhoP/PhoQ two-component systems are associated with initiation of DNA replication and cell division, however, the effects of the TorS/TorR system on cell cycle and DNA replication remains unknown. The TorS/TorR system in Escherichia coli can sense changes in trimethylamine oxide (TMAO) concentration around the cells. However, it is unknown if it also affects initiation of DNA replication. We detected DNA replication patterns in ΔtorS and ΔtorR mutant strains by flow cytometry. We found that the average number of replication origins (oriCs) per cell and doubling time in ΔtorS mutants were the same while the average number of oriCs in ΔtorR mutants was increased compared with that in wild-type cells. These results indicated that absence of TorR led to an earlier initiation of DNA replication than that in wild-type cells. Strangely, neither overexpression of TorR nor co-expression of TorR and TorS could restore ΔtorR mutant phenotype to the wild type. However, overexpression of SufD in both wild type and ΔtorR mutants promoted initiation of DNA replication, while mutation of SufD delayed it in ΔtorR mutants. Thus, TorR may affect initiation of DNA replication indirectly through regulating gene expression of sufD.

  18. Independent and combined associations of total sedentary time and television viewing time with food intake patterns of 9- to 11-year-old Canadian children.

    Science.gov (United States)

    Borghese, Michael M; Tremblay, Mark S; Leduc, Genevieve; Boyer, Charles; Bélanger, Priscilla; LeBlanc, Allana G; Francis, Claire; Chaput, Jean-Philippe

    2014-08-01

    The relationships among sedentary time, television viewing time, and dietary patterns in children are not fully understood. The aim of this paper was to determine which of self-reported television viewing time or objectively measured sedentary time is a better correlate of the frequency of consumption of healthy and unhealthy foods. A cross-sectional study was conducted of 9- to 11-year-old children (n = 523; 57.1% female) from Ottawa, Ontario, Canada. Accelerometers were used to determine total sedentary time, and questionnaires were used to determine the number of hours of television watching and the frequency of consumption of foods per week. Television viewing was negatively associated with the frequency of consumption of fruits, vegetables, and green vegetables, and positively associated with the frequency of consumption of sweets, soft drinks, diet soft drinks, pastries, potato chips, French fries, fruit juices, ice cream, fried foods, and fast food. Except for diet soft drinks and fruit juices, these associations were independent of covariates, including sedentary time. Total sedentary time was negatively associated with the frequency of consumption of sports drinks, independent of covariates, including television viewing. In combined sedentary time and television viewing analyses, children watching >2 h of television per day consumed several unhealthy food items more frequently than did children watching ≤2 h of television, regardless of sedentary time. In conclusion, this paper provides evidence to suggest that television viewing time is more strongly associated with unhealthy dietary patterns than is total sedentary time. Future research should focus on reducing television viewing time, as a means of improving dietary patterns and potentially reducing childhood obesity.

  19. Diurnal fatigue patterns, sleep timing, and mental health outcomes among healthy postpartum women.

    Science.gov (United States)

    McBean, Amanda L; Montgomery-Downs, Hawley E

    2015-01-01

    Postpartum women have frequently interrupted sleep, report high levels of fatigue, and may experience circadian rhythm disruptions. They are also susceptible to mood impairments, anxiety, and stress. The current study explored associations between maternal postpartum daily fatigue patterns, which should vary according to circadian influences and mental health. Seventy-one primiparous, healthy mothers completed multiple daily self-reports of fatigue during postpartum Weeks 2 and 12 and were categorized at each week as having either a rhythmic or random fatigue pattern during the daytime. Wrist actigraphy data were used to calculate sleep midpoints. Surveys assessed chronotype, mood, anxiety, and stress. At postpartum Week 2, there were no differences in mental health measures between fatigue groups. At postpartum Week 12, higher overall fatigue levels were associated with increased anxiety, stress, and mood disruption. However, overall fatigue levels did not differ between fatigue groups. Women with a rhythmic fatigue pattern reported significantly less stress and more vigor than women with a random fatigue pattern. An earlier sleep midpoint was associated with a rhythmic fatigue pattern during postpartum Week 12. These data suggest that, despite similar average daily fatigue levels, having a rhythmic daily pattern of fatigue may be advantageous for mental health outcomes among postpartum women.

  20. Pattern Formation in Predator-Prey Model with Delay and Cross Diffusion

    Directory of Open Access Journals (Sweden)

    Xinze Lian

    2013-01-01

    Full Text Available We consider the effect of time delay and cross diffusion on the dynamics of a modified Leslie-Gower predator-prey model incorporating a prey refuge. Based on the stability analysis, we demonstrate that delayed feedback may generate Hopf and Turing instability under some conditions, resulting in spatial patterns. One of the most interesting findings is that the model exhibits complex pattern replication: the model dynamics exhibits a delay and diffusion controlled formation growth not only to spots, stripes, and holes, but also to spiral pattern self-replication. The results indicate that time delay and cross diffusion play important roles in pattern formation.

  1. Pattern Formation in a Bacterial Colony Model

    Directory of Open Access Journals (Sweden)

    Xinze Lian

    2014-01-01

    Full Text Available We investigate the spatiotemporal dynamics of a bacterial colony model. Based on the stability analysis, we derive the conditions for Hopf and Turing bifurcations. Furthermore, we present novel numerical evidence of time evolution of patterns controlled by parameters in the model and find that the model dynamics exhibit a diffusion controlled formation growth to spots, holes and stripes pattern replication, which show that the bacterial colony model is useful in revealing the spatial predation dynamics in the real world.

  2. Oscillation-Driven Spike-Timing Dependent Plasticity Allows Multiple Overlapping Pattern Recognition in Inhibitory Interneuron Networks.

    Science.gov (United States)

    Garrido, Jesús A; Luque, Niceto R; Tolu, Silvia; D'Angelo, Egidio

    2016-08-01

    The majority of operations carried out by the brain require learning complex signal patterns for future recognition, retrieval and reuse. Although learning is thought to depend on multiple forms of long-term synaptic plasticity, the way this latter contributes to pattern recognition is still poorly understood. Here, we have used a simple model of afferent excitatory neurons and interneurons with lateral inhibition, reproducing a network topology found in many brain areas from the cerebellum to cortical columns. When endowed with spike-timing dependent plasticity (STDP) at the excitatory input synapses and at the inhibitory interneuron-interneuron synapses, the interneurons rapidly learned complex input patterns. Interestingly, induction of plasticity required that the network be entrained into theta-frequency band oscillations, setting the internal phase-reference required to drive STDP. Inhibitory plasticity effectively distributed multiple patterns among available interneurons, thus allowing the simultaneous detection of multiple overlapping patterns. The addition of plasticity in intrinsic excitability made the system more robust allowing self-adjustment and rescaling in response to a broad range of input patterns. The combination of plasticity in lateral inhibitory connections and homeostatic mechanisms in the inhibitory interneurons optimized mutual information (MI) transfer. The storage of multiple complex patterns in plastic interneuron networks could be critical for the generation of sparse representations of information in excitatory neuron populations falling under their control.

  3. Control of DNA replication by anomalous reaction-diffusion kinetics

    Science.gov (United States)

    Bechhoefer, John; Gauthier, Michel

    2010-03-01

    DNA replication requires two distinct processes: the initiation of pre-licensed replication origins and the propagation of replication forks away from the fired origins. Experiments indicate that these origins are triggered over the whole genome at a rate I(t) (the number of initiations per unreplicated length per time) that increases throughout most of the synthesis (S) phase, before rapidly decreasing to zero at the end of the replication process. We propose a simple model for the control of DNA replication in which the rate of initiation of replication origins is controlled by protein-DNA interactions. Analyzing recent data from Xenopus frog embryos, we find that the initiation rate is reaction limited until nearly the end of replication, when it becomes diffusion limited. Initiation of origins is suppressed when the diffusion-limited search time dominates. To fit the experimental data, we find that the interaction between DNA and the rate-limiting protein must be subdiffusive.

  4. Two-Dimensional Time-Domain Antenna Arrays for Optimum Steerable Energy Pattern with Low Side Lobes

    Directory of Open Access Journals (Sweden)

    Alberto Reyna

    2014-01-01

    Full Text Available This document presents the synthesis of different two-dimensional time-domain antenna arrays for steerable energy patterns with side lobe levels. The research is focused on the uniform and nonuniform distributions of true-time exciting delays and positions of antenna elements. The uniform square array, random array, uniform concentric ring array, and rotated nonuniform concentric ring array geometries are particularly studied. These geometries are synthesized by using the well-known sequential quadratic programming. The synthesis regards the optimal true-time exciting delays and optimal positions of pulsed antenna elements. The results show the capabilities of the different antenna arrays to steer the beam in their energy pattern in time domain and how their performance is in frequency domain after the synthesis in time domain.

  5. Reversible Switching of Cooperating Replicators

    Science.gov (United States)

    Urtel, Georg C.; Rind, Thomas; Braun, Dieter

    2017-02-01

    How can molecules with short lifetimes preserve their information over millions of years? For evolution to occur, information-carrying molecules have to replicate before they degrade. Our experiments reveal a robust, reversible cooperation mechanism in oligonucleotide replication. Two inherently slow replicating hairpin molecules can transfer their information to fast crossbreed replicators that outgrow the hairpins. The reverse is also possible. When one replication initiation site is missing, single hairpins reemerge from the crossbreed. With this mechanism, interacting replicators can switch between the hairpin and crossbreed mode, revealing a flexible adaptation to different boundary conditions.

  6. Virtual Machine Replication on Achieving Energy-Efficiency in a Cloud

    Directory of Open Access Journals (Sweden)

    Subrota K. Mondal

    2016-07-01

    Full Text Available The rapid growth in cloud service demand has led to the establishment of large-scale virtualized data centers in which virtual machines (VMs are used to handle user requests for service. A user’s request cannot be completed if the VM fails. Replication mechanisms can be used to mitigate the impact of failures. Further, data centers consume a large amount of energy resulting in high operating costs and contributing to significant greenhouse gas (GHG emissions. In this paper, we focus on Infrastructure as a Service (IaaS cloud where user job requests are processed by VMs and analyze the effectiveness of VM replications in terms of job completion time performance as well as energy consumption. Three different schemes: cold, warm, and hot replications are considered. The trade-offs between job completion time and energy consumption in different replication schemes are characterized through comprehensive analytical models which capture VM state transitions and associated power consumption patterns. The effectiveness of replication schemes are demonstrated through experimental results. To verify the validity of the proposed analytical models, we extend the widely used cloud simulator CloudSim and compare the simulation results with analytical solutions.

  7. No time for the gym? Housework and other non-labor market time use patterns are associated with meeting physical activity recommendations among adults in full-time, sedentary jobs.

    Science.gov (United States)

    Smith, Lindsey P; Ng, Shu Wen; Popkin, Barry M

    2014-11-01

    Physical activity and inactivity have distinct cardio-metabolic consequences, suggesting that combinations of activities can impact health above and beyond the effects of a single activity. However, little work has examined patterns of non-labor market time activity in the US population, particularly among full-time employees in sedentary occupations, who are at increased risk of adverse health consequences associated with a sedentary lifestyle. Identification of these patterns, and how they are related to total physical activity levels, is important for developing effective, attainable physical activity recommendations among sedentary employees, who typically have less time available for exercise. This is especially the case for low-income employees who face the highest time and financial barriers to achieving physical activity goals. This study uses cluster analysis to examine patterns of non-labor market time use among full-time (≥40 h/week) employed adults in sedentary occupations (improve physical activity among similarly sedentary groups. Alternately, non-labor market time use patterns characterized by housework and caregiving represented feasible avenues for increasing overall physical activity levels, especially for those with low financial and time resources. Consideration of non-labor market time use patterns may improve strategies to increase physical activity and decrease inactivity among full-time employed adults in sedentary jobs.

  8. Using areas of known occupancy to identify sources of variation in detection probability of raptors: taking time lowers replication effort for surveys.

    Science.gov (United States)

    Murn, Campbell; Holloway, Graham J

    2016-10-01

    Species occurring at low density can be difficult to detect and if not properly accounted for, imperfect detection will lead to inaccurate estimates of occupancy. Understanding sources of variation in detection probability and how they can be managed is a key part of monitoring. We used sightings data of a low-density and elusive raptor (white-headed vulture Trigonoceps occipitalis) in areas of known occupancy (breeding territories) in a likelihood-based modelling approach to calculate detection probability and the factors affecting it. Because occupancy was known a priori to be 100%, we fixed the model occupancy parameter to 1.0 and focused on identifying sources of variation in detection probability. Using detection histories from 359 territory visits, we assessed nine covariates in 29 candidate models. The model with the highest support indicated that observer speed during a survey, combined with temporal covariates such as time of year and length of time within a territory, had the highest influence on the detection probability. Averaged detection probability was 0.207 (s.e. 0.033) and based on this the mean number of visits required to determine within 95% confidence that white-headed vultures are absent from a breeding area is 13 (95% CI: 9-20). Topographical and habitat covariates contributed little to the best models and had little effect on detection probability. We highlight that low detection probabilities of some species means that emphasizing habitat covariates could lead to spurious results in occupancy models that do not also incorporate temporal components. While variation in detection probability is complex and influenced by effects at both temporal and spatial scales, temporal covariates can and should be controlled as part of robust survey methods. Our results emphasize the importance of accounting for detection probability in occupancy studies, particularly during presence/absence studies for species such as raptors that are widespread and

  9. How much time do nurses have for patients? a longitudinal study quantifying hospital nurses' patterns of task time distribution and interactions with health professionals

    Directory of Open Access Journals (Sweden)

    Westbrook Johanna I

    2011-11-01

    Full Text Available Abstract Background Time nurses spend with patients is associated with improved patient outcomes, reduced errors, and patient and nurse satisfaction. Few studies have measured how nurses distribute their time across tasks. We aimed to quantify how nurses distribute their time across tasks, with patients, in individual tasks, and engagement with other health care providers; and how work patterns changed over a two year period. Methods Prospective observational study of 57 nurses for 191.3 hours (109.8 hours in 2005/2006 and 81.5 in 2008, on two wards in a teaching hospital in Australia. The validated Work Observation Method by Activity Timing (WOMBAT method was applied. Proportions of time in 10 categories of work, average time per task, time with patients and others, information tools used, and rates of interruptions and multi-tasking were calculated. Results Nurses spent 37.0%[95%CI: 34.5, 39.3] of their time with patients, which did not change in year 3 [35.7%; 95%CI: 33.3, 38.0]. Direct care, indirect care, medication tasks and professional communication together consumed 76.4% of nurses' time in year 1 and 81.0% in year 3. Time on direct and indirect care increased significantly (respectively 20.4% to 24.8%, P Conclusions Nurses spent around 37% of their time with patients which did not change. Work patterns were increasingly fragmented with rapid changes between tasks of short length. Interruptions were modest but their substantial over-representation among medication tasks raises potential safety concerns. There was no evidence of an increase in team-based, multi-disciplinary care. Over time nurses spent significantly less time talking with colleagues and more time alone.

  10. Analysis of risk factors for the interval time, number and pattern of hepatic metastases from gastric cancer after radical gastrectomy

    Institute of Scientific and Technical Information of China (English)

    Jing-Yu Deng; Han Liang; Dan Sun; Hong-Jie Zhan; Ru-Peng Zhang

    2008-01-01

    AIM: To analyze the risk factors for interval time,number and pattern of hepatic metastases from gastric cancer after radical gastrectomy, and provide evidence for predicting and preventing hepatic metastasis from gastric cancer after radical gastrectomy. METHODS: A retrospective study of 87 patients with hepatic metastasis who underwent radical gastrectomy for gastric cancer from 1996 to 2001. The data was analyzed to evaluate significant risk factors for interval time, number and pattern of hepatic metastases originating from gastric cancer after radical gastrectomy.RESULTS: The size of gastric cancer and lymph node metastases were independently correlated with the interval time of hepatic metastases; the depth of invasion was independently correlated with the number of hepatic metastases; while the depth of invasion and Lauren classification were independently correlated with the pattern of hepatic metastases.CONCLUSION: We evaluated the interval time of hepatic metastases with the size of gastric cancer and lymph node metastases. The depth of invasion could be used to evaluate the number of hepatic metastases, while the depth of invasion and the Lauren classification could be used to evaluate the pattern of hepatic metastases in patients who underwent radical gastrectomy.

  11. Counting forbidden patterns in irregularly sampled time series. II. Reliability in the presence of highly irregular sampling

    Science.gov (United States)

    Sakellariou, Konstantinos; McCullough, Michael; Stemler, Thomas; Small, Michael

    2016-12-01

    We are motivated by real-world data that exhibit severe sampling irregularities such as geological or paleoclimate measurements. Counting forbidden patterns has been shown to be a powerful tool towards the detection of determinism in noisy time series. They constitute a set of ordinal symbolic patterns that cannot be realised in time series generated by deterministic systems. The reliability of the estimator of the relative count of forbidden patterns from irregularly sampled data has been explored in two recent studies. In this paper, we explore highly irregular sampling frequency schemes. Using numerically generated data, we examine the reliability of the estimator when the sampling period has been drawn from exponential, Pareto and Gamma distributions of varying skewness. Our investigations demonstrate that some statistical properties of the sampling distribution are useful heuristics for assessing the estimator's reliability. We find that sampling in the presence of large chronological gaps can still yield relatively accurate estimates as long as the time series contains sufficiently many densely sampled areas. Furthermore, we show that the reliability of the estimator of forbidden patterns is poor when there is a high number of sampling intervals, which are larger than a typical correlation time of the underlying system.

  12. Predicting different patterns of sexual identity development over time among lesbian, gay, and bisexual youths: a cluster analytic approach.

    Science.gov (United States)

    Rosario, Margaret; Schrimshaw, Eric W; Hunter, Joyce

    2008-12-01

    Recent research has suggested that the sexual identity development of lesbian, gay, and bisexual (LGB) youths may not follow a single pattern, but may follow a variety of pathways. Although some research documenting variability in identity development exists, unclear are the potential individual and social contexts that predict these different patterns, as well as the contexts that predict changes in identity integration over time. This report longitudinally examined these issues in an ethnically diverse sample of 156 LGB youths (ages 14-21) in New York City. Cluster analytic techniques identified two patterns of sexual identity formation (i.e., early and more recent), and three patterns of sexual identity integration (i.e., high, middling, and low). Gender and sexual abuse were found to predict identity formation; and, gay-related stress, social support, negative social relationships, sexual orientation, sexual identity, and gender were found to predict patterns of sexual identity integration and changes in integration over 1 year. These findings document different patterns of sexual identity development and identify potential contextual barriers and facilitating factors that may be used to develop interventions to promote healthy LGB identity development.

  13. A comparison of the real-time controllability of pattern recognition to conventional myoelectric control for discrete and simultaneous movements.

    Science.gov (United States)

    Young, Aaron J; Smith, Lauren H; Rouse, Elliott J; Hargrove, Levi J

    2014-01-10

    Myoelectric control has been used for decades to control powered upper limb prostheses. Conventional, amplitude-based control has been employed to control a single prosthesis degree of freedom (DOF) such as closing and opening of the hand. Within the last decade, new and advanced arm and hand prostheses have been constructed that are capable of actuating numerous DOFs. Pattern recognition control has been proposed to control a greater number of DOFs than conventional control, but has traditionally been limited to sequentially controlling DOFs one at a time. However, able-bodied individuals use multiple DOFs simultaneously, and it may be beneficial to provide amputees the ability to perform simultaneous movements. In this study, four amputees who had undergone targeted motor reinnervation (TMR) surgery with previous training using myoelectric prostheses were configured to use three control strategies: 1) conventional amplitude-based myoelectric control, 2) sequential (one-DOF) pattern recognition control, 3) simultaneous pattern recognition control. Simultaneous pattern recognition was enabled by having amputees train each simultaneous movement as a separate motion class. For tasks that required control over just one DOF, sequential pattern recognition based control performed the best with the lowest average completion times, completion rates and length error. For tasks that required control over 2 DOFs, the simultaneous pattern recognition controller performed the best with the lowest average completion times, completion rates and length error compared to the other control strategies. In the two strategies in which users could employ simultaneous movements (conventional and simultaneous pattern recognition), amputees chose to use simultaneous movements 78% of the time with simultaneous pattern recognition and 64% of the time with conventional control for tasks that required two DOF motions to reach the target. These results suggest that when amputees are given the

  14. Isometric fatigue patterns in time and time-frequency domains of triceps surae muscle in different knee positions.

    Science.gov (United States)

    Pereira, Glauber Ribeiro; de Oliveira, Liliam Fernandes; Nadal, Jurandir

    2011-08-01

    The occurrence of fatigue in triceps surae (TS) muscles during sustained plantar flexion contraction is investigated by means of the RMS electromyogram (EMG) and the instantaneous median frequency (IMF) of the short time Fourier transform (STFT). Six male subjects realized a 40% maximal plantar flexion isometric voluntary contraction until fatigue in two knee positions. Electrodes were positioned on gastrocnemius medialis, gastrocnemius lateralis and soleus muscles. The torque (TO) and EMG signals were synchronized. The RMS and the median of the IMF values were obtained, respectively, for each 250 ms and 1s windows of signal. Each signal was segmented into 10 epochs, from which the mean values of IMF, RMS and TO were obtained and submitted to linear regressions to determine parameter trends. Friedman test with the Dunn's post hoc were used to test for differences among muscles activation for each knee position and among slopes of regression curves, as well as to observe changes in TS RMS values over time. The results indicate different activation strategies with the knee extended (KE) in contrast to knee flexed (KF). With the KE, the gastrocnemii showed typical fatigue behavior with significant (p<0.05) IMF reductions and RMS increases over time, while soleus showed concomitant RMS and IMF increases (p<0.05) suggesting an increased soleus contribution to the torque production. With KF, the gastrocnemii were under activated, increasing the role of soleus. Thus, time-frequency analysis represented an important tool for TS muscular fatigue evaluation, allowing differentiates the role of soleus muscle.

  15. The relative dependence of Spanish landscape pattern on environmental and geographical variables over time

    NARCIS (Netherlands)

    Ortega, M.; Bunce, R.G.H.; Barrio, del J.M.G.; Elena-Rossello, R.

    2008-01-01

    The analysis of the dependence of landscape patterns on environment was carried out in order to investigate the landscape structure evolution of Spain. The underlying concept was that the dependence between landscape spatial structure and environmental factors could be gradually decreasing over

  16. Dynamics in cancer caregiver's health over time : Gender-specific patterns and determinants

    NARCIS (Netherlands)

    Nijboer, C; Triemstra, M; Sanderman, R; van den Bos, GAM

    2001-01-01

    This study examined patterns and determinants of three dimensions of caregiver's health of newly diagnosed colorectal cancer patients, i.e. physical, mental and social functioning (N = 148). Physical functioning declined within a 6-month period in female caregivers, while no change was observed in m

  17. Time-resolved double-slit interference pattern measurement with entangled photons.

    Science.gov (United States)

    Kolenderski, Piotr; Scarcella, Carmelo; Johnsen, Kelsey D; Hamel, Deny R; Holloway, Catherine; Shalm, Lynden K; Tisa, Simone; Tosi, Alberto; Resch, Kevin J; Jennewein, Thomas

    2014-04-28

    The double-slit experiment strikingly demonstrates the wave-particle duality of quantum objects. In this famous experiment, particles pass one-by-one through a pair of slits and are detected on a distant screen. A distinct wave-like pattern emerges after many discrete particle impacts as if each particle is passing through both slits and interfering with itself. Here we present a temporally- and spatially-resolved measurement of the double-slit interference pattern using single photons. We send single photons through a birefringent double-slit apparatus and use a linear array of single-photon detectors to observe the developing interference pattern. The analysis of the buildup allows us to compare quantum mechanics and the corpuscular model, which aims to explain the mystery of single-particle interference. Finally, we send one photon from an entangled pair through our double-slit setup and show the dependence of the resulting interference pattern on the twin photon's measured state. Our results provide new insight into the dynamics of the buildup process in the double-slit experiment, and can be used as a valuable resource in quantum information applications.

  18. Adapting to Hard Times: Family Participation Patterns in Local Thrift Economies

    Science.gov (United States)

    James, Spencer; Brown, Ralph B.; Goodsell, Todd L.; Stovall, Josh; Flaherty, Jeremy

    2010-01-01

    Using survey data from a western U.S. county (N = 595), we examined how lower, middle, and higher income families negotiate a period of economic stress--the closing of a major employer in the community--through their shopping patterns. Specifically, we examined their participation in local thrift economies such as yard sales and secondhand stores.…

  19. Are clusters of dietary patterns and cluster membership stable over time? Results of a longitudinal cluster analysis study.

    Science.gov (United States)

    Walthouwer, Michel Jean Louis; Oenema, Anke; Soetens, Katja; Lechner, Lilian; de Vries, Hein

    2014-11-01

    Developing nutrition education interventions based on clusters of dietary patterns can only be done adequately when it is clear if distinctive clusters of dietary patterns can be derived and reproduced over time, if cluster membership is stable, and if it is predictable which type of people belong to a certain cluster. Hence, this study aimed to: (1) identify clusters of dietary patterns among Dutch adults, (2) test the reproducibility of these clusters and stability of cluster membership over time, and (3) identify sociodemographic predictors of cluster membership and cluster transition. This study had a longitudinal design with online measurements at baseline (N=483) and 6 months follow-up (N=379). Dietary intake was assessed with a validated food frequency questionnaire. A hierarchical cluster analysis was performed, followed by a K-means cluster analysis. Multinomial logistic regression analyses were conducted to identify the sociodemographic predictors of cluster membership and cluster transition. At baseline and follow-up, a comparable three-cluster solution was derived, distinguishing a healthy, moderately healthy, and unhealthy dietary pattern. Male and lower educated participants were significantly more likely to have a less healthy dietary pattern. Further, 251 (66.2%) participants remained in the same cluster, 45 (11.9%) participants changed to an unhealthier cluster, and 83 (21.9%) participants shifted to a healthier cluster. Men and people living alone were significantly more likely to shift toward a less healthy dietary pattern. Distinctive clusters of dietary patterns can be derived. Yet, cluster membership is unstable and only few sociodemographic factors were associated with cluster membership and cluster transition. These findings imply that clusters based on dietary intake may not be suitable as a basis for nutrition education interventions. Copyright © 2014 Elsevier Ltd. All rights reserved.

  20. Replication Research and Special Education

    Science.gov (United States)

    Travers, Jason C.; Cook, Bryan G.; Therrien, William J.; Coyne, Michael D.

    2016-01-01

    Replicating previously reported empirical research is a necessary aspect of an evidence-based field of special education, but little formal investigation into the prevalence of replication research in the special education research literature has been conducted. Various factors may explain the lack of attention to replication of special education…

  1. Replication Research and Special Education

    Science.gov (United States)

    Travers, Jason C.; Cook, Bryan G.; Therrien, William J.; Coyne, Michael D.

    2016-01-01

    Replicating previously reported empirical research is a necessary aspect of an evidence-based field of special education, but little formal investigation into the prevalence of replication research in the special education research literature has been conducted. Various factors may explain the lack of attention to replication of special education…

  2. Longitudinal variability of time-location/activity patterns of population at different ages: a longitudinal study in California

    Directory of Open Access Journals (Sweden)

    Cassady Diana L

    2011-09-01

    Full Text Available Abstract Background Longitudinal time-activity data are important for exposure modeling, since the extent to which short-term time-activity data represent long-term activity patterns is not well understood. This study was designed to evaluate longitudinal variations in human time-activity patterns. Method We report on 24-hour recall diaries and questionnaires collected via the internet from 151 parents of young children (mostly under age 55, and from 55 older adults of ages 55 and older, for both a weekday and a weekend day every three months over an 18-month period. Parents also provided data for their children. The self-administrated diary and questionnaire distinguished ~30 frequently visited microenvironments and ~20 activities which we selected to represent opportunities for exposure to toxic environmental compounds. Due to the non-normal distribution of time-location/activity data, we employed generalized linear mixed-distribution mixed-effect models to examine intra- and inter-individual variations. Here we describe variation in the likelihood of and time spent engaging in an activity or being in a microenvironment by age group, day-type (weekday/weekend, season (warm/cool, sex, employment status, and over the follow-up period. Results As expected, day-type and season influence time spent in many location and activity categories. Longitudinal changes were also observed, e.g., young children slept less with increasing follow-up, transit time increased, and time spent on working and shopping decreased during the study, possibly related to human physiological changes with age and changes in macro-economic factors such as gas prices and the economic recession. Conclusions This study provides valuable new information about time-activity assessed longitudinally in three major age groups and greatly expands our knowledge about intra- and inter-individual variations in time-location/activity patterns. Longitudinal variations beyond weekly and

  3. The Alleged Crisis and the Illusion of Exact Replication.

    Science.gov (United States)

    Stroebe, Wolfgang; Strack, Fritz

    2014-01-01

    There has been increasing criticism of the way psychologists conduct and analyze studies. These critiques as well as failures to replicate several high-profile studies have been used as justification to proclaim a "replication crisis" in psychology. Psychologists are encouraged to conduct more "exact" replications of published studies to assess the reproducibility of psychological research. This article argues that the alleged "crisis of replicability" is primarily due to an epistemological misunderstanding that emphasizes the phenomenon instead of its underlying mechanisms. As a consequence, a replicated phenomenon may not serve as a rigorous test of a theoretical hypothesis because identical operationalizations of variables in studies conducted at different times and with different subject populations might test different theoretical constructs. Therefore, we propose that for meaningful replications, attempts at reinstating the original circumstances are not sufficient. Instead, replicators must ascertain that conditions are realized that reflect the theoretical variable(s) manipulated (and/or measured) in the original study.

  4. Eukaryotic Mismatch Repair in Relation to DNA Replication.

    Science.gov (United States)

    Kunkel, Thomas A; Erie, Dorothy A

    2015-01-01

    Three processes act in series to accurately replicate the eukaryotic nuclear genome. The major replicative DNA polymerases strongly prevent mismatch formation, occasional mismatches that do form are proofread during replication, and rare mismatches that escape proofreading are corrected by mismatch repair (MMR). This review focuses on MMR in light of increasing knowledge about nuclear DNA replication enzymology and the rate and specificity with which mismatches are generated during leading- and lagging-strand replication. We consider differences in MMR efficiency in relation to mismatch recognition, signaling to direct MMR to the nascent strand, mismatch removal, and the timing of MMR. These studies are refining our understanding of relationships between generating and repairing replication errors to achieve accurate replication of both DNA strands of the nuclear genome.

  5. Replication data collection highlights value in diversity of replication attempts

    Science.gov (United States)

    DeSoto, K. Andrew; Schweinsberg, Martin

    2017-01-01

    Researchers agree that replicability and reproducibility are key aspects of science. A collection of Data Descriptors published in Scientific Data presents data obtained in the process of attempting to replicate previously published research. These new replication data describe published and unpublished projects. The different papers in this collection highlight the many ways that scientific replications can be conducted, and they reveal the benefits and challenges of crucial replication research. The organizers of this collection encourage scientists to reuse the data contained in the collection for their own work, and also believe that these replication examples can serve as educational resources for students, early-career researchers, and experienced scientists alike who are interested in learning more about the process of replication. PMID:28291224

  6. A systemic increase in the recombination frequency upon local infection of Arabidopsis thaliana plants with oilseed rape mosaic virus depends on plant age, the initial inoculum concentration and the time for virus replication.

    Science.gov (United States)

    Yao, Youli; Kathiria, Palak; Kovalchuk, Igor

    2013-01-01

    In the past, we showed that local infection of tobacco leaves with either tobacco mosaic virus or oilseed rape mosaic virus (ORMV) resulted in a systemic increase in the homologous recombination frequency (HRF). Later on, we showed that a similar phenomenon occurs in Arabidopsis thaliana plants infected with ORMV. Here, we tested whether the time of removing the infected leaves as well as viral titer have any effect on the degree of changes in HRF in systemic tissues. An increase in HRF in systemic non-infected tissues was more pronounced when the infected leaves were detached from the infected plants at 60-96 h post-infection, rather than at earlier time. Next, we found that exposure to higher concentrations of inoculum was much more efficient in triggering an increase in HRF than exposure to lower concentrations. Finally, we showed that older plants exhibited a higher increase in HRF than younger plants. We found that an increase in genome instability in systemic tissues of locally infected plants depends on plant age, the concentration of initial inoculums and the time of viral replication.

  7. A systemic increase in the recombination frequency upon local infection of Arabidopsis thaliana plants with oilseed rape mosaic virus depends on plant age, the initial inoculum concentration and the time for virus replication

    Directory of Open Access Journals (Sweden)

    Youli eYao

    2013-03-01

    Full Text Available In the past, we showed that local infection of tobacco leaves with either Tobacco mosaic virus (TMV or Oilseed rape mosaic virus (ORMV resulted in a systemic increase in the homologous recombination frequency (HRF. Later on, we showed that a similar phenomenon occurs in Arabidopsis thaliana plants infected with ORMV. Here, we tested whether the time of removing the infected leaves as well as viral titer have any effect on the degree of changes in HRF in systemic tissues. An increase in HRF in systemic non-infected tissues was more pronounced when the infected leaves were detached from the infected plants at 60-96 hours post infection, rather than at earlier time. Next, we found that exposure to higher concentrations of inoculum was much more efficient in triggering an increase in HRF than exposure to lower concentrations. Finally, we showed that older plants exhibited a higher increase in HRF than younger plants. We found that an increase in genome instability in systemic tissues of locally infected plants depends on plant age, the concentration of initial inoculums and the time of viral replication.

  8. Adapting to Hard Times: Family Participation Patterns in Local Thrift Economies

    OpenAIRE

    James, Spencer; Brown, Ralph B.; Goodsell, Todd L.; Stovall, Josh; Flaherty, Jeremy

    2010-01-01

    Using survey data from a western U.S. county (N = 595), we examined how lower, middle, and higher income families negotiate a period of economic stress—the closing of a major employer in the community—through their shopping patterns. Specifically, we examined their participation in local thrift economies such as yard sales and secondhand stores. We found that lower and middle income households shop more frequently at these venues. They also tend to shop more for furniture and clothing, wherea...

  9. Anatomy of Mammalian Replication Domains

    Science.gov (United States)

    Takebayashi, Shin-ichiro; Ogata, Masato; Okumura, Katsuzumi

    2017-01-01

    Genetic information is faithfully copied by DNA replication through many rounds of cell division. In mammals, DNA is replicated in Mb-sized chromosomal units called “replication domains.” While genome-wide maps in multiple cell types and disease states have uncovered both dynamic and static properties of replication domains, we are still in the process of understanding the mechanisms that give rise to these properties. A better understanding of the molecular basis of replication domain regulation will bring new insights into chromosome structure and function. PMID:28350365

  10. Oscillation-Driven Spike-Timing Dependent Plasticity Allows Multiple Overlapping Pattern Recognition in Inhibitory Interneuron Networks

    DEFF Research Database (Denmark)

    Garrido, Jesús A.; Luque, Niceto R.; Tolu, Silvia

    2016-01-01

    understood. Here, we have used a simple model of afferent excitatory neurons and interneurons with lateral inhibition, reproducing a network topology found in many brain areas from the cerebellum to cortical columns. When endowed with spike-timing dependent plasticity (STDP) at the excitatory input synapses...... and at the inhibitory interneuron-interneuron synapses, the interneurons rapidly learned complex input patterns. Interestingly, induction of plasticity required that the network be entrained into theta-frequency band oscillations, setting the internal phase-reference required to drive STDP. Inhibitory plasticity...... patterns. The combination of plasticity in lateral inhibitory connections and homeostatic mechanisms in the inhibitory interneurons optimized mutual information (MI) transfer. The storage of multiple complex patterns in plastic interneuron networks could be critical for the generation of sparse...

  11. Time allocation shifts and pollutant exposure due to traffic congestion: an analysis using the national human activity pattern survey.

    Science.gov (United States)

    Zhang, Kai; Batterman, Stuart A

    2009-10-15

    Traffic congestion increases air pollutant exposures of commuters and urban populations due to the increased time spent in traffic and the increased vehicular emissions that occur in congestion, especially "stop-and-go" traffic. Increased time in traffic also decreases time in other microenvironments, a trade-off that has not been considered in previous time activity pattern (TAP) analyses conducted for exposure assessment purposes. This research investigates changes in time allocations and exposures that result from traffic congestion. Time shifts were derived using data from the National Human Activity Pattern Survey (NHAPS), which was aggregated to nine microenvironments (six indoor locations, two outdoor locations and one transport location). After imputing missing values, handling outliers, and conducting other quality checks, these data were stratified by respondent age, employment status and period (weekday/weekend). Trade-offs or time-shift coefficients between time spent in vehicles and the eight other microenvironments were then estimated using robust regression. For children and retirees, congestion primarily reduced the time spent at home; for older children and working adults, congestion shifted the time spent at home as well as time in schools, public buildings, and other indoor environments. Changes in benzene and PM(2.5) exposure were estimated for the current average travel delay in the U.S. (9 min day(-1)) and other scenarios using the estimated time shifts coefficients, concentrations in key microenvironments derived from the literature, and a probabilistic analysis. Changes in exposures depended on the duration of the congestion and the pollutant. For example, a 30 min day(-1) travel delay was determined to account for 21+/-12% of current exposure to benzene and 14+/-8% of PM(2.5) exposure. The time allocation shifts and the dynamic approach to TAPs improve estimates of exposure impacts from congestion and other recurring events.

  12. Calculation of Taper Rolling Time in Plan View Pattern Control Process

    Institute of Scientific and Technical Information of China (English)

    JIAO Zhi-jie; HU Xian-lei; ZHAO Zhong; LIU Xiang-hua; WANG Guo-dong

    2006-01-01

    The forward slip model with adhesion was used to derive the formula of calculating taper rolling time. The relation between the rolling time and the taper length and the relation between the rolling time and the taper thickness can be obtained. The numerical solution for this formula was used on-site. According to the simulation result, the roll gap value should be changed linearly with rolling time.

  13. High-Resolution Replication Profiles Define the Stochastic Nature of Genome Replication Initiation and Termination

    Directory of Open Access Journals (Sweden)

    Michelle Hawkins

    2013-11-01

    Full Text Available Eukaryotic genome replication is stochastic, and each cell uses a different cohort of replication origins. We demonstrate that interpreting high-resolution Saccharomyces cerevisiae genome replication data with a mathematical model allows quantification of the stochastic nature of genome replication, including the efficiency of each origin and the distribution of termination events. Single-cell measurements support the inferred values for stochastic origin activation time. A strain, in which three origins were inactivated, confirmed that the distribution of termination events is primarily dictated by the stochastic activation time of origins. Cell-to-cell variability in origin activity ensures that termination events are widely distributed across virtually the whole genome. We propose that the heterogeneity in origin usage contributes to genome stability by limiting potentially deleterious events from accumulating at particular loci.

  14. Evaluating the different laser fragmentation patterns used in laser cataract surgeries in terms of effective phacoemulsification time and power

    Directory of Open Access Journals (Sweden)

    Huseynova T

    2015-11-01

    Full Text Available Tukezban Huseynova,1 Mariko Mita,2 Christine Carole C Corpuz,1 Yuko Sotoyama,1 Minoru Tomita2,3 1Shinagawa LASIK Center, Tokyo, Japan; 2Tomita Minoru Eye Clinic Ginza, Tokyo, Japan; 3Wenzhou Medical College, Wenzhou, People’s Republic of China Purpose: To evaluate the effects of the different fragmentation patterns for the lens nucleus in terms of the effective phacoemulsification time (EPT and power. Setting: Shinagawa LASIK Center, Tokyo, Japan. Design: Comparison study. Methods: Seventy-one eyes of 71 patients had preoperative lens opacity grading based on the Emery-Little Classification (Grade 1 and Grade 2. Eyes underwent femtosecond laser-assisted cataract surgery (Catalys™ Precision Laser System, for capsulotomy and lens fragmentation. For the lens fragmentation, either the quadrants softened (Quadrant or the quadrants complete (Complete pattern was used. The mean EPT and phacoemulsification (phaco power for each cutting pattern of Grades 1 and 2 cataracts were evaluated. Results: The mean EPT was 28.96 seconds in the Quadrant Group and 16.31 seconds in the Complete Group (P=0.006. The mean phaco power was 8.07% in the Quadrant Group and 4.77% in the Complete Group (P=0.0002. Comparing the Quadrant and Complete Groups of Grade 1 cataract showed no significant difference in EPT (P=0.16, but showed a significant difference in phaco power (P=0.033. Comparing the Quadrant and Complete patterns of Grade 2 cataract showed significant differences in both EPT (P=0.012 and phaco power (P=0.003. Using the Complete pattern showed a 44.7% reduction in EPT and a 40.9% reduction in phaco power when compared to the Quadrant Group. Conclusion: Using the smaller fragmentation pattern in femtosecond laser cataract surgery, the phaco time and power were reduced significantly when compared to the procedure with the larger fragmentation pattern. Keywords: effective phacoemulsification time (EPT, complete and quadrant fragmentation pattern

  15. GIS oriented analysis of tourist time-space patterns to support sustainable tourism development

    NARCIS (Netherlands)

    Knaap, van der W.G.M.

    1999-01-01

    Tourism and tourism development create major changes in the environment. To determine their impact on environmental sustainability, it is necessary to understand tourist behaviour. Time, space and context are important components in describing tourist time-space behaviour. Tourist time-space

  16. GIS oriented analysis of tourist time-space patterns to support sustainable tourism development

    NARCIS (Netherlands)

    Knaap, van der W.G.M.

    1999-01-01

    Tourism and tourism development create major changes in the environment. To determine their impact on environmental sustainability, it is necessary to understand tourist behaviour. Time, space and context are important components in describing tourist time-space behaviour. Tourist time-space analysi

  17. Revisiting the daily human birth pattern: time of delivery at Casa de Maternidad in Madrid (1887-1892).

    Science.gov (United States)

    Varea, Carlos; Fernández-Cerezo, Susana

    2014-01-01

    Among the ancestral characteristics of the primate group to which Homo sapiens belongs we find a pattern of daytime physical activity, but one notable exception is birthing which usually begins with night-time labor. In populations with a moderate or high level of medicalized labor, there is evidence that the medical preferences interfere with the underlying biological mechanism for the circadian pattern of human birth. This study analyses the hourly patterns of 4,599 single live births in the House of Maternity in Madrid between 1887 and 1892, a period of very limited obstetric intervention and without the influence of artificial lighting. In order to determine the influence of natural light on labor, two periods of maximum and minimum light have been established around the summer and winter solstices of the years in question. A clear circadian pattern of births emerges, with very early morning and early morning births dominating, and a sharp drop from midday until nightfall. The hourly distribution on both solstices follows this pattern, but with a clear peak shift: in winter, there is a greater concentration of deliveries in the early morning, whereas in the summer, the highest concentration is between 8 and 12 in the morning. The results confirm that non-intervened human birth has a clear diurnal cycle, with a higher incidence of deliveries in the early morning or morning. The shift in distribution during the winter and summer solstices seems to confirm the effect of light on the labor process. © 2014 Wiley Periodicals, Inc.

  18. Who sleeps best? Longitudinal patterns and covariates of change in sleep quantity, quality, and timing across four university years.

    Science.gov (United States)

    Galambos, Nancy L; Vargas Lascano, Dayuma I; Howard, Andrea L; Maggs, Jennifer L

    2013-01-01

    This study tracked change over time in sleep quantity, disturbance, and timing, and sleep's covariations with living situation, stress, social support, alcohol use, and grade point average (GPA) across four years of university in 186 Canadian students. Women slept longer as they moved through university, and men slept less; rise times were later each year. Students reported sleeping fewer hours, more sleep disturbances, and later rise times during years with higher stress. In years when students lived away from home, they reported more sleep disturbances, later bedtimes, and later rise times. Living on campus was associated with later bedtimes and rise times. Alcohol use was higher and GPA was lower when bedtimes were later. The implications of these observed patterns for understanding the correlates and consequences of university students' sleep are discussed.

  19. Wing patterning genes and coevolution of Müllerian mimicry in Heliconius butterflies: Support from phylogeography, cophylogeny, and divergence times.

    Science.gov (United States)

    Hoyal Cuthill, Jennifer F; Charleston, Michael

    2015-12-01

    Examples of long-term coevolution are rare among free-living organisms. Müllerian mimicry in Heliconius butterflies had been suggested as a key example of coevolution by early genetic studies. However, research over the last two decades has been dominated by the idea that the best-studied comimics, H. erato and H. melpomene, did not coevolve at all. Recently sequenced genes associated with wing color pattern phenotype offer a new opportunity to resolve this controversy. Here, we test the hypothesis of coevolution between H. erato and H. melpomene using Bayesian multilocus analysis of five color pattern genes and five neutral genetic markers. We first explore the extent of phylogenetic agreement versus conflict between the different genes. Coevolution is then tested against three aspects of the mimicry diversifications: phylogenetic branching patterns, divergence times, and, for the first time, phylogeographic histories. We show that all three lines of evidence are compatible with strict coevolution of the diverse mimicry wing patterns, contrary to some recent suggestions. Instead, these findings tally with a coevolutionary diversification driven primarily by the ecological force of Müllerian mimicry. © 2015 The Author(s). Evolution © 2015 The Society for the Study of Evolution.

  20. Norwegian Priority Setting in Practice – an Analysis of Waiting Time Patterns Across Medical Disciplines

    Directory of Open Access Journals (Sweden)

    Jurgita Januleviciute Gangstøe

    2016-06-01

    Full Text Available Background: Different strategies for addressing the challenge of prioritizing elective patients efficiently and fairly have been introduced in Norway. In the time period studied, there were three possible outcomes for elective patients that had been through the process of priority setting: (i high priority with assigned individual maximum waiting time; (ii low priority without a maximum waiting time; and (iii refusal (not in need for specialized services. We study variation in priority status and waiting time of the first two groups across different medical disciplines. Methods: Data was extracted from the Norwegian Patient Register (NPR and contains information on elective referrals to 41 hospitals in the Western Norway Regional Health Authority in 2010. The hospital practice across different specialties was measured by patient priority status and waiting times. The distributions of assigned maximum waiting times and the actual ones were analyzed using standard Kernel density estimation. The perspective of the planning process was studied by measuring the time interval between the actual start of healthcare and the maximum waiting time. Results: Considerable variation was found across medical specialties concerning proportion of priority patients and their maximum waiting times. The degree of differentiation in terms of maximum waiting times also varied by medical discipline. We found that the actual waiting time was very close to the assigned maximum waiting time. Furthermore, there was no clear correspondence between the actual waiting time for patients and their priority status. Conclusion: Variations across medical disciplines are often interpreted as differences in clinical judgment and capacity. Alternatively they primarily reflect differences in patient characteristics, patient case-mix, as well as capacity. One hypothesis for further research is that the introduction of maximum waiting times may have contributed to push the actual

  1. Just in time: circadian defense patterns and the optimal defense hypothesis.

    Science.gov (United States)

    Baldwin, Ian T; Meldau, Stefan

    2013-06-01

    The optimal defense hypothesis (ODH) provides a functional explanation for the inhomogeneous distribution of defensive structures and defense metabolites throughout a plant's body: tissues that are most valuable in terms of fitness and have the highest probability of attack are generally the best defended. In a previous review, we argue that ontogenically-controlled accumulations of defense metabolites are likely regulated through an integration of developmental and defense signaling pathways. In this addendum, we extend the discussion of ODH patterns by including the recent discoveries of circadian clock-controlled defenses in plants.

  2. Microfluidic Immunoassays Based on Self-Assembled Magnetic Bead Patterns and Time-Resolved Luminescence Detection

    OpenAIRE

    Sivagnanam, Venkataragavalu

    2010-01-01

    Microfluidic bio-assays have emerged as the most privileged solutions and provide the basis for the realization of miniaturized bio-analytical systems and clinical diagnostic devices that are portable, user-friendly and cost-effective (Lab-on-a-chip). Two important steps that are implemented in a microfluidic bio-assay are: (a) the immobilization and/or patterning of target-specific bio-molecules on the surface of a microfluidic channel, for selectively capturing bio-targets like antigens or ...

  3. Developing a complex independent component analysis technique to extract non-stationary patterns from geophysical time-series

    Science.gov (United States)

    Forootan, Ehsan; Kusche, Jürgen

    2016-04-01

    Geodetic/geophysical observations, such as the time series of global terrestrial water storage change or sea level and temperature change, represent samples of physical processes and therefore contain information about complex physical interactionswith many inherent time scales. Extracting relevant information from these samples, for example quantifying the seasonality of a physical process or its variability due to large-scale ocean-atmosphere interactions, is not possible by rendering simple time series approaches. In the last decades, decomposition techniques have found increasing interest for extracting patterns from geophysical observations. Traditionally, principal component analysis (PCA) and more recently independent component analysis (ICA) are common techniques to extract statistical orthogonal (uncorrelated) and independent modes that represent the maximum variance of observations, respectively. PCA and ICA can be classified as stationary signal decomposition techniques since they are based on decomposing the auto-covariance matrix or diagonalizing higher (than two)-order statistical tensors from centered time series. However, the stationary assumption is obviously not justifiable for many geophysical and climate variables even after removing cyclic components e.g., the seasonal cycles. In this paper, we present a new decomposition method, the complex independent component analysis (CICA, Forootan, PhD-2014), which can be applied to extract to non-stationary (changing in space and time) patterns from geophysical time series. Here, CICA is derived as an extension of real-valued ICA (Forootan and Kusche, JoG-2012), where we (i) define a new complex data set using a Hilbert transformation. The complex time series contain the observed values in their real part, and the temporal rate of variability in their imaginary part. (ii) An ICA algorithm based on diagonalization of fourth-order cumulants is then applied to decompose the new complex data set in (i

  4. Automated analysis of art object surfaces using time-averaged digital speckle pattern interferometry

    Science.gov (United States)

    Lukomski, Michal; Krzemien, Leszek

    2013-05-01

    Technical development and practical evaluation of a laboratory built, out-of-plane digital speckle pattern interferometer (DSPI) are reported. The instrument was used for non-invasive, non-contact detection and characterization of early-stage damage, like fracturing and layer separation, of painted objects of art. A fully automated algorithm was developed for recording and analysis of vibrating objects utilizing continuous-wave laser light. The algorithm uses direct, numerical fitting or Hilbert transformation for an independent, quantitative evaluation of the Bessel function at every point of the investigated surface. The procedure does not require phase modulation and thus can be implemented within any, even the simplest, DSPI apparatus. The proposed deformation analysis is fast and computationally inexpensive. Diagnosis of physical state of the surface of a panel painting attributed to Nicolaus Haberschrack (a late-mediaeval painter active in Krakow) from the collection of the National Museum in Krakow is presented as an example of an in situ application of the developed methodology. It has allowed the effectiveness of the deformation analysis to be evaluated for the surface of a real painting (heterogeneous colour and texture) in a conservation studio where vibration level was considerably higher than in the laboratory. It has been established that the methodology, which offers automatic analysis of the interferometric fringe patterns, has a considerable potential to facilitate and render more precise the condition surveys of works of art.

  5. Internal dispersal of seeds by waterfowl: effect of seed size on gut passage time and germination patterns

    OpenAIRE

    Figuerola, Jordi; Charalambidou, Iris; Santamaría, Luis; Andy J Green

    2010-01-01

    Long distance dispersal may have important consequences for gene flow and community structure. The dispersal of many plants depends on transport by vertebrate seed dispersers. The shapes of seed shadows produced by vertebrates depend both on movement patterns of the dispersers and on the dynamics and effects of passage through the disperser’s gut (i.e. the retention time, survival and germination of ingested seeds). A combination of experiments with captive waterbirds and aquatic plant seeds ...

  6. Contemporary Fertility Patterns and First-Birth Timing among Mexican-Origin Women

    Science.gov (United States)

    Batson, Christie D.

    2013-01-01

    This article examines first-birth timing among Mexican women in the United States over two birth cohorts. Currently, Mexican women are one of a small group that maintains above-replacement fertility in the United States, contributing to both Mexican population growth and overall national population growth. Yet, the fertility timing of Mexican…

  7. Association between dietary patterns and depressive symptoms over time: a 10-year follow-up study of the GAZEL cohort.

    Directory of Open Access Journals (Sweden)

    Agnès Le Port

    Full Text Available BACKGROUND: Data on the association between dietary patterns and depression are scarce. The objective of this study was to examine the longitudinal association between dietary patterns and depressive symptoms assessed repeatedly over 10 years in the French occupational GAZEL cohort. METHODS: A total of 9,272 men and 3,132 women, aged 45-60 years in 1998, completed a 35-item Food Frequency Questionnaire (FFQ at baseline. Dietary patterns were derived by Principal Component Analysis. Depressive symptoms were assessed by the Center for Epidemiologic Studies Depression scale (CES-D in 1999, 2002, 2005 and 2008. The main outcome measure was the repeated measures of CES-D. Longitudinal analyses were performed with logistic regression based on generalized estimating equations. PRINCIPAL FINDINGS: The highest quartile of low-fat, western, high snack and high fat-sweet diets in men and low-fat and high snack diets in women were associated with higher likelihood of depressive symptoms at the start of the follow-up compared to the lowest quartile (OR between 1.16 and 1.50. Conversely, the highest quartile of traditional diet (characterized by fish and fruit consumption was associated with a lower likelihood of depressive symptoms in women compared to the lowest quartile, with OR = 0.63 [95%CI, 0.50 to 0.80], as the healthy pattern (characterized by vegetables consumption with OR = 0.72 [95%CI, 0.63 to 0.83] and OR = 0.75 [95%CI, 0.61 to 0.93] in men and women, respectively. However, there was probably a reverse causality effect for the healthy pattern. CONCLUSION: This longitudinal study shows that several dietary patterns are associated with depressive symptoms and these associations track over time.

  8. Epigenetic control of DNA replication dynamics in mammals

    OpenAIRE

    Casas Delucchi, Corella Susana

    2011-01-01

    One of the most critically important processes in any living organism, essential for development and reproduction, is that of the accurate replication of its genome before each cell division. The process of DNA replication can take place millions of times in a single organism and any mistake, if left unrepaired, is potentially transmitted into the next generation. Errors during replication can result in genetic mutations or karyotype aberrations, both of which can lead to disease or death. ...

  9. A Novel Approach to Extract Significant Patterns of Travel Time Intervals of Vehicles from Freeway Gantry Timestamp Sequences

    Directory of Open Access Journals (Sweden)

    Jing-Doo Wang

    2017-08-01

    Full Text Available It is attractive to extract and determine the key features of traffic patterns for mitigating road congestion and predicting travel time of vehicles in traffic analysis. Based on the previous work that is a scalable approach via a Hadoop MapReduce programming model, this paper aims to extract significant patterns of travel time intervals of vehicles from freeway traffic in Taiwan, and meanwhile to compute the statistics of these patterns from the point of view one may concern. Experimental resources are the records of timestamp gantry sequences of vehicles passed in five months from 2016/11 to 2017/3 that were downloaded from the Traffic Data Collection System, one of Taiwan government open data platforms. To select one specific gantry sequence for demonstration, the longest sequence on the trip within the Taiwan National Freeway No. 5 is selected. Experimental results show that some statistics of vehicle travel time intervals according to 24 h per day are computed for illustration. These statistics can not only provide clues to experts to analyze traffic congestions, but also help drivers how to avoid rush hours. Furthermore, this work is able to handle a larger amount of real data and be promising for further traffic and transportation research in the future.

  10. Replicated Spectrographs in Astronomy

    CERN Document Server

    Hill, Gary J

    2014-01-01

    As telescope apertures increase, the challenge of scaling spectrographic astronomical instruments becomes acute. The next generation of extremely large telescopes (ELTs) strain the availability of glass blanks for optics and engineering to provide sufficient mechanical stability. While breaking the relationship between telescope diameter and instrument pupil size by adaptive optics is a clear path for small fields of view, survey instruments exploiting multiplex advantages will be pressed to find cost-effective solutions. In this review we argue that exploiting the full potential of ELTs will require the barrier of the cost and engineering difficulty of monolithic instruments to be broken by the use of large-scale replication of spectrographs. The first steps in this direction have already been taken with the soon to be commissioned MUSE and VIRUS instruments for the Very Large Telescope and the Hobby-Eberly Telescope, respectively. MUSE employs 24 spectrograph channels, while VIRUS has 150 channels. We compa...

  11. An efficient method for mining cross-timepoint gene regulation sequential patterns from time course gene expression datasets.

    Science.gov (United States)

    Cheng, Chun-Pei; Liu, Yu-Cheng; Tsai, Yi-Lin; Tseng, Vincent S

    2013-01-01

    Observation of gene expression changes implying gene regulations using a repetitive experiment in time course has become more and more important. However, there is no effective method which can handle such kind of data. For instance, in a clinical/biological progression like inflammatory response or cancer formation, a great number of differentially expressed genes at different time points could be identified through a large-scale microarray approach. For each repetitive experiment with different samples, converting the microarray datasets into transactional databases with significant singleton genes at each time point would allow sequential patterns implying gene regulations to be identified. Although traditional sequential pattern mining methods have been successfully proposed and widely used in different interesting topics, like mining customer purchasing sequences from a transactional database, to our knowledge, the methods are not suitable for such biological dataset because every transaction in the converted database may contain too many items/genes. In this paper, we propose a new algorithm called CTGR-Span (Cross-Timepoint Gene Regulation Sequential pattern) to efficiently mine CTGR-SPs (Cross-Timepoint Gene Regulation Sequential Patterns) even on larger datasets where traditional algorithms are infeasible. The CTGR-Span includes several biologically designed parameters based on the characteristics of gene regulation. We perform an optimal parameter tuning process using a GO enrichment analysis to yield CTGR-SPs more meaningful biologically. The proposed method was evaluated with two publicly available human time course microarray datasets and it was shown that it outperformed the traditional methods in terms of execution efficiency. After evaluating with previous literature, the resulting patterns also strongly correlated with the experimental backgrounds of the datasets used in this study. We propose an efficient CTGR-Span to mine several biologically

  12. SUMO and KSHV Replication

    Energy Technology Data Exchange (ETDEWEB)

    Chang, Pei-Ching [Institute of Microbiology and Immunology, National Yang-Ming University, Taipei 112, Taiwan (China); Kung, Hsing-Jien, E-mail: hkung@nhri.org.tw [Institute for Translational Medicine, College of Medical Science and Technology, Taipei Medical University, Taipei 110, Taiwan (China); Department of Biochemistry and Molecular Medicine, University of California, Davis, CA 95616 (United States); UC Davis Cancer Center, University of California, Davis, CA 95616 (United States); Division of Molecular and Genomic Medicine, National Health Research Institutes, 35 Keyan Road, Zhunan, Miaoli County 35053, Taiwan (China)

    2014-09-29

    Small Ubiquitin-related MOdifier (SUMO) modification was initially identified as a reversible post-translational modification that affects the regulation of diverse cellular processes, including signal transduction, protein trafficking, chromosome segregation, and DNA repair. Increasing evidence suggests that the SUMO system also plays an important role in regulating chromatin organization and transcription. It is thus not surprising that double-stranded DNA viruses, such as Kaposi’s sarcoma-associated herpesvirus (KSHV), have exploited SUMO modification as a means of modulating viral chromatin remodeling during the latent-lytic switch. In addition, SUMO regulation allows the disassembly and assembly of promyelocytic leukemia protein-nuclear bodies (PML-NBs), an intrinsic antiviral host defense, during the viral replication cycle. Overcoming PML-NB-mediated cellular intrinsic immunity is essential to allow the initial transcription and replication of the herpesvirus genome after de novo infection. As a consequence, KSHV has evolved a way as to produce multiple SUMO regulatory viral proteins to modulate the cellular SUMO environment in a dynamic way during its life cycle. Remarkably, KSHV encodes one gene product (K-bZIP) with SUMO-ligase activities and one gene product (K-Rta) that exhibits SUMO-targeting ubiquitin ligase (STUbL) activity. In addition, at least two viral products are sumoylated that have functional importance. Furthermore, sumoylation can be modulated by other viral gene products, such as the viral protein kinase Orf36. Interference with the sumoylation of specific viral targets represents a potential therapeutic strategy when treating KSHV, as well as other oncogenic herpesviruses. Here, we summarize the different ways KSHV exploits and manipulates the cellular SUMO system and explore the multi-faceted functions of SUMO during KSHV’s life cycle and pathogenesis.

  13. 3D replicon distributions arise from stochastic initiation and domino-like DNA replication progression.

    Science.gov (United States)

    Löb, D; Lengert, N; Chagin, V O; Reinhart, M; Casas-Delucchi, C S; Cardoso, M C; Drossel, B

    2016-04-07

    DNA replication dynamics in cells from higher eukaryotes follows very complex but highly efficient mechanisms. However, the principles behind initiation of potential replication origins and emergence of typical patterns of nuclear replication sites remain unclear. Here, we propose a comprehensive model of DNA replication in human cells that is based on stochastic, proximity-induced replication initiation. Critical model features are: spontaneous stochastic firing of individual origins in euchromatin and facultative heterochromatin, inhibition of firing at distances below the size of chromatin loops and a domino-like effect by which replication forks induce firing of nearby origins. The model reproduces the empirical temporal and chromatin-related properties of DNA replication in human cells. We advance the one-dimensional DNA replication model to a spatial model by taking into account chromatin folding in the nucleus, and we are able to reproduce the spatial and temporal characteristics of the replication foci distribution throughout S-phase.

  14. USP7 is a SUMO deubiquitinase essential for DNA replication

    DEFF Research Database (Denmark)

    Lecona, Emilio; Rodriguez-Acebes, Sara; Specks, Julia

    2016-01-01

    Post-translational modification of proteins by ubiquitin (Ub) and Ub-like modifiers regulates DNA replication. We have previously shown that chromatin around replisomes is rich in SUMO and poor in Ub, whereas mature chromatin exhibits an opposite pattern. How this SUMO-rich, Ub-poor environment...... is maintained at sites of DNA replication in mammalian cells remains unexplored. Here we identify USP7 as a replisome-enriched SUMO deubiquitinase that is essential for DNA replication. By acting on SUMO and SUMOylated proteins, USP7 counteracts their ubiquitination. Inhibition or genetic deletion of USP7 leads...... to the accumulation of Ub on SUMOylated proteins, which are displaced away from replisomes. Our findings provide a model explaining the differential accumulation of SUMO and Ub at replication forks and identify an essential role of USP7 in DNA replication that should be considered in the development of USP7...

  15. USP7 is a SUMO deubiquitinase essential for DNA replication.

    Science.gov (United States)

    Lecona, Emilio; Rodriguez-Acebes, Sara; Specks, Julia; Lopez-Contreras, Andres J; Ruppen, Isabel; Murga, Matilde; Muñoz, Javier; Mendez, Juan; Fernandez-Capetillo, Oscar

    2016-04-01

    Post-translational modification of proteins by ubiquitin (Ub) and Ub-like modifiers regulates DNA replication. We have previously shown that chromatin around replisomes is rich in SUMO and poor in Ub, whereas mature chromatin exhibits an opposite pattern. How this SUMO-rich, Ub-poor environment is maintained at sites of DNA replication in mammalian cells remains unexplored. Here we identify USP7 as a replisome-enriched SUMO deubiquitinase that is essential for DNA replication. By acting on SUMO and SUMOylated proteins, USP7 counteracts their ubiquitination. Inhibition or genetic deletion of USP7 leads to the accumulation of Ub on SUMOylated proteins, which are displaced away from replisomes. Our findings provide a model explaining the differential accumulation of SUMO and Ub at replication forks and identify an essential role of USP7 in DNA replication that should be considered in the development of USP7 inhibitors as anticancer agents.

  16. Pattern Recognition of Non-Stationary Time Series with Finite Length

    Institute of Scientific and Technical Information of China (English)

    FEI Wanchun; BAI Lun

    2006-01-01

    Statistical learning and recognition methods were used to extract the characteristics of size series measurements of cocoon filaments that are non-stationary in terms of mean and auto-covariance, by using the time varying parameter auto-regressive (TVPAR) model. After the system was taught to recognize the size data, the system correctly recognized the size of series of cocoon filaments as much as 96.95% of the time for a single series and 98.72% of the time for the mean of two series. The correct recognition rate was higher after suitable filtering. The theory and method can be used to analyze other types of non-stationary finite length time series.

  17. Content replication and placement in mobile networks

    CERN Document Server

    La, Chi-Anh; Casetti, Claudio; Chiasserini, Carla-Fabiana; Fiore, Marco

    2011-01-01

    Performance and reliability of content access in mobile networks is conditioned by the number and location of content replicas deployed at the network nodes. Location theory has been the traditional, centralized approach to study content replication: computing the number and placement of replicas in a static network can be cast as a facility location problem. The endeavor of this work is to design a practical solution to the above joint optimization problem that is suitable for mobile wireless environments. We thus seek a replication algorithm that is lightweight, distributed, and reactive to network dynamics. We devise a solution that lets nodes (i) share the burden of storing and providing content, so as to achieve load balancing, and (ii) autonomously decide whether to replicate or drop the information, so as to adapt the content availability to dynamic demands and time-varying network topologies. We evaluate our mechanism through simulation, by exploring a wide range of settings, including different node ...

  18. MIXING PATTERNS AND RESIDENCE TIME DETERMINATION IN A BUBBLING FLUIDIZED BED SYSTEM

    Directory of Open Access Journals (Sweden)

    A. E. Ghaly

    2012-01-01

    Full Text Available Fluidized bed gasification can be used to convert the solar energy stored as carboneous compounds in bio-mass into a carbon neutral fuel with reduced emissions. Canada produces 20.57 million tonnes of wheat straw annually which could be used for green energy production. Wheat straw residue gasification has the capability of replacing 7.5 % (0.62 EJ of Canada’s annual fossil fuel consumption. To achieve efficient gasification in a fluidized bed proper fuel mixing and residence time must be achieved. The aim of this study was to investigate the effects of sand particle size, distributor plate shape and angle, bed height and fluidizing velocity on particle mixing and residence time in the fluidized bed reactor. Greater values of the residence time were obtained with course sand whereas lower values were obtained with fine sand. An in-crease in the angle of convex or a decrease in the angle of a concave of the distributor plate resulted in an increase in the residence time. Both the concave and convex distributor plates achieved vertical upward and downward movements of the bed material resulting in continuous bed material turnover and, thus, good mixing. However, the concave plate achieved longer residence time which will result in better conversion efficiency. To improve the mixing properties of the binary mixture, which has great tendency for segregation due to density differences, an angled distributor plate (concave or convex should be used. Considerable increases in the residence time were recorded with increases in the bed height. Increasing the fluidizing velocity decreased the residence time due to the increase in the bubble velocity. However, since the conversion efficiency is affected by the degree of mixing, it will also be improved by increasing the fluidization velocity. A velocity above 1.50 Umf is recommended for better fluidization and improved mixing.

  19. The pattern of time management in college students of Kerman University of Medical Sciences in the year 2006

    Directory of Open Access Journals (Sweden)

    Ali Ravari

    2008-09-01

    Full Text Available Background: One potential coping strategy frequently offered by university counseling services is time management for studying. Besides stress relief, time management skills will positively influence key outcomes such as academic performance, problem-solving ability, and health. Thus, it is necessary to investigate how college students manage their timing for studying. The aim of the present study was to assess the pattern of college students' time management in Kerman University of Medical Sciences. Methods: This cross-sectional study was conducted on 300 students who were selected by stratified random sampling method among students of Kerman University of Medical Sciences. Information about how students managed their study time during their educational course was collected using a questionnaire which consisted time management stages such as planning, prioritizing, time allocation, listing all study-related tasks and goal setting. Study time management was measured according to Likert scale in range of “never” to “always”. Results: There was a significant difference between the course of study and the mean of study duration (p<0.004. Mean scores of the study time management showed that the medical students (mean=67.5 ±12.87 had the highest scores and the bachelor students (mean= 61.1±15.1 had the lowest scores, but the ANOVA test did not show any significant difference between the mean scores of study time management and the course of study (p=0.07. The majority of students (186 persons=62% “occasionally” and only 48 persons (16% “always” were managing their study time. A total of 26.2% of medical students always managed their study time, and in this criterion they had the highest scores in comparison with others. There was no significant difference between the course of study and the pattern of study management (p<0.05. Conclusion: Most of the students of medical sciences have no scheduled programming for their study time

  20. Increasing streamflow forecast lead time for snowmelt-driven catchment based on large-scale climate patterns

    Science.gov (United States)

    Kalra, Ajay; Ahmad, Sajjad; Nayak, Anurag

    2013-03-01

    This study focuses on improving the spring-summer streamflow forecast lead time using large scale climate patterns. An artificial intelligence type data-driven model, Support Vector Machine (SVM), was developed incorporating oceanic-atmospheric oscillations to increase the forecast lead time. The application of SVM model is tested on three unimpaired gages in the North Platte River Basin. Seasonal averages of oceanic-atmospheric indices for the period of 1940-2007 are used to generate spring-summer streamflow volumes with 3-, 6- and 9-month lead times. The results reveal a strong association between coupled indices compared to their individual effects. The best streamflow estimates are obtained at 6-month compared to 3-month and 9-month lead times. The proposed modeling technique is expected to provide useful information to water managers and help in better managing the water resources and the operation of water systems.

  1. Time for children: trends in the employment patterns of parents, 1967-2009.

    Science.gov (United States)

    Fox, Liana; Han, Wen-Jui; Ruhm, Christopher; Waldfogel, Jane

    2013-02-01

    Using data from the 1967-2009 years of the March Current Population Surveys (CPS), we examine two important resources for children's well-being: time and money. We document trends in parental employment, from the perspective of children, and show what underlies these trends. We find that increases in family work hours mainly reflect movements into jobs by parents-particularly mothers, who in prior decades would have remained at home. This increase in market work has raised incomes for children in the typical two-parent family but not for those in lone-parent households. Time use data from 1975 and 2003-2008 reveal that working parents spend less time engaged in primary childcare than their counterparts without jobs but more than employed peers in previous cohorts. Analysis of 2004 work schedule data suggests that non-daytime work provides an alternative method of coordinating employment schedules for some dual-earner families.

  2. Patterns of change in timing of spring migration in North European songbird populations

    DEFF Research Database (Denmark)

    Tøttrup, Anders Peter; Thorup, Kasper; Rahbek, Carsten

    2006-01-01

    to be important for our understanding of population-dynamic changes in relation to climate change. These differences may also have long-term evolutionary consequences. Migration distance seems to affect the degree of change in arrival time, but we found no difference between species wintering in different regions......From 1976 to 1997 passerines were mist-netted and ringed on the island of Christiansø, in the Baltic Sea. Here we present analyses of phenological changes (i.e. time of arrival) for 25 species based on the entire populations of mist-netted songbirds during spring migration. We used two approaches...... (least square and quantile regression) to test for changes in arrival time of first individuals and three different parts of the songbird populations (i.e. first 5%, 50% and 95% of the total number of trapped individuals corrected for trapping effort). Our results generally confirm earlier spring arrival...

  3. The effect of rf pulse pattern on bremsstrahlung and ion current time evolution of an ECRIS

    Energy Technology Data Exchange (ETDEWEB)

    Ropponen, T.; Tarvainen, O.; Toivanen, V.; Peura, P.; Jones, P.; Kalvas, T.; Koivisto, H. [Department of Physics, University of Jyvaeskylae, Jyvaeskylae FI-40014 (Finland); Noland, J.; Leitner, D. [Lawrence Berkeley National Laboratory, Berkeley, California 94720 (United States)

    2010-02-15

    Time-resolved helium ion production and bremsstrahlung emission from JYFL 14 GHz ECRIS is presented with different radio frequency pulse lengths. rf on times are varied from 5 to 50 ms and rf off times from 10 to 1000 ms between different measurement sets. It is observed that the plasma breakdown occurs a few milliseconds after launching the rf power into the plasma chamber, and in the beginning of the rf pulses a preglow transient is seen. During this transient the ion beam currents are increased by several factors compared to a steady state situation. By adjusting the rf pulse separation the maximum ion beam currents can be maintained during the so-called preglow regime while the amount of bremsstrahlung radiation is significantly decreased.

  4. Efficient usage of Adabas replication

    CERN Document Server

    Storr, Dieter W

    2011-01-01

    In today's IT organization replication becomes more and more an essential technology. This makes Software AG's Event Replicator for Adabas an important part of your data processing. Setting the right parameters and establishing the best network communication, as well as selecting efficient target components, is essential for successfully implementing replication. This book provides comprehensive information and unique best-practice experience in the field of Event Replicator for Adabas. It also includes sample codes and configurations making your start very easy. It describes all components ne

  5. Solving the Telomere Replication Problem

    Science.gov (United States)

    Maestroni, Laetitia; Matmati, Samah; Coulon, Stéphane

    2017-01-01

    Telomeres are complex nucleoprotein structures that protect the extremities of linear chromosomes. Telomere replication is a major challenge because many obstacles to the progression of the replication fork are concentrated at the ends of the chromosomes. This is known as the telomere replication problem. In this article, different and new aspects of telomere replication, that can threaten the integrity of telomeres, will be reviewed. In particular, we will focus on the functions of shelterin and the replisome for the preservation of telomere integrity. PMID:28146113

  6. DETERMINATION OF SPACE-TIME PATTERNS AND RAINFALL HOMOGENEOUS AREAS AT MINAS GERAIS STATE

    Directory of Open Access Journals (Sweden)

    Leandro Rodrigues Souza

    2011-07-01

    Full Text Available The present study aimed to determine the spatial and temporal rainfall in Minas Gerais State relating to their respective rainfall weather systems and to identify homogeneous regions. The method of Factorial Analysis in Principal Components and Hierarchical Grouping were used to determine the seasonal and spatial patterns and homogeneous groups of rainfall. It was observed that the three first principal components describe 80.4% of the total variance of rainfall observed, in that the first factor explains 34.3% of the variance and showed high correlations with the rains from December to April in the southern State, which is influenced, mainly by the performance of frontal systems. The second factor explains 26.6% of data variance and showed significant correlations with rainfall from May to September in the northwest and southwest, and is possibly related to cold fronts and the South Atlantic Convergence Zone. Finally, the relative contributions to the third factor, with 19.5% of data variance accounted for the months of October and November, and are associated with mesoscale and microscale systems. Four homogeneous regions in relation to seasonal and interannual variability of rainfall were found. It concludes that statistical methods tested showed satisfactory results for this type of analyze, corroborates previous studies.

  7. Short time sports exercise boosts motor imagery patterns: Implications of mental practice in rehabilitation programs

    Directory of Open Access Journals (Sweden)

    Selina Christin Wriessnegger

    2014-06-01

    Full Text Available Motor imagery (MI is a commonly used paradigm for the study of motor learning or cognitive aspects of action control. The rationale for using MI training to promote the relearning of motor function arises from research on the functional correlates that MI shares with the execution of physical movements. While most of the previous studies investigating MI were based on simple movements in the present study a more attractive mental practice was used to investigate cortical activation during MI. We measured cerebral responses with functional magnetic resonance imaging (fMRI in twenty three healthy volunteers as they imagined playing soccer or tennis before and after a short physical sports exercise. Our results demonstrated that only 10 minutes of training are enough to boost motor imagery patterns in motor related brain regions including premotor cortex and supplementary motor area (SMA but also fronto-parietal and subcortical structures. This supports previous findings that motor imagery has beneficial effects especially in combination with motor execution when used in motor rehabilitation or motor learning processes. We conclude that sports MI combined with an interactive game environment could be a promising additional tool in future rehabilitation programs aiming to improve upper or lower limb functions or support neuroplasticity.

  8. Myosin Ⅷ Regulates Protonemal Patterning and Developmental Timing in the Moss Physcomitrella patens

    Institute of Scientific and Technical Information of China (English)

    Shu-Zon Wua; Julie A. Ritchie; Ai-Hong Pan; Ralph S. Quatrano; Magdalena Bezanilla

    2011-01-01

    Plants have two classes of myosins.While recent work has focused on class Ⅺ myosins showing that myosin Ⅺ is responsible for organelle motility and cytoplasmic streaming,much less is known about the role of myosin Ⅷ in plant growth and development.We have used a combination of RNAi and insertional knockouts to probe myosin Ⅷ function in the moss Physcomitrella patens.We isolated △myo8ABCDE plants demonstrating that myosin Ⅷ is not required for plant viability.However,myosin Ⅷ mutants are smaller than wild-type plants in part due to a defect in cell size.Additionally,△myo8ABCDE plants produce more side branches and form gametophores much earlier than wild-type plants.In the absence of nutrient media,△myo8ABCDE plants exhibit significant protonemal patterning defects,including highly curved protonemal filaments,morphologically defective side branches,as well as an increase in the number of branches.Exogenous auxin partially rescues protonemal defects in △myo8ABCDE plants grown in the absence of nutrients.This result,together with defects in protonemal branching,smaller caulonemal cells,and accelerated development in the △myo8ABCDE plants,suggests that myosin Ⅷ is involved in hormone homeostasis in P patens.

  9. Analysis of log-periodic power law singularity patterns in time series related to credit risk

    Science.gov (United States)

    Wosnitza, Jan Henrik; Sornette, Didier

    2015-04-01

    The log-periodic (super-exponential) power law singularity (LPPLS) has become a promising tool for predicting extreme behavior of self-organizing systems in natural sciences and finance. Some researchers have recently proposed to employ the LPPLS on credit risk markets. The review article at hand summarizes four papers in this field and shows how they are linked. After structuring the research questions, we collect the corresponding answers from the four articles. This eventually gives us an overall picture of the application of the LPPLS to credit risk data. Our literature review begins with grounding the view that credit default swap (CDS) spreads are hotbeds for LPPLS patterns and it ends up with drawing attention to the recently proposed alarm index for the prediction of institutional bank runs. By presenting a new field of application for the LPPLS, the reviewed strand of literature further substantiates the LPPLS hypothesis. Moreover, the results suggest that CDS spread trajectories belong to a different universality class than, for instance, stock prices.

  10. The effects of native language on Indian English sounds and timing patterns.

    Science.gov (United States)

    Sirsa, Hema; Redford, Melissa A

    2013-11-01

    This study explored whether the sound structure of Indian English (IE) varies with the divergent native languages of its speakers or whether it is similar regardless of speakers' native languages. Native Hindi (Indo-Aryan) and Telugu (Dravidian) speakers produced comparable phrases in IE and in their native languages. Naïve and experienced IE listeners were then asked to judge whether different sentences had been spoken by speakers with the same or different native language backgrounds. The findings were an interaction between listener experience and speaker background such that only experienced listeners appropriately distinguished IE sentences produced by speakers with different native language backgrounds. Naïve listeners were nonetheless very good at distinguishing between Hindi and Telugu phrases. Acoustic measurements on monophthongal vowels, select obstruent consonants, and suprasegmental temporal patterns all differentiated between Hindi and Telugu, but only 3 of the measures distinguished between IE produced by speakers of the different native languages. The overall results are largely consistent with the idea that IE has a target phonology that is distinct from the phonology of native Indian languages. The subtle L1 effects on IE may reflect either the incomplete acquisition of the target phonology or, more plausibly, the influence of sociolinguistic factors on the use and evolution of IE.

  11. Linear time distances between fuzzy sets with applications to pattern matching and classification.

    Science.gov (United States)

    Lindblad, Joakim; Sladoje, Nataša

    2014-01-01

    We present four novel point-to-set distances defined for fuzzy or gray-level image data, two based on integration over α-cuts and two based on the fuzzy distance transform. We explore their theoretical properties. Inserting the proposed point-to-set distances in existing definitions of set-to-set distances, among which are the Hausdorff distance and the sum of minimal distances, we define a number of distances between fuzzy sets. These set distances are directly applicable for comparing gray-level images or fuzzy segmented objects, but also for detecting patterns and matching parts of images. The distance measures integrate shape and intensity/membership of observed entities, providing a highly applicable tool for image processing and analysis. Performance evaluation of derived set distances in real image processing tasks is conducted and presented. It is shown that the considered distances have a number of appealing theoretical properties and exhibit very good performance in template matching and object classification for fuzzy segmented images as well as when applied directly on gray-level intensity images. Examples include recognition of hand written digits and identification of virus particles. The proposed set distances perform excellently on the MNIST digit classification task, achieving the best reported error rate for classification using only rigid body transformations and a kNN classifier.

  12. Patterns of mammalian diversification in recent evolutionary times: global tendencies and methodological issues.

    Science.gov (United States)

    Soria-Carrasco, V; Castresana, J

    2011-12-01

    Changes in diversification patterns estimated from phylogenetic trees are an important source of information about the dynamics of evolution. To study the diversification of mammals, we reconstructed phylogenetic trees of 29 families and fitted both constant-rate and variable-rate models of diversification. In addition, we investigated the effect of clock models and phylogenetic reconstruction problems on diversification analyses. We observed, first, that none of the families increased its diversification rate during the last few million years, including the Pleistocene. Furthermore, we detected a decrease in diversification that, after application of different tests, was significant only for a minority of families. However, when diversification variation was analysed in a combined tree of all families, a global decline in diversification became significant. Therefore, although distorted by some methodological artefacts, we found an underlying signal of gradually decreasing diversification that suggests that ecological factors may have shaped the recent diversification of mammals. © 2011 The Authors. Journal of Evolutionary Biology © 2011 European Society For Evolutionary Biology.

  13. Classification of Hazelnut Kernels by Using Impact Acoustic Time-Frequency Patterns

    Science.gov (United States)

    Kalkan, Habil; Ince, Nuri Firat; Tewfik, Ahmed H.; Yardimci, Yasemin; Pearson, Tom

    2007-12-01

    Hazelnuts with damaged or cracked shells are more prone to infection with aflatoxin producing molds ( Aspergillus flavus). These molds can cause cancer. In this study, we introduce a new approach that separates damaged/cracked hazelnut kernels from good ones by using time-frequency features obtained from impact acoustic signals. The proposed technique requires no prior knowledge of the relevant time and frequency locations. In an offline step, the algorithm adaptively segments impact signals from a training data set in time using local cosine packet analysis and a Kullback-Leibler criterion to assess the discrimination power of different segmentations. In each resulting time segment, the signal is further decomposed into subbands using an undecimated wavelet transform. The most discriminative subbands are selected according to the Euclidean distance between the cumulative probability distributions of the corresponding subband coefficients. The most discriminative subbands are fed into a linear discriminant analysis classifier. In the online classification step, the algorithm simply computes the learned features from the observed signal and feeds them to the linear discriminant analysis (LDA) classifier. The algorithm achieved a throughput rate of 45 nuts/s and a classification accuracy of 96% with the 30 most discriminative features, a higher rate than those provided with prior methods.

  14. Classification of Hazelnut Kernels by Using Impact Acoustic Time-Frequency Patterns

    Directory of Open Access Journals (Sweden)

    Tom Pearson

    2007-12-01

    Full Text Available Hazelnuts with damaged or cracked shells are more prone to infection with aflatoxin producing molds (Aspergillus flavus. These molds can cause cancer. In this study, we introduce a new approach that separates damaged/cracked hazelnut kernels from good ones by using time-frequency features obtained from impact acoustic signals. The proposed technique requires no prior knowledge of the relevant time and frequency locations. In an offline step, the algorithm adaptively segments impact signals from a training data set in time using local cosine packet analysis and a Kullback-Leibler criterion to assess the discrimination power of different segmentations. In each resulting time segment, the signal is further decomposed into subbands using an undecimated wavelet transform. The most discriminative subbands are selected according to the Euclidean distance between the cumulative probability distributions of the corresponding subband coefficients. The most discriminative subbands are fed into a linear discriminant analysis classifier. In the online classification step, the algorithm simply computes the learned features from the observed signal and feeds them to the linear discriminant analysis (LDA classifier. The algorithm achieved a throughput rate of 45 nuts/s and a classification accuracy of 96% with the 30 most discriminative features, a higher rate than those provided with prior methods.

  15. The Effect of Feedback Schedule Manipulation on Speech Priming Patterns and Reaction Time

    Science.gov (United States)

    Slocomb, Dana; Spencer, Kristie A.

    2009-01-01

    Speech priming tasks are frequently used to delineate stages in the speech process such as lexical retrieval and motor programming. These tasks, often measured in reaction time (RT), require fast and accurate responses, reflecting maximized participant performance, to result in robust priming effects. Encouraging speed and accuracy in responding…

  16. Modelling and analysis of time-lags in some basic patterns of cell proliferation.

    Science.gov (United States)

    Baker, C T; Bocharov, G A; Paul, C A; Rihan, F A

    1998-10-01

    In this paper, we present a systematic approach for obtaining qualitatively and quantitatively correct mathematical models of some biological phenomena with time-lags. Features of our approach are the development of a hierarchy of related models and the estimation of parameter values, along with their non-linear biases and standard deviations, for sets of experimental data. We demonstrate our method of solving parameter estimation problems for neutral delay differential equations by analyzing some models of cell growth that incorporate a time-lag in the cell division phase. We show that these models are more consistent with certain reported data than the classic exponential growth model. Although the exponential growth model provides estimates of some of the growth characteristics, such as the population-doubling time, the time-lag growth models can additionally provide estimates of: (i) the fraction of cells that are dividing, (ii) the rate of commitment of cells to cell division, (iii) the initial distribution of cells in the cell cycle, and (iv) the degree of synchronization of cells in the (initial) cell population.

  17. Quirky patterns in time-series of estimates of recruitment could be artefacts

    NARCIS (Netherlands)

    Dickey-Collas, M.; Hintzen, N.T.; Nash, R.D.M.; Schoen, P.J.; Payne, M.R.

    2015-01-01

    The accessibility of databases of global or regional stock assessment outputs is leading to an increase in meta-analysis of the dynamics of fish stocks. In most of these analyses, each of the time-series is generally assumed to be directly comparable. However, the approach to stock assessment

  18. Quirky patterns in time-series of estimates of recruitment could be artefacts

    DEFF Research Database (Denmark)

    Dickey-Collas, M.; Hinzen, N.T.; Nash, R.D.M.

    2015-01-01

    , and non-parametric “free” estimation of recruitment.Weshow that the recruitment time-series is sensitive to model assumptions and this can impact reference points in management, the perception of variability in recruitment and thus undermine meta-analyses. The assumption of the direct comparability....... This is especially true when information about cohort abundance is noisy or lacking...

  19. Hierarchical Bayesian modeling of the space - time diffusion patterns of cholera epidemic in Kumasi, Ghana

    NARCIS (Netherlands)

    Osei, Frank B.; Osei, F.B.; Duker, Alfred A.; Stein, A.

    2011-01-01

    This study analyses the joint effects of the two transmission routes of cholera on the space-time diffusion dynamics. Statistical models are developed and presented to investigate the transmission network routes of cholera diffusion. A hierarchical Bayesian modelling approach is employed for a joint

  20. Adaptive Liquid Crystal TV Based Joint Transform Correlator as Applied to Real-Time Pattern Recognition

    Science.gov (United States)

    1993-01-05

    DAAL03-87-0147. * Professor Pedro Andres was taking sabbatical leave from Departamento de I Optica. Facultad de Fisicas, Universidad de Valencia...filter blocking the dc term at the compensate for the motion as a time delay. At. onU Fourier plane, will result in a null output for a sta- the conjugate

  1. Timed and Untimed Grammaticality Judgments Measure Distinct Types of Knowledge: Evidence from Eye-Movement Patterns

    Science.gov (United States)

    Godfroid, Aline; Loewen, Shawn; Jung, Sehoon; Park, Ji-Hyun; Gass, Susan; Ellis, Rod

    2015-01-01

    Grammaticality judgment tests (GJTs) have been used to elicit data reflecting second language (L2) speakers' knowledge of L2 grammar. However, the exact constructs measured by GJTs, whether primarily implicit or explicit knowledge, are disputed and have been argued to differ depending on test-related variables (i.e., time pressure and item…

  2. Cross-continental patterns in the timing of southward Peregrine Falcon migration in North America

    NARCIS (Netherlands)

    Worcester, R.; Ydenberg, R.C.

    2008-01-01

    We analyzed the timing of southward migration of Peregrine Falcons (Falco peregrinus) across North America, based on passage data compiled by the Hawk Migration Association of North America, supplemented with two other similar datasets collected by individual observers at sites in western Canada. Th

  3. Hierarchical Bayesian modeling of the space-time diffusion patterns of cholera epidemic in Kumasi, Ghana

    NARCIS (Netherlands)

    Osei, Frank B.; Duker, Alfred A.; Stein, Alfred

    2011-01-01

    This study analyses the joint effects of the two transmission routes of cholera on the space-time diffusion dynamics. Statistical models are developed and presented to investigate the transmission network routes of cholera diffusion. A hierarchical Bayesian modelling approach is employed for a joint

  4. Discovering gene expression patterns in time course microarray experiments by ANOVA-SCA.

    NARCIS (Netherlands)

    M.J. Nueda; A. Conessa; J.A. Westerhuis; H.C.J. Hoefsloot; A.K. Smilde; M. Talon; A. Ferrer

    2007-01-01

    In this work, we develop the application of the Analysis of variance-simultaneous component analysis (ANOVA-SCA) Smilde et al. Bioinformatics, (2005) to the analysis of multiple series time course microarray data as an example of multifactorial gene expression profiling experiments. We denoted this

  5. Replication of Avocado Sunblotch Viroid in the Yeast Saccharomyces cerevisiae▿

    Science.gov (United States)

    Delan-Forino, Clémentine; Maurel, Marie-Christine; Torchet, Claire

    2011-01-01

    Viroids are the smallest known pathogenic agents. They are noncoding, single-stranded, closed-circular, “naked” RNAs, which replicate through RNA-RNA transcription. Viroids of the Avsunviroidae family possess a hammerhead ribozyme in their sequence, allowing self-cleavage during their replication. To date, viroids have only been detected in plant cells. Here, we investigate the replication of Avocado sunblotch viroid (ASBVd) of the Avsunviroidae family in a nonconventional host, the yeast Saccharomyces cerevisiae. We demonstrate that ASBVd RNA strands of both polarities are able to self-cleave and to replicate in a unicellular eukaryote cell. We show that the viroid monomeric RNA is destabilized by the nuclear 3′ and the cytoplasmic 5′ RNA degradation pathways. For the first time, our results provide evidence that viroids can replicate in other organisms than plants and that yeast contains all of the essential cellular elements for the replication of ASBVd. PMID:21270165

  6. Time-Qualified Patterns of Variation of PPARγ, DNMT1, and DNMT3B Expression in Pancreatic Cancer Cell Lines

    Directory of Open Access Journals (Sweden)

    Valerio Pazienza

    2012-01-01

    Full Text Available Carcinogenesis is related to the loss of homeostatic control of cellular processes regulated by transcriptional circuits and epigenetic mechanisms. Among these, the activities of peroxisome proliferator-activated receptors (PPARs and DNA methyltransferases (DNMTs are crucial and intertwined. PPARγ is a key regulator of cell fate, linking nutrient sensing to transcription processes, and its expression oscillates with circadian rhythmicity. Aim of our study was to assess the periodicity of PPARγ and DNMTs in pancreatic cancer (PC. We investigated the time-related patterns of PPARG, DNMT1, and DNMT3B expression monitoring their mRNA levels by qRT-PCR at different time points over a 28-hour span in BxPC-3, CFPAC-1, PANC-1, and MIAPaCa-2 PC cells after synchronization with serum shock. PPARG and DNMT1 expression in PANC-1 cells and PPARG expression in MIAPaCa-2 cells were characterized by a 24 h period oscillation, and a borderline significant rhythm was observed for the PPARG, DNMT1, and DNMT3B expression profiles in the other cell lines. The time-qualified profiles of gene expression showed different shapes and phase relationships in the PC cell lines examined. In conclusion, PPARG and DNMTs expression is characterized by different time-qualified patterns in cell lines derived from human PC, and this heterogeneity could influence cell phenotype and human disease behaviour.

  7. Blink patterns and lid-contact times in dry-eye and normal subjects

    Directory of Open Access Journals (Sweden)

    Ousler GW 3rd

    2014-05-01

    Full Text Available George W Ousler 3rd,1 Mark B Abelson,1,2 Patrick R Johnston,1 John Rodriguez,1 Keith Lane,1 Lisa M Smith11Ora, Andover, MA, USA; 2Department of Ophthalmology, Harvard Medical School, Boston, MA, USAPurpose: To classify blinks in dry eye and normal subjects into six subtypes, and to define the blink rate and duration within each type of blink, as well as the total lid-contact time/minute.Materials and methods: This was a single-centered, prospective, double-blind study of eleven dry-eye and ten normal subjects. Predefined subjects watched a video while blinks were recorded for 10 minutes. Partial blinks were classified by percentage closure of maximal palpebral fissure opening: 25%, 50%, 75%. Complete blinks were characterized as full (>0 seconds, extended (>0.1 seconds, or superextended (>0.5 seconds. The mean duration of each type of blink was determined and standardized per minute as total lid-contact time.Results: Total blinks observed were 4,990 (1,414 normal, 3,756 dry eye: 1,809 (50.59% partial and 1,767 (49.41% complete blinks among dry-eye subjects versus 741 (52.90% partial and 673 (47.60% complete blinks among normal subjects. Only superextended blinks of ≥0.5-second duration were significantly more frequent in dry-eye subjects than normals (2.3% versus 0.2%, respectively; P=0.023. Total contact time was seven times higher in dry-eye subjects than normals (0.565 versus 0.080 seconds, respectively; P<0.001. Isolating only extended blinks (>0.1 second, the average contact time (seconds was four times longer in dry-eye versus normal subjects (2.459 in dry eye, 0.575 in normals; P=0.003. Isolating only superextended blinks (>0.5 seconds, average contact time was also significantly different (7.134 in dry eye, 1.589 in normals; P<0.001. The contact rate for all full closures was 6.4 times longer in dry-eye (0.045 versus 0.007, P<0.001 than normal subjects.Conclusion: Dry-eye subjects spent 4.5% of a

  8. Analysis of Tidal DC Resistivity Time Series for Periodic Saltwater Mixing Patterns and Determination of Hydraulic Ground Properties

    Science.gov (United States)

    Sutter, E. M.; Ingham, M.

    2016-12-01

    Saline intrusion research using geoelectrical time-lapse monitoring, is often directed towards imaging the saltwater-freshwater boundary and the amount of seawater mixing within a coastal aquifer. However, these time series can contain additional information about subsurface hydrologic properties like hydraulic conductivity and permeability which are crucial elements in coastal groundwater management. In this study, DC resistivity time series from tidal time-lapse monitoring surveys of a shallow coastal sand and gravel aquifer in New Zealand have been analysed for recurring patterns of percentage seawater mixing in different portions of the aquifer. The results show a distinctly different behaviour of percentage seawater change with time for several horizontal locations along two profile lines with varying depth. In addition, the geoelectric time series have been cross-correlated with tidal stage data approximated near the survey location in order to find portions of the aquifer that exhibit different time lags with respect to a diurnal tidal cycle. First results yield a remarkably similar picture to resistivity ratios obtained between high and low tide inversion models of the DC resistivity time series both at different locations and for different seasons. The two methods indicate a correlation between rising and falling tides and the resistivity changes observed from geoelectrical monitoring studies .This may be used to distinguish between more or less hydraulically conductive portions of a coastal aquifer.

  9. From time-series to complex networks: Application to the cerebrovascular flow patterns in atrial fibrillation

    Science.gov (United States)

    Scarsoglio, Stefania; Cazzato, Fabio; Ridolfi, Luca

    2017-09-01

    A network-based approach is presented to investigate the cerebrovascular flow patterns during atrial fibrillation (AF) with respect to normal sinus rhythm (NSR). AF, the most common cardiac arrhythmia with faster and irregular beating, has been recently and independently associated with the increased risk of dementia. However, the underlying hemodynamic mechanisms relating the two pathologies remain mainly undetermined so far; thus, the contribution of modeling and refined statistical tools is valuable. Pressure and flow rate temporal series in NSR and AF are here evaluated along representative cerebral sites (from carotid arteries to capillary brain circulation), exploiting reliable artificially built signals recently obtained from an in silico approach. The complex network analysis evidences, in a synthetic and original way, a dramatic signal variation towards the distal/capillary cerebral regions during AF, which has no counterpart in NSR conditions. At the large artery level, networks obtained from both AF and NSR hemodynamic signals exhibit elongated and chained features, which are typical of pseudo-periodic series. These aspects are almost completely lost towards the microcirculation during AF, where the networks are topologically more circular and present random-like characteristics. As a consequence, all the physiological phenomena at the microcerebral level ruled by periodicity—such as regular perfusion, mean pressure per beat, and average nutrient supply at the cellular level—can be strongly compromised, since the AF hemodynamic signals assume irregular behaviour and random-like features. Through a powerful approach which is complementary to the classical statistical tools, the present findings further strengthen the potential link between AF hemodynamic and cognitive decline.

  10. Pattern and timing of late Cenozoic rapid exhumation and uplift of the Helan Mountain,China

    Institute of Scientific and Technical Information of China (English)

    2010-01-01

    The Helan Mountain, an intraplate deformation belt in the North China Craton, is located in the northern portion of the China North-South seismic belt, and at the northwestern margin of the Ordos Block. The Cenozoic deformation history of the Helan Mountain is characterized by extension along the eastern Helan Mountain fault (EHSF), resulting in the exhumation and uplift of the Helan Mountain, relative to the rifting of the adjacent Yinchuan Basin. Here we present new apatite fission track (AFT) data from several transects adjacent to the EHSF in the central and northern Helan Mountain. AFT ages from the northern Helan Mountain (Dawukou and Zhengyiguan transects) range from 10 Ma to 89 Ma, whereas AFT ages from the southern Helan Mountain (Suyukou transect) are greater than 71 Ma. The AFT data analysis reveals initiation of rapid uplift and exhumation of the Helan Mountain at 10–12 Ma. Additionally, a plot of the AFT ages versus their mean track length shows a distinctive "boomerang" pattern indicating that the Helan Mountain experienced a discrete phase of accelerated exhumation beginning at 10-12 Ma. Spatially, AFT samples systematically increase in age away from the EHSF and are consistent with late Cenozoic exhumation that was slow in the southwestern Helan Mountain and rapid in the northeastern Helan Mountain, as well more rapid adjacent to the EHSF and slower away from the EHSF. Obviously, the spatial distribution of late Cenozoic exhumation indicates that normal faulting of the EHSF is related to southwestward tilting and rapid exhumation of the Helan Mountain beginning at 10–12 Ma. The uplift and exhumation of the Helan Mountain was a response to the intensive extension of the northwestern margin of the Ordos Block in the late Cenozoic; this occurred under a regional extensional stress field oriented NW-SE along the Yinchuan-Jilantai-Hetao and the Weihe-Shanxi graben systems adjacent to the Ordos Block.

  11. Multifork chromosome replication in slow-growing bacteria

    Science.gov (United States)

    Trojanowski, Damian; Hołówka, Joanna; Ginda, Katarzyna; Jakimowicz, Dagmara; Zakrzewska-Czerwińska, Jolanta

    2017-01-01

    The growth rates of bacteria must be coordinated with major cell cycle events, including chromosome replication. When the doubling time (Td) is shorter than the duration of chromosome replication (C period), a new round of replication begins before the previous round terminates. Thus, newborn cells inherit partially duplicated chromosomes. This phenomenon, which is termed multifork replication, occurs among fast-growing bacteria such as Escherichia coli and Bacillus subtilis. In contrast, it was historically believed that slow-growing bacteria (including mycobacteria) do not reinitiate chromosome replication until the previous round has been completed. Here, we use single-cell time-lapse analyses to reveal that mycobacterial cell populations exhibit heterogeneity in their DNA replication dynamics. In addition to cells with non-overlapping replication rounds, we observed cells in which the next replication round was initiated before completion of the previous replication round. We speculate that this heterogeneity may reflect a relaxation of cell cycle checkpoints, possibly increasing the ability of slow-growing mycobacteria to adapt to environmental conditions. PMID:28262767

  12. The pattern for waiting time in the context of multiple stochastic process

    CERN Document Server

    Jamali, Tayeb; Farahani, S Vasheghani

    2015-01-01

    The aim here is to provide a deeper understanding on the concept of waiting time in application to multiple stochastic processes. This obliges us to work with the vector stochastic process which enables considering at least two stochastic process at simultaneous time instances. In the present study the plan is to master vector stochastic processes by developing the level crossing method. The reason that the previous level-crossing methods lack generality is based on their individual element studies, where the coupling between the components of the vector stochastic process had been simply neglected. In the present work by introducing the generalized level crossing method, consideration of coupling between the components has become possible. This enables analyzing and hence extracting information out of coupled processes usually faced when working in tensor environments. The results obtained by this technique state that in addition to the point distribution of the vector stochastic process, the coupling plays ...

  13. Adaptive pattern recognition in real-time video-based soccer analysis

    DEFF Research Database (Denmark)

    Schlipsing, Marc; Salmen, Jan; Tschentscher, Marc

    2017-01-01

    to the identification of players in uncertain situations. Our experiments showed high performance in the classification task achieving an average error rate of 3 % on three real-world datasets. The system was proved to collect accurate tracking statistics throughout different soccer matches in real......, human interaction is required at different stages including system setup, calibration, supervision of classifier training, and resolution of tracking conflicts. Furthermore, the real-time constraints are challenging: in contrast to other object recognition and tracking applications, we cannot treat data...... collection, annotation, and learning as an offline task. A semi-automatic labeling of training data and robust learning given few examples from unbalanced classes are required. We present a real-time system acquiring and analyzing video sequences from soccer matches. It estimates each player's position...

  14. Phylogenetic diversification patterns and divergence times in ground beetles (Coleoptera: Carabidae: Harpalinae

    Directory of Open Access Journals (Sweden)

    Ober Karen A

    2010-08-01

    Full Text Available Abstract Background Harpalinae is a species rich clade of carabid beetles with many unusual morphological forms and ecological interactions. How this diversity evolved has been difficult to reconstruct, perhaps because harpalines underwent a rapid burst of diversification early in their evolutionary history. Here we investigate the tempo of evolution in harpalines using molecular divergence dating techniques and explore the rates of lineage accumulation in harpalines and their sister group. Results According to molecular divergence date estimates, harpalines originated in the mid Cretaceous but did not diversify extensively until the late Cretaceous or early Paleogene about 32 million years after their origin. In a relatively small window of time, harpalines underwent rapid speciation. Harpalines have a relative high net diversification rate and increased cladogenesis in some regions of the clade. We did not see a significant decrease in diversification rate through time in the MCCR test, but a model of diversification with two shift points to lower diversification rates fit the harpaline lineage accumulation through time the best. Conclusions Our results indicate harpalines are significantly more diverse and have higher diversification than their sistergroup. Instead of an immediate burst of explosive diversification, harpalines may have had a long "fuse" before major lineages diversified during the early Paleogene when other taxa such as mammals, birds, and some flowering plants were also rapidly diversifying.

  15. Time course of spatial contextual interference: event history analyses of simultaneous masking by nonoverlapping patterns.

    Science.gov (United States)

    Panis, Sven; Hermens, Frouke

    2014-02-01

    Simultaneous masking refers to the impairment of performance on a visual target by simultaneously presented flankers. Whereas the spatial aspects of simultaneous masking have been studied extensively, the time course of these spatial influences is much less well understood. We here measure response latency and accuracy in a simultaneous masking paradigm and apply event history analysis to study the time course of target-flanker interactions. In our experiments, we presented a central target vernier flanked on both sides by 12 aligned distractor verniers that were either shorter, longer, or equal in length (Experiment 1), and that also were congruent or incongruent in their spatial offset with the target (Experiment 2). Response time distributions showed that there were more fast responses when the target was flanked by short flankers. Conditional accuracy functions showed that accuracy of responses dropped when the flankers had the same length as the target, but only for slow responses. These results are at odds with accounts based solely on lateral neural interactions or response competition, and instead suggest that top-down visual object-to-feature interference occurs when the target is not selected fast enough, congruent with object substitution theory. PsycINFO Database Record (c) 2014 APA, all rights reserved.

  16. Mining Fuzzy Weighted Browsing Patterns from Time Duration and with Linguistic Thresholds

    Directory of Open Access Journals (Sweden)

    Tzung P. Hong

    2008-01-01

    Full Text Available World-wide-web applications have grown very rapidly and have made a significant impact on computer systems. Among them, web browsing for useful information may be most commonly seen. Due to its tremendous amounts of use, efficient and effective web retrieval has become a very important research topic in this field. Techniques of web mining have thus been requested and developed to achieve this purpose. In this research, a new fuzzy weighted web-mining algorithm is proposed, which can process web-server logs to discover useful users’ browsing behaviors from the time durations of the paged browsed. Since the time durations are numeric, fuzzy concepts are used here to process them and to form linguistic terms. Besides, different web pages may have different importance. The importance of web pages are evaluated by managers as linguistic terms, which are then transformed and averaged as fuzzy sets of weights. Each linguistic term is then weighted by the importance for its page. Only the linguistic term with the maximum cardinality for a page is chosen in later mining processes, thus reducing the time complexity. The minimum support is set linguistic, which is more natural and understandable for human beings. An example is given to clearly illustrate the proposed approach.

  17. Space-time patterns of meteorological drought events in the European Greater Alpine Region.

    Science.gov (United States)

    Haslinger, Klaus; Blöschl, Günter

    2017-04-01

    Drought is a natural hazard impacting tremendously on human systems as latest events, like the summer 2015 drought in Central and Eastern Europe, show. However, extreme events are rare and only a few of the most recent ones are analyzed in detail concerning their emergence in space and time. With the study presented here, we aim to investigate spatiotemporal drought characteristics on a much larger sample of events covering the past 200+ years. The area of interest is the European Greater Alpine Region located at the intersection of three major climate divisions in Europe: Mediterranean climate as well as temperate oceanic and continental climate. We use gridded data of 3-month moving average precipitation sums which are transformed into percentile values for each grid point and each month individually to ensure comparability across regions and seasons. A threshold is applied to detect contiguous areas within the gridded fields below a given percentile threshold (20th percentile). Subsequently, all areas overlapping to a certain degree along time are treated as the same space-time object to form a meteorological drought event. Distinct attributes are derived for every event like duration, spatial extent, intensity, overall severity, season of peak intensity, temperature anomaly etc., which are analyzed in terms of their long-term temporal evolution, seasonality, spatial clustering and temperature characteristics. Our results indicate on one hand only minor changes in drought frequency and duration over the last 200 years, but on the other hand large variations in drought intensity and overall severity on multidecadal time scales. The time period from 1850-1880 shows highest drought intensities and also highest severities followed by a second peak from around 1930-1950. Furthermore, the top 10% of events in terms of their severity reveal a general shift in seasonality from winter/spring events in the late 19th century towards autumn events during the last decades of

  18. What Controls Space-Time Patterns of Magmatism in Western North America: Plate Tectonics, Delamination, or Convection?

    Science.gov (United States)

    Glazner, A. F.

    2007-05-01

    Mesozoic and Cenozoic magmatism in western North America is commonly explained by shallowing and steepening of subduction along the west coast of North America, and progressive destruction of the subduction system by development of the San Andreas transform fault system. This hypothesis makes several specific predictions about space-time patterns of magmatism, including eastward and westward sweeps, development of slab-window magmatism, and progressive northward extinction of an ancestral Cascade arc. However, analysis of space-time patterns using the NAVDAT database indicates that these predicted patterns are curiously obscure in the magmatic record, although other unexplained patterns are strong. Animation of about 29,000 Cenozoic U.S. points from NAVDAT (www.navdat.org) demonstrates that: (1) calc- alkaline, intermediate volcanism is poorly linked to the subduction system; (2) there is little evidence for slab- window magmatism; (3) there was no ancestral Cascade arc south of Oregon until ca. 10 Ma; (4) magmatism shifted from primarily silicic to dominantly basaltic throughout the Miocene; and (5) magmatism was clearly migratory in several directions in ways that cannot be explained by plate-tectonic processes, at length scales ranging from 1000s to 10s of km. Space-time patterns that cannot be readily linked to plate-tectonic control include: (1) a silicic sweep from Montana into Nevada from 50 to 20 Ma; (2) a clockwise sweep around the Colorado Plateau from New Mexico to southern Nevada from about 30 to 15 Ma; (3) a burst of magmatism at about 16 Ma in northern Nevada, followed by outward sweeps to Yellowstone, Oregon, and the Sierra Nevada; (4) progressive encroachment of basaltic magmatism onto the Colorado Plateau, and (5) several local migrations, including from Phoenix north onto the Colorado Plateau and from the San Francisco Bay area north to the Geysers geothermal field. These migrations typically occurred at 20-50 mm/yr. Possible origins include

  19. Analysis of short time-space range seismicity patterns in Italy

    Directory of Open Access Journals (Sweden)

    M. Imotof

    1997-06-01

    Full Text Available In our paper we analyze the data base obtained from the observations of the Italian Seismological Network from 1975 to 1994 by using a simple algotithm to determine the rate of occurrence of seismic events condi- tioned by the occurrence of previous events after a period of quiescence. The number of observed pairs of earthquakes depends on several parameters: the magnitude threshold of the two events, the spatial and tempo- ral ranges of the quiescence period preceding the first (non aftershock event, the time elapsed between the first and the second events and the spatial dimension of the alarm area. The Akaike information criterion was adopted to assess the optimal set of space-time parameters used in the definition of non-aftershock (events not related to a stronger previous one. In Central Italy, the rate of M ³3.8 earthquakes preceded by at least one M ~ 3.3 foreshock within 14.1 km and 2 days is 30%, while the rate of M ~ 3.3 earthquakes followed by a M ~ 3.8 mainshock in the same space time range is 7%. We observed that the probability that an earthquake of magnitude MI will be followed by an earthquake of magnitude M2 (success rate fits the law log À = a+b (Mi -M2 with b approximately equal to l. By computing the success rate for given values of magnitude threshold of the first and the second events over a dense grid of spatial coordinates, we obtained maps of this feature over the investigated area. The results of this process document variations larger than a factor of five in the success rate over the Italian territory.

  20. KEY FACTORS AND TIMING PATTERNS IN THE TENNIS FOREHAND OF DIFFERENT SKILL LEVELS

    Directory of Open Access Journals (Sweden)

    Johannes Landlinger

    2010-12-01

    Full Text Available The main purpose of the present study was to quantify and compare selected kinematic variables and their timing during the tennis forehand of different skill levels. An eight-camera 400 Hz, Vicon motion analysis system recorded kinematic data of six ATP- professionals (elite and seven high performance (HP players when shots were played cross court and down the line. Timing of the maximum angles, linear and angular velocities was measured prior to and after impact. A total of twelve strokes per subject were analyzed from the beginning to the end of horizontal racquet movement. Significant differences (p < 0.01 and large effect sizes were observed between elite and HP players in the timing of maximum pelvis (-0.075 ± 0.008 vs. -0.093 ± 0.012 s and trunk angular velocities (-0.057 ± 0.004 vs. -0.075 ± 0.011 s before impact. The elite group showed a tendency (p < 0.05 towards higher peak horizontal shoulder (3.0 ± 0.4 vs. 2.5 ± 0.4 m·s-1 and racquet velocities (33.1 ± 2.4 vs. 31.1 ± 1.9 m·s-1 compared to the HP players. Depending on the situation (cross court vs. down the line, different peak hip, racquet and separation angles were found for both groups. Similar peak values were detected between groups for maximum angular velocities and displacement of key variables that had been selected for analysis. The findings of this study can be vital for successful player development, improved performance or injury prevention. The later occurrence of maximum angular pelvis and trunk rotations were the main reasons for the tendency towards higher horizontal shoulder and racquet velocities in the elite group.

  1. Emerging Risks Due to New Injecting Patterns in Hungary During Austerity Times.

    Science.gov (United States)

    Tarján, Anna; Dudás, Mária; Gyarmathy, V Anna; Rusvai, Erzsébet; Tresó, Bálint; Csohán, Ágnes

    2015-01-01

    As a consequence of the massive restructuring of drug availability, heroin injection in Hungary was largely replaced by the injecting of new psychoactive substances (NPS) starting in 2010. In the following years in our sero-prevalence studies we documented higher levels of injecting paraphernalia sharing, daily injection-times, syringe reuse, and HCV prevalence among stimulant injectors, especially among NPS injectors. Despite the increasing demand, in 2012 the number of syringes distributed dropped by 35% due to austerity measures. Effects of drug market changes and the economic recession may have future epidemiological consequences. Study limitations are noted and future needed research is suggested.

  2. Charter School Replication. Policy Guide

    Science.gov (United States)

    Rhim, Lauren Morando

    2009-01-01

    "Replication" is the practice of a single charter school board or management organization opening several more schools that are each based on the same school model. The most rapid strategy to increase the number of new high-quality charter schools available to children is to encourage the replication of existing quality schools. This policy guide…

  3. Timing and patterns in the taxonomic diversification of Lepidoptera (butterflies and moths.

    Directory of Open Access Journals (Sweden)

    Niklas Wahlberg

    Full Text Available The macroevolutionary history of the megadiverse insect order Lepidoptera remains little-known, yet coevolutionary dynamics with their angiospermous host plants are thought to have influenced their diversification significantly. We estimate the divergence times of all higher-level lineages of Lepidoptera, including most extant families. We find that the diversification of major lineages in Lepidoptera are approximately equal in age to the crown group of angiosperms and that there appear to have been three significant increases in diversification rates among Lepidoptera over evolutionary time: 1 at the origin of the crown group of Ditrysia about 150 million years ago (mya, 2 at the origin of the stem group of Apoditrysia about 120 mya and finally 3 a spectacular increase at the origin of the stem group of the quadrifid noctuoids about 70 mya. In addition, there appears to be a significant increase in diversification rate in multiple lineages around 90 mya, which is concordant with the radiation of angiosperms. Almost all extant families appear to have begun diversifying soon after the Cretaceous/Paleogene event 65.51 mya.

  4. The pattern of colorectal dysfunction changes with time since spinal cord injury

    DEFF Research Database (Denmark)

    Faaborg, Pia Møller; Christensen, Peter; Finnerup, N

    2008-01-01

    Background:Cross-sectional studies suggest that colorectal dysfunction after spinal cord injuries (SCI) worsens as time goes by. However, follow-up studies are needed to prove this.Study design:Prospective study.Objective:To describe long-term colorectal function in SCI patients.Setting:Members o......Background:Cross-sectional studies suggest that colorectal dysfunction after spinal cord injuries (SCI) worsens as time goes by. However, follow-up studies are needed to prove this.Study design:Prospective study.Objective:To describe long-term colorectal function in SCI patients.......Setting:Members of the Danish Spinal Cord Injuries Association.Methods:In 1996, 424 members of the Danish Paraplegic Association answered a detailed questionnaire describing their colorectal function. In 2006, those who continued as members (n=284) received an identical questionnaire. Data for patients responding both in 1996...... defecation; in 2006, it was 19% (Pstimulation or evacuation was performed at least once every week by 48% in 1996 and by 56% in 2006 (P

  5. Middle Eocene rodents from Peruvian Amazonia reveal the pattern and timing of caviomorph origins and biogeography

    Science.gov (United States)

    Antoine, Pierre-Olivier; Marivaux, Laurent; Croft, Darin A.; Billet, Guillaume; Ganerød, Morgan; Jaramillo, Carlos; Martin, Thomas; Orliac, Maëva J.; Tejada, Julia; Altamirano, Ali J.; Duranthon, Francis; Fanjat, Grégory; Rousse, Sonia; Gismondi, Rodolfo Salas

    2012-01-01

    The long-term isolation of South America during most of the Cenozoic produced a highly peculiar terrestrial vertebrate biota, with a wide array of mammal groups, among which caviomorph rodents and platyrrhine primates are Mid-Cenozoic immigrants. In the absence of indisputable pre-Oligocene South American rodents or primates, the mode, timing and biogeography of these extraordinary dispersals remained debated. Here, we describe South America's oldest known rodents, based on a new diverse caviomorph assemblage from the late Middle Eocene (approx. 41 Ma) of Peru, including five small rodents with three stem caviomorphs. Instead of being tied to the Eocene/Oligocene global cooling and drying episode (approx. 34 Ma), as previously considered, the arrival of caviomorphs and their initial radiation in South America probably occurred under much warmer and wetter conditions, around the Mid-Eocene Climatic Optimum. Our phylogenetic results reaffirm the African origin of South American rodents and support a trans-Atlantic dispersal of these mammals during Middle Eocene times. This discovery further extends the gap (approx. 15 Myr) between first appearances of rodents and primates in South America. PMID:21993503

  6. Middle Eocene rodents from Peruvian Amazonia reveal the pattern and timing of caviomorph origins and biogeography.

    Science.gov (United States)

    Antoine, Pierre-Olivier; Marivaux, Laurent; Croft, Darin A; Billet, Guillaume; Ganerød, Morgan; Jaramillo, Carlos; Martin, Thomas; Orliac, Maëva J; Tejada, Julia; Altamirano, Ali J; Duranthon, Francis; Fanjat, Grégory; Rousse, Sonia; Gismondi, Rodolfo Salas

    2012-04-07

    The long-term isolation of South America during most of the Cenozoic produced a highly peculiar terrestrial vertebrate biota, with a wide array of mammal groups, among which caviomorph rodents and platyrrhine primates are Mid-Cenozoic immigrants. In the absence of indisputable pre-Oligocene South American rodents or primates, the mode, timing and biogeography of these extraordinary dispersals remained debated. Here, we describe South America's oldest known rodents, based on a new diverse caviomorph assemblage from the late Middle Eocene (approx. 41 Ma) of Peru, including five small rodents with three stem caviomorphs. Instead of being tied to the Eocene/Oligocene global cooling and drying episode (approx. 34 Ma), as previously considered, the arrival of caviomorphs and their initial radiation in South America probably occurred under much warmer and wetter conditions, around the Mid-Eocene Climatic Optimum. Our phylogenetic results reaffirm the African origin of South American rodents and support a trans-Atlantic dispersal of these mammals during Middle Eocene times. This discovery further extends the gap (approx. 15 Myr) between first appearances of rodents and primates in South America.

  7. LHCb experience with LFC replication

    CERN Document Server

    Bonifazi, F; Perez, E D; D'Apice, A; dell'Agnello, L; Düllmann, D; Girone, M; Re, G L; Martelli, B; Peco, G; Ricci, P P; Sapunenko, V; Vagnoni, V; Vitlacil, D

    2008-01-01

    Database replication is a key topic in the framework of the LHC Computing Grid to allow processing of data in a distributed environment. In particular, the LHCb computing model relies on the LHC File Catalog, i.e. a database which stores information about files spread across the GRID, their logical names and the physical locations of all the replicas. The LHCb computing model requires the LFC to be replicated at Tier-1s. The LCG 3D project deals with the database replication issue and provides a replication service based on Oracle Streams technology. This paper describes the deployment of the LHC File Catalog replication to the INFN National Center for Telematics and Informatics (CNAF) and to other LHCb Tier-1 sites. We performed stress tests designed to evaluate any delay in the propagation of the streams and the scalability of the system. The tests show the robustness of the replica implementation with performance going much beyond the LHCb requirements.

  8. LHCb experience with LFC replication

    CERN Document Server

    Carbone, Angelo; Dafonte Perez, Eva; D'Apice, Antimo; dell'Agnello, Luca; Duellmann, Dirk; Girone, Maria; Lo Re, Giuseppe; Martelli, Barbara; Peco, Gianluca; Ricci, Pier Paolo; Sapunenko, Vladimir; Vagnoni, Vincenzo; Vitlacil, Dejan

    2007-01-01

    Database replication is a key topic in the framework of the LHC Computing Grid to allow processing of data in a distributed environment. In particular, the LHCb computing model relies on the LHC File Catalog, i.e. database which stores information about files spread across the GRID, their logical names and the physical locations of all the replicas. The LHCb computing model requires the LFC to be replicated at Tier-1s. The LCG 3D project deals with the database replication issue and provides a replication service based on Oracle Streams technology. This paper describes the deployment of the LHC File Catalog replication to the INFN National Center for Telematics and Informations (CNAF) and to other LHCb Tier-1 sites. We performed stress tests designed to evaluate any delay in the propagation of the streams and the scalability of the system. The tests show the robustness of the replica implementation with performance going much beyond the LHCb requirements.

  9. Anthropogenic and solar forcing in δ13C time pattern of coralline sponges.

    Science.gov (United States)

    Madonia, Paolo; Reitner, Joachim

    2014-01-01

    We present the results of a re-analysis of a previously published carbon isotope data-set related to coralline sponges in the Caribbean Sea. The original interpretation led to the discrimination between a pre-industrial period, with a signal controlled by solar-induced climatic variations, followed by the industrial era, characterized by a progressive δ(13)C negative shift due to the massive anthropogenic carbon emissions. Our re-analysis allowed to extract from the raw isotopic data evidence of a solar forcing still visible during the industrial era, with a particular reference to the 88-year Gleissberg periods. These signals are related to slope changes in both the δ(13)C versus time and the δ(13)C versus carbon emission curves.

  10. Maximum isometric knee flexor and extensor muscle contractions: normal patterns of torque versus time.

    Science.gov (United States)

    Murray, M P; Baldwin, J M; Gardner, G M; Sepic, S B; Downs, W J

    1977-06-01

    Isometric torque of the knee flexor and extensor muscles were recorded for 5 seconds at three knee joint positions. The subjects included healthy men in age groups from 20 to 35 and 45 to 65 years of age. The amplitudes and duration of peak torque and the time to peak torque were measured for each contraction. Peak torque was usually maintaned less than 0.1 second and never longer than 0.9 second. At each of the three angles, the mean extensor muscle torque was higher than the mean flexor muscle torque in both age groups, and the mean torque for both muscle group was higher among the younger than among the older man. The highest average torque was recorded at the knee angle of 60 degrees for the extensor muscles and 45 degrees for the flexor muscles, but this was not always a stereotyped response either for a given individual or among individuals.

  11. Effects of iron deficiency in infancy on patterns of motor development over time

    Science.gov (United States)

    Shafir, Tal; Angulo-Barroso, Rosa; Calatroni, Agustin; Jimenez, Elias; Lozoff, Betsy

    2007-01-01

    This longitudinal study of the effects of iron deficiency in infancy assessed motor development over time in 185 healthy Costa Rican children who varied in iron status at 12–23 months. Longitudinal analyses (hierarchical linear modeling) used the Bayley Psychomotor Index before and both 1 week and 3 months after iron treatment in infancy and the Bruninks-Oseretsky Test of Motor Proficiency – long form at 5 years and short form at 11–14 years. Children with chronic severe iron deficiency in infancy had lower motor scores at the beginning of the study and a lower but parallel trajectory for motor scores through early adolescence. Thus, there was no evidence of catch-up in motor development, despite iron therapy in infancy that corrected iron deficiency anemia in all cases. PMID:17050023

  12. Response of vegetation to different time-scales drought across China: Spatiotemporal patterns, causes and implications

    Science.gov (United States)

    Zhang, Qiang; Kong, Dongdong; Singh, Vijay P.; Shi, Peijun

    2017-05-01

    Based on Normalized Difference Vegetation Index (NDVI) and Standardized Precipitation Evapotranspiration Index (SPEI), we investigated vegetation response to different time-scales drought across different vegetation types and homogeneous clusters in China, by annual maximum Pearson correlation (Rmax) and the corresponding time-scales of drought. Results showed that: (1) 8 subregions with homogeneous climate-vegetation conditions were identified using Fuzzy C-Means algorithm; (2) SPEI and NDVI's annual Rmax were in significantly positive correlation in most regions of China, indicating that vegetation biomass were influenced mainly by the spatiotemporal characteristics of the water availability. The southeastern Yangtze River basin and the lower Pearl River basin are dominated by abundant precipitation, and vegetation is not sensitive to droughts in these regions. The northeastern Heilongjiang province, the Changbai Mountains and western Sichuan province are characterized by weak NDVI versus SPEI relations, indicating a relatively small effect of drought on vegetation; (3) The effects of annual average water balance, annual average annual precipitation, annual average effective accumulative temperature, and annual average daily sunshine hours on the NDVI versus SPEI correlation show that the annual average water balance is the key factor behind the change of vegetation vigor. It can therefore be concluded that the change of water availability is the key factor behind the change of vegetation activity and biomass. Regional precipitation or water balance was significantly related to the correlation between SPEI and NDVI. Vegetation in the regions with longer sunshine hours is more sensitive to droughts. In general, the sensitivity of grassland to droughts is the largest, followed by the sensitivity of shrubs and forests to droughts.

  13. Deep-time patterns of tissue consumption by terrestrial arthropod herbivores

    Science.gov (United States)

    Labandeira, Conrad C.

    2013-04-01

    A survey of the fossil record of land-plant tissues and their damage by arthropods reveals several results that shed light on trophic trends in host-plant resource use by arthropods. All 14 major plant tissues were present by the end of the Devonian, representing the earliest 20 % of the terrestrial biota. During this interval, two types of time lags separate the point between when tissues first originated from their earliest consumption by herbivorous arthropods. For epidermis, parenchyma, collenchyma and xylem, live tissue consumption was rapid, occurring on average 10 m.y. after the earliest tissue records. By contrast, structural tissues (periderm, sclerenchyma), tissues with actively dividing cells (apical, lateral, intercalary meristems), and reproductive tissues (spores, megagametophytes, integuments) experienced approximately a 9-fold (92 m.y.) delay in arthropod herbivory, extending well into the Carboniferous Period. Phloem similarly presents a delay of 85 m.y., but this incongruously long lag-time may be attributed to the lack of preservation of this tissue in early vascular plants. Nevertheless, the presence of phloem can be indicated from planar spaces adjacent well-preserved xylem, or inferred from a known anatomy of the same plant taxon in better preserved material, especially permineralisations. The trophic partitioning of epidermis, parenchyma, phloem and xylem increases considerably to the present, probably a consequence of dietary specialization or consumption of whole leaves by several herbivore functional feeding groups. Structural tissues, meristematic tissues and reproductive tissues minimally have been consumed throughout the fossil record, consistent with their long lags to herbivory during the earlier Paleozoic. Neither angiosperm dominance in floras nor global environmental perturbations had any discernible effect on herbivore trophic partitioning of plant tissues.

  14. Time patterns of changes in biomarkers, symptoms and histopathology during pelvic radiotherapy

    Energy Technology Data Exchange (ETDEWEB)

    Larsen, Annette; Dahl, Olav [Section of Oncology, Institute of Medicine, Univ. of Bergen, and Dept. of Oncology, Haukeland Univ. Hospital, Bergen (Norway); Bjoerge, Benedikte; Klementsen, Beate [National Institute of Nutrition and Seafood Research, Bergen (Norway); Helgeland, Lars [Dept. of Pathology, Haukeland Univ. Hospital, Bergen (Norway); Wentzel-Larsen, Tore [Centre for Clinical Research, Haukeland Univ. Hospital, Bergen (Norway); Fagerhol, Magne K. [Dept. of Immunology and Transfusion Medicine, Ullevaal Univ. Hospital, Oslo (Norway); Hovdenak, Nils [Dept. of Medicine, Haukeland Univ. Hospital, Bergen (Norway)

    2007-07-15

    Acute radiation proctitis was evaluated before, during and after radiotherapy (RT) for prostate cancer. The main aims of the study were to examine changes related to the increasing radiation dose, and identify surrogate markers of gastrointestinal (GI) reaction to radiation. Twenty consecutive prostate cancer patients scheduled for 7 weeks of conformal RT were prospectively included in a longitudinal study assessing symptoms, inflammation in rectal mucosa biopsies, and blood and stool samples at four time points (before RT and 2, 6 and 11 weeks after start of RT). Blood samples were examined for acute phase response-related markers, fatty acids (FAs), vitamin E and leukotriene B4 (LTB4). Lactoferrin, calprotectin and S100A12 were measured in stool samples and FAs in biopsies from rectal mucosa. The increase in histopathological inflammation reached a maximum 2 weeks after start of RT. Symptoms of GI toxicity increased with higher radiation dose and had not returned to pre-treatment level 4 weeks after RT. Lactoferrin concentrations in stool increased significantly at week 6. Significant decreases of vitamin E, leukocyte count, hemoglobin and some groups of FAs were discovered, while a few FAs increased significantly during the study period. Time courses vary between the selected indicators of acute radiation proctitis. The biopsy grading of inflammatory changes were most intense 2 weeks into the treatment period while symptoms continued to increase until week 6. Lactoferrin in stool samples could be a non-invasive marker of GI inflammation during RT. A transient decrease in vitamin E and some FAs during RT warrants further studies.

  15. Replication of micro-sized pillars in polypropylene using the extrusion coating process

    DEFF Research Database (Denmark)

    Okulova, Nastasia; Johansen, Peter; Christensen, Lars

    2017-01-01

    A recent advancement in nano-pattern replication using roll-to-roll extrusion coating (R2R-EC) shows potential for many biomimetic applications. For further development of the technique a study of the micro-replication regime is carried out. In this study a full and partial replication in polypro......A recent advancement in nano-pattern replication using roll-to-roll extrusion coating (R2R-EC) shows potential for many biomimetic applications. For further development of the technique a study of the micro-replication regime is carried out. In this study a full and partial replication...... in polypropylene (PP) of micro-sized pillars has been demonstrated using the extrusion coating process. The replication fidelity of the pillars is investigated in a systematic variation of different process parameters: the line-speed of the rolls, the extruder output, the cooling roll temperature and the pressure...

  16. The work pattern of personal care workers in two Australian nursing homes: a time-motion study

    Directory of Open Access Journals (Sweden)

    Qian Si-Yu

    2012-09-01

    Full Text Available Abstract Background The aim of the study is to describe the work pattern of personal care workers (PCWs in nursing homes. This knowledge is important for staff performance appraisal, task allocation and scheduling. It will also support funding allocation based on activities. Methods A time-motion study was conducted in 2010 at two Australian nursing homes. The observation at Site 1 was between the hours of 7:00 and 14:00 or 15:00 for 14 days. One PCW was observed on each day. The observation at Site 2 was from 10:00 to 17:00 for 16 days. One PCW working on a morning shift and another one working on an afternoon shift were observed on each day. Fifty-eight work activities done by PCWs were grouped into eight categories. Activity time, frequency, duration and the switch between two consecutive activities were used as measurements to describe the work pattern. Results Personal care workers spent about 70.0% of their time on four types of activities consistently at both sites: direct care (30.7%, indirect care (17.6%, infection control (6.4% and staff break (15.2%. Oral communication was the most frequently observed activity. It could occur independently or concurrently with other activities. At Site 2, PCWs spent significantly more time than their counterparts at Site 1 on oral communication (Site 1: 47.3% vs. Site 2: 63.5%, P = 0.003, transit (Site 1: 3.4% vs. Site 2: 5.5%, P  Conclusions At both nursing homes, direct care, indirect care, infection control and staff break occupied the major part of a PCW’s work, however oral communication was the most time consuming activity. Personal care workers frequently switched between activities, suggesting that looking after the elderly in nursing homes is a busy and demanding job.

  17. Studies on the mechanism of DNA replication in Physarum polycephalum

    Energy Technology Data Exchange (ETDEWEB)

    Brewer, E.N.; Evans, T.E.; Evans, H.H.

    1974-01-01

    The synthesis of single-stranded DNA subunits (4 x 10/sup 7/ daltons) in Physarum polycephalum was studied by alkaline sucrose density gradient centrifugation. The results were compared with the synthesis of the double-stranded DNA molecules (2.3 x 10/sup 8/ daltons) which they comprise, as determined from neutral sucrose density gradient centrifugation patterns. Although the initiation of synthesis of most double-stranded DNA molecules takes place relatively early in the S period, synthesis of the subunits within them is initiated throughout at least the first two hours of this period. Similarly, replicating (presumably forked) DNA molecules appear to split into daughter DNA molecules prior to the completion of synthesis of the subunits therein. The average rate of DNA chain elongation within subunits is 0.3 x 10/sup 6/ daltons/minute. It is suggested that alkaline sucrose density gradient centrifugation may be a more sensitive method for determining the time required for the completion of replication than other methods based solely on the incorporation of radioactive DNA precursors into an acid-insoluble product.

  18. Quality of life in mild dementia: patterns of change in self and caregiver ratings over time

    Directory of Open Access Journals (Sweden)

    Marcia C. Dourado

    2016-01-01

    Full Text Available Objectives: To determine changes over time in self and caregiver ratings of quality of life (QoL in people with dementia (PwD and to identify factors associated with changes in QoL ratings. Methods: In this longitudinal study, 69 people with mild Alzheimer’s disease and their caregivers were assessed at baseline and after 1 year. We examined the association of QoL ratings with the following variables at the two time points: awareness of disease, cognitive status, mood, functionality, neuropsychiatric symptoms, and caregiver burden. Multivariate regression analyses were conducted to examine the contribution of co-factors. Results: At baseline, PwD self-ratings of QoL were associated with caregiver ratings of PwD QoL (p = 0.001. Caregiver ratings were associated with PwD mood (p = 0.001 and self-rated QoL (p = 0.001. After 1 year, caregiver ratings of PwD QoL changed significantly (p = 0.049, d = -0.27, whereas PwD self-ratings did not (p = 0.89, d = 0.09. PwD awareness of disease changed significantly (p = 0.001 at 1 year, having declined in 25.4% and improved in 12.3% of participants. PwD QoL self-ratings were associated with caregiver ratings (p = 0.001. Caregiver ratings of PwD QoL after 1 year were associated with PwD mood (p = 0.029, self-reported QoL (p = 0.001, and awareness of disease (p = 0.033. Conclusions: The association between self and caregiver ratings of PwD QoL was maintained over 1 year. The primary factors accounting for the change in caregiver ratings were PwD mood and awareness of disease. QoL and cognitive impairment seem to be relatively independent in mild dementia.

  19. A generic probability based model to derive regional patterns of crops in time and space

    Science.gov (United States)

    Wattenbach, Martin; Luedtke, Stefan; Redweik, Richard; van Oijen, Marcel; Balkovic, Juraj; Reinds, Gert Jan

    2015-04-01

    Croplands are not only the key to human food supply, they also change the biophysical and biogeochemical properties of the land surface leading to changes in the water cycle, energy portioning, they influence soil erosion and substantially contribute to the amount of greenhouse gases entering the atmosphere. The effects of croplands on the environment depend on the type of crop and the associated management which both are related to the site conditions, economic boundary settings as well as preferences of individual farmers. The method described here is designed to predict the most probable crop to appear at a given location and time. The method uses statistical crop area information on NUTS2 level from EUROSTAT and the Common Agricultural Policy Regionalized Impact Model (CAPRI) as observation. These crops are then spatially disaggregated to the 1 x 1 km grid scale within the region, using the assumption that the probability of a crop appearing at a given location and a given year depends on a) the suitability of the land for the cultivation of the crop derived from the MARS Crop Yield Forecast System (MCYFS) and b) expert knowledge of agricultural practices. The latter includes knowledge concerning the feasibility of one crop following another (e.g. a late-maturing crop might leave too little time for the establishment of a winter cereal crop) and the need to combat weed infestations or crop diseases. The model is implemented in R and PostGIS. The quality of the generated crop sequences per grid cell is evaluated on the basis of the given statistics reported by the joint EU/CAPRI database. The assessment is given on NUTS2 level using per cent bias as a measure with a threshold of 15% as minimum quality. The results clearly indicates that crops with a large relative share within the administrative unit are not as error prone as crops that allocate only minor parts of the unit. However, still roughly 40% show an absolute per cent bias above the 15% threshold. This

  20. Nest survival patterns in Eurasian Bittern: effect of nest age, time and habitat variables

    Directory of Open Access Journals (Sweden)

    Marcin Polak

    2016-06-01

    Full Text Available Determining the key factors affecting the reproductive success of nesting birds is crucial in order to better understand the population dynamics of endangered species and to introduce effective conservation programmes for them. Inhabiting a variety of wetland habitats, aquatic birds actively select safe nesting sites so as to protect their nests against predators. The main aim of the present work was to assess the effect of temporal and habitat variables on the daily nest survival rate of Eurasian Bitterns colonizing semi–natural fishpond habitat in eastern Poland. MARK software was used for the modelling. Eurasian Bittern nests were most vulnerable to depredation at the beginning of the breeding season. This was probably because the reedbed vegetation at this time was not yet dense enough to effectively conceal the nests. There was a positive relationship between nest age and the daily survival rate. Two of the habitat variables analysed were of the greatest significance: water depth and vegetation density. In the Eurasian Bittern population studied here, nests built over deep water and in dense vegetation had the best chances of survival. The results of this work may be useful in the preparation of plans for the conservation and management of populations of this rare and endangered species. Conservation and restoration efforts that attempt to maintain high water levels will be especially beneficial to this avian species that is dependent on wetland ecosystems for breeding.

  1. Microbial biogeography of drinking water: patterns in phylogenetic diversity across space and time.

    Science.gov (United States)

    Roeselers, Guus; Coolen, Jordy; van der Wielen, Paul W J J; Jaspers, Marco C; Atsma, Adrie; de Graaf, Bendert; Schuren, Frank

    2015-07-01

    In this study, we collected water from different locations in 32 drinking water distribution networks in the Netherlands and analysed the spatial and temporal variation in microbial community composition by high-throughput sequencing of 16S rRNA gene amplicons. We observed that microbial community compositions of raw source and processed water were very different for each distribution network sampled. In each network, major differences in community compositions were observed between raw and processed water, although community structures of processed water did not differ substantially from end-point tap water. End-point water samples within the same distribution network revealed very similar community structures. Network-specific communities were shown to be surprisingly stable in time. Biofilm communities sampled from domestic water metres varied distinctly between households and showed no resemblance to planktonic communities within the same distribution networks. Our findings demonstrate that high-throughput sequencing provides a powerful and sensitive tool to probe microbial community composition in drinking water distribution systems. Furthermore, this approach can be used to quantitatively compare the microbial communities to match end-point water samples to specific distribution networks. Insight in the ecology of drinking water distribution systems will facilitate the development of effective control strategies that will ensure safe and high-quality drinking water.

  2. Hindcasting the continuum of Dansgaard–Oeschger variability: mechanisms, patterns and timing

    Directory of Open Access Journals (Sweden)

    L. Menviel

    2013-08-01

    Full Text Available Millennial-scale variability associated with Dansgaard–Oeschger (DO and Heinrich events (HE is arguably one of the most puzzling climate phenomena ever discovered in paleoclimate archives. Here, we set out to elucidate the underlying dynamics by conducting a transient global hindcast simulation with a 3-dimensional intermediate complexity Earth system model covering the period 50 ka BP to 30 ka BP. The model is forced by time-varying external boundary conditions (greenhouse gases, orbital forcing, and ice sheet orography and albedo and anomalous North Atlantic freshwater fluxes, which mimic the effects of changing Northern Hemisphere ice-volume on millennial timescales. Together these forcings generate a realistic global climate trajectory, as demonstrated by an extensive model/paleo data comparison. Our analysis is consistent with the idea that variations in ice sheet calving and related changes of the Atlantic Meridional Overturning Circulation were the main drivers for the continuum of DO and HE variability seen in paleorecords across the globe.

  3. A Common Rule for Integration and Suppression of Luminance Contrast across Eyes, Space, Time, and Pattern

    Directory of Open Access Journals (Sweden)

    Tim S. Meese

    2013-02-01

    Full Text Available Visual perception begins by dissecting the retinal image into millions of small patches for local analyses by local receptive fields. However, image structures extend well beyond these receptive fields and so further processes must be involved in sewing the image fragments back together to derive representations of higher order (more global structures. To investigate the integration process, we also need to understand the opposite process of suppression. To investigate both processes together, we measured triplets of dipper functions for targets and pedestals involving interdigitated stimulus pairs (A, B. Previous work has shown that summation and suppression operate over the full contrast range for the domains of ocularity and space. Here, we extend that work to include orientation and time domains. Temporal stimuli were 15-Hz counter-phase sine-wave gratings, where A and B were the positive and negative phases of the oscillation, respectively. For orientation, we used orthogonally oriented contrast patches (A, B whose sum was an isotropic difference of Gaussians. Results from all four domains could be understood within a common framework in which summation operates separately within the numerator and denominator of a contrast gain control equation. This simple arrangement of summation and counter-suppression achieves integration of various stimulus attributes without distorting the underlying contrast code.

  4. Expression patterns of Doppel gene in golden hamster: quantification using real-time RT-PCR.

    Science.gov (United States)

    Li, Y R; Li, Q; Yang, J M; Zhou, X M; Yin, X M; Zhao, D M

    2008-08-01

    Doppel (prion-like protein, Dpl) may act as a useful molecular marker in tumor diagnosis and in tumor grade definition, as over-expression of Dpl protein has been found in tumors with different histologic origin. Accordingly, the quantitative analysis of the expression of Dpl in different tissues is essential for understanding its role in tumor progression and cancer diagnostic. Herein we report Dpl mRNA quantification in golden hamster by calibrated highly sensitive externally standardized real-time RT-PCR with LightCycler instrument. Total RNA was isolated from nine different organs of golden hamster in different stages of development: from neonatal to adult golden hamster. Highest level of Dpl mRNA was detected in the testis, and lower levels of Dpl mRNA were detected in the following tissues: spleen, heart, bone marrow, skeletal muscles and neocortex (only in neonatal hamster). The expression of Dpl was not detected in kidney, liver and lung. This is the first study to report the expression of Dpl in bone marrow of murine and the difference of expression levels of Dpl in testis between adult and neonatal hamsters.

  5. Metacommunity and phylogenetic structure determine wildlife and zoonotic infectious disease patterns in time and space

    Science.gov (United States)

    Suzán, Gerardo; García-Peña, Gabriel E; Castro-Arellano, Ivan; Rico, Oscar; Rubio, André V; Tolsá, María J; Roche, Benjamin; Hosseini, Parviez R; Rizzoli, Annapaola; Murray, Kris A; Zambrana-Torrelio, Carlos; Vittecoq, Marion; Bailly, Xavier; Aguirre, A Alonso; Daszak, Peter; Prieur-Richard, Anne-Helene; Mills, James N; Guégan, Jean-Francois

    2015-01-01

    The potential for disease transmission at the interface of wildlife, domestic animals and humans has become a major concern for public health and conservation biology. Research in this subject is commonly conducted at local scales while the regional context is neglected. We argue that prevalence of infection at local and regional levels is influenced by three mechanisms occurring at the landscape level in a metacommunity context. First, (1) dispersal, colonization, and extinction of pathogens, reservoir or vector hosts, and nonreservoir hosts, may be due to stochastic and niche-based processes, thus determining distribution of all species, and then their potential interactions, across local communities (metacommunity structure). Second, (2) anthropogenic processes may drive environmental filtering of hosts, nonhosts, and pathogens. Finally, (3) phylogenetic diversity relative to reservoir or vector host(s), within and between local communities may facilitate pathogen persistence and circulation. Using a metacommunity approach, public heath scientists may better evaluate the factors that predispose certain times and places for the origin and emergence of infectious diseases. The multidisciplinary approach we describe fits within a comprehensive One Health and Ecohealth framework addressing zoonotic infectious disease outbreaks and their relationship to their hosts, other animals, humans, and the environment. PMID:25750713

  6. Arrival time pattern and waiting time distribution of patients in the emergency outpatient department of a tertiary level health care institution of North India

    Directory of Open Access Journals (Sweden)

    Yogesh Tiwari

    2014-01-01

    Full Text Available Background: Emergency Department (ED of tertiary health care institute in India is mostly overcrowded, over utilized and inappropriately staffed. The challenges of overcrowded EDs and ill-managed patient flow and admission processes result in excessively long waits for patients. Aim: The objective of the present study was to analyze the patient flow system by assessing the arrival and waiting time distribution of patients in an Emergency out Patient Department (EOPD. Materials and Methods: This short cross-sectional descriptive study was conducted in the EOPD of a Tertiary level health care Institution in North India in the month of May, 2011. The data was obtained from 591 patients, who were present in the EOPD during the month of May, 2011. The waiting time, inter arrival time between two consecutive patients were calculated in addition to the daily census data (discharge rate, admission rate and transfer out rates etc. of the emergency. Results: Arrival time pattern of patients in the EOPD was highly stochastic with the peak arrival hours to be "9.00-12.00 h" in which around 26.3% patients arrived in the EOPD. The primary waiting areas of patients included patients "under observation" (29.6%; "waiting for routine diagnostic tests" (16.4% and "waiting for discharge" (14.6%. Around 71% patients were waiting due to reasons within emergency complex. Conclusion: The patient flow of the ED could only be addressed by multifaceted, multidisciplinary and hospital wide approach.

  7. NACSA Charter School Replication Guide: The Spectrum of Replication Options. Authorizing Matters. Replication Brief 1

    Science.gov (United States)

    O'Neill, Paul

    2010-01-01

    One of the most important and high-profile issues in public education reform today is the replication of successful public charter school programs. With more than 5,000 failing public schools in the United States, there is a tremendous need for strong alternatives for parents and students. Replicating successful charter school models is an…

  8. Patterns of color phase indicate spawn timing at a Nassau grouper Epinephelus striatus spawning aggregation

    Institute of Scientific and Technical Information of China (English)

    Stephanie K ARCHER; Scott A HEPPELL; Brice X SEMMENS; Christy V PATTENGILL-SEMMENS; Phillippe G BUSH; Croy M MCCOY; Bradley C JOHNSON

    2012-01-01

    Nassau grouper Epinephelus striatus are a large bodied,top level predator that is ecologically important throughout the Caribbean.Although typically solitary,Nassau grouper form large annual spawning aggregations at predictable times in specific locations.In 2003,The Cayman Islands Marine Conservation Board established protection for a newly rediscovered Nassau grouper spawning aggregation on Little Cayman,British West Indies.The large size of this aggregation provides a unique opportunity to study the behavior of Nassau grouper on a relatively intact spawning aggregation.During non-spawning periods Nassau grouper display a reddish-brown-and-white barred coloration.However,while aggregating they exhibit three additional color phases:“bicolor”,“dark”,and “white belly”.We video sampled the population on multiple days leading up to spawning across five spawning years.Divers focused a laser caliper equipped video camera on individual fish at the aggregation.We later analyzed the video to determine the length of the fish and record the color phase.Our observations show that the relative proportion of fish in the bicolor color phase increases significantly on the day leading up to the primary night of spawning.The increase in the proportion of the bicolor color phase from 0.05 early in the aggregation to 0.40 on the day of spawning suggests that this color phase conveys that a fish is behaviorally and physiologically prepared to spawn.Additionally,82.7% of fish exhibiting dark or white belly coloration early in the aggregation period suggests that these color phases are not only shown by female fish as was previously posited [Current Zoology 58 (1):73-83,2012].

  9. Global patterns of woody residence time and its influence on model simulation of aboveground biomass

    Science.gov (United States)

    Xue, Bao-Lin; Guo, Qinghua; Hu, Tianyu; Xiao, Jingfeng; Yang, Yuanhe; Wang, Guoqiang; Tao, Shengli; Su, Yanjun; Liu, Jin; Zhao, Xiaoqian

    2017-05-01

    Woody residence time (τw) is an important parameter that expresses the balance between mature forest recruitment/growth and mortality. Using field data collected from the literature, this study explored the global forest τw and investigated its influence on model simulations of aboveground biomass (AGB) at a global scale. Specifically, τw was found to be related to forest age, annual temperature, and precipitation at a global scale, but its determinants were different among various plant function types. The estimated global forest τw based on the filed data showed large spatial heterogeneity, which plays an important role in model simulation of AGB by a dynamic global vegetation model (DGVM). The τw could change the resulting AGB in tenfold based on a site-level test using the Monte Carlo method. At the global level, different parameterization schemes of the Integrated Biosphere Simulator using the estimated τw resulted in a twofold change in the AGB simulation for 2100. Our results highlight the influences of various biotic and abiotic variables on forest τw. The estimation of τw in our study may help improve the model simulations and reduce the parameter's uncertainty over the projection of future AGB in the current DGVM or Earth System Models. A clearer understanding of the responses of τw to climate change and the corresponding sophisticated description of forest growth/mortality in model structure is also needed for the improvement of carbon stock prediction in future studies.

  10. Low precipitation events in the European Greater Alpine Region and their space-time patterns in the past 210 years.

    Science.gov (United States)

    Haslinger, Klaus; Holawe, Franz; Blöschl, Günter

    2016-04-01

    In this study space-time patterns of low precipitation events in the Greater Alpine Region (GAR) of Europe are investigated. A long term gridded dataset of monthly precipitation sums spanning the last 210 years is used to assess abnormally dry states by applying a monthly percentile deceedence threshold. Furthermore, these anomalies are calculated for 1, 3, 6 and 12 months moving averages. Contiguous areas of grid points below the threshold are recorded in a lookup table in order to assess the dry anomalies on an event-based approach. The overall event severity is determined by the mean deviation from the threshold level and the area affected. With this approach we are able to show that the most severe dry anomalies take place in the 1860s, 1850s and 1940s, although there are some differences in the occurrence over time in summer and winter. Winter dry anomalies are more frequent in the 19th century, whereas in summer no clear patterns are perceptible. A spatial clustering analysis of the anomaly fields also reveals distinct patterns in space, clearly indicating the Main Alpine Crest as a major divide of dry anomalies from North to South. A joint consideration of detected dry anomaly events and their associated temperature anomalies shows that in winter of the late 19th and early 20th century dry conditions are more often accompanied by cold temperatures in contrast to the last 50 years where dry anomalies are associated with above average winter temperatures. In general dry summers are more likely warmer than the long term mean, but there is also a considerable number of dry events with negative temperature anomalies, particularly in the late 19th and early 20th century.

  11. Variation in phenotypic plasticity and selection patterns in blue tit breeding time: between- and within-population comparisons.

    Science.gov (United States)

    Porlier, Melody; Charmantier, Anne; Bourgault, Patrice; Perret, Philippe; Blondel, Jacques; Garant, Dany

    2012-09-01

    1. Phenotypic plasticity, the response of individual phenotypes to their environment, can allow organisms to cope with spatio-temporal variation in environmental conditions. Recent studies have shown that variation exists among individuals in their capacity to adjust their traits to environmental changes and that this individual plasticity can be under strong selection. Yet, little is known on the extent and ultimate causes of variation between populations and individuals in plasticity patterns. 2. In passerines, timing of breeding is a key life-history trait strongly related to fitness and is known to vary with the environment, but few studies have investigated the within-species variation in individual plasticity. 3. Here, we studied between- and within-population variation in breeding time, phenotypic plasticity and selection patterns for this trait in four Mediterranean populations of blue tits (Cyanistes caeruleus) breeding in habitats varying in structure and quality. 4. Although there was no significant warming over the course of the study, we found evidence for earlier onset of breeding in warmer years in all populations, with reduced plasticity in the less predictable environment. In two of four populations, there was significant inter-individual variation in plasticity for laying date. Interestingly, selection for earlier laying date was significant only in populations where there was no inter-individual differences in plasticity. 5. Our results show that generalization of plasticity patterns among populations of the same species might be challenging even at a small spatial scale and that the amount of within-individual variation in phenotypic plasticity may be linked to selective pressures acting on these phenotypic traits.

  12. Different patterns of sexual identity development over time: implications for the psychological adjustment of lesbian, gay, and bisexual youths.

    Science.gov (United States)

    Rosario, Margaret; Schrimshaw, Eric W; Hunter, Joyce

    2011-01-01

    Despite research documenting variability in the sexual identity development of lesbian, gay, and bisexual (LGB) youths, it remains unclear whether different developmental patterns have implications for the psychological adjustment of LGB youths. This report longitudinally examines whether different patterns of LGB identity formation and integration are associated with indicators of psychological adjustment among an ethnically diverse sample of 156 LGB youths (ages 14-21) in New York City. Although differences in the timing of identity formation were not associated with psychological adjustment, greater identity integration was related to less depressive and anxious symptoms, fewer conduct problems, and higher self-esteem both cross-sectionally and longitudinally. Individual changes in identity integration over time were associated with all four aspects of psychological adjustment, even after controlling for rival hypotheses concerning family and friend support, gay-related stress, negative social relationships, and other covariates. These findings suggest that difficulties in developing an integrated LGB identity may have negative implications for the psychological adjustment of LGB youths and that efforts to reduce distress among LGB youths should address the youths' identity integration.

  13. Real-Time Subject-Independent Pattern Classification of Overt and Covert Movements from fNIRS Signals.

    Science.gov (United States)

    Robinson, Neethu; Zaidi, Ali Danish; Rana, Mohit; Prasad, Vinod A; Guan, Cuntai; Birbaumer, Niels; Sitaram, Ranganatha

    2016-01-01

    Recently, studies have reported the use of Near Infrared Spectroscopy (NIRS) for developing Brain-Computer Interface (BCI) by applying online pattern classification of brain states from subject-specific fNIRS signals. The purpose of the present study was to develop and test a real-time method for subject-specific and subject-independent classification of multi-channel fNIRS signals using support-vector machines (SVM), so as to determine its feasibility as an online neurofeedback system. Towards this goal, we used left versus right hand movement execution and movement imagery as study paradigms in a series of experiments. In the first two experiments, activations in the motor cortex during movement execution and movement imagery were used to develop subject-dependent models that obtained high classification accuracies thereby indicating the robustness of our classification method. In the third experiment, a generalized classifier-model was developed from the first two experimental data, which was then applied for subject-independent neurofeedback training. Application of this method in new participants showed mean classification accuracy of 63% for movement imagery tasks and 80% for movement execution tasks. These results, and their corresponding offline analysis reported in this study demonstrate that SVM based real-time subject-independent classification of fNIRS signals is feasible. This method has important applications in the field of hemodynamic BCIs, and neuro-rehabilitation where patients can be trained to learn spatio-temporal patterns of healthy brain activity.

  14. Patterns and characterization of COPD exacerbations using real-time data collection

    Directory of Open Access Journals (Sweden)

    Ejiofor SI

    2017-01-01

    Full Text Available Stanley I Ejiofor,1,2 Jan Stolk,3 Pablo Fernandez,4 Robert A Stockley1,2 1Centre for Translational Inflammation Research, University of Birmingham, 2ADAPT Project, University Hospital Birmingham, Birmingham, UK; 3Leiden University Medical Centre, Leiden, the Netherlands; 4Independent consultant, Penn, UK Introduction: Patients with chronic obstructive pulmonary disease often experience exacerbations. These events are important as they are a major cause of morbidity and mortality. Recently, it has been increasingly recognized that patients may experience symptoms suggestive of an exacerbation but do not seek treatment, which are referred to as unreported or untreated exacerbations. Symptom diaries used in clinical trials have the benefit of identifying both treated and untreated exacerbation events. Methods: The Kamada study was a multicenter, double-blind randomized controlled trial of inhaled augmentation therapy in alpha-1 antitrypsin deficiency (AATD. A retrospective review of daily electronic symptom diary cards was undertaken from the two leading centers to identify symptomatic episodes consistent with a definition of an exacerbation. The aims were to explore the relationship between exacerbation events and classical “Anthonisen” symptoms and to characterize treated and untreated episodes. Results: Forty-six AATD patients with airflow obstruction and history of exacerbations were included in the analysis. Two hundred thirty-three exacerbation episodes were identified: 103 untreated and 130 treated. Untreated episodes were significantly shorter (median 6 days; interquartile range [IQR] 3–10 days than the treated episodes (median 10 days; IQR 5–18.25 days: P<0.001. Using logistic regression analysis, Anthonisen type and length of dyspnea were significant predictors of the treatment of an exacerbation event. Conclusion: Real-time electronic diary cards provide valuable information about the characterization of exacerbations

  15. Consolidation solution for composite foundation considering a time-and depth-dependent stress increment along with three distribution patterns of soil permeability

    Institute of Scientific and Technical Information of China (English)

    Meng-meng LU; Kang-he XIE; Chuan-xun LI; Kun WANG

    2011-01-01

    In actual engineering practice, the stress increment within a composite foundation caused by external loads may varysimultaneously with depth and time. In addition, column installation always leads to a decay of soil permeability towards the column. However, almost none of the consolidation theories for composite foundation comprehensively consider these factors until now. For this reason, a stress increment due to external loads changing simultaneously with time and depth was incorporated into the analysis, and three possible variation patterns of soil's horizontal permeability coefficient were considered to account for the detrimental influence of column installation. These three patterns included a constant distribution pattern (Pattern Ⅰ), a linear distribution pattern (Pattern Ⅱ), and a parabolic distribution pattern (Pattern Ⅲ). Solutions were obtained for the average excess pore water pressures and the average degree of consolidation respectively. Then several special cases were discussed in detail based on the general solution obtained. Finally, comparisons were made, and the results show that the present solution is the most general rigorous solution in the literature, and it can be broken down into a number of previous solutions. The consolidation rate is accelerated with the increase in the value of the top to the bottom stress ratio. The consolidation rate calculated by the solution for Pattern Ⅰ is less than that for Pattern Ⅱ, which in rurn is less than that for Pattern Ⅲ.

  16. Analysis on the time/activity curve of salivary gland scintigraphy in salivary gland diseases; The correlation between the pattern of time/activity curve and the amount of saliva

    Energy Technology Data Exchange (ETDEWEB)

    Suzuki, Kazufumi; Hosokawa, Yoichiro; Kaneko, Masanori; Ohmori, Keiichi; Minowa, Kazuyuki; Fukuda, Hiroshi; Yamasaki, Michio (Hokkaido Univ., Sapporo (Japan). School of Dentistry)

    1992-04-01

    Salivary gland scintigraphy with {sup 99m}TcO{sub 4}{sup -} is a simple method to evaluate salivary gland function and has been available as a technique using a time/activity curve for a number of years. But, there were few reports on the relationship between the various patterns of the time/activity curves and the salivary flow rate from the gland. This presents correlation between the time/activity curve pattern and the salivary flow rate from the parotid gland. Sixty-five patients complaining of xerostomia were examined. Sixty-two were female and 3 male (average age 45.6 years, range 17-69 years). Their diagnosis were 26 Sjoegren Syndrome, 28 suspicion of Sjoegren Syndrome and 11 parotiditis. The salivary flow rate from parotid gland was measured by stimulation with 10% citric acid using modified Carlson crittenden cup every 10 seconds for 5 min. 185 MBq {sup 99m}TcO{sub 4}{sup -} was injected intravenously and sequential scintigraphy was performed. Time/activity curves were recorded on film. Six kinds of basic patterns were as follows: normal pattern, median pattern, flat pattern and sloped pattern (Mita et al 1981), reaccumulation flat pattern and poor secretion (Stimulant secretory ratio: less than 70%) pattern by us. The amount of saliva was as follows: normal pattern (n=31), 5.4+0.4 ml; reaccumulation flat pattern (n=3), 4.2+0.6 ml; poor secretion pattern (n=18), 4.1+0.5 ml; median pattern (n=20), 3.5+0.5 ml; flat pattern (n=11), 2.6+0.5 ml and sloped pattern (n=1), 1.5 ml. Normal pattern versus poor secretion pattern, median pattern and flat pattern in the salivary flow rate were statistically significant as determined by Students' t-test. We assessed the correlation between the pattern of time/activity curve in the salivary gland scintigraphy and the amount of saliva. (author).

  17. Patterns and perceptions of physical activity and sedentary time in male transport drivers working in regional Australia.

    Science.gov (United States)

    Wong, Jason Y L; Gilson, Nicholas D; Bush, Robert A; Brown, Wendy J

    2014-08-01

    To objectively measure physical activity (PA) patterns and sedentary time, and explore perceptions of workplace PA opportunities in regional male transport workers. A multi-method study involving 28 drivers (52.4±9.69 years) working at a bus company in South-East Queensland, Australia. PA was measured using accelerometers (n=23) to determine the proportion of time spent in sedentary (work/non-work time (n=15). Interviews were conducted with 28 drivers and six managers to explore perceptions and ideas relating to workplace PA opportunities. Sedentary time was significantly higher on off-work (64% of wear time) than work (52%) days (pworking (44%) than when not working (60%; pwork and irregular driving routines), tended to preclude some drivers from engaging with these opportunities. Findings contest the notion that a sedentary occupation such as driving necessitates an inactive work environment. This research informs ongoing intervention efforts to target inactive drivers who are struggling to take advantage of existing workplace-related PA opportunities. © 2014 Public Health Association of Australia.

  18. Internal dispersal of seeds by waterfowl: effect of seed size on gut passage time and germination patterns.

    Science.gov (United States)

    Figuerola, Jordi; Charalambidou, Iris; Santamaria, Luis; Green, Andy J

    2010-06-01

    Long distance dispersal may have important consequences for gene flow and community structure. The dispersal of many plants depends on transport by vertebrate seed dispersers. The shapes of seed shadows produced by vertebrates depend both on movement patterns of the dispersers and on the dynamics and effects of passage through the disperser's gut (i.e. the retention time, survival and germination of ingested seeds). A combination of experiments with captive waterbirds and aquatic plant seeds was used to analyse the following: (a) the effects of inter- and intra-specific variation in seed size and duck species on seed retention time in the gut and (b) the relationship between retention time and the percent germination and germination rates of seeds. Among the three Scirpus species used, those with smaller seeds showed higher survival after ingestion by birds and longer retention times inside their guts than those with larger seeds. For Potamogeton pectinatus, only seeds from the smaller size class (seeds but in a manner that varied for the different plant and bird species studied. We recorded both linear and non-linear effects of retention time on percent germination. In addition, germination rate was positively correlated with retention time in Scirpus litoralis but negatively correlated in Scirpus lacustris. Small seed size can favour dispersal over larger distances. However, the effects of retention time on percent germination can modify the seed shadows produced by birds due to higher percent germination of seeds retained for short or intermediate periods. The changes in dispersal quality associated with dispersal distance (which is expected to be positively related to retention time) will affect the probability of seedling establishment over longer distances and, thus, the spatial characteristics of the effective seed shadow.

  19. Internal dispersal of seeds by waterfowl: effect of seed size on gut passage time and germination patterns

    Science.gov (United States)

    Figuerola, Jordi; Charalambidou, Iris; Santamaria, Luis; Green, Andy J.

    2010-06-01

    Long distance dispersal may have important consequences for gene flow and community structure. The dispersal of many plants depends on transport by vertebrate seed dispersers. The shapes of seed shadows produced by vertebrates depend both on movement patterns of the dispersers and on the dynamics and effects of passage through the disperser’s gut (i.e. the retention time, survival and germination of ingested seeds). A combination of experiments with captive waterbirds and aquatic plant seeds was used to analyse the following: (a) the effects of inter- and intra-specific variation in seed size and duck species on seed retention time in the gut and (b) the relationship between retention time and the percent germination and germination rates of seeds. Among the three Scirpus species used, those with smaller seeds showed higher survival after ingestion by birds and longer retention times inside their guts than those with larger seeds. For Potamogeton pectinatus, only seeds from the smaller size class (seeds but in a manner that varied for the different plant and bird species studied. We recorded both linear and non-linear effects of retention time on percent germination. In addition, germination rate was positively correlated with retention time in Scirpus litoralis but negatively correlated in Scirpus lacustris. Small seed size can favour dispersal over larger distances. However, the effects of retention time on percent germination can modify the seed shadows produced by birds due to higher percent germination of seeds retained for short or intermediate periods. The changes in dispersal quality associated with dispersal distance (which is expected to be positively related to retention time) will affect the probability of seedling establishment over longer distances and, thus, the spatial characteristics of the effective seed shadow.

  20. International Expansion through Flexible Replication

    DEFF Research Database (Denmark)

    Jonsson, Anna; Foss, Nicolai Juul

    2011-01-01

    to local environments and under the impact of new learning. To illuminate these issues, we draw on a longitudinal in-depth study of Swedish home furnishing giant IKEA, involving more than 70 interviews. We find that IKEA has developed organizational mechanisms that support an ongoing learning process aimed......, etc.) are replicated in a uniform manner across stores, and change only very slowly (if at all) in response to learning (“flexible replication”). We conclude by discussing the factors that influence the approach to replication adopted by an international replicator....