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Sample records for interrupted coding sequences

  1. Short sequence motifs, overrepresented in mammalian conservednon-coding sequences

    Energy Technology Data Exchange (ETDEWEB)

    Minovitsky, Simon; Stegmaier, Philip; Kel, Alexander; Kondrashov,Alexey S.; Dubchak, Inna

    2007-02-21

    Background: A substantial fraction of non-coding DNAsequences of multicellular eukaryotes is under selective constraint. Inparticular, ~;5 percent of the human genome consists of conservednon-coding sequences (CNSs). CNSs differ from other genomic sequences intheir nucleotide composition and must play important functional roles,which mostly remain obscure.Results: We investigated relative abundancesof short sequence motifs in all human CNSs present in the human/mousewhole-genome alignments vs. three background sets of sequences: (i)weakly conserved or unconserved non-coding sequences (non-CNSs); (ii)near-promoter sequences (located between nucleotides -500 and -1500,relative to a start of transcription); and (iii) random sequences withthe same nucleotide composition as that of CNSs. When compared tonon-CNSs and near-promoter sequences, CNSs possess an excess of AT-richmotifs, often containing runs of identical nucleotides. In contrast, whencompared to random sequences, CNSs contain an excess of GC-rich motifswhich, however, lack CpG dinucleotides. Thus, abundance of short sequencemotifs in human CNSs, taken as a whole, is mostly determined by theiroverall compositional properties and not by overrepresentation of anyspecific short motifs. These properties are: (i) high AT-content of CNSs,(ii) a tendency, probably due to context-dependent mutation, of A's andT's to clump, (iii) presence of short GC-rich regions, and (iv) avoidanceof CpG contexts, due to their hypermutability. Only a small number ofshort motifs, overrepresented in all human CNSs are similar to bindingsites of transcription factors from the FOX family.Conclusion: Human CNSsas a whole appear to be too broad a class of sequences to possess strongfootprints of any short sequence-specific functions. Such footprintsshould be studied at the level of functional subclasses of CNSs, such asthose which flank genes with a particular pattern of expression. Overallproperties of CNSs are affected by

  2. Coding visual features extracted from video sequences.

    Science.gov (United States)

    Baroffio, Luca; Cesana, Matteo; Redondi, Alessandro; Tagliasacchi, Marco; Tubaro, Stefano

    2014-05-01

    Visual features are successfully exploited in several applications (e.g., visual search, object recognition and tracking, etc.) due to their ability to efficiently represent image content. Several visual analysis tasks require features to be transmitted over a bandwidth-limited network, thus calling for coding techniques to reduce the required bit budget, while attaining a target level of efficiency. In this paper, we propose, for the first time, a coding architecture designed for local features (e.g., SIFT, SURF) extracted from video sequences. To achieve high coding efficiency, we exploit both spatial and temporal redundancy by means of intraframe and interframe coding modes. In addition, we propose a coding mode decision based on rate-distortion optimization. The proposed coding scheme can be conveniently adopted to implement the analyze-then-compress (ATC) paradigm in the context of visual sensor networks. That is, sets of visual features are extracted from video frames, encoded at remote nodes, and finally transmitted to a central controller that performs visual analysis. This is in contrast to the traditional compress-then-analyze (CTA) paradigm, in which video sequences acquired at a node are compressed and then sent to a central unit for further processing. In this paper, we compare these coding paradigms using metrics that are routinely adopted to evaluate the suitability of visual features in the context of content-based retrieval, object recognition, and tracking. Experimental results demonstrate that, thanks to the significant coding gains achieved by the proposed coding scheme, ATC outperforms CTA with respect to all evaluation metrics.

  3. Some Algebraic Aspects of MorseCode Sequences

    OpenAIRE

    Johann Cigler

    2003-01-01

    Morse code sequences are very useful to give combinatorial interpretations of various properties of Fibonacci numbers. In this note we study some algebraic and combinatorial aspects of Morse code sequences and obtain several q-analogues of Fibonacci numbers and Fibonacci polynomials and their generalizations.

  4. Some Algebraic Aspects of MorseCode Sequences

    Directory of Open Access Journals (Sweden)

    Johann Cigler

    2003-06-01

    Full Text Available Morse code sequences are very useful to give combinatorial interpretations of various properties of Fibonacci numbers. In this note we study some algebraic and combinatorial aspects of Morse code sequences and obtain several q-analogues of Fibonacci numbers and Fibonacci polynomials and their generalizations.

  5. Purifying selection acts on coding and non-coding sequences of paralogous genes in Arabidopsis thaliana.

    Science.gov (United States)

    Hoffmann, Robert D; Palmgren, Michael

    2016-06-13

    Whole-genome duplications in the ancestors of many diverse species provided the genetic material for evolutionary novelty. Several models explain the retention of paralogous genes. However, how these models are reflected in the evolution of coding and non-coding sequences of paralogous genes is unknown. Here, we analyzed the coding and non-coding sequences of paralogous genes in Arabidopsis thaliana and compared these sequences with those of orthologous genes in Arabidopsis lyrata. Paralogs with lower expression than their duplicate had more nonsynonymous substitutions, were more likely to fractionate, and exhibited less similar expression patterns with their orthologs in the other species. Also, lower-expressed genes had greater tissue specificity. Orthologous conserved non-coding sequences in the promoters, introns, and 3' untranslated regions were less abundant at lower-expressed genes compared to their higher-expressed paralogs. A gene ontology (GO) term enrichment analysis showed that paralogs with similar expression levels were enriched in GO terms related to ribosomes, whereas paralogs with different expression levels were enriched in terms associated with stress responses. Loss of conserved non-coding sequences in one gene of a paralogous gene pair correlates with reduced expression levels that are more tissue specific. Together with increased mutation rates in the coding sequences, this suggests that similar forces of purifying selection act on coding and non-coding sequences. We propose that coding and non-coding sequences evolve concurrently following gene duplication.

  6. Interrupt Handlers in Java

    DEFF Research Database (Denmark)

    Korsholm, Stephan; Schoeberl, Martin; Ravn, Anders Peter

    2008-01-01

    An important part of implementing device drivers is to control the interrupt facilities of the hardware platform and to program interrupt handlers. Current methods for handling interrupts in Java use a server thread waiting for the VM to signal an interrupt occurrence. It means that the interrupt...... is handled at a later time, which has some disadvantages. We present constructs that allow interrupts to be handled directly and not at a later point decided by a scheduler. A desirable feature of our approach is that we do not require a native middleware layer but can handle interrupts entirely with Java...... code. We have implemented our approach using an interpreter and a Java processor, and give an example demonstrating its use....

  7. Novel overlapping coding sequences in Chlamydia trachomatis

    DEFF Research Database (Denmark)

    Jensen, Klaus Thorleif; Petersen, Lise; Falk, Søren

    2006-01-01

    that are in agreement with the primary annotation. Forty two genes from the primary annotation are not predicted by EasyGene. The majority of these genes are listed as hypothetical in the primary annotation. The 15 novel predicted genes all overlap with genes on the complementary strand. We find homologues of several...... of the novel genes in C. trachomatis Serovar A and Chlamydia muridarum. Several of the genes have typical gene-like and protein-like features. Furthermore, we confirm transcriptional activity from 10 of the putative genes. The combined evidence suggests that at least seven of the 15 are protein coding genes...

  8. Genetic Code Analysis Toolkit: A novel tool to explore the coding properties of the genetic code and DNA sequences

    Science.gov (United States)

    Kraljić, K.; Strüngmann, L.; Fimmel, E.; Gumbel, M.

    2018-01-01

    The genetic code is degenerated and it is assumed that redundancy provides error detection and correction mechanisms in the translation process. However, the biological meaning of the code's structure is still under current research. This paper presents a Genetic Code Analysis Toolkit (GCAT) which provides workflows and algorithms for the analysis of the structure of nucleotide sequences. In particular, sets or sequences of codons can be transformed and tested for circularity, comma-freeness, dichotomic partitions and others. GCAT comes with a fertile editor custom-built to work with the genetic code and a batch mode for multi-sequence processing. With the ability to read FASTA files or load sequences from GenBank, the tool can be used for the mathematical and statistical analysis of existing sequence data. GCAT is Java-based and provides a plug-in concept for extensibility. Availability: Open source Homepage:http://www.gcat.bio/

  9. An Auto sequence Code to Integrate a Neutron Unfolding Code with thePC-MCA Accuspec

    International Nuclear Information System (INIS)

    Darsono

    2000-01-01

    In a neutron spectrometry using proton recoil method, the neutronunfolding code is needed to unfold the measured proton spectrum to become theneutron spectrum. The process of the unfolding neutron in the existingneutron spectrometry which was successfully installed last year was doneseparately. This manuscript reports that the auto sequence code to integratethe neutron unfolding code UNFSPEC.EXE with the software facility of thePC-MCA Accuspec has been made and run successfully so that the new neutronspectrometry become compact. The auto sequence code was written based on therules in application program facility of PC-MCA Accuspec and then it wascompiled using AC-EXE. Result of the test of the auto sequence code showedthat for binning width 20, 30, and 40 giving a little different spectrumshape. The binning width around 30 gives a better spectrum in mean of givingsmall error compared to the others. (author)

  10. Algebraic solution of the synthesis problem for coded sequences

    International Nuclear Information System (INIS)

    Leukhin, Anatolii N

    2005-01-01

    The algebraic solution of a 'complex' problem of synthesis of phase-coded (PC) sequences with the zero level of side lobes of the cyclic autocorrelation function (ACF) is proposed. It is shown that the solution of the synthesis problem is connected with the existence of difference sets for a given code dimension. The problem of estimating the number of possible code combinations for a given code dimension is solved. It is pointed out that the problem of synthesis of PC sequences is related to the fundamental problems of discrete mathematics and, first of all, to a number of combinatorial problems, which can be solved, as the number factorisation problem, by algebraic methods by using the theory of Galois fields and groups. (fourth seminar to the memory of d.n. klyshko)

  11. Sequence Coding and Search System Backfit Quality Assurance Program Plan

    International Nuclear Information System (INIS)

    Lovell, C.J.; Stepina, P.L.

    1985-03-01

    The Sequence Coding and Search System is a computer-based encoding system for events described in Licensee Event Reports. This data system contains LERs from 1981 to present. Backfit of the data system to include LERs prior to 1981 is required. This report documents the Quality Assurance Program Plan that EG and G Idaho, Inc. will follow while encoding 1980 LERs

  12. Machine-Checked Sequencer for Critical Embedded Code Generator

    Science.gov (United States)

    Izerrouken, Nassima; Pantel, Marc; Thirioux, Xavier

    This paper presents the development of a correct-by-construction block sequencer for GeneAuto a qualifiable (according to DO178B/ED12B recommendation) automatic code generator. It transforms Simulink models to MISRA C code for safety critical systems. Our approach which combines classical development process and formal specification and verification using proof-assistants, led to preliminary fruitful exchanges with certification authorities. We present parts of the classical user and tools requirements and derived formal specifications, implementation and verification for the correctness and termination of the block sequencer. This sequencer has been successfully applied to real-size industrial use cases from various transportation domain partners and led to requirement errors detection and a correct-by-construction implementation.

  13. SinEx DB: a database for single exon coding sequences in mammalian genomes.

    Science.gov (United States)

    Jorquera, Roddy; Ortiz, Rodrigo; Ossandon, F; Cárdenas, Juan Pablo; Sepúlveda, Rene; González, Carolina; Holmes, David S

    2016-01-01

    Eukaryotic genes are typically interrupted by intragenic, noncoding sequences termed introns. However, some genes lack introns in their coding sequence (CDS) and are generally known as 'single exon genes' (SEGs). In this work, a SEG is defined as a nuclear, protein-coding gene that lacks introns in its CDS. Whereas, many public databases of Eukaryotic multi-exon genes are available, there are only two specialized databases for SEGs. The present work addresses the need for a more extensive and diverse database by creating SinEx DB, a publicly available, searchable database of predicted SEGs from 10 completely sequenced mammalian genomes including human. SinEx DB houses the DNA and protein sequence information of these SEGs and includes their functional predictions (KOG) and the relative distribution of these functions within species. The information is stored in a relational database built with My SQL Server 5.1.33 and the complete dataset of SEG sequences and their functional predictions are available for downloading. SinEx DB can be interrogated by: (i) a browsable phylogenetic schema, (ii) carrying out BLAST searches to the in-house SinEx DB of SEGs and (iii) via an advanced search mode in which the database can be searched by key words and any combination of searches by species and predicted functions. SinEx DB provides a rich source of information for advancing our understanding of the evolution and function of SEGs.Database URL: www.sinex.cl. © The Author(s) 2016. Published by Oxford University Press.

  14. DNA watermarks in non-coding regulatory sequences

    Directory of Open Access Journals (Sweden)

    Pyka Martin

    2009-07-01

    Full Text Available Abstract Background DNA watermarks can be applied to identify the unauthorized use of genetically modified organisms. It has been shown that coding regions can be used to encrypt information into living organisms by using the DNA-Crypt algorithm. Yet, if the sequence of interest presents a non-coding DNA sequence, either the function of a resulting functional RNA molecule or a regulatory sequence, such as a promoter, could be affected. For our studies we used the small cytoplasmic RNA 1 in yeast and the lac promoter region of Escherichia coli. Findings The lac promoter was deactivated by the integrated watermark. In addition, the RNA molecules displayed altered configurations after introducing a watermark, but surprisingly were functionally intact, which has been verified by analyzing the growth characteristics of both wild type and watermarked scR1 transformed yeast cells. In a third approach we introduced a second overlapping watermark into the lac promoter, which did not affect the promoter activity. Conclusion Even though the watermarked RNA and one of the watermarked promoters did not show any significant differences compared to the wild type RNA and wild type promoter region, respectively, it cannot be generalized that other RNA molecules or regulatory sequences behave accordingly. Therefore, we do not recommend integrating watermark sequences into regulatory regions.

  15. Prevalence of transcription promoters within archaeal operons and coding sequences.

    Science.gov (United States)

    Koide, Tie; Reiss, David J; Bare, J Christopher; Pang, Wyming Lee; Facciotti, Marc T; Schmid, Amy K; Pan, Min; Marzolf, Bruz; Van, Phu T; Lo, Fang-Yin; Pratap, Abhishek; Deutsch, Eric W; Peterson, Amelia; Martin, Dan; Baliga, Nitin S

    2009-01-01

    Despite the knowledge of complex prokaryotic-transcription mechanisms, generalized rules, such as the simplified organization of genes into operons with well-defined promoters and terminators, have had a significant role in systems analysis of regulatory logic in both bacteria and archaea. Here, we have investigated the prevalence of alternate regulatory mechanisms through genome-wide characterization of transcript structures of approximately 64% of all genes, including putative non-coding RNAs in Halobacterium salinarum NRC-1. Our integrative analysis of transcriptome dynamics and protein-DNA interaction data sets showed widespread environment-dependent modulation of operon architectures, transcription initiation and termination inside coding sequences, and extensive overlap in 3' ends of transcripts for many convergently transcribed genes. A significant fraction of these alternate transcriptional events correlate to binding locations of 11 transcription factors and regulators (TFs) inside operons and annotated genes-events usually considered spurious or non-functional. Using experimental validation, we illustrate the prevalence of overlapping genomic signals in archaeal transcription, casting doubt on the general perception of rigid boundaries between coding sequences and regulatory elements.

  16. Performance Analysis for Cooperative Communication System with QC-LDPC Codes Constructed with Integer Sequences

    Directory of Open Access Journals (Sweden)

    Yan Zhang

    2015-01-01

    Full Text Available This paper presents four different integer sequences to construct quasi-cyclic low-density parity-check (QC-LDPC codes with mathematical theory. The paper introduces the procedure of the coding principle and coding. Four different integer sequences constructing QC-LDPC code are compared with LDPC codes by using PEG algorithm, array codes, and the Mackey codes, respectively. Then, the integer sequence QC-LDPC codes are used in coded cooperative communication. Simulation results show that the integer sequence constructed QC-LDPC codes are effective, and overall performance is better than that of other types of LDPC codes in the coded cooperative communication. The performance of Dayan integer sequence constructed QC-LDPC is the most excellent performance.

  17. Licensee Event Report sequence coding and search procedure workshop

    International Nuclear Information System (INIS)

    Cottrell, W.B.; Gallaher, R.B.

    1981-01-01

    Since mid-1980, the Office for Analysis and Evaluation of Operational Data (AEOD) of the Nuclear Regulatory Commission (NRC) has been developing procedures for the systematic review and analysis of Licensee Event Reports (LERs). These procedures generally address several areas of concern, including identification of significant trends and patterns, event sequence of occurrences, component failures, and system and plant effects. The AEOD and NSIC conducted a workshop on the new coding procedure at the American Museum of Science and Energy in Oak Ridge, TN, on November 24, 1980

  18. Sequence Coding and Search System for licensee event reports: code listings. Volume 2

    International Nuclear Information System (INIS)

    Gallaher, R.B.; Guymon, R.H.; Mays, G.T.; Poore, W.P.; Cagle, R.J.; Harrington, K.H.; Johnson, M.P.

    1985-04-01

    Operating experience data from nuclear power plants are essential for safety and reliability analyses, especially analyses of trends and patterns. The licensee event reports (LERs) that are submitted to the Nuclear Regulatory Commission (NRC) by the nuclear power plant utilities contain much of this data. The NRC's Office for Analysis and Evaluation of Operational Data (AEOD) has developed, under contract with NSIC, a system for codifying the events reported in the LERs. The primary objective of the Sequence Coding and Search System (SCSS) is to reduce the descriptive text of the LERs to coded sequences that are both computer-readable and computer-searchable. This system provides a structured format for detailed coding of component, system, and unit effects as well as personnel errors. The database contains all current LERs submitted by nuclear power plant utilities for events occurring since 1981 and is updated on a continual basis. Volume 2 contains all valid and acceptable codes used for searching and encoding the LER data. This volume contains updated material through amendment 1 to revision 1 of the working version of ORNL/NSIC-223, Vol. 2

  19. Network interruptions

    CERN Multimedia

    2005-01-01

    On Sunday 12 June 2005, a site-wide security software upgrade will be performed on all CERN network equipment. This maintenance operation will cause at least 2 short network interruptions of 2 minutes on each equipment item. There are hundreds of such items across the CERN site (Meyrin, Prévessin and all SPS and LHC pits), and it will thus take the whole day to treat them all. All network users and services will be affected. Central batch computing services will be interrupted during this period, expected to last from 8 a.m. until late evening. Job submission will still be possible but no jobs will actually be run. It is hoped to complete the computer centre upgrades in the morning so that stable access can be restored to lxplus, afs and nice services as soon as possible; this cannot be guaranteed, however. The opportunity will be used to interrupt and perform upgrades on the CERN Document Servers.

  20. Properties of Sequence Conservation in Upstream Regulatory and Protein Coding Sequences among Paralogs in Arabidopsis thaliana

    Science.gov (United States)

    Richardson, Dale N.; Wiehe, Thomas

    Whole genome duplication (WGD) has catalyzed the formation of new species, genes with novel functions, altered expression patterns, complexified signaling pathways and has provided organisms a level of genetic robustness. We studied the long-term evolution and interrelationships of 5’ upstream regulatory sequences (URSs), protein coding sequences (CDSs) and expression correlations (EC) of duplicated gene pairs in Arabidopsis. Three distinct methods revealed significant evolutionary conservation between paralogous URSs and were highly correlated with microarray-based expression correlation of the respective gene pairs. Positional information on exact matches between sequences unveiled the contribution of micro-chromosomal rearrangements on expression divergence. A three-way rank analysis of URS similarity, CDS divergence and EC uncovered specific gene functional biases. Transcription factor activity was associated with gene pairs exhibiting conserved URSs and divergent CDSs, whereas a broad array of metabolic enzymes was found to be associated with gene pairs showing diverged URSs but conserved CDSs.

  1. Mutations Related to Antiretroviral Resistance Identified by Ultra-Deep Sequencing in HIV-1 Infected Children under Structured Interruptions of HAART.

    Directory of Open Access Journals (Sweden)

    Jose Manuel Vazquez-Guillen

    Full Text Available Although Structured Treatment Interruptions (STI are currently not considered an alternative strategy for antiretroviral treatment, their true benefits and limitations have not been fully established. Some studies suggest the possibility of improving the quality of life of patients with this strategy; however, the information that has been obtained corresponds mostly to studies conducted in adults, with a lack of knowledge about its impact on children. Furthermore, mutations associated with antiretroviral resistance could be selected due to sub-therapeutic levels of HAART at each interruption period. Genotyping methods to determine the resistance profiles of the infecting viruses have become increasingly important for the management of patients under STI, thus low-abundance antiretroviral drug-resistant mutations (DRM's at levels under limit of detection of conventional genotyping (<20% of quasispecies could increase the risk of virologic failure. In this work, we analyzed the protease and reverse transcriptase regions of the pol gene by ultra-deep sequencing in pediatric patients under STI with the aim of determining the presence of high- and low-abundance DRM's in the viral rebounds generated by the STI. High-abundance mutations in protease and high- and low-abundance mutations in reverse transcriptase were detected but no one of these are directly associated with resistance to antiretroviral drugs. The results could suggest that the evaluated STI program is virologically safe, but strict and carefully planned studies, with greater numbers of patients and interruption/restart cycles, are still needed to evaluate the selection of DRM's during STI.

  2. Coding patient emotional cues and concerns in medical consultations: the Verona coding definitions of emotional sequences (VR-CoDES).

    NARCIS (Netherlands)

    Zimmermann, C.; Piccolo, L. del; Bensing, J.; Bergvik, S.; Haes, H. de; Eide, H.; Fletcher, I.; Goss, C.; Heaven, C.; Humphris, G.; Young-Mi, K.; Langewitz, W.; Meeuwesen, L.; Nuebling, M.; Rimondini, M.; Salmon, P.; Dulmen, S. van; Wissow, L.; Zandbelt, L.; Finset, A.

    2011-01-01

    Objective: To present the Verona Coding Definitions of Emotional Sequences (VR-CoDES CC), a consensus based system for coding patient expressions of emotional distress in medical consultations, defined as Cues or Concerns. Methods: The system was developed by an international group of communication

  3. Genome-wide identification of coding and non-coding conserved sequence tags in human and mouse genomes

    Directory of Open Access Journals (Sweden)

    Maggi Giorgio P

    2008-06-01

    Full Text Available Abstract Background The accurate detection of genes and the identification of functional regions is still an open issue in the annotation of genomic sequences. This problem affects new genomes but also those of very well studied organisms such as human and mouse where, despite the great efforts, the inventory of genes and regulatory regions is far from complete. Comparative genomics is an effective approach to address this problem. Unfortunately it is limited by the computational requirements needed to perform genome-wide comparisons and by the problem of discriminating between conserved coding and non-coding sequences. This discrimination is often based (thus dependent on the availability of annotated proteins. Results In this paper we present the results of a comprehensive comparison of human and mouse genomes performed with a new high throughput grid-based system which allows the rapid detection of conserved sequences and accurate assessment of their coding potential. By detecting clusters of coding conserved sequences the system is also suitable to accurately identify potential gene loci. Following this analysis we created a collection of human-mouse conserved sequence tags and carefully compared our results to reliable annotations in order to benchmark the reliability of our classifications. Strikingly we were able to detect several potential gene loci supported by EST sequences but not corresponding to as yet annotated genes. Conclusion Here we present a new system which allows comprehensive comparison of genomes to detect conserved coding and non-coding sequences and the identification of potential gene loci. Our system does not require the availability of any annotated sequence thus is suitable for the analysis of new or poorly annotated genomes.

  4. Complete cDNA sequence coding for human docking protein

    Energy Technology Data Exchange (ETDEWEB)

    Hortsch, M; Labeit, S; Meyer, D I

    1988-01-11

    Docking protein (DP, or SRP receptor) is a rough endoplasmic reticulum (ER)-associated protein essential for the targeting and translocation of nascent polypeptides across this membrane. It specifically interacts with a cytoplasmic ribonucleoprotein complex, the signal recognition particle (SRP). The nucleotide sequence of cDNA encoding the entire human DP and its deduced amino acid sequence are given.

  5. Rfam: annotating families of non-coding RNA sequences.

    Science.gov (United States)

    Daub, Jennifer; Eberhardt, Ruth Y; Tate, John G; Burge, Sarah W

    2015-01-01

    The primary task of the Rfam database is to collate experimentally validated noncoding RNA (ncRNA) sequences from the published literature and facilitate the prediction and annotation of new homologues in novel nucleotide sequences. We group homologous ncRNA sequences into "families" and related families are further grouped into "clans." We collate and manually curate data cross-references for these families from other databases and external resources. Our Web site offers researchers a simple interface to Rfam and provides tools with which to annotate their own sequences using our covariance models (CMs), through our tools for searching, browsing, and downloading information on Rfam families. In this chapter, we will work through examples of annotating a query sequence, collating family information, and searching for data.

  6. Fast comparison of IS radar code sequences for lag profile inversion

    Directory of Open Access Journals (Sweden)

    M. S. Lehtinen

    2008-08-01

    Full Text Available A fast method for theoretically comparing the posteriori variances produced by different phase code sequences in incoherent scatter radar (ISR experiments is introduced. Alternating codes of types 1 and 2 are known to be optimal for selected range resolutions, but the code sets are inconveniently long for many purposes like ground clutter estimation and in cases where coherent echoes from lower ionospheric layers are to be analyzed in addition to standard F-layer spectra.

    The method is used in practice for searching binary code quads that have estimation accuracy almost equal to that of much longer alternating code sets. Though the code sequences can consist of as few as four different transmission envelopes, the lag profile estimation variances are near to the theoretical minimum. Thus the short code sequence is equally good as a full cycle of alternating codes with the same pulse length and bit length. The short code groups cannot be directly decoded, but the decoding is done in connection with more computationally expensive lag profile inversion in data analysis.

    The actual code searches as well as the analysis and real data results from the found short code searches are explained in other papers sent to the same issue of this journal. We also discuss interesting subtle differences found between the different alternating codes by this method. We assume that thermal noise dominates the incoherent scatter signal.

  7. RNA-DNA sequence differences spell genetic code ambiguities

    DEFF Research Database (Denmark)

    Bentin, Thomas; Nielsen, Michael L

    2013-01-01

    A recent paper in Science by Li et al. 2011(1) reports widespread sequence differences in the human transcriptome between RNAs and their encoding genes termed RNA-DNA differences (RDDs). The findings could add a new layer of complexity to gene expression but the study has been criticized. ...

  8. The Coding and Effector Transfer of Movement Sequences

    Science.gov (United States)

    Kovacs, Attila J.; Muhlbauer, Thomas; Shea, Charles H.

    2009-01-01

    Three experiments utilizing a 14-element arm movement sequence were designed to determine if reinstating the visual-spatial coordinates, which require movements to the same spatial locations utilized during acquisition, results in better effector transfer than reinstating the motor coordinates, which require the same pattern of homologous muscle…

  9. SEAPATH: A microcomputer code for evaluating physical security effectiveness using adversary sequence diagrams

    International Nuclear Information System (INIS)

    Darby, J.L.

    1986-01-01

    The Adversary Sequence Diagram (ASD) concept was developed by Sandia National Laboratories (SNL) to examine physical security system effectiveness. Sandia also developed a mainframe computer code, PANL, to analyze the ASD. The authors have developed a microcomputer code, SEAPATH, which also analyzes ASD's. The Authors are supporting SNL in software development of the SAVI code; SAVI utilizes the SEAPATH algorithm to identify and quantify paths

  10. Highly conserved non-coding sequences are associated with vertebrate development.

    Directory of Open Access Journals (Sweden)

    Adam Woolfe

    2005-01-01

    Full Text Available In addition to protein coding sequence, the human genome contains a significant amount of regulatory DNA, the identification of which is proving somewhat recalcitrant to both in silico and functional methods. An approach that has been used with some success is comparative sequence analysis, whereby equivalent genomic regions from different organisms are compared in order to identify both similarities and differences. In general, similarities in sequence between highly divergent organisms imply functional constraint. We have used a whole-genome comparison between humans and the pufferfish, Fugu rubripes, to identify nearly 1,400 highly conserved non-coding sequences. Given the evolutionary divergence between these species, it is likely that these sequences are found in, and furthermore are essential to, all vertebrates. Most, and possibly all, of these sequences are located in and around genes that act as developmental regulators. Some of these sequences are over 90% identical across more than 500 bases, being more highly conserved than coding sequence between these two species. Despite this, we cannot find any similar sequences in invertebrate genomes. In order to begin to functionally test this set of sequences, we have used a rapid in vivo assay system using zebrafish embryos that allows tissue-specific enhancer activity to be identified. Functional data is presented for highly conserved non-coding sequences associated with four unrelated developmental regulators (SOX21, PAX6, HLXB9, and SHH, in order to demonstrate the suitability of this screen to a wide range of genes and expression patterns. Of 25 sequence elements tested around these four genes, 23 show significant enhancer activity in one or more tissues. We have identified a set of non-coding sequences that are highly conserved throughout vertebrates. They are found in clusters across the human genome, principally around genes that are implicated in the regulation of development

  11. SRComp: short read sequence compression using burstsort and Elias omega coding.

    Directory of Open Access Journals (Sweden)

    Jeremy John Selva

    Full Text Available Next-generation sequencing (NGS technologies permit the rapid production of vast amounts of data at low cost. Economical data storage and transmission hence becomes an increasingly important challenge for NGS experiments. In this paper, we introduce a new non-reference based read sequence compression tool called SRComp. It works by first employing a fast string-sorting algorithm called burstsort to sort read sequences in lexicographical order and then Elias omega-based integer coding to encode the sorted read sequences. SRComp has been benchmarked on four large NGS datasets, where experimental results show that it can run 5-35 times faster than current state-of-the-art read sequence compression tools such as BEETL and SCALCE, while retaining comparable compression efficiency for large collections of short read sequences. SRComp is a read sequence compression tool that is particularly valuable in certain applications where compression time is of major concern.

  12. Optical orthogonal code-division multiple-access system - Part 2: Multibits/sequence-period OOCDMA

    Science.gov (United States)

    Kwon, Hyuck M.

    1994-08-01

    In a recently proposed optical orthogonal code division multiple-access (OOCDMA) system, one bit of user's data is transmitted per sequence-period, and a threshold is employed for the final bit decision. In this paper, a system that can transmit multibits per sequence-period is introduced, and avalanche photodiode (APD) noise, thermal noise, and interference, are included. This system, derived by exploiting orthogonal properties of the OOCDMA code sequence and using a maximum search (instead of a threshold) in the final decision, is log(sub 2) F times higher in throughput, where F is sequence-period. For example, four orders of magnitude are better in bit error probability at - 56 dBW received laser power, with F = 1000 chips, 10 'marks' in a sequence, and 10 users of 30 Mb/s data rate for one-bit/sequence-period and 270 Mb/s data rate for multibits/sequence-period system. Furthermore, an exact analysis is performed for the log(sub 2)F bits/sequence-period system with a hard-limiter placed before the receiver, and its performance is compared to the performance without hard-limiter, for the chip-synchronous case. The improvement from using a hard-limiter is significant in the log(sub 2)F bits/sequence-period OCCDMA system.

  13. Modelling of blackout sequence at Atucha-1 using the MARCH3 code

    International Nuclear Information System (INIS)

    Baron, J.; Bastianelli, B.

    1997-01-01

    This paper presents the modelling of a complete blackout at the Atucha-1 NPP as preliminary phase for a Level II safety probabilistic analysis. The MARCH3 code of the STCP (Source Term Code Package) is used, based on a plant model made in accordance with particularities of the plant design. The analysis covers all the severe accident phases. The results allow to view the time sequence of the events, and provide the basis for source term studies. (author). 6 refs., 2 figs

  14. Analysis of the AD sequence in Zion plant using the March 1.1 code

    International Nuclear Information System (INIS)

    Oriolo, F.; Paci, S.

    1985-01-01

    The analyses of the AD sequences for the Zion power plant, made at the Pisa University, in the framework of the participation in the Source Tern Working Group. After a short description of the plant and the sequence under analysis, the model used for the reference computation and the results obtained using the March 1.1 code are shown. Together with the reference computation a series of parametric tests have been also made, concerning some input code variables, in order to ascertain their influence on the transient trend. The results of these analyses are shown in Appendix

  15. Sub-grouping of Plasmodium falciparum 3D7 var genes based on sequence analysis of coding and non-coding regions

    DEFF Research Database (Denmark)

    Lavstsen, Thomas; Salanti, Ali; Jensen, Anja T R

    2003-01-01

    and organization of the 3D7 PfEMP1 repertoire was investigated on the basis of the complete genome sequence. METHODS: Using two tree-building methods we analysed the coding and non-coding sequences of 3D7 var and rif genes as well as var genes of other parasite strains. RESULTS: var genes can be sub...

  16. Current interruption transients calculation

    CERN Document Server

    Peelo, David F

    2014-01-01

    Provides an original, detailed and practical description of current interruption transients, origins, and the circuits involved, and how they can be calculated Current Interruption Transients Calculationis a comprehensive resource for the understanding, calculation and analysis of the transient recovery voltages (TRVs) and related re-ignition or re-striking transients associated with fault current interruption and the switching of inductive and capacitive load currents in circuits. This book provides an original, detailed and practical description of current interruption transients, origins,

  17. Modeling compositional dynamics based on GC and purine contents of protein-coding sequences

    KAUST Repository

    Zhang, Zhang; Yu, Jun

    2010-01-01

    Background: Understanding the compositional dynamics of genomes and their coding sequences is of great significance in gaining clues into molecular evolution and a large number of publically-available genome sequences have allowed us to quantitatively predict deviations of empirical data from their theoretical counterparts. However, the quantification of theoretical compositional variations for a wide diversity of genomes remains a major challenge.Results: To model the compositional dynamics of protein-coding sequences, we propose two simple models that take into account both mutation and selection effects, which act differently at the three codon positions, and use both GC and purine contents as compositional parameters. The two models concern the theoretical composition of nucleotides, codons, and amino acids, with no prerequisite of homologous sequences or their alignments. We evaluated the two models by quantifying theoretical compositions of a large collection of protein-coding sequences (including 46 of Archaea, 686 of Bacteria, and 826 of Eukarya), yielding consistent theoretical compositions across all the collected sequences.Conclusions: We show that the compositions of nucleotides, codons, and amino acids are largely determined by both GC and purine contents and suggest that deviations of the observed from the expected compositions may reflect compositional signatures that arise from a complex interplay between mutation and selection via DNA replication and repair mechanisms.Reviewers: This article was reviewed by Zhaolei Zhang (nominated by Mark Gerstein), Guruprasad Ananda (nominated by Kateryna Makova), and Daniel Haft. 2010 Zhang and Yu; licensee BioMed Central Ltd.

  18. Modeling compositional dynamics based on GC and purine contents of protein-coding sequences

    KAUST Repository

    Zhang, Zhang

    2010-11-08

    Background: Understanding the compositional dynamics of genomes and their coding sequences is of great significance in gaining clues into molecular evolution and a large number of publically-available genome sequences have allowed us to quantitatively predict deviations of empirical data from their theoretical counterparts. However, the quantification of theoretical compositional variations for a wide diversity of genomes remains a major challenge.Results: To model the compositional dynamics of protein-coding sequences, we propose two simple models that take into account both mutation and selection effects, which act differently at the three codon positions, and use both GC and purine contents as compositional parameters. The two models concern the theoretical composition of nucleotides, codons, and amino acids, with no prerequisite of homologous sequences or their alignments. We evaluated the two models by quantifying theoretical compositions of a large collection of protein-coding sequences (including 46 of Archaea, 686 of Bacteria, and 826 of Eukarya), yielding consistent theoretical compositions across all the collected sequences.Conclusions: We show that the compositions of nucleotides, codons, and amino acids are largely determined by both GC and purine contents and suggest that deviations of the observed from the expected compositions may reflect compositional signatures that arise from a complex interplay between mutation and selection via DNA replication and repair mechanisms.Reviewers: This article was reviewed by Zhaolei Zhang (nominated by Mark Gerstein), Guruprasad Ananda (nominated by Kateryna Makova), and Daniel Haft. 2010 Zhang and Yu; licensee BioMed Central Ltd.

  19. Non-codingRNA sequence variations in human chronic lymphocytic leukemia and colorectal cancer.

    Science.gov (United States)

    Wojcik, Sylwia E; Rossi, Simona; Shimizu, Masayoshi; Nicoloso, Milena S; Cimmino, Amelia; Alder, Hansjuerg; Herlea, Vlad; Rassenti, Laura Z; Rai, Kanti R; Kipps, Thomas J; Keating, Michael J; Croce, Carlo M; Calin, George A

    2010-02-01

    Cancer is a genetic disease in which the interplay between alterations in protein-coding genes and non-coding RNAs (ncRNAs) plays a fundamental role. In recent years, the full coding component of the human genome was sequenced in various cancers, whereas such attempts related to ncRNAs are still fragmentary. We screened genomic DNAs for sequence variations in 148 microRNAs (miRNAs) and ultraconserved regions (UCRs) loci in patients with chronic lymphocytic leukemia (CLL) or colorectal cancer (CRC) by Sanger technique and further tried to elucidate the functional consequences of some of these variations. We found sequence variations in miRNAs in both sporadic and familial CLL cases, mutations of UCRs in CLLs and CRCs and, in certain instances, detected functional effects of these variations. Furthermore, by integrating our data with previously published data on miRNA sequence variations, we have created a catalog of DNA sequence variations in miRNAs/ultraconserved genes in human cancers. These findings argue that ncRNAs are targeted by both germ line and somatic mutations as well as by single-nucleotide polymorphisms with functional significance for human tumorigenesis. Sequence variations in ncRNA loci are frequent and some have functional and biological significance. Such information can be exploited to further investigate on a genome-wide scale the frequency of genetic variations in ncRNAs and their functional meaning, as well as for the development of new diagnostic and prognostic markers for leukemias and carcinomas.

  20. Complete coding sequence of Zika virus from Martinique outbreak in 2015

    Directory of Open Access Journals (Sweden)

    G. Piorkowski

    2016-05-01

    Full Text Available Zika virus is an Aedes-borne Flavivirus causing fever, arthralgia, myalgia rash, associated with Guillain–Barré syndrome and suspected to induce microcephaly in the fetus. We report here the complete coding sequence of the first characterized Caribbean Zika virus strain, isolated from a patient from Martinique in December, 2015.

  1. Multiple Access Interference Reduction Using Received Response Code Sequence for DS-CDMA UWB System

    Science.gov (United States)

    Toh, Keat Beng; Tachikawa, Shin'ichi

    This paper proposes a combination of novel Received Response (RR) sequence at the transmitter and a Matched Filter-RAKE (MF-RAKE) combining scheme receiver system for the Direct Sequence-Code Division Multiple Access Ultra Wideband (DS-CDMA UWB) multipath channel model. This paper also demonstrates the effectiveness of the RR sequence in Multiple Access Interference (MAI) reduction for the DS-CDMA UWB system. It suggests that by using conventional binary code sequence such as the M sequence or the Gold sequence, there is a possibility of generating extra MAI in the UWB system. Therefore, it is quite difficult to collect the energy efficiently although the RAKE reception method is applied at the receiver. The main purpose of the proposed system is to overcome the performance degradation for UWB transmission due to the occurrence of MAI during multiple accessing in the DS-CDMA UWB system. The proposed system improves the system performance by improving the RAKE reception performance using the RR sequence which can reduce the MAI effect significantly. Simulation results verify that significant improvement can be obtained by the proposed system in the UWB multipath channel models.

  2. Systematic analysis of coding and noncoding DNA sequences using methods of statistical linguistics

    Science.gov (United States)

    Mantegna, R. N.; Buldyrev, S. V.; Goldberger, A. L.; Havlin, S.; Peng, C. K.; Simons, M.; Stanley, H. E.

    1995-01-01

    We compare the statistical properties of coding and noncoding regions in eukaryotic and viral DNA sequences by adapting two tests developed for the analysis of natural languages and symbolic sequences. The data set comprises all 30 sequences of length above 50 000 base pairs in GenBank Release No. 81.0, as well as the recently published sequences of C. elegans chromosome III (2.2 Mbp) and yeast chromosome XI (661 Kbp). We find that for the three chromosomes we studied the statistical properties of noncoding regions appear to be closer to those observed in natural languages than those of coding regions. In particular, (i) a n-tuple Zipf analysis of noncoding regions reveals a regime close to power-law behavior while the coding regions show logarithmic behavior over a wide interval, while (ii) an n-gram entropy measurement shows that the noncoding regions have a lower n-gram entropy (and hence a larger "n-gram redundancy") than the coding regions. In contrast to the three chromosomes, we find that for vertebrates such as primates and rodents and for viral DNA, the difference between the statistical properties of coding and noncoding regions is not pronounced and therefore the results of the analyses of the investigated sequences are less conclusive. After noting the intrinsic limitations of the n-gram redundancy analysis, we also briefly discuss the failure of the zeroth- and first-order Markovian models or simple nucleotide repeats to account fully for these "linguistic" features of DNA. Finally, we emphasize that our results by no means prove the existence of a "language" in noncoding DNA.

  3. Blackout sequence modeling for Atucha-I with MARCH3 code

    International Nuclear Information System (INIS)

    Baron, J.; Bastianelli, B.

    1997-01-01

    The modeling of a blackout sequence in Atucha I nuclear power plant is presented in this paper, as a preliminary phase for a level II probabilistic safety assessment. Such sequence is analyzed with the code MARCH3 from STCP (Source Term Code Package), based on a specific model developed for Atucha, that takes into accounts it peculiarities. The analysis includes all the severe accident phases, from the initial transient (loss of heat sink), loss of coolant through the safety valves, core uncovered, heatup, metal-water reaction, melting and relocation, heatup and failure of the pressure vessel, core-concrete interaction in the reactor cavity, heatup and failure of the containment building (multi-compartmented) due to quasi-static overpressurization. The results obtained permit to visualize the time sequence of these events, as well as provide the basis for source term studies. (author) [es

  4. Consensus coding sequence (CCDS) database: a standardized set of human and mouse protein-coding regions supported by expert curation.

    Science.gov (United States)

    Pujar, Shashikant; O'Leary, Nuala A; Farrell, Catherine M; Loveland, Jane E; Mudge, Jonathan M; Wallin, Craig; Girón, Carlos G; Diekhans, Mark; Barnes, If; Bennett, Ruth; Berry, Andrew E; Cox, Eric; Davidson, Claire; Goldfarb, Tamara; Gonzalez, Jose M; Hunt, Toby; Jackson, John; Joardar, Vinita; Kay, Mike P; Kodali, Vamsi K; Martin, Fergal J; McAndrews, Monica; McGarvey, Kelly M; Murphy, Michael; Rajput, Bhanu; Rangwala, Sanjida H; Riddick, Lillian D; Seal, Ruth L; Suner, Marie-Marthe; Webb, David; Zhu, Sophia; Aken, Bronwen L; Bruford, Elspeth A; Bult, Carol J; Frankish, Adam; Murphy, Terence; Pruitt, Kim D

    2018-01-04

    The Consensus Coding Sequence (CCDS) project provides a dataset of protein-coding regions that are identically annotated on the human and mouse reference genome assembly in genome annotations produced independently by NCBI and the Ensembl group at EMBL-EBI. This dataset is the product of an international collaboration that includes NCBI, Ensembl, HUGO Gene Nomenclature Committee, Mouse Genome Informatics and University of California, Santa Cruz. Identically annotated coding regions, which are generated using an automated pipeline and pass multiple quality assurance checks, are assigned a stable and tracked identifier (CCDS ID). Additionally, coordinated manual review by expert curators from the CCDS collaboration helps in maintaining the integrity and high quality of the dataset. The CCDS data are available through an interactive web page (https://www.ncbi.nlm.nih.gov/CCDS/CcdsBrowse.cgi) and an FTP site (ftp://ftp.ncbi.nlm.nih.gov/pub/CCDS/). In this paper, we outline the ongoing work, growth and stability of the CCDS dataset and provide updates on new collaboration members and new features added to the CCDS user interface. We also present expert curation scenarios, with specific examples highlighting the importance of an accurate reference genome assembly and the crucial role played by input from the research community. Published by Oxford University Press on behalf of Nucleic Acids Research 2017.

  5. The Evolution of Bony Vertebrate Enhancers at Odds with Their Coding Sequence Landscape.

    Science.gov (United States)

    Yousaf, Aisha; Sohail Raza, Muhammad; Ali Abbasi, Amir

    2015-08-06

    Enhancers lie at the heart of transcriptional and developmental gene regulation. Therefore, changes in enhancer sequences usually disrupt the target gene expression and result in disease phenotypes. Despite the well-established role of enhancers in development and disease, evolutionary sequence studies are lacking. The current study attempts to unravel the puzzle of bony vertebrates' conserved noncoding elements (CNE) enhancer evolution. Bayesian phylogenetics of enhancer sequences spotlights promising interordinal relationships among placental mammals, proposing a closer relationship between humans and laurasiatherians while placing rodents at the basal position. Clock-based estimates of enhancer evolution provided a dynamic picture of interspecific rate changes across the bony vertebrate lineage. Moreover, coelacanth in the study augmented our appreciation of the vertebrate cis-regulatory evolution during water-land transition. Intriguingly, we observed a pronounced upsurge in enhancer evolution in land-dwelling vertebrates. These novel findings triggered us to further investigate the evolutionary trend of coding as well as CNE nonenhancer repertoires, to highlight the relative evolutionary dynamics of diverse genomic landscapes. Surprisingly, the evolutionary rates of enhancer sequences were clearly at odds with those of the coding and the CNE nonenhancer sequences during vertebrate adaptation to land, with land vertebrates exhibiting significantly reduced rates of coding sequence evolution in comparison to their fast evolving regulatory landscape. The observed variation in tetrapod cis-regulatory elements caused the fine-tuning of associated gene regulatory networks. Therefore, the increased evolutionary rate of tetrapods' enhancer sequences might be responsible for the variation in developmental regulatory circuits during the process of vertebrate adaptation to land. © The Author(s) 2015. Published by Oxford University Press on behalf of the Society for

  6. Identification of evolutionarily conserved non-AUG-initiated N-terminal extensions in human coding sequences.

    LENUS (Irish Health Repository)

    Ivanov, Ivaylo P

    2011-05-01

    In eukaryotes, it is generally assumed that translation initiation occurs at the AUG codon closest to the messenger RNA 5\\' cap. However, in certain cases, initiation can occur at codons differing from AUG by a single nucleotide, especially the codons CUG, UUG, GUG, ACG, AUA and AUU. While non-AUG initiation has been experimentally verified for a handful of human genes, the full extent to which this phenomenon is utilized--both for increased coding capacity and potentially also for novel regulatory mechanisms--remains unclear. To address this issue, and hence to improve the quality of existing coding sequence annotations, we developed a methodology based on phylogenetic analysis of predicted 5\\' untranslated regions from orthologous genes. We use evolutionary signatures of protein-coding sequences as an indicator of translation initiation upstream of annotated coding sequences. Our search identified novel conserved potential non-AUG-initiated N-terminal extensions in 42 human genes including VANGL2, FGFR1, KCNN4, TRPV6, HDGF, CITED2, EIF4G3 and NTF3, and also affirmed the conservation of known non-AUG-initiated extensions in 17 other genes. In several instances, we have been able to obtain independent experimental evidence of the expression of non-AUG-initiated products from the previously published literature and ribosome profiling data.

  7. Golay sequences coded coherent optical OFDM for long-haul transmission

    Science.gov (United States)

    Qin, Cui; Ma, Xiangrong; Hua, Tao; Zhao, Jing; Yu, Huilong; Zhang, Jian

    2017-09-01

    We propose to use binary Golay sequences in coherent optical orthogonal frequency division multiplexing (CO-OFDM) to improve the long-haul transmission performance. The Golay sequences are generated by binary Reed-Muller codes, which have low peak-to-average power ratio and certain error correction capability. A low-complexity decoding algorithm for the Golay sequences is then proposed to recover the signal. Under same spectral efficiency, the QPSK modulated OFDM with binary Golay sequences coding with and without discrete Fourier transform (DFT) spreading (DFTS-QPSK-GOFDM and QPSK-GOFDM) are compared with the normal BPSK modulated OFDM with and without DFT spreading (DFTS-BPSK-OFDM and BPSK-OFDM) after long-haul transmission. At a 7% forward error correction code threshold (Q2 factor of 8.5 dB), it is shown that DFTS-QPSK-GOFDM outperforms DFTS-BPSK-OFDM by extending the transmission distance by 29% and 18%, in non-dispersion managed and dispersion managed links, respectively.

  8. The sequence coding and search system: an approach for constructing and analyzing event sequences at commercial nuclear power plants

    International Nuclear Information System (INIS)

    Mays, G.T.

    1990-01-01

    The U.S. Nuclear Regulatory Commission (NRC) has recognized the importance of the collection, assessment, and feedback of operating experience data from commercial nuclear power plants and has centralized these activities in the Office for Analysis and Evaluation of Operational Data (AEOD). Such data is essential for performing safety and reliability analyses, especially analyses of trends and patterns to identify undesirable changes in plant performance at the earliest opportunity to implement corrective measures to preclude the occurrence of a more serious event. One of NRC's principal tools for collecting and evaluating operating experience data is the Sequence Coding and Search System (SCSS). The SCSS consists of a methodology for structuring event sequences and the requisite computer system to store and search the data. The source information for SCSS is the Licensee Event Report (LER), which is a legally required document. This paper describes the objectives of SCSS, the information it contains, and the format and approach for constructing SCSS event sequences. Examples are presented demonstrating the use of SCSS to support the analysis of LER data. The SCSS contains over 30,000 LERs describing events from 1980 through the present. Insights gained from working with a complex data system from the initial developmental stage to the point of a mature operating system are highlighted. Considerable experience has been gained in the areas of evolving and changing data requirements, staffing requirements, and quality control and quality assurance procedures for addressing consistency, software/hardware considerations for developing and maintaining a complex system, documentation requirements, and end-user needs. Two other approaches for constructing and evaluating event sequences are examined including the Accident Precursor Program (ASP) where sequences having the potential for core damage are identified and analyzed, and the Significant Event Compilation Tree

  9. Coding and decoding libraries of sequence-defined functional copolymers synthesized via photoligation.

    Science.gov (United States)

    Zydziak, Nicolas; Konrad, Waldemar; Feist, Florian; Afonin, Sergii; Weidner, Steffen; Barner-Kowollik, Christopher

    2016-11-30

    Designing artificial macromolecules with absolute sequence order represents a considerable challenge. Here we report an advanced light-induced avenue to monodisperse sequence-defined functional linear macromolecules up to decamers via a unique photochemical approach. The versatility of the synthetic strategy-combining sequential and modular concepts-enables the synthesis of perfect macromolecules varying in chemical constitution and topology. Specific functions are placed at arbitrary positions along the chain via the successive addition of monomer units and blocks, leading to a library of functional homopolymers, alternating copolymers and block copolymers. The in-depth characterization of each sequence-defined chain confirms the precision nature of the macromolecules. Decoding of the functional information contained in the molecular structure is achieved via tandem mass spectrometry without recourse to their synthetic history, showing that the sequence information can be read. We submit that the presented photochemical strategy is a viable and advanced concept for coding individual monomer units along a macromolecular chain.

  10. PATACSDB—the database of polyA translational attenuators in coding sequences

    Directory of Open Access Journals (Sweden)

    Malgorzata Habich

    2016-02-01

    Full Text Available Recent additions to the repertoire of gene expression regulatory mechanisms are polyadenylate (polyA tracks encoding for poly-lysine runs in protein sequences. Such tracks stall the translation apparatus and induce frameshifting independently of the effects of charged nascent poly-lysine sequence on the ribosome exit channel. As such, they substantially influence the stability of mRNA and the amount of protein produced from a given transcript. Single base changes in these regions are enough to exert a measurable response on both protein and mRNA abundance; this makes each of these sequences a potentially interesting case study for the effects of synonymous mutation, gene dosage balance and natural frameshifting. Here we present PATACSDB, a resource that contain a comprehensive list of polyA tracks from over 250 eukaryotic genomes. Our data is based on the Ensembl genomic database of coding sequences and filtered with algorithm of 12A-1 which selects sequences of polyA tracks with a minimal length of 12 A’s allowing for one mismatched base. The PATACSDB database is accessible at: http://sysbio.ibb.waw.pl/patacsdb. The source code is available at http://github.com/habich/PATACSDB, and it includes the scripts with which the database can be recreated.

  11. RevTrans: multiple alignment of coding DNA from aligned amino acid sequences

    DEFF Research Database (Denmark)

    Wernersson, Rasmus; Pedersen, Anders Gorm

    2003-01-01

    The simple fact that proteins are built from 20 amino acids while DNA only contains four different bases, means that the 'signal-to-noise ratio' in protein sequence alignments is much better than in alignments of DNA. Besides this information-theoretical advantage, protein alignments also benefit...... proteins. It is therefore preferable to align coding DNA at the amino acid level and it is for this purpose we have constructed the program RevTrans. RevTrans constructs a multiple DNA alignment by: (i) translating the DNA; (ii) aligning the resulting peptide sequences; and (iii) building a multiple DNA...

  12. Application of Melcor code for the calculo of TMLB sequence in PWR with natural circulating into the vessel

    International Nuclear Information System (INIS)

    Marten-Fuertes, F.

    1995-01-01

    The use of computer codes to analyze the phenomena of severe accidents is very important to take decisions in Nuclear Safety. This paper presents the MELCOR code used to calculate the TMLB sequence of PWR with natural circulation into the vessels. The main goal of this code is its application for the PSA (probabilistic safety analysis)

  13. Current interruption by density depression

    International Nuclear Information System (INIS)

    Wagner, J.S.; Tajima, T.; Akasofu, S.I.

    1985-04-01

    Using a one-dimensional electrostatic particle code, we examine processes associated with current interruption in a collisionless plasma when a density depression is present along the current channel. Current interruption due to double layers was suggested by Alfven and Carlqvist (1967) as a cause of solar flares. At a local density depression, plasma instabilities caused by an electron current flow are accentuated, leading to current disruption. Our simulation study encompasses a wide range of the parameters in such a way that under appropriate conditions, both the Alfven and Carlqvist (1967) regime and the Smith and Priest (1972) regime take place. In the latter regime the density depression decays into a stationary structure (''ion-acoustic layer'') which spawns a series of ion-acoustic ''solitons'' and ion phase space holes travelling upstream. A large inductance of the current circuit tends to enhance the plasma instabilities

  14. Episodic sequence memory is supported by a theta-gamma phase code

    OpenAIRE

    Heusser, Andrew C.; Poeppel, David; Ezzyat, Youssef; Davachi, Lila

    2016-01-01

    The meaning we derive from our experiences is not a simple static extraction of the elements, but is largely based on the order in which those elements occur. Models propose that sequence encoding is supported by interactions between high and low frequency oscillations, such that elements within an experience are represented by neural cell assemblies firing at higher frequencies (i.e. gamma) and sequential order is coded by the specific timing of firing with respect to a lower frequency oscil...

  15. Sequence Coding and Search System for licensee event reports: coder's manual. Volume 4

    International Nuclear Information System (INIS)

    Gallaher, R.B.; Guymon, R.H.; Mays, G.T.; Poore, W.P.; Cagle, R.J.; Harrington, K.H.; Johnson, M.P.

    1985-04-01

    Operating experience data from nuclear power plants are essential for safety and reliability analyses, especially analyses of trends and patterns. The licensee event reports (LERs) that are submitted to the Nuclear Regulatory Commission (NRC) by the nuclear power plant utilities contain much of this data. The NRC's Office for Analysis and Evaluation of Operational Data (AEOD) has developed, under contract with NSIC, a system for codifying the events reported in the LERs. The primary objective of the Sequence Coding and Search System (SCSS) is to reduce the descriptive text of the LERs to coded sequences that are both computer-readable and computer-searchable. This four volume report documents and describes SCSS in detail. Volume 3 and 4 provide a technical processor, new to SCSS, the information and methodology necessary to capture descriptive data from the LER and to codify that data into a structured format and serve as reference material for the more experienced technical processor, and contains information that is essential for the more advanced user who needs to be familiar with the intricate coding techniques in order to retrieve specific details in a sequence. This volume contains updated material through amendment 1 to revision 1 of the working version of ORNL/NSIC-223, Vol. 4

  16. Sequence Coding and Search System for licensee event reports: coder's manual. Volume 3

    International Nuclear Information System (INIS)

    Gallaher, R.B.; Guymon, R.H.; Mays, G.T.; Poore, W.P.; Cagle, R.J.; Harrington, K.H.; Johnson, M.P.

    1985-04-01

    Operating experience data from nuclear power plants are essential for safety and reliability analyses, especially analyses of trends and patterns. The licensee event reports (LERs) that are submitted to the Nuclear Regulatory Commission (NRC) by the nuclear power plant utilities contain much of this data. The NRC's Office for Analysis and Evaluation of Operational Data (AEOD) has developed, under contract with NSIC, a system for codifying the events reported in the LERs. The primary objective of the Sequence Coding and Search System (SCSS) is to reduce the descriptive text of the LERs to coded sequences that are both computer-readable and computer-searchable. This four volume report documents and describes SCSS in detail. Volumes 3 and 4 provide a technical processor, new to SCSS, the information and methodology necessary to capture descriptive data from the LER and to codify that data into a structured format and serve as reference material for the more experienced technical processor, and contains information is essential for the more advanced user who needs to be familiar with the intricate coding techniques in order to retrieve specific details in a sequence. This volume contains updated material through amendment 1 to revision 1 of the working version of ORNL/NSIC-223, Vol. 3

  17. The sequence coding and search system: An approach for constructing and analyzing event sequences at commercial nuclear power plants

    International Nuclear Information System (INIS)

    Mays, G.T.

    1989-04-01

    The US Nuclear Regulatory Commission (NRC) has recognized the importance of the collection, assessment, and feedstock of operating experience data from commercial nuclear power plants and has centralized these activities in the Office for Analysis and Evaluation of Operational Data (AEOD). Such data is essential for performing safety and reliability analyses, especially analyses of trends and patterns to identify undesirable changes in plant performance at the earliest opportunity to implement corrective measures to preclude the occurrences of a more serious event. One of NRC's principal tools for collecting and evaluating operating experience data is the Sequence Coding and Search System (SCSS). The SCSS consists of a methodology for structuring event sequences and the requisite computer system to store and search the data. The source information for SCSS is the Licensee Event Report (LER), which is a legally required document. This paper describes the objective SCSS, the information it contains, and the format and approach for constructuring SCSS event sequences. Examples are presented demonstrating the use SCSS to support the analysis of LER data. The SCSS contains over 30,000 LERs describing events from 1980 through the present. Insights gained from working with a complex data system from the initial developmental stage to the point of a mature operating system are highlighted

  18. Coding sequence of human rho cDNAs clone 6 and clone 9

    Energy Technology Data Exchange (ETDEWEB)

    Chardin, P; Madaule, P; Tavitian, A

    1988-03-25

    The authors have isolated human cDNAs including the complete coding sequence for two rho proteins corresponding to the incomplete isolates previously described as clone 6 and clone 9. The deduced a.a. sequences, when compared to the a.a. sequence deduced from clone 12 cDNA, show that there are in human at least three highly homologous rho genes. They suggest that clone 12 be named rhoA, clone 6 : rhoB and clone 9 : rhoC. RhoA, B and C proteins display approx. 30% a.a. identity with ras proteins,. mainly clustered in four highly homologous internal regions corresponding to the GTP binding site; however at least one significant difference is found; the 3 rho proteins have an Alanine in position corresponding to ras Glycine 13, suggesting that rho and ras proteins might have slightly different biochemical properties.

  19. Enhanced Protein Production in Escherichia coli by Optimization of Cloning Scars at the Vector-Coding Sequence Junction

    DEFF Research Database (Denmark)

    Mirzadeh, Kiavash; Martinez, Virginia; Toddo, Stephen

    2015-01-01

    are poorly expressed even when they are codon-optimized and expressed from vectors with powerful genetic elements. In this study, we show that poor expression can be caused by certain nucleotide sequences (e.g., cloning scars) at the junction between the vector and the coding sequence. Since these sequences...

  20. cDNA sequence of human transforming gene hst and identification of the coding sequence required for transforming activity

    International Nuclear Information System (INIS)

    Taira, M.; Yoshida, T.; Miyagawa, K.; Sakamoto, H.; Terada, M.; Sugimura, T.

    1987-01-01

    The hst gene was originally identified as a transforming gene in DNAs from human stomach cancers and from a noncancerous portion of stomach mucosa by DNA-mediated transfection assay using NIH3T3 cells. cDNA clones of hst were isolated from the cDNA library constructed from poly(A) + RNA of a secondary transformant induced by the DNA from a stomach cancer. The sequence analysis of the hst cDNA revealed the presence of two open reading frames. When this cDNA was inserted into an expression vector containing the simian virus 40 promoter, it efficiently induced the transformation of NIH3T3 cells upon transfection. It was found that one of the reading frames, which coded for 206 amino acids, was responsible for the transforming activity

  1. Sequence Coding and Search System for licensee event reports: user's guide. Volume 1, Revision 1

    International Nuclear Information System (INIS)

    Greene, N.M.; Mays, G.T.; Johnson, M.P.

    1985-04-01

    Operating experience data from nuclear power plants are essential for safety and reliability analyses, especially analyses of trends and patterns. The licensee event reports (LERs) that are submitted to the Nuclear Regulatory Commission (NRC) by the nuclear power plant utilities contain much of this data. The NRC's Office for Analysis and Evaluation of Operational Data (AEOD) has developed, under contract with NSIC, a system for codifying the events reported in the LERs. The primary objective of the Sequence Coding and Search System (SCSS) is to reduce the descriptive text of the LERs to coded sequences that are both computer-readable and computer-searchable. This system provides a structured format for detailed coding of component, system, and unit effects as well as personnel errors. The database contains all current LERs submitted by nuclear power plant utilities for events occurring since 1981 and is updated on a continual basis. This four volume report documents and describes SCSS in detail. Volume 1 is a User's Guide for searching the SCSS database. This volume contains updated material through February 1985 of the working version of ORNL/NSIC-223, Vol. 1

  2. Hybridization-based reconstruction of small non-coding RNA transcripts from deep sequencing data.

    Science.gov (United States)

    Ragan, Chikako; Mowry, Bryan J; Bauer, Denis C

    2012-09-01

    Recent advances in RNA sequencing technology (RNA-Seq) enables comprehensive profiling of RNAs by producing millions of short sequence reads from size-fractionated RNA libraries. Although conventional tools for detecting and distinguishing non-coding RNAs (ncRNAs) from reference-genome data can be applied to sequence data, ncRNA detection can be improved by harnessing the full information content provided by this new technology. Here we present NorahDesk, the first unbiased and universally applicable method for small ncRNAs detection from RNA-Seq data. NorahDesk utilizes the coverage-distribution of small RNA sequence data as well as thermodynamic assessments of secondary structure to reliably predict and annotate ncRNA classes. Using publicly available mouse sequence data from brain, skeletal muscle, testis and ovary, we evaluated our method with an emphasis on the performance for microRNAs (miRNAs) and piwi-interacting small RNA (piRNA). We compared our method with Dario and mirDeep2 and found that NorahDesk produces longer transcripts with higher read coverage. This feature makes it the first method particularly suitable for the prediction of both known and novel piRNAs.

  3. A versatile palindromic amphipathic repeat coding sequence horizontally distributed among diverse bacterial and eucaryotic microbes

    Directory of Open Access Journals (Sweden)

    Glass John I

    2010-07-01

    repeat may be disseminated by HGT and intra-genomic shuffling. Conclusions We describe novel features of PARCELs (Palindromic Amphipathic Repeat Coding ELements, a set of widely distributed repeat protein domains and coding sequences that were likely acquired through HGT by diverse unicellular microbes, further mobilized and diversified within genomes, and co-opted for expression in the membrane proteome of some taxa. Disseminated by multiple gene-centric vehicles, ORFs harboring these elements enhance accessory gene pools as part of the "mobilome" connecting genomes of various clades, in taxa sharing common niches.

  4. Whole-Exome Sequencing Identifies Rare and Low-Frequency Coding Variants Associated with LDL Cholesterol

    Science.gov (United States)

    Lange, Leslie A.; Hu, Youna; Zhang, He; Xue, Chenyi; Schmidt, Ellen M.; Tang, Zheng-Zheng; Bizon, Chris; Lange, Ethan M.; Smith, Joshua D.; Turner, Emily H.; Jun, Goo; Kang, Hyun Min; Peloso, Gina; Auer, Paul; Li, Kuo-ping; Flannick, Jason; Zhang, Ji; Fuchsberger, Christian; Gaulton, Kyle; Lindgren, Cecilia; Locke, Adam; Manning, Alisa; Sim, Xueling; Rivas, Manuel A.; Holmen, Oddgeir L.; Gottesman, Omri; Lu, Yingchang; Ruderfer, Douglas; Stahl, Eli A.; Duan, Qing; Li, Yun; Durda, Peter; Jiao, Shuo; Isaacs, Aaron; Hofman, Albert; Bis, Joshua C.; Correa, Adolfo; Griswold, Michael E.; Jakobsdottir, Johanna; Smith, Albert V.; Schreiner, Pamela J.; Feitosa, Mary F.; Zhang, Qunyuan; Huffman, Jennifer E.; Crosby, Jacy; Wassel, Christina L.; Do, Ron; Franceschini, Nora; Martin, Lisa W.; Robinson, Jennifer G.; Assimes, Themistocles L.; Crosslin, David R.; Rosenthal, Elisabeth A.; Tsai, Michael; Rieder, Mark J.; Farlow, Deborah N.; Folsom, Aaron R.; Lumley, Thomas; Fox, Ervin R.; Carlson, Christopher S.; Peters, Ulrike; Jackson, Rebecca D.; van Duijn, Cornelia M.; Uitterlinden, André G.; Levy, Daniel; Rotter, Jerome I.; Taylor, Herman A.; Gudnason, Vilmundur; Siscovick, David S.; Fornage, Myriam; Borecki, Ingrid B.; Hayward, Caroline; Rudan, Igor; Chen, Y. Eugene; Bottinger, Erwin P.; Loos, Ruth J.F.; Sætrom, Pål; Hveem, Kristian; Boehnke, Michael; Groop, Leif; McCarthy, Mark; Meitinger, Thomas; Ballantyne, Christie M.; Gabriel, Stacey B.; O’Donnell, Christopher J.; Post, Wendy S.; North, Kari E.; Reiner, Alexander P.; Boerwinkle, Eric; Psaty, Bruce M.; Altshuler, David; Kathiresan, Sekar; Lin, Dan-Yu; Jarvik, Gail P.; Cupples, L. Adrienne; Kooperberg, Charles; Wilson, James G.; Nickerson, Deborah A.; Abecasis, Goncalo R.; Rich, Stephen S.; Tracy, Russell P.; Willer, Cristen J.; Gabriel, Stacey B.; Altshuler, David M.; Abecasis, Gonçalo R.; Allayee, Hooman; Cresci, Sharon; Daly, Mark J.; de Bakker, Paul I.W.; DePristo, Mark A.; Do, Ron; Donnelly, Peter; Farlow, Deborah N.; Fennell, Tim; Garimella, Kiran; Hazen, Stanley L.; Hu, Youna; Jordan, Daniel M.; Jun, Goo; Kathiresan, Sekar; Kang, Hyun Min; Kiezun, Adam; Lettre, Guillaume; Li, Bingshan; Li, Mingyao; Newton-Cheh, Christopher H.; Padmanabhan, Sandosh; Peloso, Gina; Pulit, Sara; Rader, Daniel J.; Reich, David; Reilly, Muredach P.; Rivas, Manuel A.; Schwartz, Steve; Scott, Laura; Siscovick, David S.; Spertus, John A.; Stitziel, Nathaniel O.; Stoletzki, Nina; Sunyaev, Shamil R.; Voight, Benjamin F.; Willer, Cristen J.; Rich, Stephen S.; Akylbekova, Ermeg; Atwood, Larry D.; Ballantyne, Christie M.; Barbalic, Maja; Barr, R. Graham; Benjamin, Emelia J.; Bis, Joshua; Boerwinkle, Eric; Bowden, Donald W.; Brody, Jennifer; Budoff, Matthew; Burke, Greg; Buxbaum, Sarah; Carr, Jeff; Chen, Donna T.; Chen, Ida Y.; Chen, Wei-Min; Concannon, Pat; Crosby, Jacy; Cupples, L. Adrienne; D’Agostino, Ralph; DeStefano, Anita L.; Dreisbach, Albert; Dupuis, Josée; Durda, J. Peter; Ellis, Jaclyn; Folsom, Aaron R.; Fornage, Myriam; Fox, Caroline S.; Fox, Ervin; Funari, Vincent; Ganesh, Santhi K.; Gardin, Julius; Goff, David; Gordon, Ora; Grody, Wayne; Gross, Myron; Guo, Xiuqing; Hall, Ira M.; Heard-Costa, Nancy L.; Heckbert, Susan R.; Heintz, Nicholas; Herrington, David M.; Hickson, DeMarc; Huang, Jie; Hwang, Shih-Jen; Jacobs, David R.; Jenny, Nancy S.; Johnson, Andrew D.; Johnson, Craig W.; Kawut, Steven; Kronmal, Richard; Kurz, Raluca; Lange, Ethan M.; Lange, Leslie A.; Larson, Martin G.; Lawson, Mark; Lewis, Cora E.; Levy, Daniel; Li, Dalin; Lin, Honghuang; Liu, Chunyu; Liu, Jiankang; Liu, Kiang; Liu, Xiaoming; Liu, Yongmei; Longstreth, William T.; Loria, Cay; Lumley, Thomas; Lunetta, Kathryn; Mackey, Aaron J.; Mackey, Rachel; Manichaikul, Ani; Maxwell, Taylor; McKnight, Barbara; Meigs, James B.; Morrison, Alanna C.; Musani, Solomon K.; Mychaleckyj, Josyf C.; Nettleton, Jennifer A.; North, Kari; O’Donnell, Christopher J.; O’Leary, Daniel; Ong, Frank; Palmas, Walter; Pankow, James S.; Pankratz, Nathan D.; Paul, Shom; Perez, Marco; Person, Sharina D.; Polak, Joseph; Post, Wendy S.; Psaty, Bruce M.; Quinlan, Aaron R.; Raffel, Leslie J.; Ramachandran, Vasan S.; Reiner, Alexander P.; Rice, Kenneth; Rotter, Jerome I.; Sanders, Jill P.; Schreiner, Pamela; Seshadri, Sudha; Shea, Steve; Sidney, Stephen; Silverstein, Kevin; Smith, Nicholas L.; Sotoodehnia, Nona; Srinivasan, Asoke; Taylor, Herman A.; Taylor, Kent; Thomas, Fridtjof; Tracy, Russell P.; Tsai, Michael Y.; Volcik, Kelly A.; Wassel, Chrstina L.; Watson, Karol; Wei, Gina; White, Wendy; Wiggins, Kerri L.; Wilk, Jemma B.; Williams, O. Dale; Wilson, Gregory; Wilson, James G.; Wolf, Phillip; Zakai, Neil A.; Hardy, John; Meschia, James F.; Nalls, Michael; Singleton, Andrew; Worrall, Brad; Bamshad, Michael J.; Barnes, Kathleen C.; Abdulhamid, Ibrahim; Accurso, Frank; Anbar, Ran; Beaty, Terri; Bigham, Abigail; Black, Phillip; Bleecker, Eugene; Buckingham, Kati; Cairns, Anne Marie; Caplan, Daniel; Chatfield, Barbara; Chidekel, Aaron; Cho, Michael; Christiani, David C.; Crapo, James D.; Crouch, Julia; Daley, Denise; Dang, Anthony; Dang, Hong; De Paula, Alicia; DeCelie-Germana, Joan; Drumm, Allen DozorMitch; Dyson, Maynard; Emerson, Julia; Emond, Mary J.; Ferkol, Thomas; Fink, Robert; Foster, Cassandra; Froh, Deborah; Gao, Li; Gershan, William; Gibson, Ronald L.; Godwin, Elizabeth; Gondor, Magdalen; Gutierrez, Hector; Hansel, Nadia N.; Hassoun, Paul M.; Hiatt, Peter; Hokanson, John E.; Howenstine, Michelle; Hummer, Laura K.; Kanga, Jamshed; Kim, Yoonhee; Knowles, Michael R.; Konstan, Michael; Lahiri, Thomas; Laird, Nan; Lange, Christoph; Lin, Lin; Lin, Xihong; Louie, Tin L.; Lynch, David; Make, Barry; Martin, Thomas R.; Mathai, Steve C.; Mathias, Rasika A.; McNamara, John; McNamara, Sharon; Meyers, Deborah; Millard, Susan; Mogayzel, Peter; Moss, Richard; Murray, Tanda; Nielson, Dennis; Noyes, Blakeslee; O’Neal, Wanda; Orenstein, David; O’Sullivan, Brian; Pace, Rhonda; Pare, Peter; Parker, H. Worth; Passero, Mary Ann; Perkett, Elizabeth; Prestridge, Adrienne; Rafaels, Nicholas M.; Ramsey, Bonnie; Regan, Elizabeth; Ren, Clement; Retsch-Bogart, George; Rock, Michael; Rosen, Antony; Rosenfeld, Margaret; Ruczinski, Ingo; Sanford, Andrew; Schaeffer, David; Sell, Cindy; Sheehan, Daniel; Silverman, Edwin K.; Sin, Don; Spencer, Terry; Stonebraker, Jackie; Tabor, Holly K.; Varlotta, Laurie; Vergara, Candelaria I.; Weiss, Robert; Wigley, Fred; Wise, Robert A.; Wright, Fred A.; Wurfel, Mark M.; Zanni, Robert; Zou, Fei; Nickerson, Deborah A.; Rieder, Mark J.; Green, Phil; Shendure, Jay; Akey, Joshua M.; Bustamante, Carlos D.; Crosslin, David R.; Eichler, Evan E.; Fox, P. Keolu; Fu, Wenqing; Gordon, Adam; Gravel, Simon; Jarvik, Gail P.; Johnsen, Jill M.; Kan, Mengyuan; Kenny, Eimear E.; Kidd, Jeffrey M.; Lara-Garduno, Fremiet; Leal, Suzanne M.; Liu, Dajiang J.; McGee, Sean; O’Connor, Timothy D.; Paeper, Bryan; Robertson, Peggy D.; Smith, Joshua D.; Staples, Jeffrey C.; Tennessen, Jacob A.; Turner, Emily H.; Wang, Gao; Yi, Qian; Jackson, Rebecca; Peters, Ulrike; Carlson, Christopher S.; Anderson, Garnet; Anton-Culver, Hoda; Assimes, Themistocles L.; Auer, Paul L.; Beresford, Shirley; Bizon, Chris; Black, Henry; Brunner, Robert; Brzyski, Robert; Burwen, Dale; Caan, Bette; Carty, Cara L.; Chlebowski, Rowan; Cummings, Steven; Curb, J. David; Eaton, Charles B.; Ford, Leslie; Franceschini, Nora; Fullerton, Stephanie M.; Gass, Margery; Geller, Nancy; Heiss, Gerardo; Howard, Barbara V.; Hsu, Li; Hutter, Carolyn M.; Ioannidis, John; Jiao, Shuo; Johnson, Karen C.; Kooperberg, Charles; Kuller, Lewis; LaCroix, Andrea; Lakshminarayan, Kamakshi; Lane, Dorothy; Lasser, Norman; LeBlanc, Erin; Li, Kuo-Ping; Limacher, Marian; Lin, Dan-Yu; Logsdon, Benjamin A.; Ludlam, Shari; Manson, JoAnn E.; Margolis, Karen; Martin, Lisa; McGowan, Joan; Monda, Keri L.; Kotchen, Jane Morley; Nathan, Lauren; Ockene, Judith; O’Sullivan, Mary Jo; Phillips, Lawrence S.; Prentice, Ross L.; Robbins, John; Robinson, Jennifer G.; Rossouw, Jacques E.; Sangi-Haghpeykar, Haleh; Sarto, Gloria E.; Shumaker, Sally; Simon, Michael S.; Stefanick, Marcia L.; Stein, Evan; Tang, Hua; Taylor, Kira C.; Thomson, Cynthia A.; Thornton, Timothy A.; Van Horn, Linda; Vitolins, Mara; Wactawski-Wende, Jean; Wallace, Robert; Wassertheil-Smoller, Sylvia; Zeng, Donglin; Applebaum-Bowden, Deborah; Feolo, Michael; Gan, Weiniu; Paltoo, Dina N.; Sholinsky, Phyliss; Sturcke, Anne

    2014-01-01

    Elevated low-density lipoprotein cholesterol (LDL-C) is a treatable, heritable risk factor for cardiovascular disease. Genome-wide association studies (GWASs) have identified 157 variants associated with lipid levels but are not well suited to assess the impact of rare and low-frequency variants. To determine whether rare or low-frequency coding variants are associated with LDL-C, we exome sequenced 2,005 individuals, including 554 individuals selected for extreme LDL-C (>98th or <2nd percentile). Follow-up analyses included sequencing of 1,302 additional individuals and genotype-based analysis of 52,221 individuals. We observed significant evidence of association between LDL-C and the burden of rare or low-frequency variants in PNPLA5, encoding a phospholipase-domain-containing protein, and both known and previously unidentified variants in PCSK9, LDLR and APOB, three known lipid-related genes. The effect sizes for the burden of rare variants for each associated gene were substantially higher than those observed for individual SNPs identified from GWASs. We replicated the PNPLA5 signal in an independent large-scale sequencing study of 2,084 individuals. In conclusion, this large whole-exome-sequencing study for LDL-C identified a gene not known to be implicated in LDL-C and provides unique insight into the design and analysis of similar experiments. PMID:24507775

  5. Verona Coding Definitions of Emotional Sequences (VR-CoDES): Conceptual framework and future directions.

    Science.gov (United States)

    Piccolo, Lidia Del; Finset, Arnstein; Mellblom, Anneli V; Figueiredo-Braga, Margarida; Korsvold, Live; Zhou, Yuefang; Zimmermann, Christa; Humphris, Gerald

    2017-12-01

    To discuss the theoretical and empirical framework of VR-CoDES and potential future direction in research based on the coding system. The paper is based on selective review of papers relevant to the construction and application of VR-CoDES. VR-CoDES system is rooted in patient-centered and biopsychosocial model of healthcare consultations and on a functional approach to emotion theory. According to the VR-CoDES, emotional interaction is studied in terms of sequences consisting of an eliciting event, an emotional expression by the patient and the immediate response by the clinician. The rationale for the emphasis on sequences, on detailed classification of cues and concerns, and on the choices of explicit vs. non-explicit responses and providing vs. reducing room for further disclosure, as basic categories of the clinician responses, is described. Results from research on VR-CoDES may help raise awareness of emotional sequences. Future directions in applying VR-CoDES in research may include studies on predicting patient and clinician behavior within the consultation, qualitative analyses of longer sequences including several VR-CoDES triads, and studies of effects of emotional communication on health outcomes. VR-CoDES may be applied to develop interventions to promote good handling of patients' emotions in healthcare encounters. Copyright © 2017 Elsevier B.V. All rights reserved.

  6. An Explicit Construction of a sequence of codes attaining the Tsfasman-Vladut-Zink Bound:The first steps

    DEFF Research Database (Denmark)

    Høholdt, Tom; Voss, Cornelia

    1997-01-01

    We present a sequence of codes attaining the Tsfasman-Vladut-Zink bound. The construction is based on the tower of Artin-Schreier extensions described by Garcia and Stichtenoth (1995). We also determine the dual codes. The first steps of the constructions are explicitly given as generator matrices...

  7. Sequence-based heuristics for faster annotation of non-coding RNA families.

    Science.gov (United States)

    Weinberg, Zasha; Ruzzo, Walter L

    2006-01-01

    Non-coding RNAs (ncRNAs) are functional RNA molecules that do not code for proteins. Covariance Models (CMs) are a useful statistical tool to find new members of an ncRNA gene family in a large genome database, using both sequence and, importantly, RNA secondary structure information. Unfortunately, CM searches are extremely slow. Previously, we created rigorous filters, which provably sacrifice none of a CM's accuracy, while making searches significantly faster for virtually all ncRNA families. However, these rigorous filters make searches slower than heuristics could be. In this paper we introduce profile HMM-based heuristic filters. We show that their accuracy is usually superior to heuristics based on BLAST. Moreover, we compared our heuristics with those used in tRNAscan-SE, whose heuristics incorporate a significant amount of work specific to tRNAs, where our heuristics are generic to any ncRNA. Performance was roughly comparable, so we expect that our heuristics provide a high-quality solution that--unlike family-specific solutions--can scale to hundreds of ncRNA families. The source code is available under GNU Public License at the supplementary web site.

  8. Code-Switching to Know a TL Equivalent of an L1 Word: Request-Provision-Acknowledgement (RPA) Sequence

    Science.gov (United States)

    Lucero, Edgar

    2011-01-01

    This article focuses on the learner's use of Code-switching to learn the TL (Target Language) equivalent of an L1 word. The interactional pattern that this situation creates defines the Request-Provision-Acknowledgement (RPA) sequence. The article explains each of the turns of the sequence under the combination of the Ethnomethodological…

  9. Complete coding sequence of the human raf oncogene and the corresponding structure of the c-raf-1 gene

    Energy Technology Data Exchange (ETDEWEB)

    Bonner, T I; Oppermann, H; Seeburg, P; Kerby, S B; Gunnell, M A; Young, A C; Rapp, U R

    1986-01-24

    The complete 648 amino acid sequence of the human raf oncogene was deduced from the 2977 nucleotide sequence of a fetal liver cDNA. The cDNA has been used to obtain clones which extend the human c-raf-1 locus by an additional 18.9 kb at the 5' end and contain all the remaining coding exons.

  10. Capsid coding sequences of foot-and-mouth disease viruses are determinants of pathogenicity in pigs

    DEFF Research Database (Denmark)

    Lohse, Louise; Jackson, Terry; Bøtner, Anette

    2012-01-01

    The surface exposed capsid proteins, VP1, VP2 and VP3, of foot-and-mouth disease virus (FMDV) determine its antigenicity and the ability of the virus to interact with host-cell receptors. Hence, modification of these structural proteins may alter the properties of the virus. In the present study we...... compared the pathogenicity of different FMDVs in young pigs. In total 32 pigs, 7-weeks-old, were exposed to virus, either by direct inoculation or through contact with inoculated pigs, using cell culture adapted (O1K B64), chimeric (O1K/A-TUR and O1K/O-UKG) or field strain (O-UKG/34/2001) viruses. The O1K...... coding sequences are determinants of FMDV pathogenicity in pigs....

  11. The use of coded PCR primers enables high-throughput sequencing of multiple homolog amplification products by 454 parallel sequencing

    DEFF Research Database (Denmark)

    Binladen, Jonas; Gilbert, M Thomas P; Bollback, Jonathan P

    2007-01-01

    BACKGROUND: The invention of the Genome Sequence 20 DNA Sequencing System (454 parallel sequencing platform) has enabled the rapid and high-volume production of sequence data. Until now, however, individual emulsion PCR (emPCR) reactions and subsequent sequencing runs have been unable to combine...... primers that is dependent on the 5' nucleotide of the tag. In particular, primers 5' labelled with a cytosine are heavily overrepresented among the final sequences, while those 5' labelled with a thymine are strongly underrepresented. A weaker bias also exists with regards to the distribution...

  12. Deep Sequencing Reveals Uncharted Isoform Heterogeneity of the Protein-Coding Transcriptome in Cerebral Ischemia.

    Science.gov (United States)

    Bhattarai, Sunil; Aly, Ahmed; Garcia, Kristy; Ruiz, Diandra; Pontarelli, Fabrizio; Dharap, Ashutosh

    2018-06-03

    Gene expression in cerebral ischemia has been a subject of intense investigations for several years. Studies utilizing probe-based high-throughput methodologies such as microarrays have contributed significantly to our existing knowledge but lacked the capacity to dissect the transcriptome in detail. Genome-wide RNA-sequencing (RNA-seq) enables comprehensive examinations of transcriptomes for attributes such as strandedness, alternative splicing, alternative transcription start/stop sites, and sequence composition, thus providing a very detailed account of gene expression. Leveraging this capability, we conducted an in-depth, genome-wide evaluation of the protein-coding transcriptome of the adult mouse cortex after transient focal ischemia at 6, 12, or 24 h of reperfusion using RNA-seq. We identified a total of 1007 transcripts at 6 h, 1878 transcripts at 12 h, and 1618 transcripts at 24 h of reperfusion that were significantly altered as compared to sham controls. With isoform-level resolution, we identified 23 splice variants arising from 23 genes that were novel mRNA isoforms. For a subset of genes, we detected reperfusion time-point-dependent splice isoform switching, indicating an expression and/or functional switch for these genes. Finally, for 286 genes across all three reperfusion time-points, we discovered multiple, distinct, simultaneously expressed and differentially altered isoforms per gene that were generated via alternative transcription start/stop sites. Of these, 165 isoforms derived from 109 genes were novel mRNAs. Together, our data unravel the protein-coding transcriptome of the cerebral cortex at an unprecedented depth to provide several new insights into the flexibility and complexity of stroke-related gene transcription and transcript organization.

  13. Phylogenomic Resolution of the Phylogeny of Laurasiatherian Mammals: Exploring Phylogenetic Signals within Coding and Noncoding Sequences.

    Science.gov (United States)

    Chen, Meng-Yun; Liang, Dan; Zhang, Peng

    2017-08-01

    The interordinal relationships of Laurasiatherian mammals are currently one of the most controversial questions in mammalian phylogenetics. Previous studies mainly relied on coding sequences (CDS) and seldom used noncoding sequences. Here, by data mining public genome data, we compiled an intron data set of 3,638 genes (all introns from a protein-coding gene are considered as a gene) (19,055,073 bp) and a CDS data set of 10,259 genes (20,994,285 bp), covering all major lineages of Laurasiatheria (except Pholidota). We found that the intron data contained stronger and more congruent phylogenetic signals than the CDS data. In agreement with this observation, concatenation and species-tree analyses of the intron data set yielded well-resolved and identical phylogenies, whereas the CDS data set produced weakly supported and incongruent results. Further analyses showed that the phylogeny inferred from the intron data is highly robust to data subsampling and change in outgroup, but the CDS data produced unstable results under the same conditions. Interestingly, gene tree statistical results showed that the most frequently observed gene tree topologies for the CDS and intron data are identical, suggesting that the major phylogenetic signal within the CDS data is actually congruent with that within the intron data. Our final result of Laurasiatheria phylogeny is (Eulipotyphla,((Chiroptera, Perissodactyla),(Carnivora, Cetartiodactyla))), favoring a close relationship between Chiroptera and Perissodactyla. Our study 1) provides a well-supported phylogenetic framework for Laurasiatheria, representing a step towards ending the long-standing "hard" polytomy and 2) argues that intron within genome data is a promising data resource for resolving rapid radiation events across the tree of life. © The Author 2017. Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution.

  14. The use of coded PCR primers enables high-throughput sequencing of multiple homolog amplification products by 454 parallel sequencing.

    Directory of Open Access Journals (Sweden)

    Jonas Binladen

    2007-02-01

    Full Text Available The invention of the Genome Sequence 20 DNA Sequencing System (454 parallel sequencing platform has enabled the rapid and high-volume production of sequence data. Until now, however, individual emulsion PCR (emPCR reactions and subsequent sequencing runs have been unable to combine template DNA from multiple individuals, as homologous sequences cannot be subsequently assigned to their original sources.We use conventional PCR with 5'-nucleotide tagged primers to generate homologous DNA amplification products from multiple specimens, followed by sequencing through the high-throughput Genome Sequence 20 DNA Sequencing System (GS20, Roche/454 Life Sciences. Each DNA sequence is subsequently traced back to its individual source through 5'tag-analysis.We demonstrate that this new approach enables the assignment of virtually all the generated DNA sequences to the correct source once sequencing anomalies are accounted for (miss-assignment rate<0.4%. Therefore, the method enables accurate sequencing and assignment of homologous DNA sequences from multiple sources in single high-throughput GS20 run. We observe a bias in the distribution of the differently tagged primers that is dependent on the 5' nucleotide of the tag. In particular, primers 5' labelled with a cytosine are heavily overrepresented among the final sequences, while those 5' labelled with a thymine are strongly underrepresented. A weaker bias also exists with regards to the distribution of the sequences as sorted by the second nucleotide of the dinucleotide tags. As the results are based on a single GS20 run, the general applicability of the approach requires confirmation. However, our experiments demonstrate that 5'primer tagging is a useful method in which the sequencing power of the GS20 can be applied to PCR-based assays of multiple homologous PCR products. The new approach will be of value to a broad range of research areas, such as those of comparative genomics, complete mitochondrial

  15. On randomly interrupted diffusion

    International Nuclear Information System (INIS)

    Luczka, J.

    1993-01-01

    Processes driven by randomly interrupted Gaussian white noise are considered. An evolution equation for single-event probability distributions in presented. Stationary states are considered as a solution of a second-order ordinary differential equation with two imposed conditions. A linear model is analyzed and its stationary distributions are explicitly given. (author). 10 refs

  16. Biased Gene Conversion and GC-Content Evolution in the Coding Sequences of Reptiles and Vertebrates

    Science.gov (United States)

    Figuet, Emeric; Ballenghien, Marion; Romiguier, Jonathan; Galtier, Nicolas

    2015-01-01

    Mammalian and avian genomes are characterized by a substantial spatial heterogeneity of GC-content, which is often interpreted as reflecting the effect of local GC-biased gene conversion (gBGC), a meiotic repair bias that favors G and C over A and T alleles in high-recombining genomic regions. Surprisingly, the first fully sequenced nonavian sauropsid (i.e., reptile), the green anole Anolis carolinensis, revealed a highly homogeneous genomic GC-content landscape, suggesting the possibility that gBGC might not be at work in this lineage. Here, we analyze GC-content evolution at third-codon positions (GC3) in 44 vertebrates species, including eight newly sequenced transcriptomes, with a specific focus on nonavian sauropsids. We report that reptiles, including the green anole, have a genome-wide distribution of GC3 similar to that of mammals and birds, and we infer a strong GC3-heterogeneity to be already present in the tetrapod ancestor. We further show that the dynamic of coding sequence GC-content is largely governed by karyotypic features in vertebrates, notably in the green anole, in agreement with the gBGC hypothesis. The discrepancy between third-codon positions and noncoding DNA regarding GC-content dynamics in the green anole could not be explained by the activity of transposable elements or selection on codon usage. This analysis highlights the unique value of third-codon positions as an insertion/deletion-free marker of nucleotide substitution biases that ultimately affect the evolution of proteins. PMID:25527834

  17. Transduplication resulted in the incorporation of two protein-coding sequences into the Turmoil-1 transposable element of C. elegans

    Directory of Open Access Journals (Sweden)

    Pupko Tal

    2008-10-01

    Full Text Available Abstract Transposable elements may acquire unrelated gene fragments into their sequences in a process called transduplication. Transduplication of protein-coding genes is common in plants, but is unknown of in animals. Here, we report that the Turmoil-1 transposable element in C. elegans has incorporated two protein-coding sequences into its inverted terminal repeat (ITR sequences. The ITRs of Turmoil-1 contain a conserved RNA recognition motif (RRM that originated from the rsp-2 gene and a fragment from the protein-coding region of the cpg-3 gene. We further report that an open reading frame specific to C. elegans may have been created as a result of a Turmoil-1 insertion. Mutations at the 5' splice site of this open reading frame may have reactivated the transduplicated RRM motif. Reviewers This article was reviewed by Dan Graur and William Martin. For the full reviews, please go to the Reviewers' Reports section.

  18. The role of interruptions in polyQ in the pathology of SCA1.

    Directory of Open Access Journals (Sweden)

    Rajesh P Menon

    Full Text Available At least nine dominant neurodegenerative diseases are caused by expansion of CAG repeats in coding regions of specific genes that result in abnormal elongation of polyglutamine (polyQ tracts in the corresponding gene products. When above a threshold that is specific for each disease the expanded polyQ repeats promote protein aggregation, misfolding and neuronal cell death. The length of the polyQ tract inversely correlates with the age at disease onset. It has been observed that interruption of the CAG tract by silent (CAA or missense (CAT mutations may strongly modulate the effect of the expansion and delay the onset age. We have carried out an extensive study in which we have complemented DNA sequence determination with cellular and biophysical models. By sequencing cloned normal and expanded SCA1 alleles taken from our cohort of ataxia patients we have determined sequence variations not detected by allele sizing and observed for the first time that repeat instability can occur even in the presence of CAG interruptions. We show that histidine interrupted pathogenic alleles occur with relatively high frequency (11% and that the age at onset inversely correlates linearly with the longer uninterrupted CAG stretch. This could be reproduced in a cellular model to support the hypothesis of a linear behaviour of polyQ. We clarified by in vitro studies the mechanism by which polyQ interruption slows down aggregation. Our study contributes to the understanding of the role of polyQ interruption in the SCA1 phenotype with regards to age at disease onset, prognosis and transmission.

  19. SHARAKU: an algorithm for aligning and clustering read mapping profiles of deep sequencing in non-coding RNA processing.

    Science.gov (United States)

    Tsuchiya, Mariko; Amano, Kojiro; Abe, Masaya; Seki, Misato; Hase, Sumitaka; Sato, Kengo; Sakakibara, Yasubumi

    2016-06-15

    Deep sequencing of the transcripts of regulatory non-coding RNA generates footprints of post-transcriptional processes. After obtaining sequence reads, the short reads are mapped to a reference genome, and specific mapping patterns can be detected called read mapping profiles, which are distinct from random non-functional degradation patterns. These patterns reflect the maturation processes that lead to the production of shorter RNA sequences. Recent next-generation sequencing studies have revealed not only the typical maturation process of miRNAs but also the various processing mechanisms of small RNAs derived from tRNAs and snoRNAs. We developed an algorithm termed SHARAKU to align two read mapping profiles of next-generation sequencing outputs for non-coding RNAs. In contrast with previous work, SHARAKU incorporates the primary and secondary sequence structures into an alignment of read mapping profiles to allow for the detection of common processing patterns. Using a benchmark simulated dataset, SHARAKU exhibited superior performance to previous methods for correctly clustering the read mapping profiles with respect to 5'-end processing and 3'-end processing from degradation patterns and in detecting similar processing patterns in deriving the shorter RNAs. Further, using experimental data of small RNA sequencing for the common marmoset brain, SHARAKU succeeded in identifying the significant clusters of read mapping profiles for similar processing patterns of small derived RNA families expressed in the brain. The source code of our program SHARAKU is available at http://www.dna.bio.keio.ac.jp/sharaku/, and the simulated dataset used in this work is available at the same link. Accession code: The sequence data from the whole RNA transcripts in the hippocampus of the left brain used in this work is available from the DNA DataBank of Japan (DDBJ) Sequence Read Archive (DRA) under the accession number DRA004502. yasu@bio.keio.ac.jp Supplementary data are available

  20. FOURTH SEMINAR TO THE MEMORY OF D.N. KLYSHKO: Algebraic solution of the synthesis problem for coded sequences

    Science.gov (United States)

    Leukhin, Anatolii N.

    2005-08-01

    The algebraic solution of a 'complex' problem of synthesis of phase-coded (PC) sequences with the zero level of side lobes of the cyclic autocorrelation function (ACF) is proposed. It is shown that the solution of the synthesis problem is connected with the existence of difference sets for a given code dimension. The problem of estimating the number of possible code combinations for a given code dimension is solved. It is pointed out that the problem of synthesis of PC sequences is related to the fundamental problems of discrete mathematics and, first of all, to a number of combinatorial problems, which can be solved, as the number factorisation problem, by algebraic methods by using the theory of Galois fields and groups.

  1. Sound, memory and interruption

    DEFF Research Database (Denmark)

    Pinder, David

    2016-01-01

    This chapter considers how art can interrupt the times and spaces of urban development so they might be imagined, experienced and understood differently. It focuses on the construction of the M11 Link Road through north-east London during the 1990s that demolished hundreds of homes and displaced...... around a thousand people. The highway was strongly resisted and it became the site of one of the country’s longest and largest anti-road struggles. The chapter addresses specifically Graeme Miller’s sound walk LINKED (2003), which for more than a decade has been broadcasting memories and stories...... of people who were violently displaced by the road as well as those who actively sought to halt it. Attention is given to the walk’s interruption of senses of the given and inevitable in two main ways. The first is in relation to the pace of the work and its deployment of slowness and arrest in a context...

  2. IdentiCS – Identification of coding sequence and in silico reconstruction of the metabolic network directly from unannotated low-coverage bacterial genome sequence

    Directory of Open Access Journals (Sweden)

    Zeng An-Ping

    2004-08-01

    Full Text Available Abstract Background A necessary step for a genome level analysis of the cellular metabolism is the in silico reconstruction of the metabolic network from genome sequences. The available methods are mainly based on the annotation of genome sequences including two successive steps, the prediction of coding sequences (CDS and their function assignment. The annotation process takes time. The available methods often encounter difficulties when dealing with unfinished error-containing genomic sequence. Results In this work a fast method is proposed to use unannotated genome sequence for predicting CDSs and for an in silico reconstruction of metabolic networks. Instead of using predicted genes or CDSs to query public databases, entries from public DNA or protein databases are used as queries to search a local database of the unannotated genome sequence to predict CDSs. Functions are assigned to the predicted CDSs simultaneously. The well-annotated genome of Salmonella typhimurium LT2 is used as an example to demonstrate the applicability of the method. 97.7% of the CDSs in the original annotation are correctly identified. The use of SWISS-PROT-TrEMBL databases resulted in an identification of 98.9% of CDSs that have EC-numbers in the published annotation. Furthermore, two versions of sequences of the bacterium Klebsiella pneumoniae with different genome coverage (3.9 and 7.9 fold, respectively are examined. The results suggest that a 3.9-fold coverage of the bacterial genome could be sufficiently used for the in silico reconstruction of the metabolic network. Compared to other gene finding methods such as CRITICA our method is more suitable for exploiting sequences of low genome coverage. Based on the new method, a program called IdentiCS (Identification of Coding Sequences from Unfinished Genome Sequences is delivered that combines the identification of CDSs with the reconstruction, comparison and visualization of metabolic networks (free to download

  3. Interruption Practice Reduces Errors

    Science.gov (United States)

    2014-01-01

    miscalculations (Koppel et al., 2005). There are cases where the user (medical staff, MD, Nurse , etc.) forgets to complete the PCS which is to log off or...13. SUPPLEMENTARY NOTES Proceedings of the Human Factors and Ergonomics Society Annual Meeting, vol. 58, 1 vol. pp. 265-269, 2014. 14. ABSTRACT...2000). The effects of interruptions in work activ- ity: Field and laboratory results. Applied Ergonomics , 31(5), 537– 543. González, V. M., & Mark, G

  4. Capsid coding sequences of foot-and-mouth disease viruses are determinants of pathogenicity in pigs.

    Science.gov (United States)

    Lohse, Louise; Jackson, Terry; Bøtner, Anette; Belsham, Graham J

    2012-05-24

    The surface exposed capsid proteins, VP1, VP2 and VP3, of foot-and-mouth disease virus (FMDV) determine its antigenicity and the ability of the virus to interact with host-cell receptors. Hence, modification of these structural proteins may alter the properties of the virus.In the present study we compared the pathogenicity of different FMDVs in young pigs. In total 32 pigs, 7-weeks-old, were exposed to virus, either by direct inoculation or through contact with inoculated pigs, using cell culture adapted (O1K B64), chimeric (O1K/A-TUR and O1K/O-UKG) or field strain (O-UKG/34/2001) viruses. The O1K B64 virus and the two chimeric viruses are identical to each other except for the capsid coding region.Animals exposed to O1K B64 did not exhibit signs of disease, while pigs exposed to each of the other viruses showed typical clinical signs of foot-and-mouth disease (FMD). All pigs infected with the O1K/O-UKG chimera or the field strain (O-UKG/34/2001) developed fulminant disease. Furthermore, 3 of 4 in-contact pigs exposed to the O1K/O-UKG virus died in the acute phase of infection, likely from myocardial infection. However, in the group exposed to the O1K/A-TUR chimeric virus, only 1 pig showed symptoms of disease within the time frame of the experiment (10 days). All pigs that developed clinical disease showed a high level of viral RNA in serum and infected pigs that survived the acute phase of infection developed a serotype specific antibody response. It is concluded that the capsid coding sequences are determinants of FMDV pathogenicity in pigs.

  5. [Transposition errors during learning to reproduce a sequence by the right- and the left-hand movements: simulation of positional and movement coding].

    Science.gov (United States)

    Liakhovetskiĭ, V A; Bobrova, E V; Skopin, G N

    2012-01-01

    Transposition errors during the reproduction of a hand movement sequence make it possible to receive important information on the internal representation of this sequence in the motor working memory. Analysis of such errors showed that learning to reproduce sequences of the left-hand movements improves the system of positional coding (coding ofpositions), while learning of the right-hand movements improves the system of vector coding (coding of movements). Learning of the right-hand movements after the left-hand performance involved the system of positional coding "imposed" by the left hand. Learning of the left-hand movements after the right-hand performance activated the system of vector coding. Transposition errors during learning to reproduce movement sequences can be explained by neural network using either vector coding or both vector and positional coding.

  6. PACCMIT/PACCMIT-CDS: identifying microRNA targets in 3' UTRs and coding sequences.

    Science.gov (United States)

    Šulc, Miroslav; Marín, Ray M; Robins, Harlan S; Vaníček, Jiří

    2015-07-01

    The purpose of the proposed web server, publicly available at http://paccmit.epfl.ch, is to provide a user-friendly interface to two algorithms for predicting messenger RNA (mRNA) molecules regulated by microRNAs: (i) PACCMIT (Prediction of ACcessible and/or Conserved MIcroRNA Targets), which identifies primarily mRNA transcripts targeted in their 3' untranslated regions (3' UTRs), and (ii) PACCMIT-CDS, designed to find mRNAs targeted within their coding sequences (CDSs). While PACCMIT belongs among the accurate algorithms for predicting conserved microRNA targets in the 3' UTRs, the main contribution of the web server is 2-fold: PACCMIT provides an accurate tool for predicting targets also of weakly conserved or non-conserved microRNAs, whereas PACCMIT-CDS addresses the lack of similar portals adapted specifically for targets in CDS. The web server asks the user for microRNAs and mRNAs to be analyzed, accesses the precomputed P-values for all microRNA-mRNA pairs from a database for all mRNAs and microRNAs in a given species, ranks the predicted microRNA-mRNA pairs, evaluates their significance according to the false discovery rate and finally displays the predictions in a tabular form. The results are also available for download in several standard formats. © The Author(s) 2015. Published by Oxford University Press on behalf of Nucleic Acids Research.

  7. PACCMIT/PACCMIT-CDS: identifying microRNA targets in 3′ UTRs and coding sequences

    Science.gov (United States)

    Šulc, Miroslav; Marín, Ray M.; Robins, Harlan S.; Vaníček, Jiří

    2015-01-01

    The purpose of the proposed web server, publicly available at http://paccmit.epfl.ch, is to provide a user-friendly interface to two algorithms for predicting messenger RNA (mRNA) molecules regulated by microRNAs: (i) PACCMIT (Prediction of ACcessible and/or Conserved MIcroRNA Targets), which identifies primarily mRNA transcripts targeted in their 3′ untranslated regions (3′ UTRs), and (ii) PACCMIT-CDS, designed to find mRNAs targeted within their coding sequences (CDSs). While PACCMIT belongs among the accurate algorithms for predicting conserved microRNA targets in the 3′ UTRs, the main contribution of the web server is 2-fold: PACCMIT provides an accurate tool for predicting targets also of weakly conserved or non-conserved microRNAs, whereas PACCMIT-CDS addresses the lack of similar portals adapted specifically for targets in CDS. The web server asks the user for microRNAs and mRNAs to be analyzed, accesses the precomputed P-values for all microRNA–mRNA pairs from a database for all mRNAs and microRNAs in a given species, ranks the predicted microRNA–mRNA pairs, evaluates their significance according to the false discovery rate and finally displays the predictions in a tabular form. The results are also available for download in several standard formats. PMID:25948580

  8. Nucleotide sequence of the melA gene, coding for alpha-galactosidase in Escherichia coli K-12.

    OpenAIRE

    Liljeström, P L; Liljeström, P

    1987-01-01

    Melibiose uptake and hydrolysis in E.coli is performed by the MelB and MelA proteins, respectively. We report the cloning and sequencing of the melA gene. The nucleotide sequence data showed that melA codes for a 450 amino acid long protein with a molecular weight of 50.6 kd. The sequence data also supported the assumption that the mel locus forms an operon with melA in proximal position. A comparison of MelA with alpha-galactosidase proteins from yeast and human origin showed that these prot...

  9. ICRPfinder: a fast pattern design algorithm for coding sequences and its application in finding potential restriction enzyme recognition sites

    Directory of Open Access Journals (Sweden)

    Stafford Phillip

    2009-09-01

    Full Text Available Abstract Background Restriction enzymes can produce easily definable segments from DNA sequences by using a variety of cut patterns. There are, however, no software tools that can aid in gene building -- that is, modifying wild-type DNA sequences to express the same wild-type amino acid sequences but with enhanced codons, specific cut sites, unique post-translational modifications, and other engineered-in components for recombinant applications. A fast DNA pattern design algorithm, ICRPfinder, is provided in this paper and applied to find or create potential recognition sites in target coding sequences. Results ICRPfinder is applied to find or create restriction enzyme recognition sites by introducing silent mutations. The algorithm is shown capable of mapping existing cut-sites but importantly it also can generate specified new unique cut-sites within a specified region that are guaranteed not to be present elsewhere in the DNA sequence. Conclusion ICRPfinder is a powerful tool for finding or creating specific DNA patterns in a given target coding sequence. ICRPfinder finds or creates patterns, which can include restriction enzyme recognition sites, without changing the translated protein sequence. ICRPfinder is a browser-based JavaScript application and it can run on any platform, in on-line or off-line mode.

  10. Source coherence impairments in a direct detection direct sequence optical code-division multiple-access system.

    Science.gov (United States)

    Fsaifes, Ihsan; Lepers, Catherine; Lourdiane, Mounia; Gallion, Philippe; Beugin, Vincent; Guignard, Philippe

    2007-02-01

    We demonstrate that direct sequence optical code- division multiple-access (DS-OCDMA) encoders and decoders using sampled fiber Bragg gratings (S-FBGs) behave as multipath interferometers. In that case, chip pulses of the prime sequence codes generated by spreading in time-coherent data pulses can result from multiple reflections in the interferometers that can superimpose within a chip time duration. We show that the autocorrelation function has to be considered as the sum of complex amplitudes of the combined chip as the laser source coherence time is much greater than the integration time of the photodetector. To reduce the sensitivity of the DS-OCDMA system to the coherence time of the laser source, we analyze the use of sparse and nonperiodic quadratic congruence and extended quadratic congruence codes.

  11. Source coherence impairments in a direct detection direct sequence optical code-division multiple-access system

    Science.gov (United States)

    Fsaifes, Ihsan; Lepers, Catherine; Lourdiane, Mounia; Gallion, Philippe; Beugin, Vincent; Guignard, Philippe

    2007-02-01

    We demonstrate that direct sequence optical code- division multiple-access (DS-OCDMA) encoders and decoders using sampled fiber Bragg gratings (S-FBGs) behave as multipath interferometers. In that case, chip pulses of the prime sequence codes generated by spreading in time-coherent data pulses can result from multiple reflections in the interferometers that can superimpose within a chip time duration. We show that the autocorrelation function has to be considered as the sum of complex amplitudes of the combined chip as the laser source coherence time is much greater than the integration time of the photodetector. To reduce the sensitivity of the DS-OCDMA system to the coherence time of the laser source, we analyze the use of sparse and nonperiodic quadratic congruence and extended quadratic congruence codes.

  12. Comparisons between Arabidopsis thaliana and Drosophila melanogaster in relation to Coding and Noncoding Sequence Length and Gene Expression

    Directory of Open Access Journals (Sweden)

    Rachel Caldwell

    2015-01-01

    Full Text Available There is a continuing interest in the analysis of gene architecture and gene expression to determine the relationship that may exist. Advances in high-quality sequencing technologies and large-scale resource datasets have increased the understanding of relationships and cross-referencing of expression data to the large genome data. Although a negative correlation between expression level and gene (especially transcript length has been generally accepted, there have been some conflicting results arising from the literature concerning the impacts of different regions of genes, and the underlying reason is not well understood. The research aims to apply quantile regression techniques for statistical analysis of coding and noncoding sequence length and gene expression data in the plant, Arabidopsis thaliana, and fruit fly, Drosophila melanogaster, to determine if a relationship exists and if there is any variation or similarities between these species. The quantile regression analysis found that the coding sequence length and gene expression correlations varied, and similarities emerged for the noncoding sequence length (5′ and 3′ UTRs between animal and plant species. In conclusion, the information described in this study provides the basis for further exploration into gene regulation with regard to coding and noncoding sequence length.

  13. Learning about interruptions

    DEFF Research Database (Denmark)

    Brandrup, Morten

    ‘Interruption’ is a well described phenomenon within health-care. This study describes a field study in which nurses at a surgical ward desired to gain insights to what they experienced as interruptions from phone calls of the coordinating nurse. Employing an effects-driven approach data about...... the frequency and types of phone calls was collected using a tailored experience sampling tool. The data as well as the data became a way for the nurses to learn about the problem and use it as a stepping stone for discussing possible solutions....

  14. The Coding of Biological Information: From Nucleotide Sequence to Protein Recognition

    Science.gov (United States)

    Štambuk, Nikola

    The paper reviews the classic results of Swanson, Dayhoff, Grantham, Blalock and Root-Bernstein, which link genetic code nucleotide patterns to the protein structure, evolution and molecular recognition. Symbolic representation of the binary addresses defining particular nucleotide and amino acid properties is discussed, with consideration of: structure and metric of the code, direct correspondence between amino acid and nucleotide information, and molecular recognition of the interacting protein motifs coded by the complementary DNA and RNA strands.

  15. An integrated PCR colony hybridization approach to screen cDNA libraries for full-length coding sequences.

    Science.gov (United States)

    Pollier, Jacob; González-Guzmán, Miguel; Ardiles-Diaz, Wilson; Geelen, Danny; Goossens, Alain

    2011-01-01

    cDNA-Amplified Fragment Length Polymorphism (cDNA-AFLP) is a commonly used technique for genome-wide expression analysis that does not require prior sequence knowledge. Typically, quantitative expression data and sequence information are obtained for a large number of differentially expressed gene tags. However, most of the gene tags do not correspond to full-length (FL) coding sequences, which is a prerequisite for subsequent functional analysis. A medium-throughput screening strategy, based on integration of polymerase chain reaction (PCR) and colony hybridization, was developed that allows in parallel screening of a cDNA library for FL clones corresponding to incomplete cDNAs. The method was applied to screen for the FL open reading frames of a selection of 163 cDNA-AFLP tags from three different medicinal plants, leading to the identification of 109 (67%) FL clones. Furthermore, the protocol allows for the use of multiple probes in a single hybridization event, thus significantly increasing the throughput when screening for rare transcripts. The presented strategy offers an efficient method for the conversion of incomplete expressed sequence tags (ESTs), such as cDNA-AFLP tags, to FL-coding sequences.

  16. Interrupting Mythic Community

    Directory of Open Access Journals (Sweden)

    Linnell Secomb

    2013-09-01

    Full Text Available If nation is increasingly perceived as a less than honourable institution formed through war, invasion and geo-political territorialisation, and government is widely denounced as the site of political intrigue and the means of subjectification of citizen–voters, community appears to escape this critique and to be viewed as an idyllic formation based on bonds of affinity. However, this romancing of community is disrupted by trans-cultural and sub-cultural formations that expose the fantasy of a harmonious, homogenous community. While community is often conceived as arising organically from familial, tribal or cultural similarity, or as constituted through a common history and shared cultural institutions, this totalising conception of community is interrupted by the demands of difference and heterogeneity and by a questioning of the idyll of community authenticated in myths of archaic origin.

  17. Application of the verona coding definitions of emotional sequences (VR-CoDES) on a pediatric data set.

    Science.gov (United States)

    Vatne, Torun M; Finset, Arnstein; Ørnes, Knut; Ruland, Cornelia M

    2010-09-01

    Adult patients present concerns as defined in the Verona Coding Definitions of Emotional Sequences (VR-CoDES), but we do not know how children express their concerns during medical consultations. This study aimed to evaluate the applicability of VR-CoDES to pediatric oncology consultations. Twenty-eight pediatric consultations were coded with the Verona Coding Definitions of Emotional Sequences (VR-CoDES), and the material was also qualitatively analyzed for descriptive purposes. Five consultations were randomly selected for reliability testing and descriptive statistics were computed. Perfect inter-rater reliability for concerns and moderate reliability for cues were obtained. Cues and/or concerns were present in over half of the consultations. Cues were more frequent than concerns, with the majority of cues being verbal hints to hidden concerns or non-verbal cues. Intensity of expressions, limitations in vocabulary, commonality of statements, and complexity of the setting complicated the use of VR-CoDES. Child-specific cues; use of the imperative, cues about past experiences, and use of onomatopoeia were observed. Children with cancer express concerns during medical consultations. VR-CoDES is a reliable tool for coding concerns in pediatric data sets. For future applications in pediatric settings an appendix should be developed to incorporate the child-specific traits. Copyright (c) 2010 Elsevier Ireland Ltd. All rights reserved.

  18. Sequencing illustrates the transcriptional response of Legionella pneumophila during infection and identifies seventy novel small non-coding RNAs.

    LENUS (Irish Health Repository)

    Weissenmayer, Barbara A

    2011-01-01

    Second generation sequencing has prompted a number of groups to re-interrogate the transcriptomes of several bacterial and archaeal species. One of the central findings has been the identification of complex networks of small non-coding RNAs that play central roles in transcriptional regulation in all growth conditions and for the pathogen\\'s interaction with and survival within host cells. Legionella pneumophila is a gram-negative facultative intracellular human pathogen with a distinct biphasic lifestyle. One of its primary environmental hosts in the free-living amoeba Acanthamoeba castellanii and its infection by L. pneumophila mimics that seen in human macrophages. Here we present analysis of strand specific sequencing of the transcriptional response of L. pneumophila during exponential and post-exponential broth growth and during the replicative and transmissive phase of infection inside A. castellanii. We extend previous microarray based studies as well as uncovering evidence of a complex regulatory architecture underpinned by numerous non-coding RNAs. Over seventy new non-coding RNAs could be identified; many of them appear to be strain specific and in configurations not previously reported. We discover a family of non-coding RNAs preferentially expressed during infection conditions and identify a second copy of 6S RNA in L. pneumophila. We show that the newly discovered putative 6S RNA as well as a number of other non-coding RNAs show evidence for antisense transcription. The nature and extent of the non-coding RNAs and their expression patterns suggests that these may well play central roles in the regulation of Legionella spp. specific traits and offer clues as to how L. pneumophila adapts to its intracellular niche. The expression profiles outlined in the study have been deposited into Genbank\\'s Gene Expression Omnibus (GEO) database under the series accession GSE27232.

  19. [Influence of "prehistory" of sequential movements of the right and the left hand on reproduction: coding of positions, movements and sequence structure].

    Science.gov (United States)

    Bobrova, E V; Liakhovetskiĭ, V A; Borshchevskaia, E R

    2011-01-01

    The dependence of errors during reproduction of a sequence of hand movements without visual feedback on the previous right- and left-hand performance ("prehistory") and on positions in space of sequence elements (random or ordered by the explicit rule) was analyzed. It was shown that the preceding information about the ordered positions of the sequence elements was used during right-hand movements, whereas left-hand movements were performed with involvement of the information about the random sequence. The data testify to a central mechanism of the analysis of spatial structure of sequence elements. This mechanism activates movement coding specific for the left hemisphere (vector coding) in case of an ordered sequence structure and positional coding specific for the right hemisphere in case of a random sequence structure.

  20. In Silico Mining of Microsatellites in Coding Sequences of the Date Palm (Arecaceae Genome, Characterization, and Transferability

    Directory of Open Access Journals (Sweden)

    Frédérique Aberlenc-Bertossi

    2014-01-01

    Full Text Available Premise of the study: To complement existing sets of primarily dinucleotide microsatellite loci from noncoding sequences of date palm, we developed primers for tri- and hexanucleotide microsatellite loci identified within genes. Due to their conserved genomic locations, the primers should be useful in other palm taxa, and their utility was tested in seven other Phoenix species and in Chamaerops, Livistona, and Hyphaene. Methods and Results: Tandem repeat motifs of 3–6 bp were searched using a simple sequence repeat (SSR–pipeline package in coding portions of the date palm draft genome sequence. Fifteen loci produced highly consistent amplification, intraspecific polymorphisms, and stepwise mutation patterns. Conclusions: These microsatellite loci showed sufficient levels of variability and transferability to make them useful for population genetic, selection signature, and interspecific gene flow studies in Phoenix and other Coryphoideae genera.

  1. Prediction and identification of sequences coding for orphan enzymes using genomic and metagenomic neighbours

    DEFF Research Database (Denmark)

    Yamada, Takuji; Waller, Alison S.; Raes, Jeroen

    2012-01-01

    Despite the current wealth of sequencing data, one-third of all biochemically characterized metabolic enzymes lack a corresponding gene or protein sequence, and as such can be considered orphan enzymes. They represent a major gap between our molecular and biochemical knowledge, and consequently a...... Systems Biology 8: 581; published online 8 May 2012; doi:10.1038/msb.2012.13...

  2. Serotype identification and VP1 coding sequence analysis of foot-and-mouth disease virus from outbreaks in Eastern and Northern Uganda in 2008/9

    DEFF Research Database (Denmark)

    Kasambula, L.; Belsham, Graham; Siegismund, H. R.

    2012-01-01

    regions, and the presence of FMDV RNA in these samples was determined using a standard diagnostic RT-PCR assay. From the total of 27 positive samples, the VP1 coding region was amplified and sequenced. Each of these sequences showed >99% identity to each other, and just five distinct sequences were...

  3. Vacuum interrupters used for the interruption of high dc currents

    International Nuclear Information System (INIS)

    Warren, R.W.

    1977-01-01

    Conventional ac vacuum interrupters are being used to interrupt currents in pulsed energy storage systems. They have been tested with dc currents of up to 37 kA. The limit to the current which can be successfully interrupted has been measured as a function of various parameters. Among these are (1) the size of the interrupter, (2) the magnitude of the counterpulse current, (3) the nature and flux rating of the saturable reactor used, and (4) the kind of ''snubber'' circuit used. Fragmentary data have also been collected on electrode erosion rates and on mechanical failure of the bellows. A description is given of the circuits used in these tests and of the results found for a representative selection of the commercially available domestic interrupters. More recently efforts have been made to increase the values found for the maximum interruptible current. The techniques used have included connecting interrupters in parallel and operating them in an impressed axial magnetic field. The results of this work are discussed

  4. De novo ORFs in Drosophila are important to organismal fitness and evolved rapidly from previously non-coding sequences.

    Directory of Open Access Journals (Sweden)

    Josephine A Reinhardt

    Full Text Available How non-coding DNA gives rise to new protein-coding genes (de novo genes is not well understood. Recent work has revealed the origins and functions of a few de novo genes, but common principles governing the evolution or biological roles of these genes are unknown. To better define these principles, we performed a parallel analysis of the evolution and function of six putatively protein-coding de novo genes described in Drosophila melanogaster. Reconstruction of the transcriptional history of de novo genes shows that two de novo genes emerged from novel long non-coding RNAs that arose at least 5 MY prior to evolution of an open reading frame. In contrast, four other de novo genes evolved a translated open reading frame and transcription within the same evolutionary interval suggesting that nascent open reading frames (proto-ORFs, while not required, can contribute to the emergence of a new de novo gene. However, none of the genes arose from proto-ORFs that existed long before expression evolved. Sequence and structural evolution of de novo genes was rapid compared to nearby genes and the structural complexity of de novo genes steadily increases over evolutionary time. Despite the fact that these genes are transcribed at a higher level in males than females, and are most strongly expressed in testes, RNAi experiments show that most of these genes are essential in both sexes during metamorphosis. This lethality suggests that protein coding de novo genes in Drosophila quickly become functionally important.

  5. Modeling of severe accident sequences with the new modules CESAR and DIVA of ASTEC system code

    International Nuclear Information System (INIS)

    Pignet, Sophie; Guillard, Gaetan; Barre, Francois; Repetto, Georges

    2003-01-01

    Systems of computer codes, so-called 'integral' codes, are being developed to simulate the scenario of a hypothetical severe accident in a light water reactor, from the initial event until the possible radiological release of fission products out of the containment. They couple the predominant physical phenomena that occur in the different reactor zones and simulate the actuation of safety systems by procedures and by operators. In order to allow to study a great number of scenarios, a compromise must be found between precision of results and calculation time: one day of accident time should take less than one day of real time to simulate on a PC computer. This search of compromise is a real challenge for such integral codes. The development of the ASTEC integral code was initiated jointly by IRSN and GRS as an international reference code. The latest version 1.0 of ASTEC, including the new modules CESAR and DIVA which model the behaviour of the reactor cooling system and the core degradation, is presented here. Validation of the modules and one plant application are described

  6. Locating protein-coding sequences under selection for additional, overlapping functions in 29 mammalian genomes

    DEFF Research Database (Denmark)

    Lin, Michael F; Kheradpour, Pouya; Washietl, Stefan

    2011-01-01

    conservation compared to typical protein-coding genes—especially at synonymous sites. In this study, we use genome alignments of 29 placental mammals to systematically locate short regions within human ORFs that show conspicuously low estimated rates of synonymous substitution across these species. The 29......-species alignment provides statistical power to locate more than 10,000 such regions with resolution down to nine-codon windows, which are found within more than a quarter of all human protein-coding genes and contain ~2% of their synonymous sites. We collect numerous lines of evidence that the observed...... synonymous constraint in these regions reflects selection on overlapping functional elements including splicing regulatory elements, dual-coding genes, RNA secondary structures, microRNA target sites, and developmental enhancers. Our results show that overlapping functional elements are common in mammalian...

  7. Cloning and sequence analysis of cDNA coding for rat nucleolar protein C23

    International Nuclear Information System (INIS)

    Ghaffari, S.H.; Olson, M.O.J.

    1986-01-01

    Using synthetic oligonucleotides as primers and probes, the authors have isolated and sequenced cDNA clones encoding protein C23, a putative nucleolus organizer protein. Poly(A + ) RNA was isolated from rat Novikoff hepatoma cells and enriched in C23 mRNA by sucrose density gradient ultracentrifugation. Two deoxyoligonuleotides, a 48- and a 27-mer, were synthesized on the basis of amino acid sequence from the C-terminal half of protein C23 and cDNA sequence data from CHO cell protein. The 48-mer was used a primer for synthesis of cDNA which was then inserted into plasmid pUC9. Transformed bacterial colonies were screened by hybridization with 32 P labeled 27-mer. Two clones among 5000 gave a strong positive signal. Plasmid DNAs from these clones were purified and characterized by blotting and nucleotide sequence analysis. The length of C23 mRNA was estimated to be 3200 bases in a northern blot analysis. The sequence of a 267 b.p. insert shows high homology with the CHO cDNA with only 9 nucleotide differences and an identical amino acid sequence. These studies indicate that this region of the protein is highly conserved

  8. The Purine Bias of Coding Sequences is Determined by Physicochemical Constraints on Proteins.

    Science.gov (United States)

    Ponce de Leon, Miguel; de Miranda, Antonio Basilio; Alvarez-Valin, Fernando; Carels, Nicolas

    2014-01-01

    For this report, we analyzed protein secondary structures in relation to the statistics of three nucleotide codon positions. The purpose of this investigation was to find which properties of the ribosome, tRNA or protein level, could explain the purine bias (Rrr) as it is observed in coding DNA. We found that the Rrr pattern is the consequence of a regularity (the codon structure) resulting from physicochemical constraints on proteins and thermodynamic constraints on ribosomal machinery. The physicochemical constraints on proteins mainly come from the hydropathy and molecular weight (MW) of secondary structures as well as the energy cost of amino acid synthesis. These constraints appear through a network of statistical correlations, such as (i) the cost of amino acid synthesis, which is in favor of a higher level of guanine in the first codon position, (ii) the constructive contribution of hydropathy alternation in proteins, (iii) the spatial organization of secondary structure in proteins according to solvent accessibility, (iv) the spatial organization of secondary structure according to amino acid hydropathy, (v) the statistical correlation of MW with protein secondary structures and their overall hydropathy, (vi) the statistical correlation of thymine in the second codon position with hydropathy and the energy cost of amino acid synthesis, and (vii) the statistical correlation of adenine in the second codon position with amino acid complexity and the MW of secondary protein structures. Amino acid physicochemical properties and functional constraints on proteins constitute a code that is translated into a purine bias within the coding DNA via tRNAs. In that sense, the Rrr pattern within coding DNA is the effect of information transfer on nucleotide composition from protein to DNA by selection according to the codon positions. Thus, coding DNA structure and ribosomal machinery co-evolved to minimize the energy cost of protein coding given the functional

  9. The PRC2-binding long non-coding RNAs in human and mouse genomes are associated with predictive sequence features

    Science.gov (United States)

    Tu, Shiqi; Yuan, Guo-Cheng; Shao, Zhen

    2017-01-01

    Recently, long non-coding RNAs (lncRNAs) have emerged as an important class of molecules involved in many cellular processes. One of their primary functions is to shape epigenetic landscape through interactions with chromatin modifying proteins. However, mechanisms contributing to the specificity of such interactions remain poorly understood. Here we took the human and mouse lncRNAs that were experimentally determined to have physical interactions with Polycomb repressive complex 2 (PRC2), and systematically investigated the sequence features of these lncRNAs by developing a new computational pipeline for sequences composition analysis, in which each sequence is considered as a series of transitions between adjacent nucleotides. Through that, PRC2-binding lncRNAs were found to be associated with a set of distinctive and evolutionarily conserved sequence features, which can be utilized to distinguish them from the others with considerable accuracy. We further identified fragments of PRC2-binding lncRNAs that are enriched with these sequence features, and found they show strong PRC2-binding signals and are more highly conserved across species than the other parts, implying their functional importance.

  10. Nucleotide sequence of the gene coding for human factor VII, a vitamin K-dependent protein participating in blood coagulation

    International Nuclear Information System (INIS)

    O'Hara, P.J.; Grant, F.J.; Haldeman, B.A.; Gray, C.L.; Insley, M.Y.; Hagen, F.S.; Murray, M.J.

    1987-01-01

    Activated factor VII (factor VIIa) is a vitamin K-dependent plasma serine protease that participates in a cascade of reactions leading to the coagulation of blood. Two overlapping genomic clones containing sequences encoding human factor VII were isolated and characterized. The complete sequence of the gene was determined and found to span about 12.8 kilobases. The mRNA for factor VII as demonstrated by cDNA cloning is polyadenylylated at multiple sites but contains only one AAUAAA poly(A) signal sequence. The mRNA can undergo alternative splicing, forming one transcript containing eight segments as exons and another with an additional exon that encodes a larger prepro leader sequence. The latter transcript has no known counterpart in the other vitamin K-dependent proteins. The positions of the introns with respect to the amino acid sequence encoded by the eight essential exons of factor VII are the same as those present in factor IX, factor X, protein C, and the first three exons of prothrombin. These exons code for domains generally conserved among members of this gene family. The comparable introns in these genes, however, are dissimilar with respect to size and sequence, with the exception of intron C in factor VII and protein C. The gene for factor VII also contains five regions made up of tandem repeats of oligonucleotide monomer elements. More than a quarter of the intron sequences and more than a third of the 3' untranslated portion of the mRNA transcript consist of these minisatellite tandem repeats

  11. Phylum-Level Conservation of Regulatory Information in Nematodes despite Extensive Non-coding Sequence Divergence

    Science.gov (United States)

    Gordon, Kacy L.; Arthur, Robert K.; Ruvinsky, Ilya

    2015-01-01

    Gene regulatory information guides development and shapes the course of evolution. To test conservation of gene regulation within the phylum Nematoda, we compared the functions of putative cis-regulatory sequences of four sets of orthologs (unc-47, unc-25, mec-3 and elt-2) from distantly-related nematode species. These species, Caenorhabditis elegans, its congeneric C. briggsae, and three parasitic species Meloidogyne hapla, Brugia malayi, and Trichinella spiralis, represent four of the five major clades in the phylum Nematoda. Despite the great phylogenetic distances sampled and the extensive sequence divergence of nematode genomes, all but one of the regulatory elements we tested are able to drive at least a subset of the expected gene expression patterns. We show that functionally conserved cis-regulatory elements have no more extended sequence similarity to their C. elegans orthologs than would be expected by chance, but they do harbor motifs that are important for proper expression of the C. elegans genes. These motifs are too short to be distinguished from the background level of sequence similarity, and while identical in sequence they are not conserved in orientation or position. Functional tests reveal that some of these motifs contribute to proper expression. Our results suggest that conserved regulatory circuitry can persist despite considerable turnover within cis elements. PMID:26020930

  12. Phylum-Level Conservation of Regulatory Information in Nematodes despite Extensive Non-coding Sequence Divergence.

    Directory of Open Access Journals (Sweden)

    Kacy L Gordon

    2015-05-01

    Full Text Available Gene regulatory information guides development and shapes the course of evolution. To test conservation of gene regulation within the phylum Nematoda, we compared the functions of putative cis-regulatory sequences of four sets of orthologs (unc-47, unc-25, mec-3 and elt-2 from distantly-related nematode species. These species, Caenorhabditis elegans, its congeneric C. briggsae, and three parasitic species Meloidogyne hapla, Brugia malayi, and Trichinella spiralis, represent four of the five major clades in the phylum Nematoda. Despite the great phylogenetic distances sampled and the extensive sequence divergence of nematode genomes, all but one of the regulatory elements we tested are able to drive at least a subset of the expected gene expression patterns. We show that functionally conserved cis-regulatory elements have no more extended sequence similarity to their C. elegans orthologs than would be expected by chance, but they do harbor motifs that are important for proper expression of the C. elegans genes. These motifs are too short to be distinguished from the background level of sequence similarity, and while identical in sequence they are not conserved in orientation or position. Functional tests reveal that some of these motifs contribute to proper expression. Our results suggest that conserved regulatory circuitry can persist despite considerable turnover within cis elements.

  13. Interruption of Neural Function.

    Science.gov (United States)

    1987-05-01

    applcbse) University of Colorado I Be. ADDRESS (City. Stele and ZIP Code) 10. SOURCE OF FUNDING NOS. Campus Box B-19 PROGRAM PROJECT TASK WORK UNIT Boulder...rectification, frequency-sensitive phenomena, safety, and some effects on bio - logical systems," invited review, Charles Polk, Ed., CRC Handbook of Biological...experimental test", Mathematical Bio - Sciences, Vol. 29, pp. 235-253, 1978. [131 Kuf1er. S. WV., J. G. Nicholls, and A. R. Martin, "From Nettron to Brain

  14. Coding Local and Global Binary Visual Features Extracted From Video Sequences

    Science.gov (United States)

    Baroffio, Luca; Canclini, Antonio; Cesana, Matteo; Redondi, Alessandro; Tagliasacchi, Marco; Tubaro, Stefano

    2015-11-01

    Binary local features represent an effective alternative to real-valued descriptors, leading to comparable results for many visual analysis tasks, while being characterized by significantly lower computational complexity and memory requirements. When dealing with large collections, a more compact representation based on global features is often preferred, which can be obtained from local features by means of, e.g., the Bag-of-Visual-Word (BoVW) model. Several applications, including for example visual sensor networks and mobile augmented reality, require visual features to be transmitted over a bandwidth-limited network, thus calling for coding techniques that aim at reducing the required bit budget, while attaining a target level of efficiency. In this paper we investigate a coding scheme tailored to both local and global binary features, which aims at exploiting both spatial and temporal redundancy by means of intra- and inter-frame coding. In this respect, the proposed coding scheme can be conveniently adopted to support the Analyze-Then-Compress (ATC) paradigm. That is, visual features are extracted from the acquired content, encoded at remote nodes, and finally transmitted to a central controller that performs visual analysis. This is in contrast with the traditional approach, in which visual content is acquired at a node, compressed and then sent to a central unit for further processing, according to the Compress-Then-Analyze (CTA) paradigm. In this paper we experimentally compare ATC and CTA by means of rate-efficiency curves in the context of two different visual analysis tasks: homography estimation and content-based retrieval. Our results show that the novel ATC paradigm based on the proposed coding primitives can be competitive with CTA, especially in bandwidth limited scenarios.

  15. Coding Local and Global Binary Visual Features Extracted From Video Sequences.

    Science.gov (United States)

    Baroffio, Luca; Canclini, Antonio; Cesana, Matteo; Redondi, Alessandro; Tagliasacchi, Marco; Tubaro, Stefano

    2015-11-01

    Binary local features represent an effective alternative to real-valued descriptors, leading to comparable results for many visual analysis tasks while being characterized by significantly lower computational complexity and memory requirements. When dealing with large collections, a more compact representation based on global features is often preferred, which can be obtained from local features by means of, e.g., the bag-of-visual word model. Several applications, including, for example, visual sensor networks and mobile augmented reality, require visual features to be transmitted over a bandwidth-limited network, thus calling for coding techniques that aim at reducing the required bit budget while attaining a target level of efficiency. In this paper, we investigate a coding scheme tailored to both local and global binary features, which aims at exploiting both spatial and temporal redundancy by means of intra- and inter-frame coding. In this respect, the proposed coding scheme can conveniently be adopted to support the analyze-then-compress (ATC) paradigm. That is, visual features are extracted from the acquired content, encoded at remote nodes, and finally transmitted to a central controller that performs the visual analysis. This is in contrast with the traditional approach, in which visual content is acquired at a node, compressed and then sent to a central unit for further processing, according to the compress-then-analyze (CTA) paradigm. In this paper, we experimentally compare the ATC and the CTA by means of rate-efficiency curves in the context of two different visual analysis tasks: 1) homography estimation and 2) content-based retrieval. Our results show that the novel ATC paradigm based on the proposed coding primitives can be competitive with the CTA, especially in bandwidth limited scenarios.

  16. Construction and Analysis of a Novel 2-D Optical Orthogonal Codes Based on Modified One-coincidence Sequence

    Science.gov (United States)

    Ji, Jianhua; Wang, Yanfen; Wang, Ke; Xu, Ming; Zhang, Zhipeng; Yang, Shuwen

    2013-09-01

    A new two-dimensional OOC (optical orthogonal codes) named PC/MOCS is constructed, using PC (prime code) for time spreading and MOCS (modified one-coincidence sequence) for wavelength hopping. Compared with PC/PC, the number of wavelengths for PC/MOCS is not limited to a prime number. Compared with PC/OCS, the length of MOCS need not be expanded to the same length of PC. PC/MOCS can be constructed flexibly, and also can use available wavelengths effectively. Theoretical analysis shows that PC/MOCS can reduce the bit error rate (BER) of OCDMA system, and can support more users than PC/PC and PC/OCS.

  17. Cloning, characterization and sequence comparison of the gene coding for IMP dehydrogenase from Pyrococcus furiosus.

    Science.gov (United States)

    Collart, F R; Osipiuk, J; Trent, J; Olsen, G J; Huberman, E

    1996-10-03

    We have cloned and characterized the gene encoding inosine monophosphate dehydrogenase (IMPDH) from Pyrococcus furiosus (Pf), a hyperthermophillic archeon. Sequence analysis of the Pf gene indicated an open reading frame specifying a protein of 485 amino acids (aa) with a calculated M(r) of 52900. Canonical Archaea promoter elements, Box A and Box B, are located -49 and -17 nucleotides (nt), respectively, upstream of the putative start codon. The sequence of the putative active-site region conforms to the IMPDH signature motif and contains a putative active-site cysteine. Phylogenetic relationships derived by using all available IMPDH sequences are consistent with trees developed for other molecules; they do not precisely resolve the history of Pf IMPDH but indicate a close similarity to bacterial IMPDH proteins. The phylogenetic analysis indicates that a gene duplication occurred prior to the division between rodents and humans, accounting for the Type I and II isoforms identified in mice and humans.

  18. Episodic sequence memory is supported by a theta-gamma phase code.

    Science.gov (United States)

    Heusser, Andrew C; Poeppel, David; Ezzyat, Youssef; Davachi, Lila

    2016-10-01

    The meaning we derive from our experiences is not a simple static extraction of the elements but is largely based on the order in which those elements occur. Models propose that sequence encoding is supported by interactions between high- and low-frequency oscillations, such that elements within an experience are represented by neural cell assemblies firing at higher frequencies (gamma) and sequential order is encoded by the specific timing of firing with respect to a lower frequency oscillation (theta). During episodic sequence memory formation in humans, we provide evidence that items in different sequence positions exhibit greater gamma power along distinct phases of a theta oscillation. Furthermore, this segregation is related to successful temporal order memory. Our results provide compelling evidence that memory for order, a core component of an episodic memory, capitalizes on the ubiquitous physiological mechanism of theta-gamma phase-amplitude coupling.

  19. Cracking the Code of Human Diseases Using Next-Generation Sequencing: Applications, Challenges, and Perspectives

    Directory of Open Access Journals (Sweden)

    Vincenza Precone

    2015-01-01

    Full Text Available Next-generation sequencing (NGS technologies have greatly impacted on every field of molecular research mainly because they reduce costs and increase throughput of DNA sequencing. These features, together with the technology’s flexibility, have opened the way to a variety of applications including the study of the molecular basis of human diseases. Several analytical approaches have been developed to selectively enrich regions of interest from the whole genome in order to identify germinal and/or somatic sequence variants and to study DNA methylation. These approaches are now widely used in research, and they are already being used in routine molecular diagnostics. However, some issues are still controversial, namely, standardization of methods, data analysis and storage, and ethical aspects. Besides providing an overview of the NGS-based approaches most frequently used to study the molecular basis of human diseases at DNA level, we discuss the principal challenges and applications of NGS in the field of human genomics.

  20. Multi-scale coding of genomic information: From DNA sequence to genome structure and function

    International Nuclear Information System (INIS)

    Arneodo, Alain; Vaillant, Cedric; Audit, Benjamin; Argoul, Francoise; D'Aubenton-Carafa, Yves; Thermes, Claude

    2011-01-01

    Understanding how chromatin is spatially and dynamically organized in the nucleus of eukaryotic cells and how this affects genome functions is one of the main challenges of cell biology. Since the different orders of packaging in the hierarchical organization of DNA condition the accessibility of DNA sequence elements to trans-acting factors that control the transcription and replication processes, there is actually a wealth of structural and dynamical information to learn in the primary DNA sequence. In this review, we show that when using concepts, methodologies, numerical and experimental techniques coming from statistical mechanics and nonlinear physics combined with wavelet-based multi-scale signal processing, we are able to decipher the multi-scale sequence encoding of chromatin condensation-decondensation mechanisms that play a fundamental role in regulating many molecular processes involved in nuclear functions.

  1. LZW-Kernel: fast kernel utilizing variable length code blocks from LZW compressors for protein sequence classification.

    Science.gov (United States)

    Filatov, Gleb; Bauwens, Bruno; Kertész-Farkas, Attila

    2018-05-07

    Bioinformatics studies often rely on similarity measures between sequence pairs, which often pose a bottleneck in large-scale sequence analysis. Here, we present a new convolutional kernel function for protein sequences called the LZW-Kernel. It is based on code words identified with the Lempel-Ziv-Welch (LZW) universal text compressor. The LZW-Kernel is an alignment-free method, it is always symmetric, is positive, always provides 1.0 for self-similarity and it can directly be used with Support Vector Machines (SVMs) in classification problems, contrary to normalized compression distance (NCD), which often violates the distance metric properties in practice and requires further techniques to be used with SVMs. The LZW-Kernel is a one-pass algorithm, which makes it particularly plausible for big data applications. Our experimental studies on remote protein homology detection and protein classification tasks reveal that the LZW-Kernel closely approaches the performance of the Local Alignment Kernel (LAK) and the SVM-pairwise method combined with Smith-Waterman (SW) scoring at a fraction of the time. Moreover, the LZW-Kernel outperforms the SVM-pairwise method when combined with BLAST scores, which indicates that the LZW code words might be a better basis for similarity measures than local alignment approximations found with BLAST. In addition, the LZW-Kernel outperforms n-gram based mismatch kernels, hidden Markov model based SAM and Fisher kernel, and protein family based PSI-BLAST, among others. Further advantages include the LZW-Kernel's reliance on a simple idea, its ease of implementation, and its high speed, three times faster than BLAST and several magnitudes faster than SW or LAK in our tests. LZW-Kernel is implemented as a standalone C code and is a free open-source program distributed under GPLv3 license and can be downloaded from https://github.com/kfattila/LZW-Kernel. akerteszfarkas@hse.ru. Supplementary data are available at Bioinformatics Online.

  2. Comparative analysis of protein coding sequences from human, mouse and the domesticated pig

    DEFF Research Database (Denmark)

    Jørgensen, Frank Grønlund; Hobolth, Asger; Hornshøj, Henrik

    2005-01-01

    Background: The availability of abundant sequence data from key model organisms has made large scale studies of mulecular evolution an exciting possibility. Here we use full length cDNA alignments comprising more than 700,000 nucleotides from human, mouse, pig and the Japanese pufferfish Fugu rub...... rubrices in order to investigate 1) the relationships between three major lineages of mammals: rodents, artiodactys and primates, and 2) the rate of evolution and the occurrence of positive Darwinian selection using codon based models of sequence evolution. Results: We provide evidence...

  3. Analysis of mutations in the entire coding sequence of the factor VIII gene

    Energy Technology Data Exchange (ETDEWEB)

    Bidichadani, S.I.; Lanyon, W.G.; Connor, J.M. [Glascow Univ. (United Kingdom)] [and others

    1994-09-01

    Hemophilia A is a common X-linked recessive disorder of bleeding caused by deleterious mutations in the gene for clotting factor VIII. The large size of the factor VIII gene, the high frequency of de novo mutations and its tissue-specific expression complicate the detection of mutations. We have used a combination of RT-PCR of ectopic factor VIII transcripts and genomic DNA-PCRs to amplify the entire essential sequence of the factor VIII gene. This is followed by chemical mismatch cleavage analysis and direct sequencing in order to facilitate a comprehensive search for mutations. We describe the characterization of nine potentially pathogenic mutations, six of which are novel. In each case, a correlation of the genotype with the observed phenotype is presented. In order to evaluate the pathogenicity of the five missense mutations detected, we have analyzed them for evolutionary sequence conservation and for their involvement of sequence motifs catalogued in the PROSITE database of protein sites and patterns.

  4. Sequence of maximal distance codes in graphs or other metric spaces

    Directory of Open Access Journals (Sweden)

    Charles Delorme

    2013-11-01

    Full Text Available Given a subset C in a metric space E, its successor is the subset  s(C of points at maximum distance from C in E. We study some properties of the sequence obtained by iterating this operation.  Graphs with their usual distance provide already typical examples.

  5. The structural analysis of protein sequences based on the quasi-amino acids code

    International Nuclear Information System (INIS)

    Ping, Zhu; Xu-Qing, Tang; Zhen-Yuan, Xu

    2009-01-01

    Proteomics is the study of proteins and their interactions in a cell. With the successful completion of the Human Genome Project, it comes the postgenome era when the proteomics technology is emerging. This paper studies protein molecule from the algebraic point of view. The algebraic system (Σ, +, *) is introduced, where Σ is the set of 64 codons. According to the characteristics of (Σ, +, *), a novel quasi-amino acids code classification method is introduced and the corresponding algebraic operation table over the set ZU of the 16 kinds of quasi-amino acids is established. The internal relation is revealed about quasi-amino acids. The results show that there exist some very close correlations between the properties of the quasi-amino acids and the codon. All these correlation relationships may play an important part in establishing the logic relationship between codons and the quasi-amino acids during the course of life origination. According to Ma F et al (2003 J. Anhui Agricultural University 30 439), the corresponding relation and the excellent properties about amino acids code are very difficult to observe. The present paper shows that (ZU, ⊕, ) is a field. Furthermore, the operational results display that the codon tga has different property from other stop codons. In fact, in the mitochondrion from human and ox genomic codon, tga is just tryptophane, is not the stop codon like in other genetic code, it is the case of the Chen W C et al (2002 Acta Biophysica Sinica 18(1) 87). The present theory avoids some inexplicable events of the 20 kinds of amino acids code, in other words it solves the problem of 'the 64 codon assignments of mRNA to amino acids is probably completely wrong' proposed by Yang (2006 Progress in Modern Biomedicine 6 3). (cross-disciplinary physics and related areas of science and technology)

  6. DNA methylation of miRNA coding sequences putatively associated with childhood obesity.

    Science.gov (United States)

    Mansego, M L; Garcia-Lacarte, M; Milagro, F I; Marti, A; Martinez, J A

    2017-02-01

    Epigenetic mechanisms may be involved in obesity onset and its consequences. The aim of the present study was to evaluate whether DNA methylation status in microRNA (miRNA) coding regions is associated with childhood obesity. DNA isolated from white blood cells of 24 children (identification sample: 12 obese and 12 non-obese) from the Grupo Navarro de Obesidad Infantil study was hybridized in a 450 K methylation microarray. Several CpGs whose DNA methylation levels were statistically different between obese and non-obese were validated by MassArray® in 95 children (validation sample) from the same study. Microarray analysis identified 16 differentially methylated CpGs between both groups (6 hypermethylated and 10 hypomethylated). DNA methylation levels in miR-1203, miR-412 and miR-216A coding regions significantly correlated with body mass index standard deviation score (BMI-SDS) and explained up to 40% of the variation of BMI-SDS. The network analysis identified 19 well-defined obesity-relevant biological pathways from the KEGG database. MassArray® validation identified three regions located in or near miR-1203, miR-412 and miR-216A coding regions differentially methylated between obese and non-obese children. The current work identified three CpG sites located in coding regions of three miRNAs (miR-1203, miR-412 and miR-216A) that were differentially methylated between obese and non-obese children, suggesting a role of miRNA epigenetic regulation in childhood obesity. © 2016 World Obesity Federation.

  7. CpG + CpNpG Analysis of Protein-Coding Sequences from Tomato

    DEFF Research Database (Denmark)

    Hobolth, Asger; Nielsen, Rasmus; Wang, Ying

    2006-01-01

    We develop codon-based models for simultaneously inferring the mutational effects of CpG and CpNpG methylation in coding regions. In a data set of 369 tomato genes, we show that there is very little effect of CpNpG methylation but a strong effect of CpG methylation affecting almost all genes. We...... further show that the CpNpG and CpG effects are largely uncorrelated. Our results suggest different roles of CpG and CpNpG methylation, with CpNpG methylation possibly playing a specialized role in defense against transposons and RNA viruses....

  8. Non coding RNA: sequence-specific guide for chromatin modification and DNA damage signaling

    Directory of Open Access Journals (Sweden)

    Sofia eFrancia

    2015-11-01

    Full Text Available Chromatin conformation shapes the environment in which our genome is transcribed into RNA. Transcription is a source of DNA damage, thus it often occurs concomitantly to DNA damage signaling. Growing amounts of evidence suggest that different types of RNAs can, independently from their protein-coding properties, directly affect chromatin conformation, transcription and splicing, as well as promote the activation of the DNA damage response (DDR and DNA repair. Therefore, transcription paradoxically functions to both threaten and safeguard genome integrity. On the other hand, DNA damage signaling is known to modulate chromatin to suppress transcription of the surrounding genetic unit. It is thus intriguing to understand how transcription can modulate DDR signaling while, in turn, DDR signaling represses transcription of chromatin around the DNA lesion. An unexpected player in this field is the RNA interference (RNAi machinery, which play roles in transcription, splicing and chromatin modulation in several organisms. Non-coding RNAs (ncRNAs and several protein factors involved in the RNAi pathway are well known master regulators of chromatin while only recent reports suggest that ncRNAs are involved in DDR signaling and homology-mediated DNA repair. Here, we discuss the experimental evidence supporting the idea that ncRNAs act at the genomic loci from which they are transcribed to modulate chromatin, DDR signaling and DNA repair.

  9. Natural image sequences constrain dynamic receptive fields and imply a sparse code.

    Science.gov (United States)

    Häusler, Chris; Susemihl, Alex; Nawrot, Martin P

    2013-11-06

    In their natural environment, animals experience a complex and dynamic visual scenery. Under such natural stimulus conditions, neurons in the visual cortex employ a spatially and temporally sparse code. For the input scenario of natural still images, previous work demonstrated that unsupervised feature learning combined with the constraint of sparse coding can predict physiologically measured receptive fields of simple cells in the primary visual cortex. This convincingly indicated that the mammalian visual system is adapted to the natural spatial input statistics. Here, we extend this approach to the time domain in order to predict dynamic receptive fields that can account for both spatial and temporal sparse activation in biological neurons. We rely on temporal restricted Boltzmann machines and suggest a novel temporal autoencoding training procedure. When tested on a dynamic multi-variate benchmark dataset this method outperformed existing models of this class. Learning features on a large dataset of natural movies allowed us to model spatio-temporal receptive fields for single neurons. They resemble temporally smooth transformations of previously obtained static receptive fields and are thus consistent with existing theories. A neuronal spike response model demonstrates how the dynamic receptive field facilitates temporal and population sparseness. We discuss the potential mechanisms and benefits of a spatially and temporally sparse representation of natural visual input. Copyright © 2013 The Authors. Published by Elsevier B.V. All rights reserved.

  10. Modeling coding-sequence evolution within the context of residue solvent accessibility.

    Science.gov (United States)

    Scherrer, Michael P; Meyer, Austin G; Wilke, Claus O

    2012-09-12

    Protein structure mediates site-specific patterns of sequence divergence. In particular, residues in the core of a protein (solvent-inaccessible residues) tend to be more evolutionarily conserved than residues on the surface (solvent-accessible residues). Here, we present a model of sequence evolution that explicitly accounts for the relative solvent accessibility of each residue in a protein. Our model is a variant of the Goldman-Yang 1994 (GY94) model in which all model parameters can be functions of the relative solvent accessibility (RSA) of a residue. We apply this model to a data set comprised of nearly 600 yeast genes, and find that an evolutionary-rate ratio ω that varies linearly with RSA provides a better model fit than an RSA-independent ω or an ω that is estimated separately in individual RSA bins. We further show that the branch length t and the transition-transverion ratio κ also vary with RSA. The RSA-dependent GY94 model performs better than an RSA-dependent Muse-Gaut 1994 (MG94) model in which the synonymous and non-synonymous rates individually are linear functions of RSA. Finally, protein core size affects the slope of the linear relationship between ω and RSA, and gene expression level affects both the intercept and the slope. Structure-aware models of sequence evolution provide a significantly better fit than traditional models that neglect structure. The linear relationship between ω and RSA implies that genes are better characterized by their ω slope and intercept than by just their mean ω.

  11. Modeling coding-sequence evolution within the context of residue solvent accessibility

    Directory of Open Access Journals (Sweden)

    Scherrer Michael P

    2012-09-01

    Full Text Available Abstract Background Protein structure mediates site-specific patterns of sequence divergence. In particular, residues in the core of a protein (solvent-inaccessible residues tend to be more evolutionarily conserved than residues on the surface (solvent-accessible residues. Results Here, we present a model of sequence evolution that explicitly accounts for the relative solvent accessibility of each residue in a protein. Our model is a variant of the Goldman-Yang 1994 (GY94 model in which all model parameters can be functions of the relative solvent accessibility (RSA of a residue. We apply this model to a data set comprised of nearly 600 yeast genes, and find that an evolutionary-rate ratio ω that varies linearly with RSA provides a better model fit than an RSA-independent ω or an ω that is estimated separately in individual RSA bins. We further show that the branch length t and the transition-transverion ratio κ also vary with RSA. The RSA-dependent GY94 model performs better than an RSA-dependent Muse-Gaut 1994 (MG94 model in which the synonymous and non-synonymous rates individually are linear functions of RSA. Finally, protein core size affects the slope of the linear relationship between ω and RSA, and gene expression level affects both the intercept and the slope. Conclusions Structure-aware models of sequence evolution provide a significantly better fit than traditional models that neglect structure. The linear relationship between ω and RSA implies that genes are better characterized by their ω slope and intercept than by just their mean ω.

  12. Phylogeny, character evolution, and biogeography of Cuscuta (dodders; Convolvulaceae) inferred from coding plastid and nuclear sequences.

    Science.gov (United States)

    García, Miguel A; Costea, Mihai; Kuzmina, Maria; Stefanović, Saša

    2014-04-01

    The parasitic genus Cuscuta, containing some 200 species circumscribed traditionally in three subgenera, is nearly cosmopolitan, occurring in a wide range of habitats and hosts. Previous molecular studies, on subgenera Grammica and Cuscuta, delimited major clades within these groups. However, the sequences used were unalignable among subgenera, preventing the phylogenetic comparison across the genus. We conducted a broad phylogenetic study using rbcL and nrLSU sequences covering the morphological, physiological, and geographical diversity of Cuscuta. We used parsimony methods to reconstruct ancestral states for taxonomically important characters. Biogeographical inferences were obtained using statistical and Bayesian approaches. Four well-supported major clades are resolved. Two of them correspond to subgenera Monogynella and Grammica. Subgenus Cuscuta is paraphyletic, with section Pachystigma sister to subgenus Grammica. Previously described cases of strongly supported discordance between plastid and nuclear phylogenies, interpreted as reticulation events, are confirmed here and three new cases are detected. Dehiscent fruits and globose stigmas are inferred as ancestral character states, whereas the ancestral style number is ambiguous. Biogeographical reconstructions suggest an Old World origin for the genus and subsequent spread to the Americas as a consequence of one long-distance dispersal. Hybridization may play an important yet underestimated role in the evolution of Cuscuta. Our results disagree with scenarios of evolution (polarity) previously proposed for several taxonomically important morphological characters, and with their usage and significance. While several cases of long-distance dispersal are inferred, vicariance or dispersal to adjacent areas emerges as the dominant biogeographical pattern.

  13. Validation of the Serpent 2-DYNSUB code sequence using the Special Power Excursion Reactor Test III (SPERT III)

    International Nuclear Information System (INIS)

    Knebel, Miriam; Mercatali, Luigi; Sanchez, Victor; Stieglitz, Robert; Macian-Juan, Rafael

    2016-01-01

    Highlights: • Full few-group cross section tables created by Monte Carlo lattice code Serpent 2. • Serpent 2 group constant methodology verified for HFP static and transient cases. • Serpent 2-DYNSUB tool chainvalidated using SPERT III REA experiments. • Serpent 2-DYNSUB tool chain suitable to model RIAs in PWRs. - Abstract: The Special Power Excursion Reactor Test III (SPERT III) is studied using the Serpent 2-DYNSUB code sequence in order to validate it for modeling reactivity insertion accidents (RIA) in PWRs. The SPERT III E-core was a thermal research reactor constructed to analyze reactor dynamics. Its configuration resembles a commercial PWR on terms of fuel type, choice of moderator, coolant flow and system pressure. The initial conditions of the rod ejection accident experiments (REA) performed cover cold startup, hot startup, hot standby and operating power scenarios. Eight of these experiments were analyzed in detail. Firstly, multi-dimensional nodal diffusion cross section tables were created for the three-dimensional reactor simulator DYNSUB employing the Monte Carlo neutron transport code Serpent 2. In a second step, DYNSUB stationary simulations were compared to Monte Carlo reference three-dimensional full scale solutions obtained with Serpent 2 (cold startup conditions) and Serpent 2/SUBCHANFLOW (operating power conditions) with a good agreement being observed. The latter tool is an internal coupling of Serpent 2 and the sub-channel thermal-hydraulics code SUBCHANFLOW. Finally, DYNSUB was utilized to study the eight selected transient experiments. Results were found to match measurements well. As the selected experiments cover much of the possible transient (delayed super-critical, prompt super-critical and super-prompt critical excursion) and initial conditions (cold and hot as well as zero, little and full power reactor states) one expects in commercial PWRs, the obtained results give confidence that the Serpent 2-DYNSUB tool chain is

  14. mPUMA: a computational approach to microbiota analysis by de novo assembly of operational taxonomic units based on protein-coding barcode sequences.

    Science.gov (United States)

    Links, Matthew G; Chaban, Bonnie; Hemmingsen, Sean M; Muirhead, Kevin; Hill, Janet E

    2013-08-15

    Formation of operational taxonomic units (OTU) is a common approach to data aggregation in microbial ecology studies based on amplification and sequencing of individual gene targets. The de novo assembly of OTU sequences has been recently demonstrated as an alternative to widely used clustering methods, providing robust information from experimental data alone, without any reliance on an external reference database. Here we introduce mPUMA (microbial Profiling Using Metagenomic Assembly, http://mpuma.sourceforge.net), a software package for identification and analysis of protein-coding barcode sequence data. It was developed originally for Cpn60 universal target sequences (also known as GroEL or Hsp60). Using an unattended process that is independent of external reference sequences, mPUMA forms OTUs by DNA sequence assembly and is capable of tracking OTU abundance. mPUMA processes microbial profiles both in terms of the direct DNA sequence as well as in the translated amino acid sequence for protein coding barcodes. By forming OTUs and calculating abundance through an assembly approach, mPUMA is capable of generating inputs for several popular microbiota analysis tools. Using SFF data from sequencing of a synthetic community of Cpn60 sequences derived from the human vaginal microbiome, we demonstrate that mPUMA can faithfully reconstruct all expected OTU sequences and produce compositional profiles consistent with actual community structure. mPUMA enables analysis of microbial communities while empowering the discovery of novel organisms through OTU assembly.

  15. Phylogenetic analyses of the polyprotein coding sequences of serotype O foot-and-mouth disease viruses in East Africa: evidence for interserotypic recombination

    DEFF Research Database (Denmark)

    Balinda, Sheila; Siegismund, Hans; Muwanika, Vincent

    2010-01-01

    from both serotypes A and O. Conclusions Sequences of the VP1 coding region from recent serotype O FMDVs from Kenya and Uganda are all representatives of a specific East African lineage (topotype EA-2), a probable indication that hardly any FMD introductions of this serotype have occurred from outside...... the region in the recent past. Furthermore, evidence for interserotypic recombination, within the non-structural protein coding regions, between FMDVs of serotypes A and O has been obtained. In addition to characterization using the VP1 coding region, analyses involving the non-structural protein coding...

  16. Customer interruption cost and results

    Energy Technology Data Exchange (ETDEWEB)

    Eua-Arporn, B.; Bisarnbutra, S. [Chulalongkorn Univ., Bangkok (Thailand)

    1997-12-31

    Results of a comprehensive study on short-term direct impacts and consumer interruption costs, incurred as a result of power supply interruption, were discussed. The emphasis was on questionnaire development, general responses and the average customer damage function of some selected sectors. The customer damage function was established for each category of customers (agriculture, industry, mining, wholesale, retail merchandising, residential, etc) as well as for different locations. Results showed that the average customer damage function depended mostly on customer category. Size and location were not significant factors. 5 refs., 7 tabs.

  17. Species delimitation and phylogenetic reconstruction of the sinipercids (Perciformes: Sinipercidae) based on target enrichment of thousands of nuclear coding sequences.

    Science.gov (United States)

    Song, Shuli; Zhao, Jinliang; Li, Chenhong

    2017-06-01

    The sinipercids are freshwater fishes endemic to East Asia, mainly in China. Phylogenetic studies on the sinipercids have made great progress in the last decades, but interspecific relationships and evolutionary history of the sinipercids remain unresolved. Lack of distinctive morphological characters leads to problems in validating of some species, such as Siniperca loona. Moreover, genetic data are needed to delimitate species pairs with explicit hypothesis testing, such as in S. chuatsi vs. S. kneri and Coreoperca whiteheadi vs. C. liui. Here we reconstructed phylogeny of the sinipercids with an unprecedented scale of data, 16,943 loci of single-copy coding sequence data from nine sinipercid species, eight putative sister taxa and two outgroups. Targeted sequences were collected using gene enrichment and Illumina sequencing, yielding thousands of protein coding sequences and single nucleotide polymorphisms (SNPs) data. Maximum likelihood and coalescent species tree analyses resulted in identical and highly supported trees. We confirmed that the centrarchids are sister to the sinipercids. A monophyletic Sinipercidae with two genera, Siniperca and Coreoperca was also supported. Different from most previous studies, S. scherzeri was found as the most basal taxon to other species of Siniperca, which consists of two clades: a clade having S. roulei sister to S. chuatsi and S. kneri, and a clade consisting S. loona sister to S. obscura and S. undulata. We found that both S. loona and C. liui are valid species using Bayes factor delimitation (BFD ∗ ) based on SNPs data. Species delimitation also provided decisive support for S. chuatsi and S. kneri being two distinct species. We calibrated a chronogram of the sinipercids based on 100 loci and three fossil calibration points using BEAST, and reconstructed ancestral ranges of the sinipercids using Lagrange Analysis (DEC model) and Statistical Dispersal-Vicariance Analysis (S-DIVA) implemented in RASP. Divergence time

  18. OFFSCALE: A PC input processor for the SCALE code system. The CSASIN processor for the criticality sequences

    International Nuclear Information System (INIS)

    Bowman, S.M.

    1994-11-01

    OFFSCALE is a suite of personal computer input processor programs developed at Oak Ridge National Laboratory to provide an easy-to-use interface for modules in the SCALE-4 code system. CSASIN (formerly known as OFFSCALE) is a program in the OFFSCALE suite that serves as a user-friendly interface for the Criticality Safety Analysis Sequences (CSAS) available in SCALE-4. It is designed to assist a SCALE-4 user in preparing an input file for execution of criticality safety problems. Output from CSASIN generates an input file that may be used to execute the CSAS control module in SCALE-4. CSASIN features a pulldown menu system that accesses sophisticated data entry screens. The program allows the user to quickly set up a CSAS input file and perform data checking. This capability increases productivity and decreases the chance of user error

  19. Deconstruction of archaeal genome depict strategic consensus in core pathways coding sequence assembly.

    Directory of Open Access Journals (Sweden)

    Ayon Pal

    Full Text Available A comprehensive in silico analysis of 71 species representing the different taxonomic classes and physiological genre of the domain Archaea was performed. These organisms differed in their physiological attributes, particularly oxygen tolerance and energy metabolism. We explored the diversity and similarity in the codon usage pattern in the genes and genomes of these organisms, emphasizing on their core cellular pathways. Our thrust was to figure out whether there is any underlying similarity in the design of core pathways within these organisms. Analyses of codon utilization pattern, construction of hierarchical linear models of codon usage, expression pattern and codon pair preference pointed to the fact that, in the archaea there is a trend towards biased use of synonymous codons in the core cellular pathways and the Nc-plots appeared to display the physiological variations present within the different species. Our analyses revealed that aerobic species of archaea possessed a larger degree of freedom in regulating expression levels than could be accounted for by codon usage bias alone. This feature might be a consequence of their enhanced metabolic activities as a result of their adaptation to the relatively O2-rich environment. Species of archaea, which are related from the taxonomical viewpoint, were found to have striking similarities in their ORF structuring pattern. In the anaerobic species of archaea, codon bias was found to be a major determinant of gene expression. We have also detected a significant difference in the codon pair usage pattern between the whole genome and the genes related to vital cellular pathways, and it was not only species-specific but pathway specific too. This hints towards the structuring of ORFs with better decoding accuracy during translation. Finally, a codon-pathway interaction in shaping the codon design of pathways was observed where the transcription pathway exhibited a significantly different coding

  20. Deconstruction of archaeal genome depict strategic consensus in core pathways coding sequence assembly.

    Science.gov (United States)

    Pal, Ayon; Banerjee, Rachana; Mondal, Uttam K; Mukhopadhyay, Subhasis; Bothra, Asim K

    2015-01-01

    A comprehensive in silico analysis of 71 species representing the different taxonomic classes and physiological genre of the domain Archaea was performed. These organisms differed in their physiological attributes, particularly oxygen tolerance and energy metabolism. We explored the diversity and similarity in the codon usage pattern in the genes and genomes of these organisms, emphasizing on their core cellular pathways. Our thrust was to figure out whether there is any underlying similarity in the design of core pathways within these organisms. Analyses of codon utilization pattern, construction of hierarchical linear models of codon usage, expression pattern and codon pair preference pointed to the fact that, in the archaea there is a trend towards biased use of synonymous codons in the core cellular pathways and the Nc-plots appeared to display the physiological variations present within the different species. Our analyses revealed that aerobic species of archaea possessed a larger degree of freedom in regulating expression levels than could be accounted for by codon usage bias alone. This feature might be a consequence of their enhanced metabolic activities as a result of their adaptation to the relatively O2-rich environment. Species of archaea, which are related from the taxonomical viewpoint, were found to have striking similarities in their ORF structuring pattern. In the anaerobic species of archaea, codon bias was found to be a major determinant of gene expression. We have also detected a significant difference in the codon pair usage pattern between the whole genome and the genes related to vital cellular pathways, and it was not only species-specific but pathway specific too. This hints towards the structuring of ORFs with better decoding accuracy during translation. Finally, a codon-pathway interaction in shaping the codon design of pathways was observed where the transcription pathway exhibited a significantly different coding frequency signature.

  1. Analyses of SBO sequence of VVER1000 reactor using TRACE and MELCOR codes

    International Nuclear Information System (INIS)

    Mazzini, Guido; Kyncl, Milos; Miglierini, Bruno; Kopecek, Vit

    2015-01-01

    In response to the Fukushima accident, the European Commission ordered to perform stress tests to all European Nuclear Power Plants (NPPs). Due to shortage of time a number of conclusions in national stress tests reports were based on engineering judgment only. In the Czech Republic, as a follow up, a consortium of Research Organizations and Universities has decided to simulate selected stress tests scenarios, in particular station Black-Out (SBO) and Loss of Ultimate Sink (LoUS), with the aim to verify conclusions made in the national stress report and to analyse time response of respective source term releases. These activities are carried out in the frame of the project 'Prevention, preparedness and mitigation of consequences of Severe Accident (SA) at Czech NPPs in relation to lessons learned from stress tests after Fukushima' financed by the Ministry of Interior. The Research Centre Rez has been working on the preparation of a MELCOR model for VVER1000 NPP starting with a plant systems nodalization. The basic idea of this paper is to benchmark the MELCOR model with the validated TRACE model, first comparing the steady state and continuing in a long term SBO plus another event until the beginning of the severe accident. The presented work focuses mainly on the preliminary comparison of the thermo-hydraulics of the two models created in MELCOR and TRACE codes. After that, preliminary general results of the SA progression showing the hydrogen production and the relocation phenomena will be shortly discussed. This scenario is considered closed after some seconds to the break of the lower head. (author)

  2. The Number, Organization, and Size of Polymorphic Membrane Protein Coding Sequences as well as the Most Conserved Pmp Protein Differ within and across Chlamydia Species.

    Science.gov (United States)

    Van Lent, Sarah; Creasy, Heather Huot; Myers, Garry S A; Vanrompay, Daisy

    2016-01-01

    Variation is a central trait of the polymorphic membrane protein (Pmp) family. The number of pmp coding sequences differs between Chlamydia species, but it is unknown whether the number of pmp coding sequences is constant within a Chlamydia species. The level of conservation of the Pmp proteins has previously only been determined for Chlamydia trachomatis. As different Pmp proteins might be indispensible for the pathogenesis of different Chlamydia species, this study investigated the conservation of Pmp proteins both within and across C. trachomatis,C. pneumoniae,C. abortus, and C. psittaci. The pmp coding sequences were annotated in 16 C. trachomatis, 6 C. pneumoniae, 2 C. abortus, and 16 C. psittaci genomes. The number and organization of polymorphic membrane coding sequences differed within and across the analyzed Chlamydia species. The length of coding sequences of pmpA,pmpB, and pmpH was conserved among all analyzed genomes, while the length of pmpE/F and pmpG, and remarkably also of the subtype pmpD, differed among the analyzed genomes. PmpD, PmpA, PmpH, and PmpA were the most conserved Pmp in C. trachomatis,C. pneumoniae,C. abortus, and C. psittaci, respectively. PmpB was the most conserved Pmp across the 4 analyzed Chlamydia species. © 2016 S. Karger AG, Basel.

  3. Nonsense mutation in the glycoprotein Ibα coding sequence associated with Bernard-Soulier syndrome

    International Nuclear Information System (INIS)

    Ware, J.; Russell, S.R.; Vicente, V.; Scharf, R.E.; Tomer, A.; McMillian, R.; Ruggeri, Z.M.

    1990-01-01

    Three distinct gene products, the α and β chains of glycoprotein (GP) Ib and GP IX, constitute the platelet membrane GP Ib-IX complex, a receptor for von Willebrand factor and thrombin involved in platelet adhesion and aggregation. Defective function of the GP Ib-IX complex is the hallmark of a rare congenital bleeding disorder of still undefined pathogenesis, the Bernard-Soulier syndrome. The authors have analyzed the molecular basis of the disease in one patient in whom immunoblotting of solubilized platelets demonstrated absence of normal GP Ibα but presence of a smaller immunoreactive species. The truncated polypeptide was also present, along with normal protein, in platelets from the patient's mother and two of his four children. Genetic characterization identified a nucleotide transition changing the Trp-343 codon (TGG) to a nonsense codon (TGA). Such a mutation explains the origin of the smaller GP Ibα, which by lacking half of the sequence on the carboxyl-terminal side, including the transmembrane domain, cannot be properly inserted in the platelet membrane. Both normal and mutant codons were found in the patient, suggesting that he is a compound heterozygote with a still unidentified defect in the other GP Ibα allele. Nonsense mutation and truncated GP Ibα polypeptide were found to cosegregate in four individuals through three generations and were associated with either Bernard-Soulier syndrome or carrier state phenotype. The molecular abnormality demonstrated in this family provides evidence that defective synthesis of GP Ibα alters the membrane expression of the GP Ib-IX complex and may be responsible for Bernard-Soulier syndrome

  4. Absence of mutations in the coding sequence of the potential tumor suppressor 3pK in metastatic melanoma

    Directory of Open Access Journals (Sweden)

    Houben Roland

    2005-12-01

    Full Text Available Abstract Background Activation of Ras or Raf contributes to tumorigenesis of melanoma. However, constitutive Raf activation is also a characteristic of the majority of benign melanocytic nevi and high intensity signaling of either Ras or Raf was found to induce growth inhibition and senescence rather than transformation. Since the chromosome 3p kinase (3pK is a target of the Ras/Raf/Mek/Erk signaling pathway which antagonizes the function of the oncogene and anti-differentiation factor Bmi-1, 3pK may function as a tumor suppressor in tumors with constitutive Ras/Raf activation. Consequently, we tested whether inactivating 3pK mutations are present in melanoma. Methods 30 metastatic melanoma samples, which were positive for activating mutations of either BRaf or NRas, were analyzed for possible mutations in the 3pk gene. The 10 coding exons and their flanking intron sequences were amplified by PCR and direct sequencing of the PCR products was performed. Results This analysis revealed that besides the presence of some single nucleotide polymorphisms in the 3pk gene, we could not detect any possible loss of function mutation in any of these 30 metastatic melanoma samples selected for the presence of activating mutations within the Ras/Raf/Mek/Erk signaling pathway. Conclusion Hence, in melanoma with constitutively active Ras/Raf inactivating mutations within the 3pk gene do not contribute to the oncogenic phenotype of this highly malignant tumor.

  5. Generic detection of poleroviruses using an RT-PCR assay targeting the RdRp coding sequence.

    Science.gov (United States)

    Lotos, Leonidas; Efthimiou, Konstantinos; Maliogka, Varvara I; Katis, Nikolaos I

    2014-03-01

    In this study a two-step RT-PCR assay was developed for the generic detection of poleroviruses. The RdRp coding region was selected as the primers' target, since it differs significantly from that of other members in the family Luteoviridae and its sequence can be more informative than other regions in the viral genome. Species specific RT-PCR assays targeting the same region were also developed for the detection of the six most widespread poleroviral species (Beet mild yellowing virus, Beet western yellows virus, Cucurbit aphid-borne virus, Carrot red leaf virus, Potato leafroll virus and Turnip yellows virus) in Greece and the collection of isolates. These isolates along with other characterized ones were used for the evaluation of the generic PCR's detection range. The developed assay efficiently amplified a 593bp RdRp fragment from 46 isolates of 10 different Polerovirus species. Phylogenetic analysis using the generic PCR's amplicon sequence showed that although it cannot accurately infer evolutionary relationships within the genus it can differentiate poleroviruses at the species level. Overall, the described generic assay could be applied for the reliable detection of Polerovirus infections and, in combination with the specific PCRs, for the identification of new and uncharacterized species in the genus. Copyright © 2013 Elsevier B.V. All rights reserved.

  6. Interruptions in emergency medicine: things are not always what they seem.

    Science.gov (United States)

    Walter, Scott R

    2018-06-20

    We have all felt the cognitive disjuncture of being interrupted during an important task. Most ED physicians will readily proffer the high frequency and/or burden of interruptions during their work, and of the many observational studies of interruptions in healthcare EDs do indeed have high interruption rates[2]. In experimental psychology, where many of these ideas originated, there is plenty of evidence that interruptions negatively affect performance. Interruptions have been associated with reduced performance on complex tasks[3,4], increased sequence errors[5], increased task completion time and augmented annoyance and anxiety[6]. This article is protected by copyright. All rights reserved. This article is protected by copyright. All rights reserved.

  7. Isolation and sequencing of a cDNA coding for the human DF3 breast carcinoma-associated antigen

    International Nuclear Information System (INIS)

    Siddiqui, J.; Abe, M.; Hayes, D.; Shani, E.; Yunis, E.; Kufe, D.

    1988-01-01

    The murine monoclonal antibody (mAb) DF3 reacts with a high molecular weight glycoprotein detectable in human breast carcinomas. DF3 antigen expression correlates with human breast tumor differentiation, and the detection of a cross-reactive species in human milk has suggested that this antigen might be useful as a marker of differentiated mammary epithelium. To further characterize DF3 antigen expression, the authors have isolated a cDNA clone from a λgt11 library by screening with mAb DF3. The results demonstrate that this 309-base-pair cDNA, designated pDF9.3, codes for the DF3 epitope. Southern blot analyses of EcoRI-digested DNAs from six human tumor cell lines with 32 P-labeled pDF9.3 have revealed a restriction fragment length polymorphism. Variations in size of the alleles detected by pDF9.3 were also identified in Pst I, but not in HindIII, DNA digests. Furthermore, hybridization of 32 P-labeled pDF9.3 with total cellular RNA from each of these cell lines demonstrated either one or two transcripts that varied from 4.1 to 7.1 kilobases in size. The presence of differently sized transcripts detected by pDF9.3 was also found to correspond with the polymorphic expression of DF3 glycoproteins. Nucleotide sequence analysis of pDF9.3 has revealed a highly conserved (G + C)-rich 60-base-pair tandem repeat. These findings suggest that the variation in size of alleles coding for the polymorphic DF3 glycoprotein may represent different numbers of repeats

  8. Procedural Error and Task Interruption

    Science.gov (United States)

    2016-09-30

    interruption. A cognitive model we discuss below explains this effect in terms of increases in performance speed having the effect of compressing memory for...performance, and pilot data suggest that the task can distinguish between cognitive processes that are impaired by sleep deprivation and those that are...David Z. Hambrick Technical contact: Erik M. Altmann Michigan State University Department of Psychology 316 Physics Rd, Room 298A East Lansing

  9. Early counterpulse technique applied to vacuum interrupters

    International Nuclear Information System (INIS)

    Warren, R.W.

    1979-01-01

    Interruption of dc currents using counterpulse techniques is investigated with vacuum interrupters and a novel approach in which the counterpulse is applied before contact separation. Important increases have been achieved in this way in the maximum interruptible current and large reductions in contact erosion. The factors establishing these new limits are presented and ways are discussed to make further improvements to the maximum interruptible current

  10. Effects of Interruptibility-Aware Robot Behavior

    OpenAIRE

    Banerjee, Siddhartha; Silva, Andrew; Feigh, Karen; Chernova, Sonia

    2018-01-01

    As robots become increasingly prevalent in human environments, there will inevitably be times when a robot needs to interrupt a human to initiate an interaction. Our work introduces the first interruptibility-aware mobile robot system, and evaluates the effects of interruptibility-awareness on human task performance, robot task performance, and on human interpretation of the robot's social aptitude. Our results show that our robot is effective at predicting interruptibility at high accuracy, ...

  11. Sequencing the GRHL3 Coding Region Reveals Rare Truncating Mutations and a Common Susceptibility Variant for Nonsyndromic Cleft Palate

    Science.gov (United States)

    Mangold, Elisabeth; Böhmer, Anne C.; Ishorst, Nina; Hoebel, Ann-Kathrin; Gültepe, Pinar; Schuenke, Hannah; Klamt, Johanna; Hofmann, Andrea; Gölz, Lina; Raff, Ruth; Tessmann, Peter; Nowak, Stefanie; Reutter, Heiko; Hemprich, Alexander; Kreusch, Thomas; Kramer, Franz-Josef; Braumann, Bert; Reich, Rudolf; Schmidt, Gül; Jäger, Andreas; Reiter, Rudolf; Brosch, Sibylle; Stavusis, Janis; Ishida, Miho; Seselgyte, Rimante; Moore, Gudrun E.; Nöthen, Markus M.; Borck, Guntram; Aldhorae, Khalid A.; Lace, Baiba; Stanier, Philip; Knapp, Michael; Ludwig, Kerstin U.

    2016-01-01

    Nonsyndromic cleft lip with/without cleft palate (nsCL/P) and nonsyndromic cleft palate only (nsCPO) are the most frequent subphenotypes of orofacial clefts. A common syndromic form of orofacial clefting is Van der Woude syndrome (VWS) where individuals have CL/P or CPO, often but not always associated with lower lip pits. Recently, ∼5% of VWS-affected individuals were identified with mutations in the grainy head-like 3 gene (GRHL3). To investigate GRHL3 in nonsyndromic clefting, we sequenced its coding region in 576 Europeans with nsCL/P and 96 with nsCPO. Most strikingly, nsCPO-affected individuals had a higher minor allele frequency for rs41268753 (0.099) than control subjects (0.049; p = 1.24 × 10−2). This association was replicated in nsCPO/control cohorts from Latvia, Yemen, and the UK (pcombined = 2.63 × 10−5; ORallelic = 2.46 [95% CI 1.6–3.7]) and reached genome-wide significance in combination with imputed data from a GWAS in nsCPO triads (p = 2.73 × 10−9). Notably, rs41268753 is not associated with nsCL/P (p = 0.45). rs41268753 encodes the highly conserved p.Thr454Met (c.1361C>T) (GERP = 5.3), which prediction programs denote as deleterious, has a CADD score of 29.6, and increases protein binding capacity in silico. Sequencing also revealed four novel truncating GRHL3 mutations including two that were de novo in four families, where all nine individuals harboring mutations had nsCPO. This is important for genetic counseling: given that VWS is rare compared to nsCPO, our data suggest that dominant GRHL3 mutations are more likely to cause nonsyndromic than syndromic CPO. Thus, with rare dominant mutations and a common risk variant in the coding region, we have identified an important contribution for GRHL3 in nsCPO. PMID:27018475

  12. Early counterpulse technique applied to vacuum interrupters

    International Nuclear Information System (INIS)

    Warren, R.W.

    1979-11-01

    Interruption of dc currents using counterpulse techniques is investigated with vacuum interrupters and a novel approach in which the counterpulse is applied before contact separation. Important increases have been achieved in this way in the maximum interruptible current as well as large reductions in contact erosion. The factors establishing these new limits are presented and ways are discussed to make further improvements

  13. MicroRNA-128 targets myostatin at coding domain sequence to regulate myoblasts in skeletal muscle development.

    Science.gov (United States)

    Shi, Lei; Zhou, Bo; Li, Pinghua; Schinckel, Allan P; Liang, Tingting; Wang, Han; Li, Huizhi; Fu, Lingling; Chu, Qingpo; Huang, Ruihua

    2015-09-01

    MicroRNAs (miRNAs or miRs) play a critical role in skeletal muscle development. In a previous study we observed that miR-128 was highly expressed in skeletal muscle. However, its function in regulating skeletal muscle development is not clear. Our hypothesis was that miR-128 is involved in the regulation of the proliferation and differentiation of skeletal myoblasts. In this study, through bioinformatics analyses, we demonstrate that miR-128 specifically targeted mRNA of myostatin (MSTN), a critical inhibitor of skeletal myogenesis, at coding domain sequence (CDS) region, resulting in down-regulating of myostatin post-transcription. Overexpression of miR-128 inhibited proliferation of mouse C2C12 myoblast cells but promoted myotube formation; whereas knockdown of miR-128 had completely opposite effects. In addition, ectopic miR-128 regulated the expression of myogenic factor 5 (Myf5), myogenin (MyoG), paired box (Pax) 3 and 7. Furthermore, an inverse relationship was found between the expression of miR-128 and MSTN protein expression in vivo and in vitro. Taken together, these results reveal that there is a novel pathway in skeletal muscle development in which miR-128 regulates myostatin at CDS region to inhibit proliferation but promote differentiation of myoblast cells. Copyright © 2015 Elsevier Inc. All rights reserved.

  14. Selective Constraints on Coding Sequences of Nervous System Genes Are a Major Determinant of Duplicate Gene Retention in Vertebrates.

    Science.gov (United States)

    Roux, Julien; Liu, Jialin; Robinson-Rechavi, Marc

    2017-11-01

    The evolutionary history of vertebrates is marked by three ancient whole-genome duplications: two successive rounds in the ancestor of vertebrates, and a third one specific to teleost fishes. Biased loss of most duplicates enriched the genome for specific genes, such as slow evolving genes, but this selective retention process is not well understood. To understand what drives the long-term preservation of duplicate genes, we characterized duplicated genes in terms of their expression patterns. We used a new method of expression enrichment analysis, TopAnat, applied to in situ hybridization data from thousands of genes from zebrafish and mouse. We showed that the presence of expression in the nervous system is a good predictor of a higher rate of retention of duplicate genes after whole-genome duplication. Further analyses suggest that purifying selection against the toxic effects of misfolded or misinteracting proteins, which is particularly strong in nonrenewing neural tissues, likely constrains the evolution of coding sequences of nervous system genes, leading indirectly to the preservation of duplicate genes after whole-genome duplication. Whole-genome duplications thus greatly contributed to the expansion of the toolkit of genes available for the evolution of profound novelties of the nervous system at the base of the vertebrate radiation. © The Author 2017. Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution.

  15. Older persons' worries expressed during home care visits: exploring the content of cues and concerns identified by the Verona coding definitions of emotional sequences.

    NARCIS (Netherlands)

    Hafskjold, L.; Eide, T.; Holmström, I.K.; Sundling, V.; Dulmen, S. van; Eide, H.

    2016-01-01

    Objective: Little is known about how older persons in home care express their concerns. Emotional cues and concerns can be identified by the Verona coding definitions of emotional sequences (VR-CoDES), but the method gives no insight into what causes the distress and the emotions involved. The aims

  16. 33-GVA interrupter test facility

    International Nuclear Information System (INIS)

    Parsons, W.M.; Honig, E.M.; Warren, R.W.

    1979-01-01

    The use of commercial ac circuit breakers for dc switching operations requires that they be evaluated to determine their dc limitations. Two 2.4-GVA facilities have been constructed and used for this purpose at LASL during the last several years. In response to the increased demand on switching technology, a 33-GVA facility has been constructed. Novel features incorporated into this facility include (1) separate capacitive and cryogenic inductive energy storage systems, (2) fiber-optic controls and optically-coupled data links, and (3) digital data acquisition systems. Facility details and planned tests on an experimental rod-array vacuum interrupter are presented

  17. Low-pass shotgun sequencing of the barley genome facilitates rapid identification of genes, conserved non-coding sequences and novel repeats

    Directory of Open Access Journals (Sweden)

    Graner Andreas

    2008-10-01

    Full Text Available Abstract Background Barley has one of the largest and most complex genomes of all economically important food crops. The rise of new short read sequencing technologies such as Illumina/Solexa permits such large genomes to be effectively sampled at relatively low cost. Based on the corresponding sequence reads a Mathematically Defined Repeat (MDR index can be generated to map repetitive regions in genomic sequences. Results We have generated 574 Mbp of Illumina/Solexa sequences from barley total genomic DNA, representing about 10% of a genome equivalent. From these sequences we generated an MDR index which was then used to identify and mark repetitive regions in the barley genome. Comparison of the MDR plots with expert repeat annotation drawing on the information already available for known repetitive elements revealed a significant correspondence between the two methods. MDR-based annotation allowed for the identification of dozens of novel repeat sequences, though, which were not recognised by hand-annotation. The MDR data was also used to identify gene-containing regions by masking of repetitive sequences in eight de-novo sequenced bacterial artificial chromosome (BAC clones. For half of the identified candidate gene islands indeed gene sequences could be identified. MDR data were only of limited use, when mapped on genomic sequences from the closely related species Triticum monococcum as only a fraction of the repetitive sequences was recognised. Conclusion An MDR index for barley, which was obtained by whole-genome Illumina/Solexa sequencing, proved as efficient in repeat identification as manual expert annotation. Circumventing the labour-intensive step of producing a specific repeat library for expert annotation, an MDR index provides an elegant and efficient resource for the identification of repetitive and low-copy (i.e. potentially gene-containing sequences regions in uncharacterised genomic sequences. The restriction that a particular

  18. Three new shRNA expression vectors targeting the CYP3A4 coding sequence to inhibit its expression

    Directory of Open Access Journals (Sweden)

    Siyun Xu

    2014-10-01

    Full Text Available RNA interference (RNAi is useful for selective gene silencing. Cytochrome P450 3A4 (CYP3A4, which metabolizes approximately 50% of drugs in clinical use, plays an important role in drug metabolism. In this study, we aimed to develop a short hairpin RNA (shRNA to modulate CYP3A4 expression. Three new shRNAs (S1, S2 and S3 were designed to target the coding sequence (CDS of CYP3A4, cloned into a shRNA expression vector, and tested in different cells. The mixture of three shRNAs produced optimal reduction (55% in CYP3A4 CDS-luciferase activity in both CHL and HEK293 cells. Endogenous CYP3A4 expression in HepG2 cells was decreased about 50% at both mRNA and protein level after transfection of the mixture of three shRNAs. In contrast, CYP3A5 gene expression was not altered by the shRNAs, supporting the selectivity of CYP3A4 shRNAs. In addition, HepG2 cells transfected with CYP3A4 shRNAs were less sensitive to Ginkgolic acids, whose toxic metabolites are produced by CYP3A4. These results demonstrate that vector-based shRNAs could modulate CYP3A4 expression in cells through their actions on CYP3A4 CDS, and CYP3A4 shRNAs may be utilized to define the role of CYP3A4 in drug metabolism and toxicity.

  19. Individual variation of human S1P₁ coding sequence leads to heterogeneity in receptor function and drug interactions.

    Science.gov (United States)

    Obinata, Hideru; Gutkind, Sarah; Stitham, Jeremiah; Okuno, Toshiaki; Yokomizo, Takehiko; Hwa, John; Hla, Timothy

    2014-12-01

    Sphingosine 1-phosphate receptor 1 (S1P₁), an abundantly-expressed G protein-coupled receptor which regulates key vascular and immune responses, is a therapeutic target in autoimmune diseases. Fingolimod/Gilenya (FTY720), an oral medication for relapsing-remitting multiple sclerosis, targets S1P₁ receptors on immune and neural cells to suppress neuroinflammation. However, suppression of endothelial S1P₁ receptors is associated with cardiac and vascular adverse effects. Here we report the genetic variations of the S1P₁ coding region from exon sequencing of >12,000 individuals and their functional consequences. We conducted functional analyses of 14 nonsynonymous single nucleotide polymorphisms (SNPs) of the S1PR1 gene. One SNP mutant (Arg¹²⁰ to Pro) failed to transmit sphingosine 1-phosphate (S1P)-induced intracellular signals such as calcium increase and activation of p44/42 MAPK and Akt. Two other mutants (Ile⁴⁵ to Thr and Gly³⁰⁵ to Cys) showed normal intracellular signals but impaired S1P-induced endocytosis, which made the receptor resistant to FTY720-induced degradation. Another SNP mutant (Arg¹³ to Gly) demonstrated protection from coronary artery disease in a high cardiovascular risk population. Individuals with this mutation showed a significantly lower percentage of multi-vessel coronary obstruction in a risk factor-matched case-control study. This study suggests that individual genetic variations of S1P₁ can influence receptor function and, therefore, infer differential disease risks and interaction with S1P₁-targeted therapeutics. Copyright © 2014 by the American Society for Biochemistry and Molecular Biology, Inc.

  20. The culture contributing to interruptions in the nursing work environment: An ethnography.

    Science.gov (United States)

    Hopkinson, Susan G; Wiegand, Debra L

    2017-12-01

    To understand the occurrence of interruptions within the culture of the medical nursing unit work environment. Interruptions may lead to errors in nursing work. Little is known about how the culture of the nursing work environment contributes to interruptions. A micro-focused ethnographic study was conducted. Data collection involved extensive observation of a nursing unit, 1:1 observations of nurses and follow-up interviews with the nurses. Data were analysed from unstructured field notes and interview transcripts. The definitions of interruption and culture guided coding, categorising and identification of themes. A framework was developed that describes the medical nursing unit as a complex culture full of unpredictable, nonlinear changes that affect the entire interconnected system, often in the form of an interruption. The cultural elements contributing to interruptions included (i) the value placed on excellence in patient care and meeting personal needs, (ii) the beliefs that the nurses had to do everything by themselves and that every phone call was important, (iii) the patterns of changing patients, patient transport and coordination of resources and (iv) the normative practices of communicating and adapting. Interruptions are an integral part of the culture of a medical nursing unit. Uniformly decreasing interruptions may disrupt current practices, such as communication to coordinate care, that are central to nursing work. In future research, the nursing work environment must be looked at through the lens of a complex system. Interventions to minimise the negative impact of interruptions must take into account the culture of the nursing as a complex adaptive system. Nurses should be educated on their own contribution to interruptions and issues addressed at a system level, rather than isolating the interruption as the central issue. © 2017 John Wiley & Sons Ltd.

  1. Period of an Interrupted Pendulum

    Science.gov (United States)

    Miller, Bradley E.

    2002-11-01

    While demonstrating a classic conservation-of-energy problem to my AP Physics students, I became curious about the periodic motion that ensued for certain initial conditions. The original problem consists of releasing a mass at the end of a string from an initial position horizontal to the plane of a table. The string comes in contact with a peg some distance below the point where the string is attached at the top. One is asked to find what minimum fraction of the string's length should the peg be placed to have the mass complete a circle about the peg. However, when the mass is released from much lower heights, the system undergoes periodic motion that can be thought of as an interrupted pendulum.

  2. Development of the Verona coding definitions of emotional sequences to code health providers' responses (VR-CoDES-P) to patient cues and concerns

    NARCIS (Netherlands)

    del Piccolo, Lidia; de Haes, Hanneke; Heaven, Cathy; Jansen, Jesse; Verheul, William; Bensing, Jozien; Bergvik, Svein; Deveugele, Myriam; Eide, Hilde; Fletcher, Ian; Goss, Claudia; Humphris, Gerry; Kim, Young-Mi; Langewitz, Wolf; Mazzi, Maria Angela; Mjaaland, Trond; Moretti, Francesca; Nübling, Matthias; Rimondini, Michela; Salmon, Peter; Sibbern, Tonje; Skre, Ingunn; van Dulmen, Sandra; Wissow, Larry; Young, Bridget; Zandbelt, Linda; Zimmermann, Christa; Finset, Arnstein

    2011-01-01

    Objective: To present a method to classify health provider responses to patient cues and concerns according to the VR-CoDES-CC (Del Piccolo et al. (2009) [2] and Zimmermann et al. (submitted for publication) [3]). The system permits sequence analysis and a detailed description of how providers

  3. Development of the Verona coding definitions of emotional sequences to code health providers' responses (VR-CoDES-P) to patient cues and concerns.

    NARCIS (Netherlands)

    Piccolo, L. del; Haes, H. de; Heaven, C.; Jansen, J.; Verheul, W.; Bensing, J.; Bergvik, S.; Deveugele, M.; Eide, H.; Fletcher, I.; Goss, C.; Humphris, G.; Young-Mi, K.; Langewitz, W.; Mazzi, M.A.; Mjaaland, T.; Moretti, F.; Nübling, M.; Rimondini, M.; Salmon, P.; Sibbern, T.; Skre, I.; Dulmen, S. van; Wissow, L.; Young, B.; Zandbelt, L.; Zimmermann, C.; Finset, A.

    2011-01-01

    Objective: To present a method to classify health provider responses to patient cues and concerns according to the VR-CoDES-CC (Del Piccolo et al. (2009) [2] and Zimmermann et al. (submitted for publication) [3]). The system permits sequence analysis and a detailed description of how providers

  4. Executing application function calls in response to an interrupt

    Science.gov (United States)

    Almasi, Gheorghe; Archer, Charles J.; Giampapa, Mark E.; Gooding, Thomas M.; Heidelberger, Philip; Parker, Jeffrey J.

    2010-05-11

    Executing application function calls in response to an interrupt including creating a thread; receiving an interrupt having an interrupt type; determining whether a value of a semaphore represents that interrupts are disabled; if the value of the semaphore represents that interrupts are not disabled: calling, by the thread, one or more preconfigured functions in dependence upon the interrupt type of the interrupt; yielding the thread; and if the value of the semaphore represents that interrupts are disabled: setting the value of the semaphore to represent to a kernel that interrupts are hard-disabled; and hard-disabling interrupts at the kernel.

  5. Characterization of the FoxL2 proximal promoter and coding sequence from the common snapping turtle (Chelydra serpentina).

    Science.gov (United States)

    Guo, Lei; Rhen, Turk

    2017-10-01

    Sex is determined by temperature during embryogenesis in snapping turtles, Chelydra serpentina. Previous studies in this species show that dihydrotestosterone (DHT) induces ovarian development at temperatures that normally produce males or mixed sex ratios. The feminizing effect of DHT is associated with increased expression of FoxL2, suggesting that androgens regulate transcription of FoxL2. To test this hypothesis, we cloned the proximal promoter (1.6kb) and coding sequence for snapping turtle FoxL2 (tFoxL2) in frame with mCherry to produce a fluorescent reporter. The tFoxL2-mCherry fusion plasmid or mCherry control plasmid were stably transfected into mouse KK1 granulosa cells. These cells were then treated with 0, 1, 10, or 100nM DHT to assess androgen effects on tFoxL2-mCherry expression. In contrast to the main hypothesis, DHT did not alter expression of the tFoxL2-mCherry reporter. However, normal serum increased expression of tFoxL2-mCherry when compared to charcoal-stripped serum, indicating that the cloned region of tFoxL2 contains cis regulatory elements. We also used the tFoxL2-mCherry plasmid as an expression vector to test the hypothesis that DHT and tFoxL2 interact to regulate expression of endogenous genes in granulosa cells. While tFoxL2-mCherry and DHT had independent effects on mouse FoxL2, FshR, GnRHR, and StAR expression, tFoxL2-mCherry potentiated low concentration DHT effects on mouse aromatase expression. Further studies will be required to determine whether synergistic regulation of aromatase by DHT and FoxL2 also occurs in turtle gonads during the sex-determining period, which would explain the feminizing effect of DHT in this species. Copyright © 2017 Elsevier Inc. All rights reserved.

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

    Science.gov (United States)

    Kashofer, Karl; Regauer, Sigrid

    2017-08-01

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

  7. Application of MELCOR Code to a French PWR 900 MWe Severe Accident Sequence and Evaluation of Models Performance Focusing on In-Vessel Thermal Hydraulic Results

    International Nuclear Information System (INIS)

    De Rosa, Felice

    2006-01-01

    In the ambit of the Severe Accident Network of Excellence Project (SARNET), funded by the European Union, 6. FISA (Fission Safety) Programme, one of the main tasks is the development and validation of the European Accident Source Term Evaluation Code (ASTEC Code). One of the reference codes used to compare ASTEC results, coming from experimental and Reactor Plant applications, is MELCOR. ENEA is a SARNET member and also an ASTEC and MELCOR user. During the first 18 months of this project, we performed a series of MELCOR and ASTEC calculations referring to a French PWR 900 MWe and to the accident sequence of 'Loss of Steam Generator (SG) Feedwater' (known as H2 sequence in the French classification). H2 is an accident sequence substantially equivalent to a Station Blackout scenario, like a TMLB accident, with the only difference that in H2 sequence the scram is forced to occur with a delay of 28 seconds. The main events during the accident sequence are a loss of normal and auxiliary SG feedwater (0 s), followed by a scram when the water level in SG is equal or less than 0.7 m (after 28 seconds). There is also a main coolant pumps trip when ΔTsat < 10 deg. C, a total opening of the three relief valves when Tric (core maximal outlet temperature) is above 603 K (330 deg. C) and accumulators isolation when primary pressure goes below 1.5 MPa (15 bar). Among many other points, it is worth noting that this was the first time that a MELCOR 1.8.5 input deck was available for a French PWR 900. The main ENEA effort in this period was devoted to prepare the MELCOR input deck using the code version v.1.8.5 (build QZ Oct 2000 with the latest patch 185003 Oct 2001). The input deck, completely new, was prepared taking into account structure, data and same conditions as those found inside ASTEC input decks. The main goal of the work presented in this paper is to put in evidence where and when MELCOR provides good enough results and why, in some cases mainly referring to its

  8. Static Checking of Interrupt-driven Software

    DEFF Research Database (Denmark)

    Brylow, Dennis; Damgaard, Niels; Palsberg, Jens

    2001-01-01

    at the assembly level. In this paper we present the design and implementation of a static checker for interrupt-driven Z86-based software with hard real-time requirements. For six commercial microcontrollers, our checker has produced upper bounds on interrupt latencies and stack sizes, as well as verified...

  9. A bacterial genetic screen identifies functional coding sequences of the insect mariner transposable element Famar1 amplified from the genome of the earwig, Forficula auricularia.

    Science.gov (United States)

    Barry, Elizabeth G; Witherspoon, David J; Lampe, David J

    2004-02-01

    Transposons of the mariner family are widespread in animal genomes and have apparently infected them by horizontal transfer. Most species carry only old defective copies of particular mariner transposons that have diverged greatly from their active horizontally transferred ancestor, while a few contain young, very similar, and active copies. We report here the use of a whole-genome screen in bacteria to isolate somewhat diverged Famar1 copies from the European earwig, Forficula auricularia, that encode functional transposases. Functional and nonfunctional coding sequences of Famar1 and nonfunctional copies of Ammar1 from the European honey bee, Apis mellifera, were sequenced to examine their molecular evolution. No selection for sequence conservation was detected in any clade of a tree derived from these sequences, not even on branches leading to functional copies. This agrees with the current model for mariner transposon evolution that expects neutral evolution within particular hosts, with selection for function occurring only upon horizontal transfer to a new host. Our results further suggest that mariners are not finely tuned genetic entities and that a greater amount of sequence diversification than had previously been appreciated can occur in functional copies in a single host lineage. Finally, this method of isolating active copies can be used to isolate other novel active transposons without resorting to reconstruction of ancestral sequences.

  10. Assembly of the Complete Sitka Spruce Chloroplast Genome Using 10X Genomics' GemCode Sequencing Data.

    Directory of Open Access Journals (Sweden)

    Lauren Coombe

    Full Text Available The linked read sequencing library preparation platform by 10X Genomics produces barcoded sequencing libraries, which are subsequently sequenced using the Illumina short read sequencing technology. In this new approach, long fragments of DNA are partitioned into separate micro-reactions, where the same index sequence is incorporated into each of the sequencing fragment inserts derived from a given long fragment. In this study, we exploited this property by using reads from index sequences associated with a large number of reads, to assemble the chloroplast genome of the Sitka spruce tree (Picea sitchensis. Here we report on the first Sitka spruce chloroplast genome assembled exclusively from P. sitchensis genomic libraries prepared using the 10X Genomics protocol. We show that the resulting 124,049 base pair long genome shares high sequence similarity with the related white spruce and Norway spruce chloroplast genomes, but diverges substantially from a previously published P. sitchensis- P. thunbergii chimeric genome. The use of reads from high-frequency indices enabled separation of the nuclear genome reads from that of the chloroplast, which resulted in the simplification of the de Bruijn graphs used at the various stages of assembly.

  11. Species tree phylogeny and character evolution in the genus Centipeda (Asteraceae): evidence from DNA sequences from coding and non-coding loci from the plastid and nuclear genomes.

    Science.gov (United States)

    Nylinder, Stephan; Cronholm, Bodil; de Lange, Peter J; Walsh, Neville; Anderberg, Arne A

    2013-08-01

    A species tree phylogeny of the Australian/New Zealand genus Centipeda (Asteraceae) is estimated based on nucleotide sequence data. We analysed sequences of nuclear ribosomal DNA (ETS, ITS) and three plasmid loci (ndhF, psbA-trnH, and trnL-F) using the multi-species coalescent module in BEAST. A total of 129 individuals from all 10 recognised species of Centipeda were sampled throughout the species distribution ranges, including two subspecies. We conclude that the inferred species tree topology largely conform previous assumptions on species relationships. Centipeda racemosa (Snuffweed) is the sister to remaining species, which is also the only consistently perennial representative in the genus. Centipeda pleiocephala (Tall Sneezeweed) and C. nidiformis (Cotton Sneezeweed) constitute a species pair, as does C. borealis and C. minima (Spreading Sneezeweed), all sharing the symplesiomorphic characters of spherical capitulum and convex receptacle with C. racemosa. Another species group comprising C. thespidioides (Desert Sneezeweed), C. cunninghamii (Old man weed, or Common sneeze-weed), C. crateriformis is well-supported but then include the morphologically aberrant C. aotearoana, all sharing the character of having capitula that mature more slowly relative the subtending shoot. Centipeda elatinoides takes on a weakly supported intermediate position between the two mentioned groups, and is difficult to relate to any of the former groups based on morphological characters. Copyright © 2013 Elsevier Inc. All rights reserved.

  12. Phylogenetic analyses of the polyprotein coding sequences of serotype O foot-and-mouth disease viruses in East Africa: evidence for interserotypic recombination

    Directory of Open Access Journals (Sweden)

    Balinda Sheila N

    2010-08-01

    Full Text Available Abstract Background Foot-and-mouth disease (FMD is endemic in East Africa with the majority of the reported outbreaks attributed to serotype O virus. In this study, phylogenetic analyses of the polyprotein coding region of serotype O FMD viruses from Kenya and Uganda has been undertaken to infer evolutionary relationships and processes responsible for the generation and maintenance of diversity within this serotype. FMD virus RNA was obtained from six samples following virus isolation in cell culture and in one case by direct extraction from an oropharyngeal sample. Following RT-PCR, the single long open reading frame, encoding the polyprotein, was sequenced. Results Phylogenetic comparisons of the VP1 coding region showed that the recent East African viruses belong to one lineage within the EA-2 topotype while an older Kenyan strain, K/52/1992 is a representative of the topotype EA-1. Evolutionary relationships between the coding regions for the leader protease (L, the capsid region and almost the entire coding region are monophyletic except for the K/52/1992 which is distinct. Furthermore, phylogenetic relationships for the P2 and P3 regions suggest that the K/52/1992 is a probable recombinant between serotypes A and O. A bootscan analysis of K/52/1992 with East African FMD serotype A viruses (A21/KEN/1964 and A23/KEN/1965 and serotype O viral isolate (K/117/1999 revealed that the P2 region is probably derived from a serotype A strain while the P3 region appears to be a mosaic derived from both serotypes A and O. Conclusions Sequences of the VP1 coding region from recent serotype O FMDVs from Kenya and Uganda are all representatives of a specific East African lineage (topotype EA-2, a probable indication that hardly any FMD introductions of this serotype have occurred from outside the region in the recent past. Furthermore, evidence for interserotypic recombination, within the non-structural protein coding regions, between FMDVs of serotypes A

  13. Optical Cutting Interruption Sensor for Fiber Lasers

    Directory of Open Access Journals (Sweden)

    Benedikt Adelmann

    2015-09-01

    Full Text Available We report on an optical sensor system attached to a 4 kW fiber laser cutting machine to detect cutting interruptions. The sensor records the thermal radiation from the process zone with a modified ring mirror and optical filter arrangement, which is placed between the cutting head and the collimator. The process radiation is sensed by a Si and InGaAs diode combination with the detected signals being digitalized with 20 kHz. To demonstrate the function of the sensor, signals arising during fusion cutting of 1 mm stainless steel and mild steel with and without cutting interruptions are evaluated and typical signatures derived. In the recorded signals the piercing process, the laser switch on and switch off point and waiting period are clearly resolved. To identify the cutting interruption, the signals of both Si and InGaAs diodes are high pass filtered and the signal fluctuation ranges being subsequently calculated. Introducing a correction factor, we identify that only in case of a cutting interruption the fluctuation range of the Si diode exceeds the InGaAs diode. This characteristic signature was successfully used to detect 80 cutting interruptions of 83 incomplete cuts (alpha error 3.6% and system recorded no cutting interruption from 110 faultless cuts (beta error of 0. This particularly high detection rate in combination with the easy integration of the sensor, highlight its potential for cutting interruption detection in industrial applications.

  14. Causes of unplanned interruption of radiotherapy

    International Nuclear Information System (INIS)

    Diegues, Sylvia Suelotto; Ciconelli, Rozana Mesquita; Segreto, Roberto Araujo

    2008-01-01

    Objective: To evaluate the occurrence and causes of unplanned interruption of radiotherapy. Materials and methods: Retrospective study developed in the Division of Radiotherapy of Hospital Alemao Oswaldo Cruz in Sao Paulo, SP, Brazil, with data collected from 560 dossiers of patients submitted to radiotherapy in the period between January 1, 2005 and December 31, 2005. Chi-squared and Student t tests were utilized in the data analysis, and p < 0.05 was considered as statistically significant. Results: Interruption of treatment was identified in 350 cases, corresponding to 62.5% of the patients. The reasons for treatment interruption were the following: preventive device maintenance (55%), patient's own private reasons (13%), adverse reactions to the treatment or to combined radiotherapy/chemotherapy (6%), clinical worsening (3%), two or more combined reasons (23%). The interruption time interval ranged between 1 and 24 days (mean 1.4 day). One-day interruption was mostly due to preventive device maintenance (84.4%); two-five-day interruption was due to combined reasons (48.28%). Conclusion: The most frequent cause of interruption was preventive device maintenance, with maximum two-day time interval. (author)

  15. Evolution of ASTEC V1.2 rev.1 code for WWER-1000 reactors/SBO sequence

    International Nuclear Information System (INIS)

    Georgieva, J.; Stefanova, A.; Groudev, P.; Tusheva, P.; Kalchev, B.; Passalacqua, R.

    2006-01-01

    In this paper a comparison between calculations of severe accidents occurred from WWER-1000 with ASTEC code specified for an event of full unloading with relief valves stuck opened with no hydroaccumulators intervention is presented. The purpose of the analyses provided is to present the relationship between the improvements of the actual version (ASTEC Vl.2 rev. 1) and ASTEC V1.1 p2 like: code modifications, incoming data improvements. Such discrepancies are to be examined. Case by case suggestions for ASTEC improvements are to be provided

  16. Simulation with the MELCOR code of two severe accident sequences, Station Blackout and Small Break LOCA, for the Atucha I nuclear power plant

    International Nuclear Information System (INIS)

    Valle Cepero, Reinaldo

    2004-01-01

    The results of the PSA-I applied to the Atucha I nuclear power plant (CNA I) determine the accidental sequences with the most influence related to the probability of the core reactor damage. Among those sequences are include, the Station Blackout and lost of primary coolant, combine with the failure of the emergency injection systems by pipe breaks of diameters between DN100 - DN25 or equivalent areas, Small LOCA. This paper has the objective to model and analyze the behavior of the primary circuit and the pressure vessel during the evolution of those two accidental sequences. It presented a detailed analysis of the main phenomena that occur from the initial moment of the accident to the failure moment of the pressure vessel and the melt material fall to the reactor cavity. Two sequences were taken into account, considering the main phenomena (core uncover, heating, fuel element oxidation, hydrogen generation, degradation and relocation of the melt material, failure of the support structures, etc.) and the time of occurrence, of those events will be different, if it is considered that both sequences will be developed in different scenarios. One case is an accident with the primary circuit to a high pressure (Station Blackout scenario) and the other with a early primary circuit depressurization due to the lost of primary coolant. For this work the MELCOR 1.8.5 code was used and it allows within a unified framework to modeling an extensive spectrum of phenomenology associated with the severe accidents. (author)

  17. MicroRNA-200c modulates the expression of MUC4 and MUC16 by directly targeting their coding sequences in human pancreatic cancer.

    Directory of Open Access Journals (Sweden)

    Prakash Radhakrishnan

    Full Text Available Transmembrane mucins, MUC4 and MUC16 are associated with tumor progression and metastatic potential in human pancreatic adenocarcinoma. We discovered that miR-200c interacts with specific sequences within the coding sequence of MUC4 and MUC16 mRNAs, and evaluated the regulatory nature of this association. Pancreatic cancer cell lines S2.028 and T3M-4 transfected with miR-200c showed a 4.18 and 8.50 fold down regulation of MUC4 mRNA, and 4.68 and 4.82 fold down regulation of MUC16 mRNA compared to mock-transfected cells, respectively. A significant reduction of glycoprotein expression was also observed. These results indicate that miR-200c overexpression regulates MUC4 and MUC16 mucins in pancreatic cancer cells by directly targeting the mRNA coding sequence of each, resulting in reduced levels of MUC4 and MUC16 mRNA and protein. These data suggest that, in addition to regulating proteins that modulate EMT, miR-200c influences expression of cell surface mucins in pancreatic cancer.

  18. Evidence for a novel coding sequence overlapping the 5'-terminal ~90 codons of the Gill-associated and Yellow head okavirus envelope glycoprotein gene

    Directory of Open Access Journals (Sweden)

    Atkins John F

    2009-12-01

    Full Text Available Abstract The genus Okavirus (order Nidovirales includes a number of viruses that infect crustaceans, causing major losses in the shrimp industry. These viruses have a linear positive-sense ssRNA genome of ~26-27 kb, encoding a large replicase polyprotein that is expressed from the genomic RNA, and several additional proteins that are expressed from a nested set of 3'-coterminal subgenomic RNAs. In this brief report, we describe the bioinformatic discovery of a new, apparently coding, ORF that overlaps the 5' end of the envelope glycoprotein encoding sequence, ORF3, in the +2 reading frame. The new ORF has a strong coding signature and, in fact, is more conserved at the amino acid level than the overlapping region of ORF3. We propose that translation of the new ORF initiates at a conserved AUG codon separated by just 2 nt from the ORF3 AUG initiation codon, resulting in a novel 86 amino acid protein.

  19. Accommodating interruptions: A grounded theory of young people with asthma.

    Science.gov (United States)

    Hughes, Mary; Savage, Eileen; Andrews, Tom

    2018-01-01

    The aim of this study was to develop an explanatory theory on the lives of young people with asthma, issues affecting them and the impact of asthma on their day-to-day lives. Accommodating Interruptions is a theory that explains young people's concerns about living with asthma. Although national and international asthma management guidelines exist, it is accepted that the symptom control of asthma among the young people population is poor. This study was undertaken using Classic Grounded Theory. Data were collected through in-depth interviews and clinic consultations with young people aged 11-16 years who had asthma for over 1 year. Data were also collected from participant diaries. Constant comparative analysis, theoretical coding and memo writing were used to develop the substantive theory. The theory explains how young people resolve their main concern of being restricted by Accommodating Interruptions in their lives. They do this by assimilating behaviours in balance finding, moderating influence, fitting in and assuming control minimising the effects of asthma on their everyday lives. The theory of Accommodating Interruptions explains young people's asthma management behaviours in a new way. It allows us to understand how and why young people behave the way they do because they want to participate and be included in everyday activities, events and relationships. The theory adds to the body of knowledge on how young people with asthma live their day-to-day lives and it challenges some existing viewpoints in the literature regarding their behaviours. The findings have implications for developing services to support young people in a more meaningful way as they accommodate the interruptions associated with asthma in their lives. © 2017 John Wiley & Sons Ltd.

  20. Whole-Exome Sequencing of 2,000 Danish Individuals and the Role of Rare Coding Variants in Type 2 Diabetes

    DEFF Research Database (Denmark)

    Lohmueller, Kirk E.; Sparsø, Thomas; Li, Qibin

    2013-01-01

    number of genes. We applied a series of gene-based tests to detect such susceptibility genes. However, no gene showed a significant association with disease risk after we corrected for the number of genes analyzed. Thus, we could reject a model for the genetic architecture of type 2 diabetes where rare......It has been hypothesized that, in aggregate, rare variants in coding regions of genes explain a substantial fraction of the heritability of common diseases. We sequenced the exomes of 1,000 Danish cases with common forms of type 2 diabetes (including body mass index > 27.5 kg/m2 and hypertension...

  1. Basic interrupt and command structures and applications

    International Nuclear Information System (INIS)

    Davies, R.C.

    1974-01-01

    Interrupt and command structures of a real-time system are described through specific examples. References to applications of a real-time system and programing development references are supplied. (auth)

  2. Performance Analysis of Direct-Sequence Code-Division Multiple-Access Communications with Asymmetric Quadrature Phase-Shift-Keying Modulation

    Science.gov (United States)

    Wang, C.-W.; Stark, W.

    2005-01-01

    This article considers a quaternary direct-sequence code-division multiple-access (DS-CDMA) communication system with asymmetric quadrature phase-shift-keying (AQPSK) modulation for unequal error protection (UEP) capability. Both time synchronous and asynchronous cases are investigated. An expression for the probability distribution of the multiple-access interference is derived. The exact bit-error performance and the approximate performance using a Gaussian approximation and random signature sequences are evaluated by extending the techniques used for uniform quadrature phase-shift-keying (QPSK) and binary phase-shift-keying (BPSK) DS-CDMA systems. Finally, a general system model with unequal user power and the near-far problem is considered and analyzed. The results show that, for a system with UEP capability, the less protected data bits are more sensitive to the near-far effect that occurs in a multiple-access environment than are the more protected bits.

  3. The Effects of Interruption Task Complexity and Interruptions on Student Multitasking

    OpenAIRE

    Tan, Jiun Yi

    2013-01-01

    Students commonly multitask while studying. The ubiquitous use of laptops and computers has facilitated this phenomenon and even changed the nature of multitasking in studying environments. Interruptions have an undeniable presence in these everyday studying environments and there are growing concerns about their potential to disrupt both performance and the learning process. Since interruptions are unavoidable, it is useful to identify the features that make some interruptions more disruptiv...

  4. Experiments with vacuum interrupters used for large dc-current interruption

    International Nuclear Information System (INIS)

    Warren, R.W.

    1977-10-01

    Vacuum interrupters have been tested in circuits similar to those used in theta-pinch and Tokamak fusion devices. The effects on performance of auxiliary circuit components and axial magnetic fields have been determined, and limits to lifetime caused by mechanical and electrical wear have been measured. Results show that the upper reliable limit of interruption is independent of the auxiliary components but quite dependent on interrupter size and on the axial field

  5. MCNP code

    International Nuclear Information System (INIS)

    Cramer, S.N.

    1984-01-01

    The MCNP code is the major Monte Carlo coupled neutron-photon transport research tool at the Los Alamos National Laboratory, and it represents the most extensive Monte Carlo development program in the United States which is available in the public domain. The present code is the direct descendent of the original Monte Carlo work of Fermi, von Neumaum, and Ulam at Los Alamos in the 1940s. Development has continued uninterrupted since that time, and the current version of MCNP (or its predecessors) has always included state-of-the-art methods in the Monte Carlo simulation of radiation transport, basic cross section data, geometry capability, variance reduction, and estimation procedures. The authors of the present code have oriented its development toward general user application. The documentation, though extensive, is presented in a clear and simple manner with many examples, illustrations, and sample problems. In addition to providing the desired results, the output listings give a a wealth of detailed information (some optional) concerning each state of the calculation. The code system is continually updated to take advantage of advances in computer hardware and software, including interactive modes of operation, diagnostic interrupts and restarts, and a variety of graphical and video aids

  6. Understanding Emergency Medicine Physicians Multitasking Behaviors Around Interruptions.

    Science.gov (United States)

    Fong, Allan; Ratwani, Raj M

    2018-06-11

    Interruptions can adversely impact human performance, particularly in fast-paced and high-risk environments such as the emergency department (ED). Understanding physician behaviors before, during, and after interruptions is important to the design and promotion of safe and effective workflow solutions. However, traditional human factors based interruption models do not accurately reflect the complexities of real-world environments like the ED and may not capture multiple interruptions and multitasking. We present a more comprehensive framework for understanding interruptions that is composed of three phases, each with multiple levels: Interruption Start Transition, Interruption Engagement, and Interruption End Transition. This three-phase framework is not constrained to discrete task transitions, providing a robust method to categorize multitasking behaviors around interruptions. We apply this framework in categorizing 457 interruption episodes. 457 interruption episodes were captured during 36 hours of observation. The interrupted task was immediately suspended 348 (76.1%) times. Participants engaged in new self-initiated tasks during the interrupting task 164 (35.9%) times and did not directly resume the interrupted task in 284 (62.1%) interruption episodes. Using this framework provides a more detailed description of the types of physician behaviors in complex environments. Understanding the different types of interruption and resumption patterns, which may have a different impact on performance, can support the design of interruption mitigation strategies. This article is protected by copyright. All rights reserved. This article is protected by copyright. All rights reserved.

  7. In silico Coding Sequence Analysis of Walnut GAI and PIP2 Genes and Comparison with Different Plant Species

    Directory of Open Access Journals (Sweden)

    Mahdi Mohseniazar

    2017-02-01

    Full Text Available Introduction: Dwarfism is one of the important traits in breeding of crops and horticulture plants. A dwarfing rootstock will produce trees with 15-50% of standard trees size. In modern intensive fruit tree orchards, dwarfing rootstocks are commonly used to reduce trees size, enabling high-density planting and easy management, thus achieving higher yield. Trees on dwarfing rootstocks can also exhibit other economically important traits, such as precocious flowering, increased yield and increased disease resistance. Dwarf rootstocks have been extensively studied and released in stone and pome fruits, because of presence of genetic materials and the simplicity of budding methods. Control of tree size using genetically dwarf rootstocks for achievement to higher density and mechanized orchard systems is now very important for walnut production in the world especially in Iran. Many different genes can be involved in appear of this. Mutations in GAI and PIP2 genes cause dwarf trait by two different mechanisms in some plant species. In this case, we study in silico analysis of GAI and PIP2 genes consist of conserved sequences and domains, exon and intron number, function of their proteins, targeting, secondary and tertiary structure, and post translational modification. Materials and methods: The GAI and PIP2 mRNA and protein sequences (FASTA format belonging to 17 monocotyledon and dicotyledon were downloaded from NCBI (http://www.ncbi.nlm.nih.gov accessed, on September 2014. Several online web services and software were used for analysis of GAI and PIP2 mRNA and Proteins in plants. Comparative and bioinformatics analyses of PIP2 and GAI proteins were performed online at two websites NCBI (http://www.ncbi.nih.gov and EXPASY (http://expasy.org/tools. Molecular Evolutionary Genetics Analysis (MEGA; version 4 program and CLUSTAL-W with default parameters were used for multiple alignments of sequences. The phylogenetic analysis of GAI and PIP2 protein was

  8. In silico Coding Sequence Analysis of Walnut GAI and PIP2 Genes and Comparison with Different Plant Species

    Directory of Open Access Journals (Sweden)

    Mahdi Mohseniazar

    2017-09-01

    Full Text Available Introduction: Dwarfism is one of the important traits in breeding of crops and horticulture plants. A dwarfing rootstock will produce trees with 15-50% of standard trees size. In modern intensive fruit tree orchards, dwarfing rootstocks are commonly used to reduce trees size, enabling high-density planting and easy management, thus achieving higher yield. Trees on dwarfing rootstocks can also exhibit other economically important traits, such as precocious flowering, increased yield and increased disease resistance. Dwarf rootstocks have been extensively studied and released in stone and pome fruits, because of presence of genetic materials and the simplicity of budding methods. Control of tree size using genetically dwarf rootstocks for achievement to higher density and mechanized orchard systems is now very important for walnut production in the world especially in Iran. Many different genes can be involved in appear of this. Mutations in GAI and PIP2 genes cause dwarf trait by two different mechanisms in some plant species. In this case, we study in silico analysis of GAI and PIP2 genes consist of conserved sequences and domains, exon and intron number, function of their proteins, targeting, secondary and tertiary structure, and post translational modification. Materials and methods: The GAI and PIP2 mRNA and protein sequences (FASTA format belonging to 17 monocotyledon and dicotyledon were downloaded from NCBI (http://www.ncbi.nlm.nih.gov accessed, on September 2014. Several online web services and software were used for analysis of GAI and PIP2 mRNA and Proteins in plants. Comparative and bioinformatics analyses of PIP2 and GAI proteins were performed online at two websites NCBI (http://www.ncbi.nih.gov and EXPASY (http://expasy.org/tools. Molecular Evolutionary Genetics Analysis (MEGA; version 4 program and CLUSTAL-W with default parameters were used for multiple alignments of sequences. The phylogenetic analysis of GAI and PIP2 protein was

  9. Impact of Frequent Interruption on Nurses' Patient-Controlled Analgesia Programming Performance.

    Science.gov (United States)

    Campoe, Kristi R; Giuliano, Karen K

    2017-12-01

    The purpose was to add to the body of knowledge regarding the impact of interruption on acute care nurses' cognitive workload, total task completion times, nurse frustration, and medication administration error while programming a patient-controlled analgesia (PCA) pump. Data support that the severity of medication administration error increases with the number of interruptions, which is especially critical during the administration of high-risk medications. Bar code technology, interruption-free zones, and medication safety vests have been shown to decrease administration-related errors. However, there are few published data regarding the impact of number of interruptions on nurses' clinical performance during PCA programming. Nine acute care nurses completed three PCA pump programming tasks in a simulation laboratory. Programming tasks were completed under three conditions where the number of interruptions varied between two, four, and six. Outcome measures included cognitive workload (six NASA Task Load Index [NASA-TLX] subscales), total task completion time (seconds), nurse frustration (NASA-TLX Subscale 6), and PCA medication administration error (incorrect final programming). Increases in the number of interruptions were associated with significant increases in total task completion time ( p = .003). We also found increases in nurses' cognitive workload, nurse frustration, and PCA pump programming errors, but these increases were not statistically significant. Complex technology use permeates the acute care nursing practice environment. These results add new knowledge on nurses' clinical performance during PCA pump programming and high-risk medication administration.

  10. Repeat interruptions in spinocerebellar ataxia type 10 expansions are strongly associated with epileptic seizures

    Science.gov (United States)

    McFarland, Karen N.; Liu, Jilin; Landrian, Ivette; Zeng, Desmond; Raskin, Salmo; Moscovich, Mariana; Gatto, Emilia M.; Ochoa, Adriana; Teive, Hélio A. G.; Rasmussen, Astrid; Ashizawa, Tetsuo

    2014-01-01

    Spinocerebellar ataxia type 10 (SCA10), an autosomal dominant neurodegenerative disorder, is the result of a non-coding, pentanucleotide repeat expansion within intron 9 of the Ataxin 10 gene. SCA10 patients present with pure cerebellar ataxia; yet, some families also have a high incidence of epilepsy. SCA10 expansions containing penta- and heptanucleotide interruption motifs, termed “ATCCT interruptions,” experience large contractions during germline transmission, particularly in paternal lineages. At the same time, these alleles confer an earlier age at onset which contradicts traditional rules of genetic anticipation in repeat expansions. Previously, ATCCT interruptions have been associated with a higher prevalence of epileptic seizures in one Mexican-American SCA10 family. In a large cohort of SCA10 families, we analyzed whether ATCCT interruptions confers a greater risk for developing seizures in these families. Notably, we find that the presence of repeat interruptions within the SCA10 expansion confers a 6.3-fold increase in the risk of an SCA10 patient developing epilepsy (6.2-fold when considering patients of Mexican ancestry only) and a 13.7-fold increase in having a positive family history of epilepsy (10.5-fold when considering patients of Mexican ancestry only). We conclude that the presence of repeat interruptions in SCA10 repeat expansion indicates a significant risk for the epilepsy phenotype and should be considered during genetic counseling. PMID:24318420

  11. Comprehensive search for intra- and inter-specific sequence polymorphisms among coding envelope genes of retroviral origin found in the human genome: genes and pseudogenes

    Directory of Open Access Journals (Sweden)

    Vasilescu Alexandre

    2005-09-01

    Full Text Available Abstract Background The human genome carries a high load of proviral-like sequences, called Human Endogenous Retroviruses (HERVs, which are the genomic traces of ancient infections by active retroviruses. These elements are in most cases defective, but open reading frames can still be found for the retroviral envelope gene, with sixteen such genes identified so far. Several of them are conserved during primate evolution, having possibly been co-opted by their host for a physiological role. Results To characterize further their status, we presently sequenced 12 of these genes from a panel of 91 Caucasian individuals. Genomic analyses reveal strong sequence conservation (only two non synonymous Single Nucleotide Polymorphisms [SNPs] for the two HERV-W and HERV-FRD envelope genes, i.e. for the two genes specifically expressed in the placenta and possibly involved in syncytiotrophoblast formation. We further show – using an ex vivo fusion assay for each allelic form – that none of these SNPs impairs the fusogenic function. The other envelope proteins disclose variable polymorphisms, with the occurrence of a stop codon and/or frameshift for most – but not all – of them. Moreover, the sequence conservation analysis of the orthologous genes that can be found in primates shows that three env genes have been maintained in a fully coding state throughout evolution including envW and envFRD. Conclusion Altogether, the present study strongly suggests that some but not all envelope encoding sequences are bona fide genes. It also provides new tools to elucidate the possible role of endogenous envelope proteins as susceptibility factors in a number of pathologies where HERVs have been suspected to be involved.

  12. Browning in Annona cherimola fruit: role of polyphenol oxidase and characterization of a coding sequence of the enzyme.

    Science.gov (United States)

    Prieto, Humberto; Utz, Daniella; Castro, Alvaro; Aguirre, Carlos; González-Agüero, Mauricio; Valdés, Héctor; Cifuentes, Nicolas; Defilippi, Bruno G; Zamora, Pablo; Zúñiga, Gustavo; Campos-Vargas, Reinaldo

    2007-10-31

    Cherimoya (Annona cherimola Mill.) fruit is an attractive candidate for food processing applications as fresh cut. However, along with its desirable delicate taste, cherimoya shows a marked susceptibility to browning. This condition is mainly attributed to polyphenol oxidase activity (PPO). A general lack of knowledge regarding PPO and its role in the oxidative loss of quality in processed cherimoya fruit requires a better understanding of the mechanisms involved. The work carried out included the cloning of a full-length cDNA, an analysis of its properties in the deduced amino sequence, and linkage of its mRNA levels with enzyme activity in mature and ripe fruits after wounding. The results showed one gene different at the nucleotide level when compared with previously reported genes, but a well-conserved protein, either in functional and in structural terms. Cherimoya PPO gene (Ac-ppo, GenBank DQ990911) showed to be present apparently in one copy of the genome, and its transcripts could be significantly detected in leaves and less abundantly in flowers and fruits. Analysis of wounded matured and ripened fruits revealed an inductive behavior for mRNA levels in the flesh of mature cherimoya after 16 h. Although the highest enzymatic activity was observed on rind, a consistent PPO activity was detected on flesh samples. A lack of correlation between PPO mRNA level and PPO activity was observed, especially in flesh tissue. This is probably due to the presence of monophenolic substrates inducing a lag period, enzyme inhibitors and/or diphenolic substrates causing suicide inactivation, and proenzyme or latent isoforms of PPO. To our knowledge this is the first report of a complete PPO sequence in cherimoya. Furthermore, the gene is highly divergent from known nucleotide sequences but shows a well conserved protein in terms of its function, deduced structure, and physiological role.

  13. Molecular phylogeny of Edraianthus (Grassy Bells; Campanulaceae) based on non-coding plastid DNA sequences

    DEFF Research Database (Denmark)

    Stefanovic, Sasa; Lakusic, Dmitar; Kuzmina, Maria

    2008-01-01

    The Balkan Peninsula is known as an ice-age refugium and an area with high rates of speciation and diversification. Only a few genera have their centers of distribution in the Balkans and the endemic genus Edraianthus is one of its most prominent groups. As such, Edraianthus is an excellent model...... divided into three sections: E. sect. Edraianthus, E. sect. Uniflori, and E. sect. Spathulati. We present here the first phylogenetic study of Edraianthus based on multiple plastid DNA sequences (trnL-F region and rbcL-atpB spacer) derived from a wide taxonomic sampling and geographic range. While...

  14. The Effects of Career Interruptions on Young Men and Women.

    Science.gov (United States)

    Shorten, Brett; Lewis, Donald E.

    1991-01-01

    Data from a sample of 5,837 Australians showed that (1) women had longer career interruptions; (2) regardless of number of interruptions, men had higher wages; (3) longer interruptions had a negative effect on reentry wages; and (4) 1985-88 growth in wages for males was enhanced by increased numbers and length of interruptions, with the opposite…

  15. A large-scale study of the random variability of a coding sequence: a study on the CFTR gene.

    Science.gov (United States)

    Modiano, Guido; Bombieri, Cristina; Ciminelli, Bianca Maria; Belpinati, Francesca; Giorgi, Silvia; Georges, Marie des; Scotet, Virginie; Pompei, Fiorenza; Ciccacci, Cinzia; Guittard, Caroline; Audrézet, Marie Pierre; Begnini, Angela; Toepfer, Michael; Macek, Milan; Ferec, Claude; Claustres, Mireille; Pignatti, Pier Franco

    2005-02-01

    Coding single nucleotide substitutions (cSNSs) have been studied on hundreds of genes using small samples (n(g) approximately 100-150 genes). In the present investigation, a large random European population sample (average n(g) approximately 1500) was studied for a single gene, the CFTR (Cystic Fibrosis Transmembrane conductance Regulator). The nonsynonymous (NS) substitutions exhibited, in accordance with previous reports, a mean probability of being polymorphic (q > 0.005), much lower than that of the synonymous (S) substitutions, but they showed a similar rate of subpolymorphic (q < 0.005) variability. This indicates that, in autosomal genes that may have harmful recessive alleles (nonduplicated genes with important functions), genetic drift overwhelms selection in the subpolymorphic range of variability, making disadvantageous alleles behave as neutral. These results imply that the majority of the subpolymorphic nonsynonymous alleles of these genes are selectively negative or even pathogenic.

  16. Highly conserved non-coding elements on either side of SOX9 associated with Pierre Robin sequence.

    Science.gov (United States)

    Benko, Sabina; Fantes, Judy A; Amiel, Jeanne; Kleinjan, Dirk-Jan; Thomas, Sophie; Ramsay, Jacqueline; Jamshidi, Negar; Essafi, Abdelkader; Heaney, Simon; Gordon, Christopher T; McBride, David; Golzio, Christelle; Fisher, Malcolm; Perry, Paul; Abadie, Véronique; Ayuso, Carmen; Holder-Espinasse, Muriel; Kilpatrick, Nicky; Lees, Melissa M; Picard, Arnaud; Temple, I Karen; Thomas, Paul; Vazquez, Marie-Paule; Vekemans, Michel; Roest Crollius, Hugues; Hastie, Nicholas D; Munnich, Arnold; Etchevers, Heather C; Pelet, Anna; Farlie, Peter G; Fitzpatrick, David R; Lyonnet, Stanislas

    2009-03-01

    Pierre Robin sequence (PRS) is an important subgroup of cleft palate. We report several lines of evidence for the existence of a 17q24 locus underlying PRS, including linkage analysis results, a clustering of translocation breakpoints 1.06-1.23 Mb upstream of SOX9, and microdeletions both approximately 1.5 Mb centromeric and approximately 1.5 Mb telomeric of SOX9. We have also identified a heterozygous point mutation in an evolutionarily conserved region of DNA with in vitro and in vivo features of a developmental enhancer. This enhancer is centromeric to the breakpoint cluster and maps within one of the microdeletion regions. The mutation abrogates the in vitro enhancer function and alters binding of the transcription factor MSX1 as compared to the wild-type sequence. In the developing mouse mandible, the 3-Mb region bounded by the microdeletions shows a regionally specific chromatin decompaction in cells expressing Sox9. Some cases of PRS may thus result from developmental misexpression of SOX9 due to disruption of very-long-range cis-regulatory elements.

  17. 多重随机序列在算术编码中的应用%Application of Multiple Random Sequence in Arithmetic Coding

    Institute of Scientific and Technical Information of China (English)

    周明; 冯民富

    2012-01-01

    Arithmetic coding, for its high compression ratio and moderate coding efficiency, plays an important role in the standard of image compression technology. This algorithm depends on only one argument: the occurrence probability of information source symbols. This probability determines the efficiency of compression, and the interval of information source symbols as well. However, the classical arithmetic coding considers no internal structure of the input sequence of information source symbols, but only the probability of single symbols. Finally to which special combinations the coding intervals should be allocated, and whether there exists an effective allocation algorithm, these are still problems to been considered and settled.%算术编码凭借其高效的压缩比以及适度的编码效率,在图像压缩技术标准(比如JPEG等)中有着重要的地位。该算法仅仅依赖于一个参数:信源符号出现的概率。该概率决定了压缩编码的效率,同时也决定了编码过程中信源符号的间隔。然而,经典的算术编码都没有考虑信源符号输入序列的内在结构,仅仅是考虑单个的符号。这些连续的输入组合中的某些组合若大量出现在信源符号中,就有必要考虑这些组合的出现概率了。而最终需要给哪些特定的组合分配编码区间,以及是否有行之有效的分配算法,都需要考虑。

  18. The Vulnerability Assessment Code for Physical Protection System

    International Nuclear Information System (INIS)

    Jang, Sung Soon; Yoo, Ho Sik

    2007-01-01

    To neutralize the increasing terror threats, nuclear facilities have strong physical protection system (PPS). PPS includes detectors, door locks, fences, regular guard patrols, and a hot line to a nearest military force. To design an efficient PPS and to fully operate it, vulnerability assessment process is required. Evaluating PPS of a nuclear facility is complicate process and, hence, several assessment codes have been developed. The estimation of adversary sequence interruption (EASI) code analyzes vulnerability along a single intrusion path. To evaluate many paths to a valuable asset in an actual facility, the systematic analysis of vulnerability to intrusion (SAVI) code was developed. KAERI improved SAVI and made the Korean analysis of vulnerability to intrusion (KAVI) code. Existing codes (SAVI and KAVI) have limitations in representing the distance of a facility because they use the simplified model of a PPS called adversary sequence diagram. In adversary sequence diagram the position of doors, sensors and fences is described just as the locating area. Thus, the distance between elements is inaccurate and we cannot reflect the range effect of sensors. In this abstract, we suggest accurate and intuitive vulnerability assessment based on raster map modeling of PPS. The raster map of PPS accurately represents the relative position of elements and, thus, the range effect of sensor can be easily incorporable. Most importantly, the raster map is easy to understand

  19. New insights into flavivirus evolution, taxonomy and biogeographic history, extended by analysis of canonical and alternative coding sequences.

    Directory of Open Access Journals (Sweden)

    Gregory Moureau

    Full Text Available To generate the most diverse phylogenetic dataset for the flaviviruses to date, we determined the genomic sequences and phylogenetic relationships of 14 flaviviruses, of which 10 are primarily associated with Culex spp. mosquitoes. We analyze these data, in conjunction with a comprehensive collection of flavivirus genomes, to characterize flavivirus evolutionary and biogeographic history in unprecedented detail and breadth. Based on the presumed introduction of yellow fever virus into the Americas via the transatlantic slave trade, we extrapolated a timescale for a relevant subset of flaviviruses whose evolutionary history, shows that different Culex-spp. associated flaviviruses have been introduced from the Old World to the New World on at least five separate occasions, with 2 different sets of factors likely to have contributed to the dispersal of the different viruses. We also discuss the significance of programmed ribosomal frameshifting in a central region of the polyprotein open reading frame in some mosquito-associated flaviviruses.

  20. Characterization of a polymorphism in the coding sequence of FCN3 resulting in a Ficolin-3 (Hakata antigen) deficiency state

    DEFF Research Database (Denmark)

    Munthe-Fog, Lea; Hummelshøj, Tina; Ma, Ying Jie

    2008-01-01

    Ficolin-3 (Hakata antigen or H-ficolin) is a soluble pattern recognition molecule in the lectin complement pathway. We speculated whether common genetic variations in the FCN3 gene contribute to deficiency of Ficolin-3. The FCN3 gene was sequenced in 237 healthy Danish Caucasians. The relevance...... of polymorphisms was assessed with antibodies against Ficolin-3 in a novel ELISA system and by production of recombinant Ficolin-3 variants. Ficolin-3 serum profiles were analyzed by SDS-PAGE and western blotting. Ficolin-3 serum concentration varied 10-fold (median, 24microg/ml; range, 3-54microg/ml). Out.......025). SDS-PAGE and western blotting of serum revealed a weak band corresponding to the truncated molecule in addition to the normal Ficolin-3 pattern. Characterization of recombinant Ficolin-3 derived from FCN3+1637delC showed that in the homozygous situation this allelic variant would lead to Ficolin-3...

  1. Markets and pricing for interruptible electric power

    International Nuclear Information System (INIS)

    Gedra, T.W.; Varaiya, P.P.

    1993-01-01

    The authors propose a market for interruptible, or callable, forward contracts for electric power, in which the consumer grants the power supplier the right to interrupt a given unit of load in return for a price discount. The callable forward contracts are traded continuously until the time of use. This allows recourse for those customers with uncertain demand, while risk-averse consumers can minimize their price risk by purchasing early. Callable forward contracts are simple in form, and can be directly incorporated into the utility's economic dispatch procedure

  2. A LTR copia retrotransposon and Mutator transposons interrupt Pgip genes in cultivated and wild wheats.

    Science.gov (United States)

    Di Giovanni, Michela; Cenci, Alberto; Janni, Michela; D'Ovidio, Renato

    2008-04-01

    Polygalacturonase-inhibiting proteins (PGIPs) are leucine-rich repeat (LRR) proteins involved in plant defence. Wheat pgip genes have been isolated from the B (Tapgip1) and D (Tapgip2) genomes, and now we report the identification of pgip genes from the A genomes of wild and cultivated wheats. By Southern blots and sequence analysis of BAC clones we demonstrated that wheat contains a single copy pgip gene per genome and the one from the A genome, pgip3, is inactivated by the insertion of a long terminal repeat copia retrotranspon within the fourth LRR. We demonstrated also that this retrotransposon insertion is present in Triticum urartu and all the polyploidy wheats assayed, but is absent in T. monococcum (Tmpgip3), suggesting that this insertion took place after the divergence between T. monococcum and T. urartu, but before the formation of the polyploid wheats. We identified also two independent insertion events of new Class II transposable elements, Vacuna, belonging to the Mutator superfamily, that interrupted the Tdipgip1 gene of T. turgidum ssp. dicoccoides. The occurrence of these transposons within the coding region of Tdipgip1 facilitated the mapping of the Pgip locus in the pericentric region of the short arm of chromosome group 7. We speculate that the inactivation of pgip genes are tolerated because of redundancy of PGIP activities in the wheat genome.

  3. Interactive or interruptive? Instant messaging at work

    NARCIS (Netherlands)

    Ou, C.X.J.; Davison, R.M.

    2011-01-01

    The use of instant messaging (IM) technology at work is controversial, due to the interruptions it may cause and the difficulties associated with quantifying its benefits for individuals, teams and organizations. In this study, we investigate the use and impact of IM tools in the workplace. Based on

  4. Stress Outcomes of Four Types of Perceived Interruptions.

    Science.gov (United States)

    Fletcher, Keaton A; Potter, Sean M; Telford, Britany N

    2018-03-01

    Objective We sought to define and measure four types of perceived interruptions and to examine their relationships with stress outcomes. Background Interruptions have been defined and measured in a variety of inconsistent ways. No study has simultaneously examined the subjective experience of all types of interruptions. Method First, we provide a synthesized definition and model of interruptions that aligns interruptions along two qualities: origin and degree of multitasking. Second, we create and validate a self-report measure of these four types of perceived interruptions within two samples (working undergraduate students and working engineers). Last, we correlate this measure with self-reported psychological and physical stress outcomes. Results Our results support the four-factor model of interruptions. Results further support the link between each of the four types of interruptions (intrusions, breaks, distractions, and a specific type of ruminations, discrepancies) and stress outcomes. Specifically, results suggest that distractions explain a unique portion of variance in stress outcomes above and beyond the shared variance explained by intrusions, breaks, and discrepancies. Conclusion The synthesized four-factor model of interruptions is an adequate representation of the overall construct of interruptions. Further, perceived interruptions can be measured and are significantly related to stress outcomes. Application Measuring interruptions by observation can be intrusive and resource intensive. Additionally, some types of interruptions may be internal and therefore unobservable. Our survey measure offers a practical alternative method for practitioners and researchers interested in the outcomes of interruptions, especially stress outcomes.

  5. Functional anthology of intrinsic disorder. 2. Cellular components, domains, technical terms, developmental processes, and coding sequence diversities correlated with long disordered regions.

    Science.gov (United States)

    Vucetic, Slobodan; Xie, Hongbo; Iakoucheva, Lilia M; Oldfield, Christopher J; Dunker, A Keith; Obradovic, Zoran; Uversky, Vladimir N

    2007-05-01

    Biologically active proteins without stable ordered structure (i.e., intrinsically disordered proteins) are attracting increased attention. Functional repertoires of ordered and disordered proteins are very different, and the ability to differentiate whether a given function is associated with intrinsic disorder or with a well-folded protein is crucial for modern protein science. However, there is a large gap between the number of proteins experimentally confirmed to be disordered and their actual number in nature. As a result, studies of functional properties of confirmed disordered proteins, while helpful in revealing the functional diversity of protein disorder, provide only a limited view. To overcome this problem, a bioinformatics approach for comprehensive study of functional roles of protein disorder was proposed in the first paper of this series (Xie, H.; Vucetic, S.; Iakoucheva, L. M.; Oldfield, C. J.; Dunker, A. K.; Obradovic, Z.; Uversky, V. N. Functional anthology of intrinsic disorder. 1. Biological processes and functions of proteins with long disordered regions. J. Proteome Res. 2007, 5, 1882-1898). Applying this novel approach to Swiss-Prot sequences and functional keywords, we found over 238 and 302 keywords to be strongly positively or negatively correlated, respectively, with long intrinsically disordered regions. This paper describes approximately 90 Swiss-Prot keywords attributed to the cellular components, domains, technical terms, developmental processes, and coding sequence diversities possessing strong positive and negative correlation with long disordered regions.

  6. Functional Anthology of Intrinsic Disorder. II. Cellular Components, Domains, Technical Terms, Developmental Processes and Coding Sequence Diversities Correlated with Long Disordered Regions

    Science.gov (United States)

    Vucetic, Slobodan; Xie, Hongbo; Iakoucheva, Lilia M.; Oldfield, Christopher J.; Dunker, A. Keith; Obradovic, Zoran; Uversky, Vladimir N.

    2008-01-01

    Biologically active proteins without stable ordered structure (i.e., intrinsically disordered proteins) are attracting increased attention. Functional repertoires of ordered and disordered proteins are very different, and the ability to differentiate whether a given function is associated with intrinsic disorder or with a well-folded protein is crucial for modern protein science. However, there is a large gap between the number of proteins experimentally confirmed to be disordered and their actual number in nature. As a result, studies of functional properties of confirmed disordered proteins, while helpful in revealing the functional diversity of protein disorder, provide only a limited view. To overcome this problem, a bioinformatics approach for comprehensive study of functional roles of protein disorder was proposed in the first paper of this series (Xie H., Vucetic S., Iakoucheva L.M., Oldfield C.J., Dunker A.K., Obradovic Z., Uversky V.N. (2006) Functional anthology of intrinsic disorder. I. Biological processes and functions of proteins with long disordered regions. J. Proteome Res.). Applying this novel approach to Swiss-Prot sequences and functional keywords, we found over 238 and 302 keywords to be strongly positively or negatively correlated, respectively, with long intrinsically disordered regions. This paper describes ~90 Swiss-Prot keywords attributed to the cellular components, domains, technical terms, developmental processes and coding sequence diversities possessing strong positive and negative correlation with long disordered regions. PMID:17391015

  7. Color differences among feral pigeons (Columba livia) are not attributable to sequence variation in the coding region of the melanocortin-1 receptor gene (MC1R)

    Science.gov (United States)

    2013-01-01

    Background Genetic variation at the melanocortin-1 receptor (MC1R) gene is correlated with melanin color variation in many birds. Feral pigeons (Columba livia) show two major melanin-based colorations: a red coloration due to pheomelanic pigment and a black coloration due to eumelanic pigment. Furthermore, within each color type, feral pigeons display continuous variation in the amount of melanin pigment present in the feathers, with individuals varying from pure white to a full dark melanic color. Coloration is highly heritable and it has been suggested that it is under natural or sexual selection, or both. Our objective was to investigate whether MC1R allelic variants are associated with plumage color in feral pigeons. Findings We sequenced 888 bp of the coding sequence of MC1R among pigeons varying both in the type, eumelanin or pheomelanin, and the amount of melanin in their feathers. We detected 10 non-synonymous substitutions and 2 synonymous substitution but none of them were associated with a plumage type. It remains possible that non-synonymous substitutions that influence coloration are present in the short MC1R fragment that we did not sequence but this seems unlikely because we analyzed the entire functionally important region of the gene. Conclusions Our results show that color differences among feral pigeons are probably not attributable to amino acid variation at the MC1R locus. Therefore, variation in regulatory regions of MC1R or variation in other genes may be responsible for the color polymorphism of feral pigeons. PMID:23915680

  8. CGG repeat length and AGG interruptions as indicators of fragile X-associated diminished ovarian reserve.

    Science.gov (United States)

    Lekovich, Jovana; Man, Limor; Xu, Kangpu; Canon, Chelsea; Lilienthal, Debra; Stewart, Joshua D; Pereira, Nigel; Rosenwaks, Zev; Gerhardt, Jeannine

    2017-12-21

    PurposeFragile X premutation (PM) carriers may experience difficulties conceiving a child probably due to fragile X-associated diminished ovarian reserve (FXDOR). We investigated which subgroups of carriers with a PM are at higher risk of FXDOR, and whether the number of AGG interruptions within the repeat sequence further ameliorates the risk.MethodsWe compared markers of ovarian reserve, including anti-Müllerian hormone, antral follicle count, and number of oocytes retrieved between different subgroups of patients with a PM.ResultsWe found that carriers with midrange repeats size (70-90 CGG) demonstrate significantly lower ovarian reserve. Additionally, the number of AGG interruptions directly correlated with parameters of ovarian reserve. Patients with longer uninterrupted CGG repeats post-AGG interruptions had the lowest ovarian reserve.ConclusionThis study connects AGG interruptions and certain CGG repeat length to reduced ovarian reserve in carriers with a PM. A possible explanation for our findings is the proposed gonadotoxicity of the FMR1 transcripts. Reduction of AGG interruptions could increase the likelihood that secondary RNA structures in the FMR1 messenger RNA are formed, which could cause cell dysfunction within the ovaries. These findings may provide women with guidance regarding their fertility potential and accordingly assist with their family planning.GENETICS in MEDICINE advance online publication, 21 December 2017; doi:10.1038/gim.2017.220.

  9. Sex Discrimination and Women's Labor Market Interruptions

    OpenAIRE

    David Neumark

    1993-01-01

    The human capital explanation of sex differences in wages is that women intend to work in the labor market more intermittently than men, and therefore invest less. This lower investment leads to lower wages and wage growth. The alternative "feedback" hypothesis consistent with the same facts is that women experience labor market discrimination and respond with career interruptions and specialization in household production. This paper explores the relationship between self-reported discrimina...

  10. Interrupting long periods of sitting: good STUFF

    Directory of Open Access Journals (Sweden)

    Rutten Geert M

    2013-01-01

    Full Text Available Abstract There is increasing evidence that sedentary behaviour is in itself a health risk, regardless of the daily amount of moderate to vigorous physical activity. Therefore, sedentary behaviour should be targeted as important health behaviour. It is known that even relatively small changes of health behaviour often require serious efforts from an individual and from people in their environment to become part of their lifestyle. Therefore, interventions to promote healthy behaviours should ideally be simple, easy to perform and easily available. Since sitting is likely to be highly habitual, confrontation with an intervention should almost automatically elicit a reaction of getting up, and thus break up and reduce sitting time. One important prerequisite for successful dissemination of such an intervention could be the use of a recognisable term relating to sedentary behaviour, which should have the characteristics of an effective brand name. To become wide spread, this term may need to meet three criteria: the “Law of the few”, the “Stickiness factor”, and the “Power of context”. For that purpose we introduce STUFF: Stand Up For Fitness. STUFF can be defined as “interrupting long sitting periods by short breaks”, for instance, interrupting sitting every 30 min by standing for at least five minutes. Even though we still need evidence to test the health-enhancing effects of interrupted sitting, we hope that the introduction of STUFF will facilitate the testing of the social, psychological and health effects of interventions to reduce sitting time.

  11. Older persons' worries expressed during home care visits: Exploring the content of cues and concerns identified by the Verona coding definitions of emotional sequences.

    Science.gov (United States)

    Hafskjold, Linda; Eide, Tom; Holmström, Inger K; Sundling, Vibeke; van Dulmen, Sandra; Eide, Hilde

    2016-12-01

    Little is known about how older persons in home care express their concerns. Emotional cues and concerns can be identified by the Verona coding definitions of emotional sequences (VR-CoDES), but the method gives no insight into what causes the distress and the emotions involved. The aims of this study are to explore (1) older persons' worries and (2) the content of these expressions. An observational exploratory two-step approach was used to investigate audiotaped recordings from 38 Norwegian home care visits with older persons and nurse assistants. First, 206 cues and concerns were identified using VR-CoDES. Second, the content and context of these expressions were analysed inductively. Four main categories emerged: worries about relationships with others, worries about health care-related issues, worries about aging and bodily impairment, and life narratives and value issues, with several subcategories showing the causes of worry and emotions involved. The two-step approach provides an in-depth knowledge of older persons' worries, causes of worries, and their related emotions. The subcategories described in a language close to the experience can be useful in practice development and communication training for students and health care providers. Copyright © 2016 Elsevier Ireland Ltd. All rights reserved.

  12. Energy expenditure of interruptions to sedentary behavior

    Directory of Open Access Journals (Sweden)

    Strath Scott J

    2011-06-01

    Full Text Available Abstract Background Advances in technology, social influences and environmental attributes have resulted in substan-tial portions of the day spent in sedentary pursuits. Sedentary behavior may be a cause of many chronic diseases including obesity, insulin resistance, type 2 diabetes and the metabolic syndrome. Research demonstrated that breaking up sedentary time was beneficially associated with markers of body composition, cardiovascular health and type 2 diabetes. Therefore, the purpose of this study was to quantify the total energy expenditure of three different durations of physical activity within a 30-minute sedentary period and to examine the potential benefits of interrupting sedentary behavior with physical activity for weight control. Methods Participants completed four consecutive 30-minute bouts of sedentary behavior (reading, working on the computer, or doing other desk activities with and without interruptions of walking at a self-selected pace. Bout one contained no walking interruptions. Bout two contained a 1-minute walking period. Bout three contained a 2-minute walking period. Bout four contained a 5-minute walking period. Body composition and resting metabolic rate were assessed. Result Twenty males and females (18-39 years completed this study. Results of the repeated measures analysis of variance with post-hoc testing showed that significantly more energy was expended during each 30 minute sedentary bout with a walking break than in the 30 minute sedentary bout (p Conclusions This study demonstrated that making small changes, such as taking a five minute walking break every hour could yield beneficial weight control or weight loss results. Therefore, taking breaks from sedentary time is a potential outlet to prevent obesity and the rise of obesity in developed countries.

  13. Sequence analysis of Epstein-Barr virus EBNA-2 gene coding amino acid 148-487 in nasopharyngeal and gastric carcinomas

    Directory of Open Access Journals (Sweden)

    Wang Xinying

    2012-02-01

    Full Text Available Abstract Background The Epstein-Barr virus (EBV nuclear antigen 2 (EBNA-2 plays a key role in the B-cell growth transformation by initiating and maintaining the proliferation of infected B-cell upon EBV infection in vitro. Most studies about EBNA-2 have focused on its functions yet little is known for its intertypic polymorphisms. Results Coding region for amino acid (aa 148-487 of the EBNA-2 gene was sequenced in 25 EBV-associated gastric carcinomas (EBVaGCs, 56 nasopharyngeal carcinomas (NPCs and 32 throat washings (TWs from healthy donors in Northern China. Three variations (g48991t, c48998a, t49613a were detected in all of the samples (113/113, 100%. EBNA-2 could be classified into four distinct subtypes: E2-A, E2-B, E2-C and E2-D based on the deletion status of three aa (294Q, 357K and 358G. Subtypes E2-A and E2-C were detected in 56/113 (49.6%, 38/113 (33.6% samples, respectively. E2-A was observed more in EBVaGCs samples and subtype E2-D was only detected in the NPC samples. Variation analysis in EBNA-2 functional domains: the TAD residue (I438L and the NLS residues (E476G, P484H and I486T were only detected in NPC samples which located in the carboxyl terminus of EBNA-2 gene. Conclusions The subtypes E2-A and E2-C were the dominant genotypes of the EBNA-2 gene in Northern China. The subtype E2-D may be associated with the tumorigenesis of NPC. The NPC isolates were prone harbor to more mutations than the other two groups in the functional domains.

  14. Evolutionary changes in gene expression, coding sequence and copy-number at the Cyp6g1 locus contribute to resistance to multiple insecticides in Drosophila.

    Directory of Open Access Journals (Sweden)

    Thomas W R Harrop

    Full Text Available Widespread use of insecticides has led to insecticide resistance in many populations of insects. In some populations, resistance has evolved to multiple pesticides. In Drosophila melanogaster, resistance to multiple classes of insecticide is due to the overexpression of a single cytochrome P450 gene, Cyp6g1. Overexpression of Cyp6g1 appears to have evolved in parallel in Drosophila simulans, a sibling species of D. melanogaster, where it is also associated with insecticide resistance. However, it is not known whether the ability of the CYP6G1 enzyme to provide resistance to multiple insecticides evolved recently in D. melanogaster or if this function is present in all Drosophila species. Here we show that duplication of the Cyp6g1 gene occurred at least four times during the evolution of different Drosophila species, and the ability of CYP6G1 to confer resistance to multiple insecticides exists in D. melanogaster and D. simulans but not in Drosophila willistoni or Drosophila virilis. In D. virilis, which has multiple copies of Cyp6g1, one copy confers resistance to DDT and another to nitenpyram, suggesting that the divergence of protein sequence between copies subsequent to the duplication affected the activity of the enzyme. All orthologs tested conferred resistance to one or more insecticides, suggesting that CYP6G1 had the capacity to provide resistance to anthropogenic chemicals before they existed. Finally, we show that expression of Cyp6g1 in the Malpighian tubules, which contributes to DDT resistance in D. melanogaster, is specific to the D. melanogaster-D. simulans lineage. Our results suggest that a combination of gene duplication, regulatory changes and protein coding changes has taken place at the Cyp6g1 locus during evolution and this locus may play a role in providing resistance to different environmental toxins in different Drosophila species.

  15. Estimates of thermal fatigue due to beam interruptions for an ALMR-type ATW

    International Nuclear Information System (INIS)

    Dunn, F. E.; Wade, D. C.

    1999-01-01

    Thermal fatigue due to beam interruptions has been investigated in a sodium cooled ATW using the Advanced Liquid Metal mod B design as a basis for the subcritical source driven reactor. A k eff of 0.975 was used for the reactor. Temperature response in the primary coolant system was calculated, using the SASSYS- 1 code, for a drop in beam current from full power to zero in 1 microsecond.. Temperature differences were used to calculate thermal stresses. Fatigue curves from the American Society of Mechanical Engineers Boiler and Pressure Vessel Code were used to determine the number of cycles various components should be designed for, based on these thermal stresses

  16. Are Technology Interruptions Impacting Your Bottom Line? An Innovative Proposal for Change.

    Science.gov (United States)

    Ledbetter, Tamera; Shultz, Sarah; Beckham, Roxanne

    2017-10-01

    Nursing interruptions are a costly and dangerous variable in acute care hospitals. Malfunctioning technology equipment interrupts nursing care and prevents full utilization of computer safety systems to prevent patient care errors. This paper identifies an innovative approach to nursing interruptions related to computer and computer cart malfunctions. The impact on human resources is defined and outcome measures were proposed. A multifaceted proposal, based on a literature review, aimed at reducing nursing interruptions is presented. This proposal is expected to increase patient safety, as well as patient and nurse satisfaction. Acute care hospitals utilizing electronic medical records and bar-coded medication administration technology. Nurses, information technology staff, nursing informatics staff, and all leadership teams affected by technology problems and their proposed solutions. Literature from multiple fields was reviewed to evaluate research related to computer/computer cart failures, and the approaches used to resolve these issues. Outcome measured strategic goals related to patient safety, and nurse and patient satisfaction. Specific help desk metrics will demonstrate the effect of interventions. This paper addresses a gap in the literature and proposes practical and innovative solutions. A comprehensive computer and computer cart repair program is essential for patient safety, financial stewardship, and utilization of resources. © 2015 Wiley Periodicals, Inc.

  17. Interrupting the Interruption: Neoliberalism and the Challenges of an Antiracist School

    Science.gov (United States)

    Meshulam, Assaf; Apple, Michael W.

    2014-01-01

    The article examines a US public elementary bilingual, multicultural school that attempts to interrupt the reproduction of existing relations of dominance and subordination across a variety of differences. The school's experiences illuminate the complex reality of schools as a site of struggle and compromise between at times contradictory…

  18. Analysis of Smartphone Interruptions on Academic General Internal Medicine Wards. Frequent Interruptions may cause a 'Crisis Mode' Work Climate.

    Science.gov (United States)

    Vaisman, Alon; Wu, Robert C

    2017-01-04

    Hospital-based medical services are increasingly utilizing team-based pagers and smartphones to streamline communications. However, an unintended consequence may be higher volumes of interruptions potentially leading to medical error. There is likely a level at which interruptions are excessive and cause a 'crisis mode' climate. We retrospectively collected phone, text messaging, and email interruptions directed to hospital-assigned smartphones on eight General Internal Medicine (GIM) teams at two tertiary care centres in Toronto, Ontario from April 2013 to September 2014. We also calculated the number of times these interruptions exceeded a pre-specified threshold per hour, termed 'crisis mode', defined as at least five interruptions in 30 minutes. We analyzed the correlation between interruptions and date, site, and patient volumes. A total of 187,049 interruptions were collected over an 18-month period. Daily weekday interruptions rose sharply in the morning, peaking between 11 AM to 12 PM and measuring 4.8 and 3.7 mean interruptions/hour at each site, respectively. Mean daily interruptions per team totaled 46.2 ± 3.6 at Site 1 and 39.2 ± 4.2 at Site 2. The 'crisis mode' threshold was exceeded, on average, 2.3 times/day per GIM team during weekdays. In a multivariable linear regression analysis, site (β6.43 CI95% 5.44 - 7.42, ptime.

  19. Task Interruption: Resumption Lag and the Role of Cues

    National Research Council Canada - National Science Library

    Altmann, Erik M; Trafton, J. G

    2004-01-01

    ...), indicating a substantial disruptive effect. To probe the nature of the disruption, they examined the role of external cues associated with the interrupted task and found that cues available immediately before an interruption facilitate performance immediately afterwards, thus reducing the resumption lag. This "cue-availability" effect suggests that people deploy preparatory perceptual and memory processes, apparently spontaneously, to mitigate the disruptive effects of task interruption.

  20. Diagnosis of aortic interruption by CT angiography

    International Nuclear Information System (INIS)

    Shirani, Shapour; Soleymanzadeh, Maryam

    2013-01-01

    Interrupted aortic arch (IAA) is a rare congenital malformation of the aortic arch, which might be accompanied with other coexisting cardiovascular anomalies. Many cases with IAA are diagnosed at their neonatal and newborn period but in rare cases the diagnosis is not established until adulthood. The patients may have no clinical symptoms but the signs of heart failure will gradually appear and may cause death. The development of imaging methods such as computed tomography (CT) and magnetic resonance (MR) imaging has dramatically changed the diagnostics. Here we report a 20-year-old young man with IAA associated with sinus venosus atrial septal defect (SVD) and partial anomalous pulmonary venous connection (PAPVC) referred to our hospital

  1. Pulsed interrupter and method of operation

    Science.gov (United States)

    Drake, Joel Lawton; Kratz, Robert

    2015-06-09

    Some embodiments provide interrupter systems comprising: a first electrode; a second electrode; a piston movably located at a first position and electrically coupled with the first and second electrodes establishing a closed state, the piston comprises an electrical conductor that couples with the first and second electrodes providing a conductive path; an electromagnetic launcher configured to, when activated, induce a magnetic field pulse causing the piston to move away from the electrical coupling with the first and second electrodes establishing an open circuit between the first and second electrodes; and a piston control system comprising a piston arresting system configured to control a deceleration of the piston following the movement of the piston induced by the electromagnetic launcher such that the piston is not in electrical contact with at least one of the first electrode and the second electrode when in the open state.

  2. Codes and curves

    CERN Document Server

    Walker, Judy L

    2000-01-01

    When information is transmitted, errors are likely to occur. Coding theory examines efficient ways of packaging data so that these errors can be detected, or even corrected. The traditional tools of coding theory have come from combinatorics and group theory. Lately, however, coding theorists have added techniques from algebraic geometry to their toolboxes. In particular, by re-interpreting the Reed-Solomon codes, one can see how to define new codes based on divisors on algebraic curves. For instance, using modular curves over finite fields, Tsfasman, Vladut, and Zink showed that one can define a sequence of codes with asymptotically better parameters than any previously known codes. This monograph is based on a series of lectures the author gave as part of the IAS/PCMI program on arithmetic algebraic geometry. Here, the reader is introduced to the exciting field of algebraic geometric coding theory. Presenting the material in the same conversational tone of the lectures, the author covers linear codes, inclu...

  3. Two-terminal video coding.

    Science.gov (United States)

    Yang, Yang; Stanković, Vladimir; Xiong, Zixiang; Zhao, Wei

    2009-03-01

    Following recent works on the rate region of the quadratic Gaussian two-terminal source coding problem and limit-approaching code designs, this paper examines multiterminal source coding of two correlated, i.e., stereo, video sequences to save the sum rate over independent coding of both sequences. Two multiterminal video coding schemes are proposed. In the first scheme, the left sequence of the stereo pair is coded by H.264/AVC and used at the joint decoder to facilitate Wyner-Ziv coding of the right video sequence. The first I-frame of the right sequence is successively coded by H.264/AVC Intracoding and Wyner-Ziv coding. An efficient stereo matching algorithm based on loopy belief propagation is then adopted at the decoder to produce pixel-level disparity maps between the corresponding frames of the two decoded video sequences on the fly. Based on the disparity maps, side information for both motion vectors and motion-compensated residual frames of the right sequence are generated at the decoder before Wyner-Ziv encoding. In the second scheme, source splitting is employed on top of classic and Wyner-Ziv coding for compression of both I-frames to allow flexible rate allocation between the two sequences. Experiments with both schemes on stereo video sequences using H.264/AVC, LDPC codes for Slepian-Wolf coding of the motion vectors, and scalar quantization in conjunction with LDPC codes for Wyner-Ziv coding of the residual coefficients give a slightly lower sum rate than separate H.264/AVC coding of both sequences at the same video quality.

  4. Nucleotide sequence of a cDNA coding for the amino-terminal region of human prepro. alpha. 1(III) collagen

    Energy Technology Data Exchange (ETDEWEB)

    Toman, P D; Ricca, G A [Rorer Biotechnology, Inc., Springfield, VA (USA); de Crombrugghe, B [National Institutes of Health, Bethesda, MD (USA)

    1988-07-25

    Type III Collagen is synthesized in a variety of tissues as a precursor macromolecule containing a leader sequence, a N-propeptide, a N-telopeptide, the triple helical region, a C-telopeptide, and C-propeptide. To further characterize the human type III collagen precursor, a human placental cDNA library was constructed in gt11 using an oligonucleotide derived from a partial cDNA sequence corresponding to the carboxy-terminal part of the 1(III) collagen. A cDNA was identified which contains the leader sequence, the N-propeptide and N-telopeptide regions. The DNA sequence of these regions are presented here. The triple helical, C-telopeptide and C-propeptide amino acid sequence for human type III collagen has been determined previously. A comparison of the human amino acid sequence with mouse, chicken, and calf sequence shows 81%, 81%, and 92% similarity, respectively. At the DNA level, the sequence similarity between human and mouse or chicken type III collagen sequences in this area is 82% and 77%, respectively.

  5. Molecular phylogeny of 21 tropical bamboo species reconstructed by integrating non-coding internal transcribed spacer (ITS1 and 2) sequences and their consensus secondary structure.

    Science.gov (United States)

    Ghosh, Jayadri Sekhar; Bhattacharya, Samik; Pal, Amita

    2017-06-01

    The unavailability of the reproductive structure and unpredictability of vegetative characters for the identification and phylogenetic study of bamboo prompted the application of molecular techniques for greater resolution and consensus. We first employed internal transcribed spacer (ITS1, 5.8S rRNA and ITS2) sequences to construct the phylogenetic tree of 21 tropical bamboo species. While the sequence alone could grossly reconstruct the traditional phylogeny amongst the 21-tropical species studied, some anomalies were encountered that prompted a further refinement of the phylogenetic analyses. Therefore, we integrated the secondary structure of the ITS sequences to derive individual sequence-structure matrix to gain more resolution on the phylogenetic reconstruction. The results showed that ITS sequence-structure is the reliable alternative to the conventional phenotypic method for the identification of bamboo species. The best-fit topology obtained by the sequence-structure based phylogeny over the sole sequence based one underscores closer clustering of all the studied Bambusa species (Sub-tribe Bambusinae), while Melocanna baccifera, which belongs to Sub-Tribe Melocanneae, disjointedly clustered as an out-group within the consensus phylogenetic tree. In this study, we demonstrated the dependability of the combined (ITS sequence+structure-based) approach over the only sequence-based analysis for phylogenetic relationship assessment of bamboo.

  6. Interrupter and hybrid-switch testing for fusion devices

    International Nuclear Information System (INIS)

    Parsons, W.M.; Warren, R.W.; Honig, E.M.; Lindsay, J.D.G.; Bellamo, P.; Cassel, R.L.

    1979-01-01

    This paper discusses recent and ongoing switch testing for fusion devices. The first part describes testing for the TFTR ohmic-heating circuit. In this set of tests, which simulated the stresses produced during a plasma initiation pulse, circuit breakers were required to interrupt a current of 24 kA with an associated recovery voltage of 25 kV. Two interrupter systems were tested for over 1000 operations each, and both appear to satisfy TFTR requirements. The second part discusses hybrid-switch development for superconducting coil protection. These switching systems must be capable of carrying large currents on a continuous basis as well as performing interruption duties. The third part presents preliminary results on an early-counterpulse technique applied to vacuum interrupters. Implementation of this technique has resulted in large increases in interruptible current as well as a marked reduction in contact erosion

  7. Effects of interruption of irradiation on Harwell Red Perspex (PMMA)

    International Nuclear Information System (INIS)

    Khayet Tebourbi, Mohamed anouar abdelaziz

    2010-01-01

    Harwell Red Perspex PMMA (Polymethylmethacrylate) is a dosimeter very much used in the industrial treatments by Radiations ionizing. The purpose of this work is to test the response of this dosimeter for radiation processes having undergone one or more interruptions. This experimental study based on the development of a factorial experimental design on two levels showed that the response of this dosimeter increases for the interrupted treatments. The value of the estimated amount of response increase is all the more significant as the temperature during the interruption is high. Also it made possible to determine a mathematical model binding the value of the amount posted to the factors of influence: Temperature, target amount, a number of interruptions and duration of each interruption.

  8. Code Cactus; Code Cactus

    Energy Technology Data Exchange (ETDEWEB)

    Fajeau, M; Nguyen, L T; Saunier, J [Commissariat a l' Energie Atomique, Centre d' Etudes Nucleaires de Saclay, 91 - Gif-sur-Yvette (France)

    1966-09-01

    This code handles the following problems: -1) Analysis of thermal experiments on a water loop at high or low pressure; steady state or transient behavior; -2) Analysis of thermal and hydrodynamic behavior of water-cooled and moderated reactors, at either high or low pressure, with boiling permitted; fuel elements are assumed to be flat plates: - Flowrate in parallel channels coupled or not by conduction across plates, with conditions of pressure drops or flowrate, variable or not with respect to time is given; the power can be coupled to reactor kinetics calculation or supplied by the code user. The code, containing a schematic representation of safety rod behavior, is a one dimensional, multi-channel code, and has as its complement (FLID), a one-channel, two-dimensional code. (authors) [French] Ce code permet de traiter les problemes ci-dessous: 1. Depouillement d'essais thermiques sur boucle a eau, haute ou basse pression, en regime permanent ou transitoire; 2. Etudes thermiques et hydrauliques de reacteurs a eau, a plaques, a haute ou basse pression, ebullition permise: - repartition entre canaux paralleles, couples on non par conduction a travers plaques, pour des conditions de debit ou de pertes de charge imposees, variables ou non dans le temps; - la puissance peut etre couplee a la neutronique et une representation schematique des actions de securite est prevue. Ce code (Cactus) a une dimension d'espace et plusieurs canaux, a pour complement Flid qui traite l'etude d'un seul canal a deux dimensions. (auteurs)

  9. Servicing a globally broadcast interrupt signal in a multi-threaded computer

    Science.gov (United States)

    Attinella, John E.; Davis, Kristan D.; Musselman, Roy G.; Satterfield, David L.

    2015-12-29

    Methods, apparatuses, and computer program products for servicing a globally broadcast interrupt signal in a multi-threaded computer comprising a plurality of processor threads. Embodiments include an interrupt controller indicating in a plurality of local interrupt status locations that a globally broadcast interrupt signal has been received by the interrupt controller. Embodiments also include a thread determining that a local interrupt status location corresponding to the thread indicates that the globally broadcast interrupt signal has been received by the interrupt controller. Embodiments also include the thread processing one or more entries in a global interrupt status bit queue based on whether global interrupt status bits associated with the globally broadcast interrupt signal are locked. Each entry in the global interrupt status bit queue corresponds to a queued global interrupt.

  10. Cloning and sequencing of the gene coding for alcohol dehydrogenase of Bacillus stearothermophilus and rational shift of the optimum pH.

    OpenAIRE

    Sakoda, H; Imanaka, T

    1992-01-01

    Using Bacillus subtilis as a host and pTB524 as a vector plasmid, we cloned the thermostable alcohol dehydrogenase (ADH-T) gene (adhT) from Bacillus stearothermophilus NCA1503 and determined its nucleotide sequence. The deduced amino acid sequence (337 amino acids) was compared with the sequences of ADHs from four different origins. The amino acid residues responsible for the catalytic activity of horse liver ADH had been clarified on the basis of three-dimensional structure. Since those cata...

  11. Opioid interruptions, pain, and withdrawal symptoms in nursing home residents.

    Science.gov (United States)

    Redding, Sarah E; Liu, Sophia; Hung, William W; Boockvar, Kenneth S

    2014-11-01

    Interruptions in opioid use have the potential to cause pain relapse and withdrawal symptoms. The objectives of this study were to observe patterns of opioid interruption during acute illness in nursing home residents and examine associations between interruptions and pain and withdrawal symptoms. Patients from 3 nursing homes in a metropolitan area who were prescribed opioids were assessed for symptoms of pain and withdrawal by researchers blinded to opioid dosage received, using the Brief Pain Inventory Scale and the Clinical Opioid Withdrawal Scale, respectively, during prespecified time periods. The prespecified time periods were 2 weeks after onset of acute illness (eg, urinary tract infection), and 2 weeks after hospital admission and nursing home readmission, if they occurred. Opioid dosing was recorded and a significant interruption was defined as a complete discontinuation or a reduction in dose of >50% for ≥1 day. The covariates age, sex, race, comorbid conditions, initial opioid dose, and initial pain level were recorded. Symptoms pre- and post-opioid interruptions were compared and contrasted with those in a group without opioid interruptions. Sixty-six patients receiving opioids were followed for a mean of 10.9 months and experienced a total of 104 acute illnesses. During 64 (62%) illnesses, patients experienced any reduction in opioid dosing, with a mean (SD) dose reduction of 63.9% (29.9%). During 39 (38%) illnesses, patients experienced a significant opioid interruption. In a multivariable model, residence at 1 of the 3 nursing homes was associated with a lower risk of interruption (odds ratio = 0.073; 95% CI, 0.009 to 0.597; P pain score (difference -0.50 [2.66]; 95% CI, -3.16 to 2.16) and withdrawal score (difference -0.91 [3.12]; 95% CI, -4.03 to 2.21) after the interruption as compared with before interruption. However, when compared with patients without interruptions, patients with interruptions experienced larger increases in pain scores

  12. The time-course of recovery from interruption during reading: eye movement evidence for the role of interruption lag and spatial memory.

    Science.gov (United States)

    Cane, James E; Cauchard, Fabrice; Weger, Ulrich W

    2012-01-01

    Two experiments examined how interruptions impact reading and how interruption lags and the reader's spatial memory affect the recovery from such interruptions. Participants read paragraphs of text and were interrupted unpredictably by a spoken news story while their eye movements were monitored. Time made available for consolidation prior to responding to the interruption did not aid reading resumption. However, providing readers with a visual cue that indicated the interruption location did aid task resumption substantially in Experiment 2. Taken together, the findings show that the recovery from interruptions during reading draws on spatial memory resources and can be aided by processes that support spatial memory. Practical implications are discussed.

  13. A Multiple-Reception Access Protocol with Interruptions with Mixed Priorities in CDMA Networks

    Institute of Scientific and Technical Information of China (English)

    Lu Xiaowen; Zhu Jinkang

    2003-01-01

    A novel access protocol called Multiple-Reception Access Protocol (MRAP) and its modification MRAP/WI are proposed. In this protocol, all colliding users with a common code can be identified by the base station due to the offset of arrival time Thus they can retransmit access requests under the base station's control. Furthermore new arrivals with higher priority level can interrupt the lower retransmission in order to reduce its access delay although it increases the lower priority's delay. Simulation results of MRAP and MRAP/WI are given in order to highlight the superior performance of the proposed approach.

  14. Complete genome sequence of a Chinese isolate of pepper vein yellows virus and evolutionary analysis based on the CP, MP and RdRp coding regions.

    Science.gov (United States)

    Liu, Maoyan; Liu, Xiangning; Li, Xun; Zhang, Deyong; Dai, Liangyin; Tang, Qianjun

    2016-03-01

    The genome sequence of pepper vein yellows virus (PeVYV) (PeVYV-HN, accession number KP326573), isolated from pepper plants (Capsicum annuum L.) grown at the Hunan Vegetables Institute (Changsha, Hunan, China), was determined by deep sequencing of small RNAs. The PeVYV-HN genome consists of 6244 nucleotides, contains six open reading frames (ORFs), and is similar to that of an isolate (AB594828) from Japan. Its genomic organization is similar to that of members of the genus Polerovirus. Sequence analysis revealed that PeVYV-HN shared 92% sequence identity with the Japanese PeVYV genome at both the nucleotide and amino acid levels. Evolutionary analysis based on the coat protein (CP), movement protein (MP), and RNA-dependent RNA polymerase (RdRP) showed that PeVYV could be divided into two major lineages corresponding to their geographical origins. The Asian isolates have a higher population expansion frequency than the African isolates. Negative selection and genetic drift (founder effect) were found to be the potential drivers of the molecular evolution of PeVYV. Moreover, recombination was not the distinct cause of PeVYV evolution. This is the first report of a complete genomic sequence of PeVYV in China.

  15. Neurocognition and quality of life after reinitiating antiretroviral therapy in children randomized to planned treatment interruption

    NARCIS (Netherlands)

    Ananworanich, Jintanat; Melvin, Diane; Amador, Jose T. R.; Childs, Tristan; Medin, Gabriela; Boscolo, Valentina; Compagnucci, Alexandra; Kanjanavanit, Suparat; Montero, Samuel; Gibb, Diana M.; Aboulker, J. -P.; Babiker, A.; Belfrage, E.; Bernardi, S.; Bologna, R.; Burger, D.; Butler, K.; Castelli-Gattinara, G.; Castro, H.; Clayden, P.; Compagnucci, A.; Cressey, T.; Darbyshire, J. H.; Debré, M.; de Groot, R.; della Negra, M.; Di Biagio, A.; de Rossi, A.; Duicelescu, D.; Faye, A.; Giaquinto, C.; Giacomet, V.; Gibb, D. M.; Grosch-Wörner, I.; Hainault, M.; Klein, N.; Lallemant, M.; Levy, J.; Lyall, H.; Marczynska, M.; Marques, L.; Mardarescu, M.; Mellado Peña, M. J.; Nadal, D.; Nastouli, E.; Naver, L.; Niehues, T.; Peckham, C.; Pillay, D.; Popieska, J.; Ramos Amador, J. T.; Rojo Conejo, P.; Rosado, L.; Rosso, R.; Rudin, C.; Scherpbier, H. J.; Sharland, M.; Stevanovic, M.; Thorne, C.; Tovo, P. A.; Tudor-Williams, G.; Turkova, A.; Valerius, N.; Volokha, A.; Walker, A. S.; Welch, S.; Wintergerst, U.; Aboulker, J. P.; Burger, D. M.; Green, H.; Harper, L.; Mofenson, L.; Moye, J.; Saïdi, Y.; Cressey, T. R.; Jacqz-Aigrain, E.; Khoo, S.; Regazzi, M.; Tréluyer, J. M.; Ngo-Giang-Huong, N.; Muñoz Fernandez, M. A.; Hill, C.; Lepage, P.; Pozniak, A.; Vella, S.; Chêne, G.; Vesikari, T.; Hadjou, G.; Léonardo, S.; Riault, Y.; Bleier, J.; Buck, L.; Duong, T.; Farrelly, L.; Forcat, S.; Harrison, L.; Horton, J.; Johnson, D.; Montero, S.; Taylor, C.; Chalermpantmetagul, S.; Peongjakta, R.; Khamjakkaew, W.; Than-in-at, K.; Chailert, S.; Jourdain, G.; Le Coeur, S.; Floret, D.; Costanzo, P.; Le Thi, T. T.; Monpoux, F.; Mellul, S.; Caranta, I.; Boudjoudi, N.; Firtion, G.; Denon, M.; Charlemaine, E.; Picard, F.; Hellier, E.; Heuninck, C.; Damond, F.; Alexandre, G.; Tricoire, J.; Antras, M.; Lachendowier, C.; Nicot, F.; Krivine, A.; Rivaux, D.; Notheis, G.; Strotmann, G.; Schlieben, S.; Rampon, O.; Boscolo, V.; Zanchetta, M.; Ginocchio, F.; Viscoli, C.; Martino, A.; Pontrelli, G.; Baldassar, S.; Concato, C.; Mazza, A.; Rossetti, G.; Dobosz, S.; Oldakowska, A.; Popielska, J.; Kaflik, M.; Stanczak, J.; Stanczack, G.; Dyda, T.; Kruk, M.; González Tomé, M. I.; Delgado García, R.; Fernandez Gonzalez, M. T.; Medin, G.; Mellado Peña, M. José; Martín Fontelos, P.; Garcia Mellado, M. I.; Medina, A. F.; Ascencion, B.; Garcia Bermejo, I.; Navarro Gomez, D. M. L.; Saavedra, J.; Prieto, C.; Jimenez, J. L.; Muñoz-Fernandez, M. A.; Garcia Torre, A.; de José Gómez, M. I.; García Rodriguez, M. C.; Moreno Pérez, D.; Núñez Cuadros, E.; Asensi-Botet, F.; Otero Reigada, C.; Pérez Tamarit, M. D.; Vilalta, R.; Molina Moreno, J. M.; Rainer, Truninger; Schupbach, J.; Rutishauser, M.; Bunupuradah, T.; Butterworth, O.; Phasomsap, C.; Prasitsuebsai, W.; Chuanjaroen, T.; Jupimai, T.; Ubolyam, S.; Phanuphak, P.; Puthanakit, T.; Pancharoen, C.; Mai, Chaing; Kanjanavanit, S.; Namwong, T.; Punsakoon, W.; Payakachat, S.; Chutima, D.; Raksasang, M.; Foster, C.; Hamadache, D.; Campbell, S.; Newbould, C.; Monrose, C.; Abdulla, A.; Walley, A.; Melvin, D.; Patel, D.; Kaye, S.; Seery, P.; Rankin, A.; Wildfire, A.; Novelli, V.; Shingadia, D.; Moshal, K.; Flynn, J.; Clapson, M.; Allen, A.; Spencer, L.; Rackstraw, C.; Ward, B.; Parkes, K.; Depala, M.; Jacobsen, M.; Poulsom, H.; Barkley, L.; Miah, J.; Lurie, P.; Keane, C.; McMaster, P.; Phipps, M.; Orendi, J.; Farmer, C.; Liebeschuetz, S.; Sodeinde, O.; Wong, S.; Bostock, V.; Heath, Y.; Scott, S.; Gandhi, K.; Lewis, P.; Daglish, J.; Miles, K.; Summerhill, L.; Subramaniam, B.; Weiner, L.; Famiglietti, M.; Rana, S.; Yu, P.; Roa, J.; Puga, A.; Haerry, A.

    2016-01-01

    Objective: Understanding the effects of antiretroviral treatment (ART) interruption on neurocognition and quality of life (QoL) are important for managing unplanned interruptions and planned interruptions in HIV cure research. Design: Children previously randomized to continuous (continuous ART, n =

  16. Deformation of contact surfaces in a vacuum interrupter after high-current interruptions

    Energy Technology Data Exchange (ETDEWEB)

    Wang, Haoran; Wang, Zhenxing, E-mail: zxwang@xjtu.edu.cn; Zhou, Zhipeng; Jiang, Yanjun; Wang, Jianhua; Geng, Yingsan; Liu, Zhiyuan [State Key Laboratory of Electrical Insulation and Power Equipment, Xi' an Jiaotong University, Xi' an 710049 (China)

    2016-08-07

    In a high-current interruption, the contact surface in a vacuum interrupter might be severely damaged by constricted vacuum arcs causing a molten area on it. As a result, a protrusion will be initiated by a transient recovery voltage after current zero, enhancing the local electric field and making breakdowns occur easier. The objective of this paper is to simulate the deformation process on the molten area under a high electric field by adopting the finite element method. A time-dependent Electrohydrodynamic model was established, and the liquid-gas interface was tracked by the level-set method. From the results, the liquid metal can be deformed to a Taylor cone if the applied electric field is above a critical value. This value is correlated to the initial geometry of the liquid metal, which increases as the size of the liquid metal decreases. Moreover, the buildup time of a Taylor cone obeys the power law t = k × E{sup −3}, where E is the initial electric field and k is a coefficient related to the material property, indicating a temporal self-similar characteristic. In addition, the influence of temperature has little impact on the deformation but has great impact on electron emission. Finally, the possible reason to initiate a delayed breakdown is associated with the deformation. The breakdown does not occur immediately when the voltage is just applied upon the gap but is postponed to several milliseconds later when the tip is formed on the liquid metal.

  17. Phylogenetic footprinting of non-coding RNA: hammerhead ribozyme sequences in a satellite DNA family of Dolichopoda cave crickets (Orthoptera, Rhaphidophoridae

    Directory of Open Access Journals (Sweden)

    Venanzetti Federica

    2010-01-01

    Full Text Available Abstract Background The great variety in sequence, length, complexity, and abundance of satellite DNA has made it difficult to ascribe any function to this genome component. Recent studies have shown that satellite DNA can be transcribed and be involved in regulation of chromatin structure and gene expression. Some satellite DNAs, such as the pDo500 sequence family in Dolichopoda cave crickets, have a catalytic hammerhead (HH ribozyme structure and activity embedded within each repeat. Results We assessed the phylogenetic footprints of the HH ribozyme within the pDo500 sequences from 38 different populations representing 12 species of Dolichopoda. The HH region was significantly more conserved than the non-hammerhead (NHH region of the pDo500 repeat. In addition, stems were more conserved than loops. In stems, several compensatory mutations were detected that maintain base pairing. The core region of the HH ribozyme was affected by very few nucleotide substitutions and the cleavage position was altered only once among 198 sequences. RNA folding of the HH sequences revealed that a potentially active HH ribozyme can be found in most of the Dolichopoda populations and species. Conclusions The phylogenetic footprints suggest that the HH region of the pDo500 sequence family is selected for function in Dolichopoda cave crickets. However, the functional role of HH ribozymes in eukaryotic organisms is unclear. The possible functions have been related to trans cleavage of an RNA target by a ribonucleoprotein and regulation of gene expression. Whether the HH ribozyme in Dolichopoda is involved in similar functions remains to be investigated. Future studies need to demonstrate how the observed nucleotide changes and evolutionary constraint have affected the catalytic efficiency of the hammerhead.

  18. Towards advanced code simulators

    International Nuclear Information System (INIS)

    Scriven, A.H.

    1990-01-01

    The Central Electricity Generating Board (CEGB) uses advanced thermohydraulic codes extensively to support PWR safety analyses. A system has been developed to allow fully interactive execution of any code with graphical simulation of the operator desk and mimic display. The system operates in a virtual machine environment, with the thermohydraulic code executing in one virtual machine, communicating via interrupts with any number of other virtual machines each running other programs and graphics drivers. The driver code itself does not have to be modified from its normal batch form. Shortly following the release of RELAP5 MOD1 in IBM compatible form in 1983, this code was used as the driver for this system. When RELAP5 MOD2 became available, it was adopted with no changes needed in the basic system. Overall the system has been used for some 5 years for the analysis of LOBI tests, full scale plant studies and for simple what-if studies. For gaining rapid understanding of system dependencies it has proved invaluable. The graphical mimic system, being independent of the driver code, has also been used with other codes to study core rewetting, to replay results obtained from batch jobs on a CRAY2 computer system and to display suitably processed experimental results from the LOBI facility to aid interpretation. For the above work real-time execution was not necessary. Current work now centers on implementing the RELAP 5 code on a true parallel architecture machine. Marconi Simulation have been contracted to investigate the feasibility of using upwards of 100 processors, each capable of a peak of 30 MIPS to run a highly detailed RELAP5 model in real time, complete with specially written 3D core neutronics and balance of plant models. This paper describes the experience of using RELAP5 as an analyzer/simulator, and outlines the proposed methods and problems associated with parallel execution of RELAP5

  19. Preserving the Context of Interrupted Business Process Activities

    NARCIS (Netherlands)

    Bassil, S.; Rinderle, S.B.; Keller, R.; Reichert, M.U.; Kropf, P.G.

    2005-01-01

    The capability to safely interrupt business process activities is an important requirement for advanced process-aware information systems. Indeed, exceptions stemming from the application environment often appear while one or more application-related process activities are running. Safely

  20. Preserving the Context of Interrupted Business Process Activities

    NARCIS (Netherlands)

    Bassil, S.; Rinderle, S.B.; Keller, R.; Kropf, P.G.; Reichert, M.U.; Chen, C.S.; Filipe, J.; Seruca, I.; Cordeiro, J.

    2006-01-01

    The capability to safely interrupt business process activities is an important requirement for advanced process-aware information systems. Indeed, exceptions stemming from the application environment often appear while one or more application-related process activities are running. Safely

  1. HIV models for treatment interruption: Adaptation and comparison

    Science.gov (United States)

    Hillmann, Andreas; Crane, Martin; Ruskin, Heather J.

    2017-10-01

    In recent years, Antiretroviral Therapy (ART) has become commonplace for treating HIV infections, although a cure remains elusive, given reservoirs of replicating latently-infected cells, which are resistant to normal treatment regimes. Treatment interruptions, whether ad hoc or structured, are known to cause a rapid increase in viral production to detectable levels, but numerous clinical trials remain inconclusive on the dangers inherent in this resurgence. In consequence, interest in examining interruption strategies has recently been rekindled. This overview considers modelling approaches, which have been used to explore the issue of treatment interruption. We highlight their purpose and the formalisms employed and examine ways in which clinical data have been used. Implementation of selected models is demonstrated, illustrative examples provided and model performance compared for these cases. Possible extensions to bottom-up modelling techniques for treatment interruptions are briefly discussed.

  2. Instant Messaging Usage and Interruptions in the Workplace

    Directory of Open Access Journals (Sweden)

    Hui‐Jung Chang

    2014-12-01

    Full Text Available The goal of the present study is to explore IM interruption by relating it to media choices and purposes of IM use in the workplace. Two major media choice concepts were: media richness and social influence; while four purposes of IM use were: organization work, knowledge work, socializing, and boundary spanning activities. Data (N = 283 were collected via a combination of convenience and snowball sampling of “computer‐using workers” in Taiwan, based on the Standard Occupational Classification system published by the Taiwan government. Results indicated that media choice works better than purpose of IM use to explain IM interruption. Among them, social influence was the best predictor to IM interruption in the workplace. In addition, instant feedback and personalization provided by IM, and IM usage for the purposes of knowledge work and socializing, also relate to IM interruption in the workplace.

  3. Coping with interruptions in clinical nursing - a qualitative study

    DEFF Research Database (Denmark)

    Laustsen, Sussie; Brahe, Liselotte

    2018-01-01

    phenomenological approach. METHODS: Observations were performed combined with semi-structured qualitative interviews. RESULTS: Managing interruptions depend on level of competence, working environment, dialogue and matching of expectations, collegial roles and implicit rules. Working procedures impact on how......AIMS AND OBJECTIVES: To gain knowledge on how nurses' cope with interruptions in clinical practice. BACKGROUND: Interruptions may delay work routines and result in wasted time, disorganised planning and ineffective working procedures, affecting nurses' focus and overview in different ways. Research......: Culture work and matching of expectations are important to reflect on and discuss personal- and group behaviour caused by interruptions. We need to focus on the role of each nurse in the professional team, types of personality and unspoken rules. Professional competencies for example prioritising, keeping...

  4. Length and nucleotide sequence polymorphism at the trnL and trnF non-coding regions of chloroplast genomes among Saccharum and Erianthus species

    Science.gov (United States)

    The aneupolyploidy genome of sugarcane (Saccharum hybrids spp.) and lack of a classical genetic linkage map make genetics research most difficult for sugarcane. Whole genome sequencing and genetic characterization of sugarcane and related taxa are far behind other crops. In this study, universal PCR...

  5. Characterisation of Toxoplasma gondii isolates using polymerase chain reaction (PCR) and restriction fragment length polymorphism (RFLP) of the non-coding Toxoplasma gondii (TGR)-gene sequences

    DEFF Research Database (Denmark)

    Høgdall, Estrid; Vuust, Jens; Lind, Peter

    2000-01-01

    of using TGR gene variants as markers to distinguish among T. gondii isolates from different animals and different geographical sources. Based on the band patterns obtained by restriction fragment length polymorphism (RFLP) analysis of the polymerase chain reaction (PCR) amplified TGR sequences, the T...

  6. Approximator: Predicting Interruptibility in Software Development with Commodity Computers

    DEFF Research Database (Denmark)

    Tell, Paolo; Jalaliniya, Shahram; Andersen, Kristian S. M.

    2015-01-01

    Assessing the presence and availability of a remote colleague is key in coordination in global software development but is not easily done using existing computer-mediated channels. Previous research has shown that automated estimation of interruptibility is feasible and can achieve a precision....... These early but promising results represent a starting point for designing tools with support for interruptibility capable of improving distributed awareness and cooperation to be used in global software development....

  7. A rare variant P507L in TPP1 interrupts TPP1-TIN2 interaction, influences telomere length, and confers colorectal cancer risk in Chinese population.

    Science.gov (United States)

    Li, Jiaoyuan; Chang, Jiang; Tian, Jianbo; Ke, Juntao; Zhu, Ying; Yang, Yang; Gong, Yajie; Zou, Danyi; Peng, Xiating; Yang, Nan; Mei, Shufang; Wang, Xiaoyang; Cheng, Liming; Hu, Weiguo; Gong, Jing; Zhong, Rong; Miao, Xiaoping

    2018-06-11

    Telomere dysfunction triggers cellular senescence and constitutes a driving force for cancer initiation. Genetic variants in genes involved in telomere maintenance may contribute to colorectal cancer (CRC) susceptibility. In this study, we firstly captured germline mutations in 192 CRC patients by sequencing the coding regions of 13 core components implicated in telomere biology. Five potential functional variants were then genotyped and assessed in a case-control set with 3,761 CRC cases and 3,839 healthy controls. The promising association was replicated in additional 6,765 cases and 6,906 controls. Functional experiments were used to further clarify the potential function of the significant variant and uncover the underlying mechanism in CRC development. The two-stage association studies showed that a rare missense variant rs149418249 (c.C1520T, p.P507L) in the 11th exon of TPP1 (also known as ACD, gene ID 65057) was significantly associated with CRC risk with the ORs being 2.90 (95% CI:1.04-8.07, P=0.041), 2.50 (95% CI:1.04-6.04, P=0.042), and 2.66 (95%CI:1.36-5.18, P=0.004) in discovery, replication, and the combined samples, respectively. Further functional annotation indicated that the TPP1 P507L substitution interrupted TPP1-TIN2 interaction, impaired telomerase processivity, and shortened telomere length, which subsequently facilitated cell proliferation and promoted CRC development. A rare variant P507L in TPP1 confers increased risk of CRC through interrupting TPP1-TIN2 interaction, impairing telomerase processivity, and shrinking telomere length. These findings emphasize the important role of telomere dysfunction in CRC development, and provide new insights about the prevention of this type of cancer. Copyright ©2018, American Association for Cancer Research.

  8. Surveillance of hazardous substances releases due to system interruptions, 2002.

    Science.gov (United States)

    Orr, Maureen F; Ruckart, Perri Zeitz

    2007-04-11

    The Hazardous Substances Emergency Events Surveillance (HSEES) system collected information on 9014 acute hazardous substance releases in 15 participating states in 2002. There were 3749 fixed-facility manufacturing events, of which 2100 involved "interruptions" to normal processing and 1649 "comparisons" that did not involve interruption. Equipment failure (69%) or intentional acts (20%) were the main root factor. Many events occurred in October and November in three states (Texas, Louisiana, and New Jersey), in three manufacturing industries (industrial and miscellaneous chemicals; petroleum refining; and plastics, synthetics, and resins). In interruption events, the substance categories most often released were mixtures, other inorganic substances, and volatile organic compounds and those most often causing injury were acids, chlorine, bases, and ammonia. Comparison events resulted in more acutely injured persons (408 versus 59) and more evacuees (11,318 versus 335) than interruption events and therefore may receive more public health attention. Because of the large number of interruption events, targeted prevention activities, including management of change procedures, lessons-learned implementation, process hazards analysis, and appropriate protection for workers could be economically advantageous and improve environmental quality. Efforts should focus on the identified areas of greater occurrence. The relationship of weather and equipment failure with interruption events needs further investigation.

  9. Tests of vacuum interrupters for the Tokamak Fusion Test Reactor

    International Nuclear Information System (INIS)

    Warren, R.; Parsons, M.; Honig, E.; Lindsay, J.

    1979-04-01

    The Tokamak Fusion Test Reactor (TFTR) project at Princeton University requires the insertion of a resistor in an excited ohmic-heating coil circuit to produce a plasma initiation pulse (PIP). It is expected that the maximum duty for the switching system will be an interruption of 24 kA with an associated recovery voltage of 25 kV. Vacuum interrupters were selected as the most economical means to satisfy these requirements. However, it was felt that some testing of available systems should be performed to determine their reliability under these conditions. Two interrupter systems were tested for over 1000 interruptions each at 24 kA and 25 kV. One system employed special Westinghouse type WL-33552 interrupters in a circuit designed by LASL. This circuit used a commercially available actuator and a minimum size counterpulse bank and saturable reactor. The other used Toshiba type VGB2-D20 interrupters actuated by a Toshiba mechanism in a Toshiba circuit using a larger counterpulse bank and saturable reactor

  10. Interruption of People in Human-Computer Interaction: A General Unifying Definition of Human Interruption and Taxonomy

    National Research Council Canada - National Science Library

    McFarlane, Daniel

    1997-01-01

    .... This report asserts that a single unifying definition of user-interruption and the accompanying practical taxonomy would be useful theoretical tools for driving effective investigation of this crucial...

  11. Interrupting behaviour: Minimizing decision costs via temporal commitment and low-level interrupts.

    Science.gov (United States)

    Lloyd, Kevin; Dayan, Peter

    2018-01-01

    Ideal decision-makers should constantly assess all sources of information about opportunities and threats, and be able to redetermine their choices promptly in the face of change. However, perpetual monitoring and reassessment impose inordinate sensing and computational costs, making them impractical for animals and machines alike. The obvious alternative of committing for extended periods of time to limited sensory strategies associated with particular courses of action can be dangerous and wasteful. Here, we explore the intermediate possibility of making provisional temporal commitments whilst admitting interruption based on limited broader observation. We simulate foraging under threat of predation to elucidate the benefits of such a scheme. We relate our results to diseases of distractibility and roving attention, and consider mechanistic substrates such as noradrenergic neuromodulation.

  12. Interrupting behaviour: Minimizing decision costs via temporal commitment and low-level interrupts.

    Directory of Open Access Journals (Sweden)

    Kevin Lloyd

    2018-01-01

    Full Text Available Ideal decision-makers should constantly assess all sources of information about opportunities and threats, and be able to redetermine their choices promptly in the face of change. However, perpetual monitoring and reassessment impose inordinate sensing and computational costs, making them impractical for animals and machines alike. The obvious alternative of committing for extended periods of time to limited sensory strategies associated with particular courses of action can be dangerous and wasteful. Here, we explore the intermediate possibility of making provisional temporal commitments whilst admitting interruption based on limited broader observation. We simulate foraging under threat of predation to elucidate the benefits of such a scheme. We relate our results to diseases of distractibility and roving attention, and consider mechanistic substrates such as noradrenergic neuromodulation.

  13. Interrupting behaviour: Minimizing decision costs via temporal commitment and low-level interrupts

    Science.gov (United States)

    Dayan, Peter

    2018-01-01

    Ideal decision-makers should constantly assess all sources of information about opportunities and threats, and be able to redetermine their choices promptly in the face of change. However, perpetual monitoring and reassessment impose inordinate sensing and computational costs, making them impractical for animals and machines alike. The obvious alternative of committing for extended periods of time to limited sensory strategies associated with particular courses of action can be dangerous and wasteful. Here, we explore the intermediate possibility of making provisional temporal commitments whilst admitting interruption based on limited broader observation. We simulate foraging under threat of predation to elucidate the benefits of such a scheme. We relate our results to diseases of distractibility and roving attention, and consider mechanistic substrates such as noradrenergic neuromodulation. PMID:29338004

  14. Simultaneous sequencing of coding and noncoding RNA reveals a human transcriptome dominated by a small number of highly expressed noncoding genes.

    Science.gov (United States)

    Boivin, Vincent; Deschamps-Francoeur, Gabrielle; Couture, Sonia; Nottingham, Ryan M; Bouchard-Bourelle, Philia; Lambowitz, Alan M; Scott, Michelle S; Abou-Elela, Sherif

    2018-07-01

    Comparing the abundance of one RNA molecule to another is crucial for understanding cellular functions but most sequencing techniques can target only specific subsets of RNA. In this study, we used a new fragmented ribodepleted TGIRT sequencing method that uses a thermostable group II intron reverse transcriptase (TGIRT) to generate a portrait of the human transcriptome depicting the quantitative relationship of all classes of nonribosomal RNA longer than 60 nt. Comparison between different sequencing methods indicated that FRT is more accurate in ranking both mRNA and noncoding RNA than viral reverse transcriptase-based sequencing methods, even those that specifically target these species. Measurements of RNA abundance in different cell lines using this method correlate with biochemical estimates, confirming tRNA as the most abundant nonribosomal RNA biotype. However, the single most abundant transcript is 7SL RNA, a component of the signal recognition particle. S tructured n on c oding RNAs (sncRNAs) associated with the same biological process are expressed at similar levels, with the exception of RNAs with multiple functions like U1 snRNA. In general, sncRNAs forming RNPs are hundreds to thousands of times more abundant than their mRNA counterparts. Surprisingly, only 50 sncRNA genes produce half of the non-rRNA transcripts detected in two different cell lines. Together the results indicate that the human transcriptome is dominated by a small number of highly expressed sncRNAs specializing in functions related to translation and splicing. © 2018 Boivin et al.; Published by Cold Spring Harbor Laboratory Press for the RNA Society.

  15. Sequence of the intron/exon junctions of the coding region of the human androgen receptor gene and identification of a point mutation in a family with complete androgen insensitivity

    International Nuclear Information System (INIS)

    Lubahn, D.B.; Simental, J.A.; Higgs, H.N.; Wilson, E.M.; French, F.S.; Brown, T.R.; Migeon, C.J.

    1989-01-01

    Androgens act through a receptor protein (AR) to mediate sex differentiation and development of the male phenotype. The authors have isolated the eight exons in the amino acid coding region of the AR gene from a human X chromosome library. Nucleotide sequences of the AR gene intron/exon boundaries were determined for use in designing synthetic oligonucleotide primers to bracket coding exons for amplification by the polymerase chain reaction. Genomic DNA was amplified from 46, XY phenotypic female siblings with complete androgen insensitivity syndrome. AR binding affinity for dihydrotestosterone in the affected siblings was lower than in normal males, but the binding capacity was normal. Sequence analysis of amplified exons demonstrated within the AR steroid-binding domain (exon G) a single guanine to adenine mutation, resulting in replacement of valine with methionine at amino acid residue 866. As expected, the carrier mother had both normal and mutant AR genes. Thus, a single point mutation in the steroid-binding domain of the AR gene correlated with the expression of an AR protein ineffective in stimulating male sexual development

  16. A reflection of the coding of meaning in patient-physician interaction: Jürgen Habermas' theory of communication applied to sequence analysis.

    Science.gov (United States)

    Skirbekk, Helge

    2004-08-01

    This paper introduces parts of Jürgen Habermas' theory of communication in an attempt to understand how meaning is coded in patient-physician communication. By having a closer look at how patients and physicians make assertions with their utterances, light will be shed on difficult aspects of reaching understanding in the clinical encounter. Habermas' theory will be used to differentiate assertions into validity claims referring to truth, truthfulness and rightness. An analysis of hypothetical physician-replies to a patient suffering from back pains will substantiate the necessity for such a theory.

  17. Nucleotide sequence of the Escherichia coli pyrE gene and of the DNA in front of the protein-coding region

    DEFF Research Database (Denmark)

    Poulsen, Peter; Jensen, Kaj Frank; Valentin-Hansen, Poul

    1983-01-01

    leader segment in front of the protein-coding region. This leader contains a structure with features characteristic for a (translated?) rho-independent transcriptional terminator, which is preceded by a cluster of uridylate residues. This indicates that the frequency of pyrE transcription is regulated......Orotate phosphoribosyltransferase (EC 2.4.2.10) was purified to electrophoretic homogeneity from a strain of Escherichia coli containing the pyrE gene cloned on a multicopy plasmid. The relative molecular masses (Mr) of the native enzyme and its subunit were estimated by means of gel filtration...

  18. Diversity of antisense and other non-coding RNAs in Archaea revealed by comparative small RNA sequencing in four Pyrobaculum species

    Directory of Open Access Journals (Sweden)

    David L Bernick

    2012-07-01

    Full Text Available A great diversity of small, non-coding RNA molecules with roles in gene regulation and RNA processing have been intensely studied in eukaryotic and bacterial model organisms, yet our knowledge of possible parallel roles for small RNAs in archaea is limited. We employed RNA-seq to identify novel small RNA across multiple species of the hyperthermophilic genus Pyrobaculum, known for unusual RNA gene characteristics. By comparing transcriptional data collected in parallel among four species, we were able to identify conserved RNA genes fitting into known and novel families. Among our findings, we highlight three novel cis-antisense small RNAs encoded opposite to key regulatory (ferric uptake regulator, metabolic (triose-phosphate isomerase, and core transcriptional apparatus genes (transcription factor B. We also found a large increase in the number of conserved C/D box small RNA genes over what had been previously recognized; many of these genes are encoded antisense to protein coding genes. The conserved opposition to orthologous genes across the Pyrobaculum genus suggests similarities to other cis-antisense regulatory systems. Furthermore, the genus-specific nature of these small RNAs indicates they are relatively recent, stable adaptations.

  19. Cloning and sequencing of the gene coding for alcohol dehydrogenase of Bacillus stearothermophilus and rational shift of the optimum pH.

    Science.gov (United States)

    Sakoda, H; Imanaka, T

    1992-02-01

    Using Bacillus subtilis as a host and pTB524 as a vector plasmid, we cloned the thermostable alcohol dehydrogenase (ADH-T) gene (adhT) from Bacillus stearothermophilus NCA1503 and determined its nucleotide sequence. The deduced amino acid sequence (337 amino acids) was compared with the sequences of ADHs from four different origins. The amino acid residues responsible for the catalytic activity of horse liver ADH had been clarified on the basis of three-dimensional structure. Since those catalytic amino acid residues were fairly conserved in ADH-T and other ADHs, ADH-T was inferred to have basically the same proton release system as horse liver ADH. The putative proton release system of ADH-T was elucidated by introducing point mutations at the catalytic amino acid residues, Cys-38 (cysteine at position 38), Thr-40, and His-43, with site-directed mutagenesis. The mutant enzyme Thr-40-Ser (Thr-40 was replaced by serine) showed a little lower level of activity than wild-type ADH-T did. The result indicates that the OH group of serine instead of threonine can also be used for the catalytic activity. To change the pKa value of the putative system, His-43 was replaced by the more basic amino acid arginine. As a result, the optimum pH of the mutant enzyme His-43-Arg was shifted from 7.8 (wild-type enzyme) to 9.0. His-43-Arg exhibited a higher level of activity than wild-type enzyme at the optimum pH.

  20. Identification and expression of the tig gene coding for trigger factor from psychrophilic bacteria with no information of genome sequence available.

    Science.gov (United States)

    Lee, Kyunghee; Choi, Hyojung; Im, Hana

    2009-08-01

    Trigger factor (TF) plays a key role as a molecular chaperone with a peptidyl-prolyl cis-trans isomerase (PPIase) activity by which cells promote folding of newly synthesized proteins coming out of ribosomes. Since psychrophilic bacteria grow at a quite low temperature, between 4 and 15 degrees C, TF from such bacteria was investigated and compared with that of mesophilic bacteria E. coli in order to offer an explanation of cold-adaptation at a molecular level. Using a combination of gradient PCRs with homologous primers and LA PCR in vitro cloning technology, the tig gene was fully identified from Psychromonas arctica, whose genome sequence is not yet available. The resulting amino acid sequence of the TF was compared with other homologous TFs using sequence alignments to search for common domains. In addition, we have developed a protein expression system, by which TF proteins from P. arctica (PaTF) were produced by IPTG induction upon cloning the tig gene on expression vectors, such as pAED4. We have further examined the role of expressed psychrophilic PaTF on survival against cold treatment at 4 degrees C. Finally, we have attempted the in vitro biochemical characterization of TF proteins with His-tags expressed in a pET system, such as the PPIase activity of PaTF protein. Our results demonstrate that the expressed PaTF proteins helped cells survive against cold environments in vivo and the purified PaTF in vitro display the functional PPIase activity in a concentration dependent manner.

  1. Digenic Inheritance of PROKR2 and WDR11 Mutations in Pituitary Stalk Interruption Syndrome.

    Science.gov (United States)

    McCormack, Shana E; Li, Dong; Kim, Yeon Joo; Lee, Ji Young; Kim, Soo-Hyun; Rapaport, Robert; Levine, Michael A

    2017-07-01

    Pituitary stalk interruption syndrome (PSIS, ORPHA95496) is a congenital defect of the pituitary gland characterized by the triad of a very thin/interrupted pituitary stalk, an ectopic (or absent) posterior pituitary gland, and hypoplasia or aplasia of the anterior pituitary gland. Complex genetic patterns of inheritance of this disorder are increasingly recognized. The objective of this study was to identify a genetic cause of PSIS in an affected child. Whole exome sequencing (WES) was performed by using standard techniques, with prioritized genetic variants confirmed via Sanger sequencing. To investigate the effects of one candidate variant on mutant WDR11 function, Western blotting and coimmunofluorescence were used to assess binding capacity, and leptomycin B exposure along with immunofluorescence was used to assess nuclear localization. We describe a child who presented in infancy with combined pituitary hormone deficiencies and whose brain imaging demonstrated a small anterior pituitary, ectopic posterior pituitary, and a thin, interrupted stalk. WES demonstrated heterozygous missense mutations in two genes required for pituitary development, a known loss-of-function mutation in PROKR2 (c.253C>T;p.R85C) inherited from an unaffected mother, and a WDR11 (c.1306A>G;p.I436V) mutation inherited from an unaffected father. Mutant WDR11 loses its capacity to bind to its functional partner, EMX1, and to localize to the nucleus. WES in a child with PSIS and his unaffected family implicates a digenic mechanism of inheritance. In cases of hypopituitarism in which there is incomplete segregation of a monogenic genotype with the phenotype, the possibility that a second genetic locus is involved should be considered. Copyright © 2017 Endocrine Society

  2. gEVE: a genome-based endogenous viral element database provides comprehensive viral protein-coding sequences in mammalian genomes.

    Science.gov (United States)

    Nakagawa, So; Takahashi, Mahoko Ueda

    2016-01-01

    In mammals, approximately 10% of genome sequences correspond to endogenous viral elements (EVEs), which are derived from ancient viral infections of germ cells. Although most EVEs have been inactivated, some open reading frames (ORFs) of EVEs obtained functions in the hosts. However, EVE ORFs usually remain unannotated in the genomes, and no databases are available for EVE ORFs. To investigate the function and evolution of EVEs in mammalian genomes, we developed EVE ORF databases for 20 genomes of 19 mammalian species. A total of 736,771 non-overlapping EVE ORFs were identified and archived in a database named gEVE (http://geve.med.u-tokai.ac.jp). The gEVE database provides nucleotide and amino acid sequences, genomic loci and functional annotations of EVE ORFs for all 20 genomes. In analyzing RNA-seq data with the gEVE database, we successfully identified the expressed EVE genes, suggesting that the gEVE database facilitates studies of the genomic analyses of various mammalian species.Database URL: http://geve.med.u-tokai.ac.jp. © The Author(s) 2016. Published by Oxford University Press.

  3. The mythology of anticoagulation therapy interruption for dental surgery.

    Science.gov (United States)

    Wahl, Michael J

    2018-01-01

    Continuous anticoagulation therapy is used to prevent heart attacks, strokes, and other embolic complications. When patients receiving anticoagulation therapy undergo dental surgery, a decision must be made about whether to continue anticoagulation therapy and risk bleeding complications or briefly interrupt anticoagulation therapy and increase the risk of developing embolic complications. Results from decades of studies of thousands of dental patients receiving anticoagulation therapy reveal that bleeding complications requiring more than local measures for hemostasis have been rare and never fatal. However, embolic complications (some of which were fatal and others possibly permanently debilitating) sometimes have occurred in patients whose anticoagulation therapy was interrupted for dental procedures. Although there is now virtually universal consensus among national medical and dental groups and other experts that anticoagulation therapy should not be interrupted for most dental surgery, there are still some arguments made supporting anticoagulation therapy interruption. An analysis of these arguments shows them to be based on a collection of myths and half-truths rather than on logical scientific conclusions. The time has come to stop anticoagulation therapy interruption for dental procedures. Copyright © 2018 American Dental Association. Published by Elsevier Inc. All rights reserved.

  4. Effects of interruptible natural gas service: Winter 1989--1990

    International Nuclear Information System (INIS)

    1991-07-01

    During the extreme winter conditions experienced in December 1989, petroleum products showed dramatic price increases. Supply of certain products such as propane reached critical levels. Numerous factors contributed to the heating fuel situation, including well freeze-ups and refinery problems, as well as difficulties associated with delivery of the product. An area of concern identified in the ensuing debates was the impact of customer requirements for petroleum products resulting from curtailment of natural gas purchases under interruptible contracts. The lower rates associated with interruptible contracts make them an attractive choice for electric utilities. However, they require that the customer be prepared to obtain adequate fuel supplies in the event of curtailments. Electric utilities prepare for these contingencies with stocks of alternative fuels. Particularly in cold climates, interruptible has contracts are part of doing business. The extent and duration of the interruptions faced by customers relate principally to weather factors. Previous EIA studies investigated on a national level the causes of the dramatic price increases seen in petroleum product markets in the 1989--1990 heating season. This study is in response to a request from Senator Timothy Wirth, Chairman, Subcommittee on Energy Regulation and Conservation, to study in detail the impact of interruptible natural gas contracts as one of the factors cited as contributing to the price increases. A copy of the letter requesting the study is contained in Appendix A

  5. The Effects of Interruptions on Oncologists' Patient Assessment and Medication Ordering Practices

    Directory of Open Access Journals (Sweden)

    Patricia L. Trbovich

    2013-01-01

    Full Text Available Interruptions are causal factors in medication errors. Although researchers have assessed the nature and frequency of interruptions during medication administration, there has been little focus on understanding their effects during medication ordering. The goal of this research was to examine the nature, frequency, and impact of interruptions on oncologists' ordering practices. Direct observations were conducted at a Canadian cancer treatment facility to (1 document the nature, frequency, and timing of interruptions during medication ordering, and (2 quantify the use of coping mechanisms by oncologists. On average, oncologists were interrupted 17 % of their time, and were frequently interrupted during safety-critical stages of medication ordering. When confronted with interruptions, oncologists engaged/multitasked more often than resorting to deferring/blocking. While some interruptions are necessary forms of communication, efforts must be made to reduce unnecessary interruptions during safety-critical tasks, and to develop interventions that increase oncologists' resiliency to inevitable interruptions.

  6. Nucleotide sequence of a cDNA coding for the barley seed protein CMa: an inhibitor of insect α-amylase

    DEFF Research Database (Denmark)

    Rasmussen, Søren Kjærsgård; Johansson, A.

    1992-01-01

    The primary structure of the insect alpha-amylase inhibitor CMa of barley seeds was deduced from a full-length cDNA clone pc43F6. Analysis of RNA from barley endosperm shows high levels 15 and 20 days after flowering. The cDNA predicts an amino acid sequence of 119 residues preceded by a signal...... peptide of 25 amino acids. Ala and Leu account for 55% of the signal peptide. CMa is 60-85% identical with alpha-amylase inhibitors of wheat, but shows less than 50% identity to trypsin inhibitors of barley and wheat. The 10 Cys residues are located in identical positions compared to the cereal inhibitor...

  7. Thinking aloud in the presence of interruptions and time constraints

    DEFF Research Database (Denmark)

    Hertzum, Morten; Holmegaard, Kristin Due

    2013-01-01

    and time constraints, two frequent elements of real-world activities. We find that the presence of auditory, visual, audiovisual, or no interruptions interacts with thinking aloud for task solution rate, task completion time, and participants’ fixation rate. Thinking-aloud participants also spend longer......Thinking aloud is widely used for usability evaluation and its reactivity is therefore important to the quality of evaluation results. This study investigates whether thinking aloud (i.e., verbalization at levels 1 and 2) affects the behaviour of users who perform tasks that involve interruptions...... responding to interruptions than control participants. Conversely, the absence or presence of time constraints does not interact with thinking aloud, suggesting that time pressure is less likely to make thinking aloud reactive than previously assumed. Our results inform practitioners faced with the decision...

  8. Application of customer-interruption costs for optimum distribution planning

    International Nuclear Information System (INIS)

    Mok, Y.L.; Chung, T.S.

    1996-01-01

    We present a new methodology for obtaining optimum values of the integrated cost of utility investment with customer interruption in distribution planning for electric power systems by determining the reliability cost and worth of the distribution system. Reliability cost refers to investment cost of the utility in achieving a defined level of reliability. Reliability worth is the benefit gained by the utility customer from an increase of reliability. A computer program has been developed to determine comparative reliability indices for a typical distribution network. With the average interruption cost, outage duration, average disconnected load, cost data for distribution equipment, etc. being known, the relation between reliability cost, reliability worth and reliability at the specified load point are obtained. The optimum reliability of the distribution system is then determined from the minimum cost to the utility with customer interruption. The applicability of this approach is demonstrated by several practical networks. (Author)

  9. Simulation-Based Testing of Pager Interruptions During Laparoscopic Cholecystectomy.

    Science.gov (United States)

    Sujka, Joseph A; Safcsak, Karen; Bhullar, Indermeet S; Havron, William S

    2018-01-30

    To determine if pager interruptions affect operative time, safety, or complications and management of pager issues during a simulated laparoscopic cholecystectomy. Twelve surgery resident volunteers were tested on a Simbionix Lap Mentor II simulator. Each resident performed 6 randomized simulated laparoscopic cholecystectomies; 3 with pager interruptions (INT) and 3 without pager interruptions (NO-INT). The pager interruptions were sent in the form of standardized patient vignettes and timed to distract the resident during dissection of the critical view of safety and clipping of the cystic duct. The residents were graded on a pass/fail scale for eliciting appropriate patient history and management of the pager issue. Data was extracted from the simulator for the following endpoints: operative time, safety metrics, and incidence of operative complications. The Mann-Whitney U test and contingency table analysis were used to compare the 2 groups (INT vs. NO-INT). Level I trauma center; Simulation laboratory. Twelve general surgery residents. There was no significant difference between the 2 groups in any of the operative endpoints as measured by the simulator. However, in the INT group, only 25% of the time did the surgery residents both adequately address the issue and provide effective patient management in response to the pager interruption. Pager interruptions did not affect operative time, safety, or complications during the simulated procedure. However, there were significant failures in the appropriate evaluations and management of pager issues. Consideration for diversion of patient care issues to fellow residents not operating to improve quality and safety of patient care outside the operating room requires further study. Copyright © 2018. Published by Elsevier Inc.

  10. Identification and characterization of wheat long non-protein coding RNAs responsive to powdery mildew infection and heat stress by using microarray analysis and SBS sequencing

    Directory of Open Access Journals (Sweden)

    Peng Huiru

    2011-04-01

    Full Text Available Abstract Background Biotic and abiotic stresses, such as powdery mildew infection and high temperature, are important limiting factors for yield and grain quality in wheat production. Emerging evidences suggest that long non-protein coding RNAs (npcRNAs are developmentally regulated and play roles in development and stress responses of plants. However, identification of long npcRNAs is limited to a few plant species, such as Arabidopsis, rice and maize, no systematic identification of long npcRNAs and their responses to abiotic and biotic stresses is reported in wheat. Results In this study, by using computational analysis and experimental approach we identified 125 putative wheat stress responsive long npcRNAs, which are not conserved among plant species. Among them, some were precursors of small RNAs such as microRNAs and siRNAs, two long npcRNAs were identified as signal recognition particle (SRP 7S RNA variants, and three were characterized as U3 snoRNAs. We found that wheat long npcRNAs showed tissue dependent expression patterns and were responsive to powdery mildew infection and heat stress. Conclusion Our results indicated that diverse sets of wheat long npcRNAs were responsive to powdery mildew infection and heat stress, and could function in wheat responses to both biotic and abiotic stresses, which provided a starting point to understand their functions and regulatory mechanisms in the future.

  11. Optimal treatment interruptions control of TB transmission model

    Science.gov (United States)

    Nainggolan, Jonner; Suparwati, Titik; Kawuwung, Westy B.

    2018-03-01

    A tuberculosis model which incorporates treatment interruptions of infectives is established. Optimal control of individuals infected with active TB is given in the model. It is obtained that the control reproduction numbers is smaller than the reproduction number, this means treatment controls could optimize the decrease in the spread of active TB. For this model, controls on treatment of infection individuals to reduce the actively infected individual populations, by application the Pontryagins Maximum Principle for optimal control. The result further emphasized the importance of controlling disease relapse in reducing the number of actively infected and treatment interruptions individuals with tuberculosis.

  12. A Wrist-Worn Thermohaptic Device for Graceful Interruption

    DEFF Research Database (Denmark)

    Bolton, Frank; Jalaliniya, Shahram; Pederson, Thomas

    2015-01-01

    Thermal haptics is a potential system output modality for wearable devices that promises to function at the periphery of human attention. When adequately combined with existing attention-governing mechanisms of the human mind, it could be used for interrupting the human agent at a time when......-worn thermohaptic actuator for self-mitigating interruption. We then develop a prototype and perform an insightful pilot study. We frame our empirical thermohaptic experimental work in terms of Peripheral Interaction concepts and show how this new approach to Human-Computer Interaction relates to the Context...

  13. Profiling of Long Non-coding RNAs and mRNAs by RNA-Sequencing in the Hippocampi of Adult Mice Following Propofol Sedation.

    Science.gov (United States)

    Fan, Jun; Zhou, Quan; Li, Yan; Song, Xiuling; Hu, Jijie; Qin, Zaisheng; Tang, Jing; Tao, Tao

    2018-01-01

    Propofol is a frequently used intravenous anesthetic agent. The impairment caused by propofol on the neural system, especially the hippocampus, has been widely reported. However, the molecular mechanism underlying the effects of propofol on learning and memory functions in the hippocampus is still unclear. In the present study we performed lncRNA and mRNA analysis in the hippocampi of adult mice, after propofol sedation, through RNA-Sequencing (RNA-Seq). A total of 146 differentially expressed lncRNAs and 1103 mRNAs were identified. Bioinformatics analysis, including gene ontology (GO) analysis, pathway analysis and network analysis, were done for the identified dysregulated genes. Pathway analysis indicated that the FoxO signaling pathway played an important role in the effects of propofol on the hippocampus. Finally, four lncRNAs and three proteins were selected from the FoxO-related network for further validation. The up-regulation of lncE230001N04Rik and the down-regulation of lncRP23-430H21.1 and lncB230206L02Rik showed the same fold change tendencies but changes in Gm26532 were not statistically significant in the RNA-Seq results, following propofol sedation. The FoxO pathway-related proteins, PI3K and AKT, are up-regulated in propofol-exposed group. FoxO3a is down-regulated at both mRNA and protein levels. Our study reveals that propofol sedation can influence the expression of lncRNAs and mRNAs in the hippocampus, and bioinformatics analysis have identified key biological processes and pathways associated with propofol sedation. Cumulatively, our results provide a framework for further study on the role of lncRNAs in propofol-induced or -related neurotoxicity, particularly with regards to hippocampus-related dysfunction.

  14. Profiling of Long Non-coding RNAs and mRNAs by RNA-Sequencing in the Hippocampi of Adult Mice Following Propofol Sedation

    Directory of Open Access Journals (Sweden)

    Jun Fan

    2018-03-01

    Full Text Available Propofol is a frequently used intravenous anesthetic agent. The impairment caused by propofol on the neural system, especially the hippocampus, has been widely reported. However, the molecular mechanism underlying the effects of propofol on learning and memory functions in the hippocampus is still unclear. In the present study we performed lncRNA and mRNA analysis in the hippocampi of adult mice, after propofol sedation, through RNA-Sequencing (RNA-Seq. A total of 146 differentially expressed lncRNAs and 1103 mRNAs were identified. Bioinformatics analysis, including gene ontology (GO analysis, pathway analysis and network analysis, were done for the identified dysregulated genes. Pathway analysis indicated that the FoxO signaling pathway played an important role in the effects of propofol on the hippocampus. Finally, four lncRNAs and three proteins were selected from the FoxO-related network for further validation. The up-regulation of lncE230001N04Rik and the down-regulation of lncRP23-430H21.1 and lncB230206L02Rik showed the same fold change tendencies but changes in Gm26532 were not statistically significant in the RNA-Seq results, following propofol sedation. The FoxO pathway-related proteins, PI3K and AKT, are up-regulated in propofol-exposed group. FoxO3a is down-regulated at both mRNA and protein levels. Our study reveals that propofol sedation can influence the expression of lncRNAs and mRNAs in the hippocampus, and bioinformatics analysis have identified key biological processes and pathways associated with propofol sedation. Cumulatively, our results provide a framework for further study on the role of lncRNAs in propofol-induced or -related neurotoxicity, particularly with regards to hippocampus-related dysfunction.

  15. Institutional Narcissism, Arrogant Organization Disorder and Interruptions in Organizational Learning

    Science.gov (United States)

    Godkin, Lynn; Allcorn, Seth

    2009-01-01

    Purpose: This article aims to present an alternative approach to diagnosing behavioral barriers to organizational learning. Design/methodology/approach: The paper juxtaposes interruptions in organizational learning with characteristics of narcissism and arrogant organization disorder. Psychoanalytically informed theory and DSM-IV criteria are…

  16. 18 CFR 284.9 - Interruptible transportation service.

    Science.gov (United States)

    2010-04-01

    ... transportation service. 284.9 Section 284.9 Conservation of Power and Water Resources FEDERAL ENERGY REGULATORY... AUTHORITIES CERTAIN SALES AND TRANSPORTATION OF NATURAL GAS UNDER THE NATURAL GAS POLICY ACT OF 1978 AND RELATED AUTHORITIES General Provisions and Conditions § 284.9 Interruptible transportation service. (a...

  17. Incidental right Bochdalek hernia with interruption of the inferior ...

    African Journals Online (AJOL)

    2014-05-30

    May 30, 2014 ... Case Report doi:10.4102/sajr.v18i1.592 http://sajr.org.za. Incidental right Bochdalek hernia with interruption of the inferior vena cava and hepatic venous collateral continuation: A case report. Authors: Farzanah I. Ismail1. Rule Human2. Anith Chacko1. Parmanand Naran2. Samia Ahmad1. Siraj Ellemdin2.

  18. User assistance for multitasking with interruptions on a mobile device

    NARCIS (Netherlands)

    Nagata, S.F.

    2006-01-01

    Issues users have with use of the web on a mobile device can be attributed to difficulties with the mobile interface. A major challenge that we address is improving the user experience for handling of interruptions and multitasking when using the web in a mobile context. The usability issues with a

  19. User Assistance for Multitasking with Interruptions on a Mobile Device

    NARCIS (Netherlands)

    Nagata, S.F.

    2006-01-01

    Issues users have with use of the web on a mobile device can be attributed to difficulties with the mobile interface. A major challenge that we address is improving the user experience for handling of interruptions and multitasking when using the web in a mobile context. The usability issues with a

  20. 30 CFR 18.48 - Circuit-interrupting devices.

    Science.gov (United States)

    2010-07-01

    ... energized. (f) Belt conveyors shall be equipped with control switches to automatically stop the driving motor in the event the belt is stopped, or abnormally slowed down. Note: Short transfer-type conveyors... Design Requirements § 18.48 Circuit-interrupting devices. (a) Each machine shall be equipped with a...

  1. 'Keeping healthy in the backseat': How motherhood interrupted HIV ...

    African Journals Online (AJOL)

    This study explores how motherhood in newly delivered HIV-infected mothers in Kenya interrupted their antiretroviral treatment (ART). Qualitative interviews were performed with 26 mothers on ART in a rural or urban area. The data were organised and interpreted using content analysis. The study found that adherence to ...

  2. The Needs of Others: Gender and Sleep Interruptions for Caregivers

    Science.gov (United States)

    Burgard, Sarah A.

    2011-01-01

    Received wisdom, some sociological theory and a handful of qualitative studies suggest that the "night shift" of caregiving work that interrupts sleep is a burden borne disproportionately by women. However, there is no broadly representative evidence to substantiate claims about who takes the night shift in contemporary American households.…

  3. COMPARATIVE STUDY OF RTOS AND PRIMITIVE INTERRUPT IN EMBEDDED SYSTEM

    Directory of Open Access Journals (Sweden)

    Dwi Purnomo

    2015-03-01

    Full Text Available Multitasking is one of the most challenging issues in the automation industry which is highly depended on the embedded system. There are two methods to perform multitasking in embedded system: RTOS and primitive interrupt. The main purpose of this research is to compare the performance of R¬TOS with primitive method while concurrently undertaking multiple tasks. The system, which is able to perform various tasks, has been built to evaluate the performance of both methods. There are four tasks introduced in the system: servo task, sensor task, LED task, and LCD task. The performance of each method is indicated by the success rate of the sensor task detection. Sensor task detection will be compared with the true value which is calculated and measured manually during observation time. Observation time was varied after several iterations and the data of the iteration are recorded for both RTOS and primitive interrupt methods. The results of the conducted experiments have shown that, RTOS is more accurate than interrupt method. However, the data variance of the primitive interrupt method is narrower than RTOS. Therefore, to choose a better method, an optimization is needed to be done and each product has its own standard.

  4. Reference ranges for interrupter resistance technique: the Asthma UK Initiative.

    NARCIS (Netherlands)

    Merkus, P.J.F.M.; Stocks, J.; Beydon, N.; Lombardi, E.; Jones, M.; McKenzie, S.A.; Kivastik, J.; Arets, B.G.; Stanojevic, S.

    2010-01-01

    Measuring interrupter resistance (R(int)) is an increasingly popular lung function technique and especially suitable for preschool children because it is simple, quick and requires only passive cooperation. A European Respiratory Society (ERS)/American Thoracic Society (ATS) Task Force recently

  5. Coding Partitions

    Directory of Open Access Journals (Sweden)

    Fabio Burderi

    2007-05-01

    Full Text Available Motivated by the study of decipherability conditions for codes weaker than Unique Decipherability (UD, we introduce the notion of coding partition. Such a notion generalizes that of UD code and, for codes that are not UD, allows to recover the ``unique decipherability" at the level of the classes of the partition. By tacking into account the natural order between the partitions, we define the characteristic partition of a code X as the finest coding partition of X. This leads to introduce the canonical decomposition of a code in at most one unambiguouscomponent and other (if any totally ambiguouscomponents. In the case the code is finite, we give an algorithm for computing its canonical partition. This, in particular, allows to decide whether a given partition of a finite code X is a coding partition. This last problem is then approached in the case the code is a rational set. We prove its decidability under the hypothesis that the partition contains a finite number of classes and each class is a rational set. Moreover we conjecture that the canonical partition satisfies such a hypothesis. Finally we consider also some relationships between coding partitions and varieties of codes.

  6. Detection of Multiple Budding Yeast Cells and a Partial Sequence of 43-kDa Glycoprotein Coding Gene of Paracoccidioides brasiliensis from a Case of Lacaziosis in a Female Pacific White-Sided Dolphin (Lagenorhynchus obliquidens).

    Science.gov (United States)

    Minakawa, Tomoko; Ueda, Keiichi; Tanaka, Miyuu; Tanaka, Natsuki; Kuwamura, Mitsuru; Izawa, Takeshi; Konno, Toshihiro; Yamate, Jyoji; Itano, Eiko Nakagawa; Sano, Ayako; Wada, Shinpei

    2016-08-01

    Lacaziosis, formerly called as lobomycosis, is a zoonotic mycosis, caused by Lacazia loboi, found in humans and dolphins, and is endemic in the countries on the Atlantic Ocean, Indian Ocean and Pacific Ocean of Japanese coast. Susceptible Cetacean species include the bottlenose dolphin (Tursiops truncatus), the Indian Ocean bottlenose dolphin (T. aduncus), and the estuarine dolphin (Sotalia guianensis); however, no cases have been recorded in other Cetacean species. We diagnosed a case of Lacaziosis in a Pacific white-sided dolphin (Lagenorhynchus obliquidens) nursing in an aquarium in Japan. The dolphin was a female estimated to be more than 14 years old at the end of June 2015 and was captured in a coast of Japan Sea in 2001. Multiple, lobose, and solid granulomatous lesions with or without ulcers appeared on her jaw, back, flipper and fluke skin, in July 2014. The granulomatous skin lesions from the present case were similar to those of our previous cases. Multiple budding and chains of round yeast cells were detected in the biopsied samples. The partial sequence of 43-kDa glycoprotein coding gene confirmed by a nested PCR and sequencing, which revealed a different genotype from both Amazonian and Japanese lacaziosis in bottlenose dolphins, and was 99 % identical to those derived from Paracoccidioides brasiliensis; a sister fungal species to L. loboi. This is the first case of lacaziosis in Pacific white-sided dolphin.

  7. A cryptic promoter in potato virus X vector interrupted plasmid construction

    Directory of Open Access Journals (Sweden)

    Schultz Ronald D

    2007-03-01

    Full Text Available Abstract Background Potato virus X has been developed into an expression vector for plants. It is widely used to express foreign genes. In molecular manipulation, the foreign genes need to be sub-cloned into the vector. The constructed plasmid needs to be amplified. Usually, during amplification stage, the foreign genes are not expressed. However, if the foreign gene is expressed, the construction work could be interrupted. Two different viral genes were sub-cloned into the vector, but only one foreign gene was successfully sub-cloned. The other foreign gene, canine parvovirus type 2 (CPV-2 VP1 could not be sub-cloned into the vector and amplified without mutation (frame shift mutation. Results A cryptic promoter in the PVX vector was discovered with RT-PCR. The promoter activity was studied with Northern blots and Real-time RT-PCR. Conclusion It is important to recognize the homologous promoter sequences in the vector when a virus is developed as an expression vector. During the plasmid amplification stage, an unexpected expression of the CPV-2 VP1 gene (not in the target plants, but in E. coli can interrupt the downstream work.

  8. Compensability index for compensation radiotherapy after treatment interruptions

    International Nuclear Information System (INIS)

    Putora, Paul Martin; Schmuecking, Michael; Aebersold, Daniel; Plasswilm, Ludwig

    2012-01-01

    The goal of our work was to develop a simple method to evaluate a compensation treatment after unplanned treatment interruptions with respect to their tumour- and normal tissue effect. We developed a software tool in java programming language based on existing recommendations to compensate for treatment interruptions. In order to express and visualize the deviations from the originally planned tumour and normal tissue effects we defined the compensability index. The compensability index represents an evaluation of the suitability of compensatory radiotherapy in a single number based on the number of days used for compensation and the preference of preserving the originally planned tumour effect or not exceeding the originally planned normal tissue effect. An automated tool provides a method for quick evaluation of compensation treatments. The compensability index calculation may serve as a decision support system based on existing and established recommendations

  9. Reversible harmless interruption of testicular blood supply in the ram

    International Nuclear Information System (INIS)

    van Vliet, J.; De Ruiter-Bootsma, A.L.; Oei, Y.H.; Hoekstra, A.; De Rooij, D.G.; Wensing, C.J.

    1987-01-01

    An effective method of interrupting testicular blood flow temporarily and repeatedly in the ram has been developed. Blockade of flow has been achieved mechanically by an inflatable occluder placed around the testicular artery at the level of the spermatic cord. The effect of the blockade on total testicular blood supply was investigated using Doppler flowmetry and a percutaneous Xenon-133 injection method. With both approaches, the blood flow changes after inflation or deflation of the occluders could be estimated satisfactorily. A substantial decrease of testicular blood flow was achieved in eight of the 10 testes with inflated occluders. However, there were indications that in the remaining two testes blockade of the arterial flow was not complete. After deflation of the occluders, blood flow was restored rapidly and completely in all testes. Macro- and microscopic examinations revealed no long-term damage to the testis after blood flow interruptions lasting 30 or 60 minutes

  10. Task and Interruption Management in Activity-Centric Computing

    DEFF Research Database (Denmark)

    Jeuris, Steven

    to address these not in isolation, but by fundamentally reevaluating the current computing paradigm. To this end, activity-centric computing has been brought forward as an alternative computing paradigm, addressing the increasing strain put on modern-day computing systems. Activity-centric computing follows...... the scalability and intelligibility of current research prototypes. In this dissertation, I postulate that such issues arise due to a lack of support for the full set of practices which make up activity management. Most notably, although task and interruption management are an integral part of personal...... information management, they have thus far been neglected in prior activity-centric computing systems. Advancing the research agenda of activity-centric computing, I (1) implement and evaluate an activity-centric desktop computing system, incorporating support for interruptions and long-term task management...

  11. Cold standby repairable system with working vacations and vacation interruption

    Institute of Scientific and Technical Information of China (English)

    Baoliang Liu; Lirong Cui; Yanqing Wen

    2015-01-01

    This paper studies a cold standby repairable system with working vacations and vacation interruption. The repairman’s multiple vacations policy, the working vacations policy and the vacation interruption are considered simultaneously. The lifetime of components fol ows a phase-type (PH) distribution. The repair time in the regular repair period and the working vacation period fol ow other two PH distributions at different rates. For this sys-tem, the vector-valued Markov process governing the system is constructed. We obtain several important performance measures for the system in transient and stationary regimes applying matrix-analytic methods. Final y, a numerical example is given to il ustrate the results obtained.

  12. Reactor pressure elevation preventing device upon interruption of load

    International Nuclear Information System (INIS)

    Ota, Yasuo; Okukawa, Ryutaro.

    1996-01-01

    In a power load imbalance circuit of a steam turbine control device, a power load imbalance occurrence signal is outputted for a predetermined period of time upon occurrence of load interruption. A function for suppressing increase of number of rotation of a turbine due to load interruption is not disturbed, and the power load imbalance circuit is not operated at least after a primary peak where the number of rotation of the turbine is increased. Since a steam control valve flow rate demand signal and a turbine bypass valve flow rate demand signals are corporated subsequently to control the opening degree of the steam control valve and the turbine bypass valve, elevation of reactor pressure is always suppressed and maintained constant, as well as abrupt opening of the steam control valve due to cancel of the power load imbalance circuit when steam control valve opening demand is outputted can be prevented. (N.H.)

  13. Compensability index for compensation radiotherapy after treatment interruptions

    Directory of Open Access Journals (Sweden)

    Putora Paul

    2012-12-01

    Full Text Available Abstract Background The goal of our work was to develop a simple method to evaluate a compensation treatment after unplanned treatment interruptions with respect to their tumour- and normal tissue effect. Methods We developed a software tool in java programming language based on existing recommendations to compensate for treatment interruptions. In order to express and visualize the deviations from the originally planned tumour and normal tissue effects we defined the compensability index. Results The compensability index represents an evaluation of the suitability of compensatory radiotherapy in a single number based on the number of days used for compensation and the preference of preserving the originally planned tumour effect or not exceeding the originally planned normal tissue effect. An automated tool provides a method for quick evaluation of compensation treatments. Conclusions The compensability index calculation may serve as a decision support system based on existing and established recommendations.

  14. Persistent truncus arteriosis associated with interruption of the aortic arch.

    Science.gov (United States)

    Nath, P H; Zollikofer, C; Castaneda-Zuniga, W; Formanek, A; Amplatz, K

    1980-09-01

    Five patients with a combination of truncus arteriosus and interruption of the aortic arch are reported. The combination of those defects significantly increases the surgical risk. This rare cardiac malformation can only be diagnosed radiographically. An aberrant right subclavian artery is present in 25% of patients. It is helpful in suspecting the diagnosis from plain films of the chest. The diagnosis can be made from a ventriculogram, but usually a truncogram is necessary to define the anatomy of the aortic arch.

  15. Radiogenetic and radiobiological indications for interruption of pregnancy

    International Nuclear Information System (INIS)

    Neumeister, K.

    1976-11-01

    Taking into consideration the recent literature, and based on his own experience, the author deals with the question of interruption following radiation stress in early pregnancy. At fetal doses of above 10 R, induction of abortion is thought to be necessary. In the German Democratic Republic a central consultation service has been established at the National Board of Nuclear Safety and Radiation Protection offering expert opinions on these problems. (author)

  16. Building and Verifying a Predictive Model of Interruption Resumption

    Science.gov (United States)

    2012-03-01

    the gardener to remember those plants (and whether they need to be removed), and so will not commit resources to remember that information . The overall...camera), the storyteller needed help much less often. This result suggests that when there is no one to help them remember the last thing they said...INV ITED P A P E R Building and Verifying a Predictive Model of Interruption Resumption Help from a robot, to allow a human storyteller to continue

  17. The Impact of Motion Induced Interruptions on Cognitive Performance

    Science.gov (United States)

    2014-07-23

    found that even participants presenting with minor physiological effects of motion experienced a decline in multitasking performance. Further, Yu...literature has investigated the impact of task based interruptions such as being inter- rupted by a phone call or writing an email . In these...Engineers Journal. 102 (2) 65-72. Matsangas, P. (2013). The Effect of Mild Motion Sickness and Sopite Syndrome on Multitasking Cognitive Performance

  18. Treatment interruptions: Statistics, causes and management in service radiotherapy

    International Nuclear Information System (INIS)

    Ferrando Sanchez, A.; Milanes Gaillet, A. I.; Eugui Martinez, R.; Crespo Diaz, M. P.

    2013-01-01

    Despite the clinical maximum administer the prescribed dose at a given time, treatment interruptions are unavoidable in practice. In tumors quickly reproduce no evidence that the prolongation thereof entails loss of tumor control. It has tracked two of these conditions: squamous cell cancer of the head and neck (SCCHN) and lung cancer (NSCLC) over 2011 and 2012 to evaluate both the number of stops treatment as the reason for them and its management. (Author)

  19. Realistically Rendering SoC Traffic Patterns with Interrupt Awareness

    DEFF Research Database (Denmark)

    Angiolini, Frederico; Mahadevan, Sharkar; Madsen, Jan

    2005-01-01

    to generate realistic test traffic. This paper presents a selection of applications using interrupt-based synchronization; a reference methodology to split such applications in execution subflows and to adjust the overall execution stream based upon hardware events; a reactive simulation device capable...... of correctly replicating such software behaviours in the MPSoC design phase. Additionally, we validate the proposed concept by showing cycle-accurate reproduction of a previously traced application flow....

  20. Differentiating between adductor and abductor spasmodic dysphonia using airflow interruption

    Science.gov (United States)

    Hoffman, Matthew R.; Jiang, Jack J.; Rieves, Adam L.; McElveen, Kelsey A.B.; Ford, Charles N.

    2009-01-01

    Objective To measure the laryngeal resistance (RL), subglottal pressure (Ps), and mean flow rate (MFR) of adductor (ADSD) and abductor (ABSD) spasmodic dysphonia patients using the airflow interrupter. Methods The RL of six ABSD and seven ADSD patients was measured using the airflow interrupter, a noninvasive device designed to measure MFR and Ps via mechanical balloon valve interruption. Subjects performed ten trials at each of two intensity levels, with each trial consisting of a sustained /a/ during which phonation was interrupted for 500 ms. Laryngeal resistance was calculated as subglottal pressure divided by airflow. Results Mean RL for the ADSD and ABSD subtypes at 65 dB were 24.78 cmH2O/l/s and 14.51 cmH2O/l/s, respectively (p = 0.04). Mean RL at 70 dB were 40.02 cmH2O/l/s and 15.84 cmH2O/l/s (p = 0.014). Ps for the ADSD and ABSD subtypes at 65 dB were 10.23 cmH2O and 8.32 cmH2O, respectively (p = 0.582). At the 70 dB level, Ps were 12.39 cmH2O and 11.78 cmH2O (p = 0.886). MFR for the ADSD and ABSD subtypes at 65 dB were 435 ml/s and 746 ml/s (p = 0.205). Mean MFR at 70 dB were 518 ml/s and 848 ml/s (p = 0.198). Conclusion Noninvasive measurements of RL may be useful for differentiating between ADSD and ABSD. This simple objective test which produces a quantitative output could be used to evaluate laryngeal function in patients with spasmodic dysphonia. PMID:19554636

  1. Report number codes

    Energy Technology Data Exchange (ETDEWEB)

    Nelson, R.N. (ed.)

    1985-05-01

    This publication lists all report number codes processed by the Office of Scientific and Technical Information. The report codes are substantially based on the American National Standards Institute, Standard Technical Report Number (STRN)-Format and Creation Z39.23-1983. The Standard Technical Report Number (STRN) provides one of the primary methods of identifying a specific technical report. The STRN consists of two parts: The report code and the sequential number. The report code identifies the issuing organization, a specific program, or a type of document. The sequential number, which is assigned in sequence by each report issuing entity, is not included in this publication. Part I of this compilation is alphabetized by report codes followed by issuing installations. Part II lists the issuing organization followed by the assigned report code(s). In both Parts I and II, the names of issuing organizations appear for the most part in the form used at the time the reports were issued. However, for some of the more prolific installations which have had name changes, all entries have been merged under the current name.

  2. Report number codes

    International Nuclear Information System (INIS)

    Nelson, R.N.

    1985-05-01

    This publication lists all report number codes processed by the Office of Scientific and Technical Information. The report codes are substantially based on the American National Standards Institute, Standard Technical Report Number (STRN)-Format and Creation Z39.23-1983. The Standard Technical Report Number (STRN) provides one of the primary methods of identifying a specific technical report. The STRN consists of two parts: The report code and the sequential number. The report code identifies the issuing organization, a specific program, or a type of document. The sequential number, which is assigned in sequence by each report issuing entity, is not included in this publication. Part I of this compilation is alphabetized by report codes followed by issuing installations. Part II lists the issuing organization followed by the assigned report code(s). In both Parts I and II, the names of issuing organizations appear for the most part in the form used at the time the reports were issued. However, for some of the more prolific installations which have had name changes, all entries have been merged under the current name

  3. This art of psychoanalysis. Dreaming undreamt dreams and interrupted cries.

    Science.gov (United States)

    Ogden, Thomas H

    2004-08-01

    It is the art of psychoanalysis in the making, a process inventing itself as it goes, that is the subject of this paper. The author articulates succinctly how he conceives of psychoanalysis, and offers a detailed clinical illustration. He suggests that each analysand unconsciously (and ambivalently) is seeking help in dreaming his 'night terrors' (his undreamt and undreamable dreams) and his 'nightmares' (his dreams that are interrupted when the pain of the emotional experience being dreamt exceeds his capacity for dreaming). Undreamable dreams are understood as manifestations of psychotic and psychically foreclosed aspects of the personality; interrupted dreams are viewed as reflections of neurotic and other non-psychotic parts of the personality. The analyst's task is to generate conditions that may allow the analysand--with the analyst's participation--to dream the patient's previously undreamable and interrupted dreams. A significant part of the analyst's participation in the patient's dreaming takes the form of the analyst's reverie experience. In the course of this conjoint work of dreaming in the analytic setting, the analyst may get to know the analysand sufficiently well for the analyst to be able to say something that is true to what is occurring at an unconscious level in the analytic relationship. The analyst's use of language contributes significantly to the possibility that the patient will be able to make use of what the analyst has said for purposes of dreaming his own experience, thereby dreaming himself more fully into existence.

  4. The interrupted properties of an extruded Mg alloy

    International Nuclear Information System (INIS)

    Xu, Shun; Liu, Tianmo; He, Jiejun; Lu, Liwei; Zeng, Wen

    2013-01-01

    Highlights: ► The reinforcement effect of {101 ¯ 2} twins on yield stress is reflected at low deformation. ► The recompressive yield stress equals to the stress when it is unloaded. ► The stress–strain curve of recompression seems like that without interruption. ► Twins generated in precompression could become thicker in recompression. -- Abstract: The current paper investigates the effect of {101 ¯ 2} extension twins identified by using electron backscattered diffraction on the interrupted properties of an extruded Mg–3Al–1Zn (AZ31) alloy. Compressive and recompressive tests are conducted along extrusion direction (ED). It is discovered that the yield strength of recompression is enhanced due to grain refinement by {101 ¯ 2} extension twins. The reinforcement effect of {101 ¯ 2} extension twins on the yield stress of recompression is mainly reflected at the stage of small deformation while the improvement of yield strength is mainly attributed to the pile-up and intersection of dislocations as large deformation occurs. Furthermore, the yield stress of recompression is identical to the interrupted stress of precompression. In situ observation reveals that some twins generated in precompression could also become thicker in the following recompression.

  5. Factors defining face-to-face interruptions in the office environment

    NARCIS (Netherlands)

    Matysiak, A.J.; Markopoulos, P.

    2006-01-01

    This paper presents an on-going investigation on interruptions in the office caused by face-to-face interactions between knowledge workers. The study aims to identify opportunities for interactive solutions that will support both, the interrupters and the interrupted. The study involves contextual

  6. Individual Differences in Working-Memory Capacity and Task Resumption Following Interruptions

    Science.gov (United States)

    Foroughi, Cyrus K.; Werner, Nicole E.; McKendrick, Ryan; Cades, David M.; Boehm-Davis, Deborah A.

    2016-01-01

    Previous research has shown that there is a time cost (i.e., a resumption lag) associated with resuming a task following an interruption and that the longer the duration of the interruption, the greater the time cost (i.e., resumption lag increases as interruption duration increases). The memory-for-goals model (Altmann & Trafton, 2002)…

  7. Speaking Code

    DEFF Research Database (Denmark)

    Cox, Geoff

    Speaking Code begins by invoking the “Hello World” convention used by programmers when learning a new language, helping to establish the interplay of text and code that runs through the book. Interweaving the voice of critical writing from the humanities with the tradition of computing and software...

  8. Circular codes revisited: a statistical approach.

    Science.gov (United States)

    Gonzalez, D L; Giannerini, S; Rosa, R

    2011-04-21

    In 1996 Arquès and Michel [1996. A complementary circular code in the protein coding genes. J. Theor. Biol. 182, 45-58] discovered the existence of a common circular code in eukaryote and prokaryote genomes. Since then, circular code theory has provoked great interest and underwent a rapid development. In this paper we discuss some theoretical issues related to the synchronization properties of coding sequences and circular codes with particular emphasis on the problem of retrieval and maintenance of the reading frame. Motivated by the theoretical discussion, we adopt a rigorous statistical approach in order to try to answer different questions. First, we investigate the covering capability of the whole class of 216 self-complementary, C(3) maximal codes with respect to a large set of coding sequences. The results indicate that, on average, the code proposed by Arquès and Michel has the best covering capability but, still, there exists a great variability among sequences. Second, we focus on such code and explore the role played by the proportion of the bases by means of a hierarchy of permutation tests. The results show the existence of a sort of optimization mechanism such that coding sequences are tailored as to maximize or minimize the coverage of circular codes on specific reading frames. Such optimization clearly relates the function of circular codes with reading frame synchronization. Copyright © 2011 Elsevier Ltd. All rights reserved.

  9. What Interrupts Suicide Attempts in Men: A Qualitative Study

    Science.gov (United States)

    Player, Michael J.; Proudfoot, Judy; Fogarty, Andrea; Whittle, Erin; Spurrier, Michael; Shand, Fiona; Christensen, Helen; Hadzi-Pavlovic, Dusan; Wilhelm, Kay

    2015-01-01

    Despite higher rates of suicide in men, there is a dearth of research examining the perspectives and experiences of males at risk of suicide, particularly in terms of understanding how interventions can be tailored to men’s specific needs. The current study aimed to examine factors assisting, complicating or inhibiting interventions for men at risk, as well as outlining the roles of family, friends and others in male suicide prevention. Thirty-five male suicide survivors completed one-to-one interviews, and forty-seven family and friends of male suicide survivors participated in eight focus groups. Thematic analysis revealed five major themes: (1) development of suicidal behaviours tends to follow a common path associated with specific types of risk factors (disrupted mood, unhelpful stoic beliefs and values, avoidant coping strategies, stressors), (2) men at risk of suicide tend to systematically misinterpret changes in their behaviour and thinking, (3) understanding mood and behavioural changes in men enables identification of opportunities to interrupt suicide progression, (4) distraction, provision of practical and emotional supports, along with professional intervention may effectively interrupt acute risk of harm, and (5) suicidal ideation may be reduced through provision of practical help to manage crises, and helping men to focus on obligations and their role within families. Findings suggest that interventions for men at risk of suicidal behaviours need to be tailored to specific risk indicators, developmental factors, care needs and individuals’ preferences. To our knowledge this is the first qualitative study to explore the experiences of both suicidal men and their family/friends after a suicide attempt, with the view to improve understanding of the processes which are effective in interrupting suicide and better inform interventions for men at risk. PMID:26090794

  10. What Interrupts Suicide Attempts in Men: A Qualitative Study.

    Directory of Open Access Journals (Sweden)

    Michael J Player

    Full Text Available Despite higher rates of suicide in men, there is a dearth of research examining the perspectives and experiences of males at risk of suicide, particularly in terms of understanding how interventions can be tailored to men's specific needs. The current study aimed to examine factors assisting, complicating or inhibiting interventions for men at risk, as well as outlining the roles of family, friends and others in male suicide prevention. Thirty-five male suicide survivors completed one-to-one interviews, and forty-seven family and friends of male suicide survivors participated in eight focus groups. Thematic analysis revealed five major themes: (1 development of suicidal behaviours tends to follow a common path associated with specific types of risk factors (disrupted mood, unhelpful stoic beliefs and values, avoidant coping strategies, stressors, (2 men at risk of suicide tend to systematically misinterpret changes in their behaviour and thinking, (3 understanding mood and behavioural changes in men enables identification of opportunities to interrupt suicide progression, (4 distraction, provision of practical and emotional supports, along with professional intervention may effectively interrupt acute risk of harm, and (5 suicidal ideation may be reduced through provision of practical help to manage crises, and helping men to focus on obligations and their role within families. Findings suggest that interventions for men at risk of suicidal behaviours need to be tailored to specific risk indicators, developmental factors, care needs and individuals' preferences. To our knowledge this is the first qualitative study to explore the experiences of both suicidal men and their family/friends after a suicide attempt, with the view to improve understanding of the processes which are effective in interrupting suicide and better inform interventions for men at risk.

  11. Masking interrupts figure-ground signals in V1.

    Science.gov (United States)

    Lamme, Victor A F; Zipser, Karl; Spekreijse, Henk

    2002-10-01

    In a backward masking paradigm, a target stimulus is rapidly (figure-ground segregation can be recorded. Here, we recorded from awake macaque monkeys, engaged in a task where they had to detect figures from background in a pattern backward masking paradigm. We show that the V1 figure-ground signals are selectively and fully suppressed at target-mask intervals that psychophysically result in the target being invisible. Initial response transients, signalling the features that make up the scene, are not affected. As figure-ground modulations depend on feedback from extrastriate areas, these results suggest that masking selectively interrupts the recurrent interactions between V1 and higher visual areas.

  12. Children and Career Interruptions: The Family Gap in Denmark

    DEFF Research Database (Denmark)

    Gupta, Nabanita Datta; Smith, Nina

    2002-01-01

    Abstract: The effect of children and career interruptions on the family gap is analysed based on longitudinal data covering the years 1980-1995. The estimated model controls for unobserved time-constant heterogeneity. The results show that when controlling for unobserved heterogeneity, the negative...... effect of children on mothers' wages disappear, but there are large differences between educational groups and the public and private sector. The main effect of children seems to be a loss of human capital accumulation during child-birth periods. Beside this, there is no indication that children have...

  13. Fast Interrupt Priority Management in Operating System Kernels

    Science.gov (United States)

    1993-05-01

    We present results for the Mach 3.0 microkernel operating system, although the technique is applicable to other kernel architectures, both micro and...protection in the Mach 3.0 microkernel for several different processor architectures. For example, on the Omron Luna88k, we observed a 50% reduction in...general interrupt mask raise/lower pair within the Mach 3.0 microkernel on a variety of architectures. DTIC QUALM i.N1’R%.*1IMD 5 k81tltC Avail andl

  14. The Tile-map Based Vulnerability Assessment Code of a Physical Protection System: SAPE (Systematic Analysis of Protection Effectiveness)

    International Nuclear Information System (INIS)

    Jang, Sung Soon; Kwak, Sung Woo; Yoo, Ho Sik; Kim, Jung Soo; Yoon, Wan Ki

    2008-01-01

    Increasing threats on nuclear facilities demands stronger physical protection system (PPS) within the limited budget. For this reason we need an efficient physical protection system and before making an efficient PPS we need to evaluate it. This evaluation process should faithfully reflect real situation, reveal weak points and unnecessary protection elements, and give comparable quantitative values. Performance based analysis helps to build an efficient physical protection system. Instead of regulating the number of sensors and barriers, the performance based analysis evaluates a PPS fit to the situation of a facility. The analysis assesses delay (sensors) and detection (barriers) of a PPS against an intrusion, and judges whether a response force arrives before intruders complete their job. Performance based analysis needs complicated calculation and, hence, several assessment codes have been developed. A code called the estimation of adversary sequence interruption (EASI) was developed to analyze vulnerability along a single intrusion path. The systematic analysis of vulnerability to intrusion (SAVI) code investigates multi-paths to a valuable asset in an actual facility. SAVI uses adversary sequence diagram to describe multi-paths

  15. Coding Labour

    Directory of Open Access Journals (Sweden)

    Anthony McCosker

    2014-03-01

    Full Text Available As well as introducing the Coding Labour section, the authors explore the diffusion of code across the material contexts of everyday life, through the objects and tools of mediation, the systems and practices of cultural production and organisational management, and in the material conditions of labour. Taking code beyond computation and software, their specific focus is on the increasingly familiar connections between code and labour with a focus on the codification and modulation of affect through technologies and practices of management within the contemporary work organisation. In the grey literature of spreadsheets, minutes, workload models, email and the like they identify a violence of forms through which workplace affect, in its constant flux of crisis and ‘prodromal’ modes, is regulated and governed.

  16. Compact generator with semiconductor current interrupter, voltage to 300 kV and pulse repetition rate to 2 kHz

    International Nuclear Information System (INIS)

    Lyubutin, S.K.; Rukin, S.N.; Slovikovskij, B.G.

    2000-01-01

    Compact generator with a semiconductor current interrupter (SOS-diode), forming on the resistive load pulses with the amplitude up to 300 kV, duration from 30 up to 50 ns and the pulse sequence frequency 300 Hz by long operation and up to 2 kHz in the 30-second packet, is described. The generator contains a thyristor charge unit, magnetic compressor and inductive storage with a semiconductor current interrupter on the SOS-diode basis. The generator mean output capacity by the pulse maximum sequence frequency and 250 kV voltage equals 16 kw. The generator dimensions are 0.85 x 0.65 x 0.42 m, its mass equals approximately 115 kg [ru

  17. Self-complementary circular codes in coding theory.

    Science.gov (United States)

    Fimmel, Elena; Michel, Christian J; Starman, Martin; Strüngmann, Lutz

    2018-04-01

    Self-complementary circular codes are involved in pairing genetic processes. A maximal [Formula: see text] self-complementary circular code X of trinucleotides was identified in genes of bacteria, archaea, eukaryotes, plasmids and viruses (Michel in Life 7(20):1-16 2017, J Theor Biol 380:156-177, 2015; Arquès and Michel in J Theor Biol 182:45-58 1996). In this paper, self-complementary circular codes are investigated using the graph theory approach recently formulated in Fimmel et al. (Philos Trans R Soc A 374:20150058, 2016). A directed graph [Formula: see text] associated with any code X mirrors the properties of the code. In the present paper, we demonstrate a necessary condition for the self-complementarity of an arbitrary code X in terms of the graph theory. The same condition has been proven to be sufficient for codes which are circular and of large size [Formula: see text] trinucleotides, in particular for maximal circular codes ([Formula: see text] trinucleotides). For codes of small-size [Formula: see text] trinucleotides, some very rare counterexamples have been constructed. Furthermore, the length and the structure of the longest paths in the graphs associated with the self-complementary circular codes are investigated. It has been proven that the longest paths in such graphs determine the reading frame for the self-complementary circular codes. By applying this result, the reading frame in any arbitrary sequence of trinucleotides is retrieved after at most 15 nucleotides, i.e., 5 consecutive trinucleotides, from the circular code X identified in genes. Thus, an X motif of a length of at least 15 nucleotides in an arbitrary sequence of trinucleotides (not necessarily all of them belonging to X) uniquely defines the reading (correct) frame, an important criterion for analyzing the X motifs in genes in the future.

  18. The interrupted power law and the size of shadow banking.

    Science.gov (United States)

    Fiaschi, Davide; Kondor, Imre; Marsili, Matteo; Volpati, Valerio

    2014-01-01

    Using public data (Forbes Global 2000) we show that the asset sizes for the largest global firms follow a Pareto distribution in an intermediate range, that is "interrupted" by a sharp cut-off in its upper tail, where it is totally dominated by financial firms. This flattening of the distribution contrasts with a large body of empirical literature which finds a Pareto distribution for firm sizes both across countries and over time. Pareto distributions are generally traced back to a mechanism of proportional random growth, based on a regime of constant returns to scale. This makes our findings of an "interrupted" Pareto distribution all the more puzzling, because we provide evidence that financial firms in our sample should operate in such a regime. We claim that the missing mass from the upper tail of the asset size distribution is a consequence of shadow banking activity and that it provides an (upper) estimate of the size of the shadow banking system. This estimate-which we propose as a shadow banking index-compares well with estimates of the Financial Stability Board until 2009, but it shows a sharper rise in shadow banking activity after 2010. Finally, we propose a proportional random growth model that reproduces the observed distribution, thereby providing a quantitative estimate of the intensity of shadow banking activity.

  19. Speech coding

    Energy Technology Data Exchange (ETDEWEB)

    Ravishankar, C., Hughes Network Systems, Germantown, MD

    1998-05-08

    Speech is the predominant means of communication between human beings and since the invention of the telephone by Alexander Graham Bell in 1876, speech services have remained to be the core service in almost all telecommunication systems. Original analog methods of telephony had the disadvantage of speech signal getting corrupted by noise, cross-talk and distortion Long haul transmissions which use repeaters to compensate for the loss in signal strength on transmission links also increase the associated noise and distortion. On the other hand digital transmission is relatively immune to noise, cross-talk and distortion primarily because of the capability to faithfully regenerate digital signal at each repeater purely based on a binary decision. Hence end-to-end performance of the digital link essentially becomes independent of the length and operating frequency bands of the link Hence from a transmission point of view digital transmission has been the preferred approach due to its higher immunity to noise. The need to carry digital speech became extremely important from a service provision point of view as well. Modem requirements have introduced the need for robust, flexible and secure services that can carry a multitude of signal types (such as voice, data and video) without a fundamental change in infrastructure. Such a requirement could not have been easily met without the advent of digital transmission systems, thereby requiring speech to be coded digitally. The term Speech Coding is often referred to techniques that represent or code speech signals either directly as a waveform or as a set of parameters by analyzing the speech signal. In either case, the codes are transmitted to the distant end where speech is reconstructed or synthesized using the received set of codes. A more generic term that is applicable to these techniques that is often interchangeably used with speech coding is the term voice coding. This term is more generic in the sense that the

  20. Optimal codes as Tanner codes with cyclic component codes

    DEFF Research Database (Denmark)

    Høholdt, Tom; Pinero, Fernando; Zeng, Peng

    2014-01-01

    In this article we study a class of graph codes with cyclic code component codes as affine variety codes. Within this class of Tanner codes we find some optimal binary codes. We use a particular subgraph of the point-line incidence plane of A(2,q) as the Tanner graph, and we are able to describe ...

  1. Aztheca Code

    International Nuclear Information System (INIS)

    Quezada G, S.; Espinosa P, G.; Centeno P, J.; Sanchez M, H.

    2017-09-01

    This paper presents the Aztheca code, which is formed by the mathematical models of neutron kinetics, power generation, heat transfer, core thermo-hydraulics, recirculation systems, dynamic pressure and level models and control system. The Aztheca code is validated with plant data, as well as with predictions from the manufacturer when the reactor operates in a stationary state. On the other hand, to demonstrate that the model is applicable during a transient, an event occurred in a nuclear power plant with a BWR reactor is selected. The plant data are compared with the results obtained with RELAP-5 and the Aztheca model. The results show that both RELAP-5 and the Aztheca code have the ability to adequately predict the behavior of the reactor. (Author)

  2. Effect of analytical treatment interruption and reinitiation of antiretroviral therapy on HIV reservoirs and immunologic parameters in infected individuals.

    Science.gov (United States)

    Clarridge, Katherine E; Blazkova, Jana; Einkauf, Kevin; Petrone, Mary; Refsland, Eric W; Justement, J Shawn; Shi, Victoria; Huiting, Erin D; Seamon, Catherine A; Lee, Guinevere Q; Yu, Xu G; Moir, Susan; Sneller, Michael C; Lichterfeld, Mathias; Chun, Tae-Wook

    2018-01-01

    Therapeutic strategies aimed at achieving antiretroviral therapy (ART)-free HIV remission in infected individuals are under active investigation. Considering the vast majority of HIV-infected individuals experience plasma viral rebound upon cessation of therapy, clinical trials evaluating the efficacy of curative strategies would likely require inclusion of ART interruption. However, it is unclear what impact short-term analytical treatment interruption (ATI) and subsequent reinitiation of ART have on immunologic and virologic parameters of HIV-infected individuals. Here, we show a significant increase of HIV burden in the CD4+ T cells of infected individuals during ATI that was correlated with the level of plasma viral rebound. However, the size of the HIV reservoirs as well as immune parameters, including markers of exhaustion and activation, returned to pre-ATI levels 6-12 months after the study participants resumed ART. Of note, the proportions of near full-length, genome-intact and structurally defective HIV proviral DNA sequences were similar prior to ATI and following reinitiation of ART. In addition, there was no evidence of emergence of antiretroviral drug resistance mutations within intact HIV proviral DNA sequences following reinitiation of ART. These data demonstrate that short-term ATI does not necessarily lead to expansion of the persistent HIV reservoir nor irreparable damages to the immune system in the peripheral blood, warranting the inclusion of ATI in future clinical trials evaluating curative strategies.

  3. Embedded interruptions and task complexity influence schema-related cognitive load progression in an abstract learning task.

    Science.gov (United States)

    Wirzberger, Maria; Esmaeili Bijarsari, Shirin; Rey, Günter Daniel

    2017-09-01

    Cognitive processes related to schema acquisition comprise an essential source of demands in learning situations. Since the related amount of cognitive load is supposed to change over time, plausible temporal models of load progression based on different theoretical backgrounds are inspected in this study. A total of 116 student participants completed a basal symbol sequence learning task, which provided insights into underlying cognitive dynamics. Two levels of task complexity were determined by the amount of elements within the symbol sequence. In addition, interruptions due to an embedded secondary task occurred at five predefined stages over the task. Within the resulting 2x5-factorial mixed between-within design, the continuous monitoring of efficiency in learning performance enabled assumptions on relevant resource investment. From the obtained results, a nonlinear change of learning efficiency over time seems most plausible in terms of cognitive load progression. Moreover, different effects of the induced interruptions show up in conditions of task complexity, which indicate the activation of distinct cognitive mechanisms related to structural aspects of the task. Findings are discussed in the light of evidence from research on memory and information processing. Copyright © 2017 Elsevier B.V. All rights reserved.

  4. Spliced DNA Sequences in the Paramecium Germline: Their Properties and Evolutionary Potential

    Science.gov (United States)

    Catania, Francesco; McGrath, Casey L.; Doak, Thomas G.; Lynch, Michael

    2013-01-01

    Despite playing a crucial role in germline-soma differentiation, the evolutionary significance of developmentally regulated genome rearrangements (DRGRs) has received scant attention. An example of DRGR is DNA splicing, a process that removes segments of DNA interrupting genic and/or intergenic sequences. Perhaps, best known for shaping immune-system genes in vertebrates, DNA splicing plays a central role in the life of ciliated protozoa, where thousands of germline DNA segments are eliminated after sexual reproduction to regenerate a functional somatic genome. Here, we identify and chronicle the properties of 5,286 sequences that putatively undergo DNA splicing (i.e., internal eliminated sequences [IESs]) across the genomes of three closely related species of the ciliate Paramecium (P. tetraurelia, P. biaurelia, and P. sexaurelia). The study reveals that these putative IESs share several physical characteristics. Although our results are consistent with excision events being largely conserved between species, episodes of differential IES retention/excision occur, may have a recent origin, and frequently involve coding regions. Our findings indicate interconversion between somatic—often coding—DNA sequences and noncoding IESs, and provide insights into the role of DNA splicing in creating potentially functional genetic innovation. PMID:23737328

  5. Vocable Code

    DEFF Research Database (Denmark)

    Soon, Winnie; Cox, Geoff

    2018-01-01

    a computational and poetic composition for two screens: on one of these, texts and voices are repeated and disrupted by mathematical chaos, together exploring the performativity of code and language; on the other, is a mix of a computer programming syntax and human language. In this sense queer code can...... be understood as both an object and subject of study that intervenes in the world’s ‘becoming' and how material bodies are produced via human and nonhuman practices. Through mixing the natural and computer language, this article presents a script in six parts from a performative lecture for two persons...

  6. NSURE code

    International Nuclear Information System (INIS)

    Rattan, D.S.

    1993-11-01

    NSURE stands for Near-Surface Repository code. NSURE is a performance assessment code. developed for the safety assessment of near-surface disposal facilities for low-level radioactive waste (LLRW). Part one of this report documents the NSURE model, governing equations and formulation of the mathematical models, and their implementation under the SYVAC3 executive. The NSURE model simulates the release of nuclides from an engineered vault, their subsequent transport via the groundwater and surface water pathways tot he biosphere, and predicts the resulting dose rate to a critical individual. Part two of this report consists of a User's manual, describing simulation procedures, input data preparation, output and example test cases

  7. Adaptive decoding of convolutional codes

    Directory of Open Access Journals (Sweden)

    K. Hueske

    2007-06-01

    Full Text Available Convolutional codes, which are frequently used as error correction codes in digital transmission systems, are generally decoded using the Viterbi Decoder. On the one hand the Viterbi Decoder is an optimum maximum likelihood decoder, i.e. the most probable transmitted code sequence is obtained. On the other hand the mathematical complexity of the algorithm only depends on the used code, not on the number of transmission errors. To reduce the complexity of the decoding process for good transmission conditions, an alternative syndrome based decoder is presented. The reduction of complexity is realized by two different approaches, the syndrome zero sequence deactivation and the path metric equalization. The two approaches enable an easy adaptation of the decoding complexity for different transmission conditions, which results in a trade-off between decoding complexity and error correction performance.

  8. Adaptive decoding of convolutional codes

    Science.gov (United States)

    Hueske, K.; Geldmacher, J.; Götze, J.

    2007-06-01

    Convolutional codes, which are frequently used as error correction codes in digital transmission systems, are generally decoded using the Viterbi Decoder. On the one hand the Viterbi Decoder is an optimum maximum likelihood decoder, i.e. the most probable transmitted code sequence is obtained. On the other hand the mathematical complexity of the algorithm only depends on the used code, not on the number of transmission errors. To reduce the complexity of the decoding process for good transmission conditions, an alternative syndrome based decoder is presented. The reduction of complexity is realized by two different approaches, the syndrome zero sequence deactivation and the path metric equalization. The two approaches enable an easy adaptation of the decoding complexity for different transmission conditions, which results in a trade-off between decoding complexity and error correction performance.

  9. The Aster code; Code Aster

    Energy Technology Data Exchange (ETDEWEB)

    Delbecq, J.M

    1999-07-01

    The Aster code is a 2D or 3D finite-element calculation code for structures developed by the R and D direction of Electricite de France (EdF). This dossier presents a complete overview of the characteristics and uses of the Aster code: introduction of version 4; the context of Aster (organisation of the code development, versions, systems and interfaces, development tools, quality assurance, independent validation); static mechanics (linear thermo-elasticity, Euler buckling, cables, Zarka-Casier method); non-linear mechanics (materials behaviour, big deformations, specific loads, unloading and loss of load proportionality indicators, global algorithm, contact and friction); rupture mechanics (G energy restitution level, restitution level in thermo-elasto-plasticity, 3D local energy restitution level, KI and KII stress intensity factors, calculation of limit loads for structures), specific treatments (fatigue, rupture, wear, error estimation); meshes and models (mesh generation, modeling, loads and boundary conditions, links between different modeling processes, resolution of linear systems, display of results etc..); vibration mechanics (modal and harmonic analysis, dynamics with shocks, direct transient dynamics, seismic analysis and aleatory dynamics, non-linear dynamics, dynamical sub-structuring); fluid-structure interactions (internal acoustics, mass, rigidity and damping); linear and non-linear thermal analysis; steels and metal industry (structure transformations); coupled problems (internal chaining, internal thermo-hydro-mechanical coupling, chaining with other codes); products and services. (J.S.)

  10. Complete sequence and analysis of plastid genomes of two economically important red algae: Pyropia haitanensis and Pyropia yezoensis.

    Directory of Open Access Journals (Sweden)

    Li Wang

    Full Text Available Pyropia haitanensis and P. yezoensis are two economically important marine crops that are also considered to be research models to study the physiological ecology of intertidal seaweed communities, evolutionary biology of plastids, and the origins of sexual reproduction. This plastid genome information will facilitate study of breeding, population genetics and phylogenetics.We have fully sequenced using next-generation sequencing the circular plastid genomes of P. hatanensis (195,597 bp and P. yezoensis (191,975 bp, the largest of all the plastid genomes of the red lineage sequenced to date. Organization and gene contents of the two plastids were similar, with 211-213 protein-coding genes (including 29-31 unknown-function ORFs, 37 tRNA genes, and 6 ribosomal RNA genes, suggesting a largest coding capacity in the red lineage. In each genome, 14 protein genes overlapped and no interrupted genes were found, indicating a high degree of genomic condensation. Pyropia maintain an ancient gene content and conserved gene clusters in their plastid genomes, containing nearly complete repertoires of the plastid genes known in photosynthetic eukaryotes. Similarity analysis based on the whole plastid genome sequences showed the distance between P. haitanensis and P. yezoensis (0.146 was much smaller than that of Porphyra purpurea and P. haitanensis (0.250, and P. yezoensis (0.251; this supports re-grouping the two species in a resurrected genus Pyropia while maintaining P. purpurea in genus Porphyra. Phylogenetic analysis supports a sister relationship between Bangiophyceae and Florideophyceae, though precise phylogenetic relationships between multicellular red alage and chromists were not fully resolved.These results indicate that Pyropia have compact plastid genomes. Large coding capacity and long intergenic regions contribute to the size of the largest plastid genomes reported for the red lineage. Possessing the largest coding capacity and ancient gene

  11. Coding Class

    DEFF Research Database (Denmark)

    Ejsing-Duun, Stine; Hansbøl, Mikala

    Denne rapport rummer evaluering og dokumentation af Coding Class projektet1. Coding Class projektet blev igangsat i skoleåret 2016/2017 af IT-Branchen i samarbejde med en række medlemsvirksomheder, Københavns kommune, Vejle Kommune, Styrelsen for IT- og Læring (STIL) og den frivillige forening...... Coding Pirates2. Rapporten er forfattet af Docent i digitale læringsressourcer og forskningskoordinator for forsknings- og udviklingsmiljøet Digitalisering i Skolen (DiS), Mikala Hansbøl, fra Institut for Skole og Læring ved Professionshøjskolen Metropol; og Lektor i læringsteknologi, interaktionsdesign......, design tænkning og design-pædagogik, Stine Ejsing-Duun fra Forskningslab: It og Læringsdesign (ILD-LAB) ved Institut for kommunikation og psykologi, Aalborg Universitet i København. Vi har fulgt og gennemført evaluering og dokumentation af Coding Class projektet i perioden november 2016 til maj 2017...

  12. Uplink Coding

    Science.gov (United States)

    Andrews, Ken; Divsalar, Dariush; Dolinar, Sam; Moision, Bruce; Hamkins, Jon; Pollara, Fabrizio

    2007-01-01

    This slide presentation reviews the objectives, meeting goals and overall NASA goals for the NASA Data Standards Working Group. The presentation includes information on the technical progress surrounding the objective, short LDPC codes, and the general results on the Pu-Pw tradeoff.

  13. ANIMAL code

    International Nuclear Information System (INIS)

    Lindemuth, I.R.

    1979-01-01

    This report describes ANIMAL, a two-dimensional Eulerian magnetohydrodynamic computer code. ANIMAL's physical model also appears. Formulated are temporal and spatial finite-difference equations in a manner that facilitates implementation of the algorithm. Outlined are the functions of the algorithm's FORTRAN subroutines and variables

  14. Network Coding

    Indian Academy of Sciences (India)

    Home; Journals; Resonance – Journal of Science Education; Volume 15; Issue 7. Network Coding. K V Rashmi Nihar B Shah P Vijay Kumar. General Article Volume 15 Issue 7 July 2010 pp 604-621. Fulltext. Click here to view fulltext PDF. Permanent link: https://www.ias.ac.in/article/fulltext/reso/015/07/0604-0621 ...

  15. Expander Codes

    Indian Academy of Sciences (India)

    Home; Journals; Resonance – Journal of Science Education; Volume 10; Issue 1. Expander Codes - The Sipser–Spielman Construction. Priti Shankar. General Article Volume 10 ... Author Affiliations. Priti Shankar1. Department of Computer Science and Automation, Indian Institute of Science Bangalore 560 012, India.

  16. Sequence History Update Tool

    Science.gov (United States)

    Khanampompan, Teerapat; Gladden, Roy; Fisher, Forest; DelGuercio, Chris

    2008-01-01

    The Sequence History Update Tool performs Web-based sequence statistics archiving for Mars Reconnaissance Orbiter (MRO). Using a single UNIX command, the software takes advantage of sequencing conventions to automatically extract the needed statistics from multiple files. This information is then used to populate a PHP database, which is then seamlessly formatted into a dynamic Web page. This tool replaces a previous tedious and error-prone process of manually editing HTML code to construct a Web-based table. Because the tool manages all of the statistics gathering and file delivery to and from multiple data sources spread across multiple servers, there is also a considerable time and effort savings. With the use of The Sequence History Update Tool what previously took minutes is now done in less than 30 seconds, and now provides a more accurate archival record of the sequence commanding for MRO.

  17. Improving Catastrophe Modeling for Business Interruption Insurance Needs.

    Science.gov (United States)

    Rose, Adam; Huyck, Charles K

    2016-10-01

    While catastrophe (CAT) modeling of property damage is well developed, modeling of business interruption (BI) lags far behind. One reason is the crude nature of functional relationships in CAT models that translate property damage into BI. Another is that estimating BI losses is more complicated because it depends greatly on public and private decisions during recovery with respect to resilience tactics that dampen losses by using remaining resources more efficiently to maintain business function and to recover more quickly. This article proposes a framework for improving hazard loss estimation for BI insurance needs. Improved data collection that allows for analysis at the level of individual facilities within a company can improve matching the facilities with the effectiveness of individual forms of resilience, such as accessing inventories, relocating operations, and accelerating repair, and can therefore improve estimation accuracy. We then illustrate the difference this can make in a case study example of losses from a hurricane. © 2016 Society for Risk Analysis.

  18. Early results of gate valve flow interruption blowdown tests

    International Nuclear Information System (INIS)

    DeWall, K.G.

    1988-01-01

    The preliminary results of the USNRC/INEL high-energy BWR line break flow interruption testing are presented. Two representative nuclear valve assemblies were cycled under design basis Reactor Water Cleanup pipe break conditions to provide input for the technical basis for resolving the Nuclear Regulatory Commission's Generic Issue 87. The effects of the blowdown hydraulic loadings on valve operability, especially valve closure stem forces, were studied. The blowdown tests showed that, given enough thrust, typical gate valves will close against the high flow resulting from a line break. The tests also showed that proper operator sizing depends on the correct identification of values for the sizing equation. Evidence exists that values used in the past may not be conservative for all valve applications. The tests showed that improper operator lock ring installation following test or maintenance can invalidate in-situ test results and prevent the valve from performing its design function. 2 refs., 12 figs., 2 tabs

  19. Enhanced Interrupt Response Time in the nMPRA based on Embedded Real Time Microcontrollers

    Directory of Open Access Journals (Sweden)

    GAITAN, N. C.

    2017-08-01

    Full Text Available In any real-time operating system, task switching and scheduling, interrupts, synchronization and communication between processes, represent major problems. The implementation of these mechanisms through software generates significant delays for many applications. The nMPRA (Multi Pipeline Register Architecture architecture is designed for the implementation of real-time embedded microcontrollers. It supports the competitive execution of n tasks, enabling very fast switching between them, with a usual delay of one machine cycle and a maximum of 3 machine cycles, for the memory-related work instructions. This is because each task has its own PC (Program Counter, set of pipeline registers and a general registers file. The nMPRA is provided with an advanced distributed interrupt controller that implements the concept of "interrupts as threads". This allows the attachment of one or more interrupts to the same task. In this context, the original contribution of this article is to presents the solutions for improving the response time to interrupts when a task has attached a large number of interrupts. The proposed solutions enhance the original architecture for interrupts logic in order to transfer control, to the interrupt handler as soon as possible, and to create an interrupt prioritization at task level.

  20. HVDC interrupter experiments for large Magnetic Energy Transfer and Storage (METS) systems

    International Nuclear Information System (INIS)

    Swannack, C.E.; Haarman, R.A.; Lindsay, J.D.G.; Weldon, D.M.

    1975-01-01

    Proposed fusion-test reactors will require energy storage systems of hundreds of megajoules with transfer times of the order of one millisecond. The size of the energy storage submodule (and hence, the overall system cost and complexity) is directly determined by the voltage and current limits of the switch used for the energy transfer. Experiments are being conducted on high voltage dc circuit breakers as a major part of the energy storage, pulsed power program. DC circuit interruption characteristics of a commercially available ac power vacuum interrupter are discussed. Preliminary data of interruption characteristics are reported for an interrupter developed specifically to match a present METS circuit requirement

  1. Platelet count kinetics following interruption of antiretroviral treatment.

    Science.gov (United States)

    Zetterberg, Eva; Neuhaus, Jacqueline; Baker, Jason V; Somboonwit, Charurut; Llibre, Josep M; Palfreeman, Adrian; Chini, Maria; Lundgren, Jens D

    2013-01-02

    To investigate the mechanisms of platelet kinetics in the Strategies for Management of Antiretroviral Therapy (SMART) study that demonstrated excess mortality with CD4 guided episodic antiretroviral therapy (ART) drug conservation compared with continuous treatment viral suppression. Follow-up analyses of stored plasma samples demonstrated increased activation of both inflammatory and coagulation pathways after stopping ART. SMART patients from sites that determined platelets routinely. Platelet counts were retrospectively collected from 2206 patients from visits at study entry, and during follow-up. D-dimer levels were measured at study entry, month 1, and 2. Platelet levels decreased in the drug conservation group following randomization, but remained stable in the viral suppression group [median (IQR) decline from study entry to month 4: -24 000/μl (-54 000 to 4000) vs. 3000 (-22 000 to 24 000), respectively, P conservation vs. the viral suppression arm (unadjusted drug conservation/viral suppression [HR (95%CI) = 1.8 (1.2-2.7)]. The decline in platelet count among drug conservation participants on fully suppressive ART correlated with the rise in D-dimer from study entry to either month 1 or 2 (r = -0.41; P = 0.02). Among drug conservation participants who resumed ART 74% recovered to their study entry platelet levels. Interrupting ART increases the risk of thrombocytopenia, but reinitiation of ART typically reverses it. Factors contributing to declines in platelets after interrupting ART may include activation of coagulation pathways or HIV-1 replication itself. The contribution of platelets in HIV-related procoagulant activity requires further study.

  2. Coding chaotic billiards. Pt. 3

    International Nuclear Information System (INIS)

    Ullmo, D.; Giannoni, M.J.

    1993-01-01

    Non-tiling compact billiard defined on the pseudosphere is studied 'a la Morse coding'. As for most bounded systems, the coding is non exact. However, two sets of approximate grammar rules can be obtained, one specifying forbidden codes, and the other allowed ones. In-between some sequences remain in the 'unknown' zone, but their relative amount can be reduced to zero if one lets the length of the approximate grammar rules goes to infinity. The relationship between these approximate grammar rules and the 'pruning front' introduced by Cvitanovic et al. is discussed. (authors). 13 refs., 10 figs., 1 tab

  3. Linear network error correction coding

    CERN Document Server

    Guang, Xuan

    2014-01-01

    There are two main approaches in the theory of network error correction coding. In this SpringerBrief, the authors summarize some of the most important contributions following the classic approach, which represents messages by sequences?similar to algebraic coding,?and also briefly discuss the main results following the?other approach,?that uses the theory of rank metric codes for network error correction of representing messages by subspaces. This book starts by establishing the basic linear network error correction (LNEC) model and then characterizes two equivalent descriptions. Distances an

  4. Panda code

    International Nuclear Information System (INIS)

    Altomare, S.; Minton, G.

    1975-02-01

    PANDA is a new two-group one-dimensional (slab/cylinder) neutron diffusion code designed to replace and extend the FAB series. PANDA allows for the nonlinear effects of xenon, enthalpy and Doppler. Fuel depletion is allowed. PANDA has a completely general search facility which will seek criticality, maximize reactivity, or minimize peaking. Any single parameter may be varied in a search. PANDA is written in FORTRAN IV, and as such is nearly machine independent. However, PANDA has been written with the present limitations of the Westinghouse CDC-6600 system in mind. Most computation loops are very short, and the code is less than half the useful 6600 memory size so that two jobs can reside in the core at once. (auth)

  5. CANAL code

    International Nuclear Information System (INIS)

    Gara, P.; Martin, E.

    1983-01-01

    The CANAL code presented here optimizes a realistic iron free extraction channel which has to provide a given transversal magnetic field law in the median plane: the current bars may be curved, have finite lengths and cooling ducts and move in a restricted transversal area; terminal connectors may be added, images of the bars in pole pieces may be included. A special option optimizes a real set of circular coils [fr

  6. A work observation study of nuclear medicine technologists: interruptions, resilience and implications for patient safety.

    Science.gov (United States)

    Larcos, George; Prgomet, Mirela; Georgiou, Andrew; Westbrook, Johanna

    2017-06-01

    Errors by nuclear medicine technologists during the preparation of radiopharmaceuticals or at other times can cause patient harm and may reflect the impact of interruptions, busy work environments and deficient systems or processes. We aimed to: (a) characterise the rate and nature of interruptions technologists experience and (b) identify strategies that support safety. We performed 100 hours of observation of 11 technologists at a major public hospital and measured the proportions of time spent in eight categories of work tasks, location of task, interruption rate and type and multitasking (tasks conducted in parallel). We catalogued specific safety-oriented strategies used by technologists. Technologists completed 5227 tasks and experienced 569 interruptions (mean, 4.5 times per hour; 95% CI 4.1 to 4.9). The highest interruption rate occurred when technologists were in transit between rooms (10.3 per hour (95% CI 8.3 to 12.5)). Interruptions during radiopharmaceutical preparation occurred a mean of 4.4 times per hour (95% CI 3.3 to 5.6). Most (n=426) tasks were interrupted once only and all tasks were resumed after interruption. Multitasking occurred 16.6% of the time. At least some interruptions were initiated by other technologists to convey important information and/or to render assistance. Technologists employed a variety of verbal and non-verbal strategies in all work areas (notably in the hot-lab) to minimise the impact of interruptions and optimise the safe conduct of procedures. Although most were due to individual choices, some strategies reflected overt or subliminal departmental policy. Some interruptions appear beneficial. Technologists' self-initiated strategies to support safe work practices appear to be an important element in supporting a resilient work environment in nuclear medicine. Published by the BMJ Publishing Group Limited. For permission to use (where not already granted under a licence) please go to http://www.bmj.com/company/products-services/rights-and-licensing/.

  7. Implementation of LT codes based on chaos

    International Nuclear Information System (INIS)

    Zhou Qian; Li Liang; Chen Zengqiang; Zhao Jiaxiang

    2008-01-01

    Fountain codes provide an efficient way to transfer information over erasure channels like the Internet. LT codes are the first codes fully realizing the digital fountain concept. They are asymptotically optimal rateless erasure codes with highly efficient encoding and decoding algorithms. In theory, for each encoding symbol of LT codes, its degree is randomly chosen according to a predetermined degree distribution, and its neighbours used to generate that encoding symbol are chosen uniformly at random. Practical implementation of LT codes usually realizes the randomness through pseudo-randomness number generator like linear congruential method. This paper applies the pseudo-randomness of chaotic sequence in the implementation of LT codes. Two Kent chaotic maps are used to determine the degree and neighbour(s) of each encoding symbol. It is shown that the implemented LT codes based on chaos perform better than the LT codes implemented by the traditional pseudo-randomness number generator. (general)

  8. Real time interrupt handling using FORTRAN IV plus under RSX-11M

    International Nuclear Information System (INIS)

    Schultz, D.E.

    1981-01-01

    A real-time data acquisition application for a linear accelerator is described. The important programming features of this application are use of connect to interrupt, a shared library, map to I/O page, and a shared data area. How you can provide rapid interrupt handling using these tools from FORTRAN IV PLUS is explained

  9. INFLUENCE OF INTERRUPTED PULMONARY LYMPH-DRAINAGE ON ANTIBODY-RESPONSES IN HILAR-STRIPPED LUNGS

    NARCIS (Netherlands)

    WANG, FZ; WINTER, JB; WILDEVUUR, CRH; PROP, J

    1992-01-01

    Lung transplantation interrupts hilar lymphatics. This may have an impact on immune responses to antigens entering the lung because the antigens cannot reach the lung-associated lymph nodes where the immune response is generated. We investigated the interruption and regeneration of lymphatics and

  10. Trend of Antiretroviral therapy interruption in a clinic cohort of HIV ...

    African Journals Online (AJOL)

    Over subsequent years with increasing expertise coupled with more patient education and public awareness it is expected that these interruptions would decline. We therefore determined the trend in ART interruptions in a clinic cohort of HIV-1 infected children attending the Jos University Teaching Hospital (JUTH).

  11. Combining social strategies and workload: a new design to reduce the negative effects of task interruptions

    NARCIS (Netherlands)

    de Vries, R.A.J.; Lohse, M.; Winterboer, Andi; Groen, Frans C.A.; Evers, Vanessa

    2013-01-01

    Being interrupted by notifications and reminders is common while working. In this study we consider whether system politeness reduces (negative) effects of being interrupted by system requests. We carried out a 2 (polite vs. neutral system request) x 2 (high vs. low mental load) between-participants

  12. Changes in lipids and lipoprotein particle concentrations after interruption of antiretroviral therapy

    DEFF Research Database (Denmark)

    Lampe, Fiona C; Duprez, Daniel A; Kuller, Lewis H

    2010-01-01

    The effect of interruption of antiretroviral therapy (ART) on lipoprotein particle subclasses has not been studied. We examined short-term changes in lipids and lipoprotein particles among 332 HIV-infected individuals randomized to interrupt or continue ART in the "Strategies for Management...

  13. 77 FR 26579 - Certain Ground Fault Circuit Interrupters and Products Containing Same; Notice of Final...

    Science.gov (United States)

    2012-05-04

    ... INTERNATIONAL TRADE COMMISSION [Investigation No. 337-TA-739] Certain Ground Fault Circuit... importation of certain ground fault circuit interrupters and products containing the same by reason of... entry of ground fault circuit interrupters and products containing the same that infringe one or more of...

  14. 77 FR 66080 - Certain Ground Fault Circuit Interrupters and Products Containing Same

    Science.gov (United States)

    2012-11-01

    ... INTERNATIONAL TRADE COMMISSION [Investigation No. 337-TA-739] Certain Ground Fault Circuit... States after importation of certain ground fault circuit interrupters and products containing the same by... issued a general exclusion order barring entry of ground fault circuit interrupters that infringe the...

  15. 76 FR 35014 - Certain Ground Fault Circuit Interrupters and Products Containing Same; Notice of Commission...

    Science.gov (United States)

    2011-06-15

    ... INTERNATIONAL TRADE COMMISSION [Investigation No. 337-TA-739] Certain Ground Fault Circuit Interrupters and Products Containing Same; Notice of Commission Determination Not To Review an Initial... fault circuit interrupters and products containing the same by reason of infringement of various claims...

  16. Protection of spermatogenisis during X-irradiation and chemotherapy by temporary blood flow interruption

    International Nuclear Information System (INIS)

    Vliet, J. van.

    1989-01-01

    In an animal model the possibility was tested to interrupt the blood flow to the testis temporarily and repeatedly. Subsequently, it was investigated whether blood flow interuption during irradiation or during cytostatic drug administration could limit the damage induced to the spermatogonial stem cells. The effect of repeatedly blood flow interruptions on spermatogenesis was evaluated. (author). 192 refs.; 15 figs.; 11 tabs

  17. Detecting non-coding selective pressure in coding regions

    Directory of Open Access Journals (Sweden)

    Blanchette Mathieu

    2007-02-01

    Full Text Available Abstract Background Comparative genomics approaches, where orthologous DNA regions are compared and inter-species conserved regions are identified, have proven extremely powerful for identifying non-coding regulatory regions located in intergenic or intronic regions. However, non-coding functional elements can also be located within coding region, as is common for exonic splicing enhancers, some transcription factor binding sites, and RNA secondary structure elements affecting mRNA stability, localization, or translation. Since these functional elements are located in regions that are themselves highly conserved because they are coding for a protein, they generally escaped detection by comparative genomics approaches. Results We introduce a comparative genomics approach for detecting non-coding functional elements located within coding regions. Codon evolution is modeled as a mixture of codon substitution models, where each component of the mixture describes the evolution of codons under a specific type of coding selective pressure. We show how to compute the posterior distribution of the entropy and parsimony scores under this null model of codon evolution. The method is applied to a set of growth hormone 1 orthologous mRNA sequences and a known exonic splicing elements is detected. The analysis of a set of CORTBP2 orthologous genes reveals a region of several hundred base pairs under strong non-coding selective pressure whose function remains unknown. Conclusion Non-coding functional elements, in particular those involved in post-transcriptional regulation, are likely to be much more prevalent than is currently known. With the numerous genome sequencing projects underway, comparative genomics approaches like that proposed here are likely to become increasingly powerful at detecting such elements.

  18. Anticipating Interruptions. Security and risk in a liberalized electricity infrastructure

    Energy Technology Data Exchange (ETDEWEB)

    Silvast, A.

    2013-11-01

    During the past ten years, a number of social scientists have emphasized the importance of material infrastructures like electricity supply as a research topic for the social sciences. The developing of such new perspectives concerning infrastructures also includes uncertainties and risks. This research analyzes the management of uncertainties in the Finnish electricity infrastructure by posing the following research question: how are electricity interruptions, or blackouts, anticipated in Finland and how are these interruptions managed as risks? The main research methodology of the work is multi-sited field work. The empirical materials include interviews with experts and lay people (33 interviews); participant observation in two electricity control rooms; an electricity consumer survey (115 respondents); and also a number of infrastructure and security policy documents and observations from electricity security seminars. The materials were primarily gathered between 2004 and 2008. Social science research often links risks with major current social changes or socio-cultural risk perceptions. In recent international social science discussions, however, a new research topic has emerged - those styles of reasoning and techniques of governance that are deployed to manage risk as a practical matter. My study explores these themes empirically by focusing on the specific habitual practices of risk management in the Finnish electricity infrastructure. The work develops various also semi-ethnographic inquiries into infrastructure risk techniques like monitor screening of real-time risks in electricity control rooms; the management of risks in a liberalized electricity market; the emergence of Finnish reasoning about blackouts from a specific historical background; and the ways in which electricity consumers respond to blackouts in their homes. In addition, the work reflects upon the position of a risk researcher in those situations when the research subjects do not define

  19. Interruption of Electrical Conductivity of Titanium Dental Implants Suggests a Path Towards Elimination Of Corrosion.

    Science.gov (United States)

    Pozhitkov, Alex E; Daubert, Diane; Brochwicz Donimirski, Ashley; Goodgion, Douglas; Vagin, Mikhail Y; Leroux, Brian G; Hunter, Colby M; Flemmig, Thomas F; Noble, Peter A; Bryers, James D

    2015-01-01

    Peri-implantitis is an inflammatory disease that results in the destruction of soft tissue and bone around the implant. Titanium implant corrosion has been attributed to the implant failure and cytotoxic effects to the alveolar bone. We have documented the extent of titanium release into surrounding plaque in patients with and without peri-implantitis. An in vitro model was designed to represent the actual environment of an implant in a patient's mouth. The model uses actual oral microbiota from a volunteer, allows monitoring electrochemical processes generated by biofilms growing on implants and permits control of biocorrosion electrical current. As determined by next generation DNA sequencing, microbial compositions in experiments with the in vitro model were comparable with the compositions found in patients with implants. It was determined that the electrical conductivity of titanium implants was the key factor responsible for the biocorrosion process. The interruption of the biocorrosion current resulted in a 4-5 fold reduction of corrosion. We propose a new design of dental implant that combines titanium in zero oxidation state for osseointegration and strength, interlaid with a nonconductive ceramic. In addition, we propose electrotherapy for manipulation of microbial biofilms and to induce bone healing in peri-implantitis patients.

  20. Interruption of Electrical Conductivity of Titanium Dental Implants Suggests a Path Towards Elimination Of Corrosion.

    Directory of Open Access Journals (Sweden)

    Alex E Pozhitkov

    Full Text Available Peri-implantitis is an inflammatory disease that results in the destruction of soft tissue and bone around the implant. Titanium implant corrosion has been attributed to the implant failure and cytotoxic effects to the alveolar bone. We have documented the extent of titanium release into surrounding plaque in patients with and without peri-implantitis. An in vitro model was designed to represent the actual environment of an implant in a patient's mouth. The model uses actual oral microbiota from a volunteer, allows monitoring electrochemical processes generated by biofilms growing on implants and permits control of biocorrosion electrical current. As determined by next generation DNA sequencing, microbial compositions in experiments with the in vitro model were comparable with the compositions found in patients with implants. It was determined that the electrical conductivity of titanium implants was the key factor responsible for the biocorrosion process. The interruption of the biocorrosion current resulted in a 4-5 fold reduction of corrosion. We propose a new design of dental implant that combines titanium in zero oxidation state for osseointegration and strength, interlaid with a nonconductive ceramic. In addition, we propose electrotherapy for manipulation of microbial biofilms and to induce bone healing in peri-implantitis patients.

  1. Syntactic processing in music and language: Effects of interrupting auditory streams with alternating timbres.

    Science.gov (United States)

    Fiveash, Anna; Thompson, William Forde; Badcock, Nicholas A; McArthur, Genevieve

    2018-07-01

    Music and language both rely on the processing of spectral (pitch, timbre) and temporal (rhythm) information to create structure and meaning from incoming auditory streams. Behavioral results have shown that interrupting a melodic stream with unexpected changes in timbre leads to reduced syntactic processing. Such findings suggest that syntactic processing is conditional on successful streaming of incoming sequential information. The current study used event-related potentials (ERPs) to investigate whether (1) the effect of alternating timbres on syntactic processing is reflected in a reduced brain response to syntactic violations, and (2) the phenomenon is similar for music and language. Participants listened to melodies and sentences with either one timbre (piano or one voice) or three timbres (piano, guitar, and vibraphone, or three different voices). Half the stimuli contained syntactic violations: an out-of-key note in the melodies, and a phrase-structure violation in the sentences. We found smaller ERPs to syntactic violations in music in the three-timbre compared to the one-timbre condition, reflected in a reduced early right anterior negativity (ERAN). A similar but non-significant pattern was observed for language stimuli in both the early left anterior negativity (ELAN) and the left anterior negativity (LAN) ERPs. The results suggest that disruptions to auditory streaming may interfere with syntactic processing, especially for melodic sequences. Copyright © 2018 Elsevier B.V. All rights reserved.

  2. Two-dimensional electron density characterisation of arc interruption phenomenon in current-zero phase

    Science.gov (United States)

    Inada, Yuki; Kamiya, Tomoki; Matsuoka, Shigeyasu; Kumada, Akiko; Ikeda, Hisatoshi; Hidaka, Kunihiko

    2018-01-01

    Two-dimensional electron density imaging over free burning SF6 arcs and SF6 gas-blast arcs was conducted at current zero using highly sensitive Shack-Hartmann type laser wavefront sensors in order to experimentally characterise electron density distributions for the success and failure of arc interruption in the thermal reignition phase. The experimental results under an interruption probability of 50% showed that free burning SF6 arcs with axially asymmetric electron density profiles were interrupted with a success rate of 88%. On the other hand, the current interruption of SF6 gas-blast arcs was reproducibly achieved under locally reduced electron densities and the interruption success rate was 100%.

  3. Yeast genome sequencing:

    DEFF Research Database (Denmark)

    Piskur, Jure; Langkjær, Rikke Breinhold

    2004-01-01

    For decades, unicellular yeasts have been general models to help understand the eukaryotic cell and also our own biology. Recently, over a dozen yeast genomes have been sequenced, providing the basis to resolve several complex biological questions. Analysis of the novel sequence data has shown...... of closely related species helps in gene annotation and to answer how many genes there really are within the genomes. Analysis of non-coding regions among closely related species has provided an example of how to determine novel gene regulatory sequences, which were previously difficult to analyse because...... they are short and degenerate and occupy different positions. Comparative genomics helps to understand the origin of yeasts and points out crucial molecular events in yeast evolutionary history, such as whole-genome duplication and horizontal gene transfer(s). In addition, the accumulating sequence data provide...

  4. From concatenated codes to graph codes

    DEFF Research Database (Denmark)

    Justesen, Jørn; Høholdt, Tom

    2004-01-01

    We consider codes based on simple bipartite expander graphs. These codes may be seen as the first step leading from product type concatenated codes to more complex graph codes. We emphasize constructions of specific codes of realistic lengths, and study the details of decoding by message passing...

  5. Interrupting poliovirus transmission -- new solutions to an old problem.

    Science.gov (United States)

    Aylward, R Bruce; Maher, Chris

    2006-06-01

    Since the launch of the Global Polio Eradication Initiative (GPEI) in 1988, knowledge as to the nature of circulating polioviruses and the challenges to their interruption has increased tremendously, particularly during the period 2000-2005. By January 2006, however, the systematic application of the standard polio eradication strategies, combined with recent refinements, had reduced the number of countries with ongoing transmission of indigenous wild polioviruses to just four (Nigeria, India, Pakistan, and Afghanistan), the lowest ever in history. In addition, only 8 of the 22 areas that had been re-infected by wild poliovirus in 2003-2005 still required large-scale 'mop-up' activities and circulating vaccine-derived poliovirus (cVDPV) outbreaks were being readily addressed. This progress, despite new challenges late in the GPEI, was greatly facilitated by a range of solutions that included two new monovalent oral polio vaccines (mOPVs), new and robust international standards for polio outbreak response, and renewed political commitment across the remaining infected countries.

  6. [The utility of the interrupter technique in pediatric asthma].

    Science.gov (United States)

    Iimura, Akiko; Yoshihara, Shigemi; Arisaka, Osamu

    2002-11-01

    Interrupter respiratory resistance (Rint) is a new lung function test for measuring airway resistance. We investigated the utility of the Rint lung function test in pediatric patients with asthma. Thirty seven asthmatic patients with mild or moderate asthma attack (asthma group) and 9 healthy children (control group) were enrolled in the study, and the utility of the Ring test was compared with that of the PEF lung function test. Rint and PEF were measured after the inhalation of saline or beta(2) stimulant, and the values for the asthma and control groups were compared. The rint and PEF values did not change after the inhalation of saline, but both values improved after the inhalation of beta(2) stimulant in the asthma group. In the control group, the PEF and Rint values measured after saline or beta(2) stimulant were not significantly different. Rint measurements may be more useful than PEF tests for evaluating therapeutic responses to mild asthma attacks in children. These findings suggest that Rint is a useful respiratory function test for evaluating children with asthma.

  7. Interrupted time-series analysis: studying trends in neurosurgery.

    Science.gov (United States)

    Wong, Ricky H; Smieliauskas, Fabrice; Pan, I-Wen; Lam, Sandi K

    2015-12-01

    OBJECT Neurosurgery studies traditionally have evaluated the effects of interventions on health care outcomes by studying overall changes in measured outcomes over time. Yet, this type of linear analysis is limited due to lack of consideration of the trend's effects both pre- and postintervention and the potential for confounding influences. The aim of this study was to illustrate interrupted time-series analysis (ITSA) as applied to an example in the neurosurgical literature and highlight ITSA's potential for future applications. METHODS The methods used in previous neurosurgical studies were analyzed and then compared with the methodology of ITSA. RESULTS The ITSA method was identified in the neurosurgical literature as an important technique for isolating the effect of an intervention (such as a policy change or a quality and safety initiative) on a health outcome independent of other factors driving trends in the outcome. The authors determined that ITSA allows for analysis of the intervention's immediate impact on outcome level and on subsequent trends and enables a more careful measure of the causal effects of interventions on health care outcomes. CONCLUSIONS ITSA represents a significant improvement over traditional observational study designs in quantifying the impact of an intervention. ITSA is a useful statistical procedure to understand, consider, and implement as the field of neurosurgery evolves in sophistication in big-data analytics, economics, and health services research.

  8. Interruption of Onchocerca volvulus transmission in Northern Venezuela.

    Science.gov (United States)

    Convit, Jacinto; Schuler, Harland; Borges, Rafael; Olivero, Vimerca; Domínguez-Vázquez, Alfredo; Frontado, Hortencia; Grillet, María E

    2013-10-07

    Onchocerciasis is caused by Onchocerca volvulus and transmitted by Simulium species (black flies). In the Americas, the infection has been previously described in 13 discrete regional foci distributed among six countries (Brazil, Colombia, Ecuador, Guatemala, Mexico and Venezuela) where more than 370,000 people are currently considered at risk. Since 2001, disease control in Venezuela has relied on the mass drug administration to the at-risk communities. This report provides empirical evidence of interruption of Onchocerca volvulus transmission by Simulium metallicum in 510 endemic communities from two Northern foci of Venezuela, after 10-12 years of 6-monthly Mectizan (ivermectin) treatment to all the eligible residents. In-depth entomologic and epidemiologic surveys were serially conducted from 2001-2012 in selected (sentinel and extra-sentinel) communities from the North-central (NC) and North-east (NE) onchocerciasis foci of Venezuela in order to monitor the impact of ivermectin treatment. From 2007-2009, entomological indicators in both foci confirmed that 0 out of 112,637 S. metallicum females examined by PCR contained L3 infection in insect heads. The upper bound of the 95% confidence intervals of the infective rate of the vector reached values below 1% by 2009 (NC) and 2012 (NE). Additionally, after 14 (NC) and 22 (NE) rounds of treatment, the seasonal transmission potential (±UL CIs) of S. metallicum was under the critical threshold of 20 L3 per person per season. Serological analysis in school children Venezuela.

  9. Gonadotrophic status in adolescents with pituitary stalk interruption syndrome.

    Science.gov (United States)

    Rottembourg, Diane; Linglart, Agnès; Adamsbaum, Catherine; Lahlou, Najiba; Teinturier, Cécile; Bougnères, Pierre; Carel, Jean-Claude

    2008-07-01

    Pituitary stalk interruption syndrome (PSIS) is a frequent cause of GH deficiency (GHD) and is commonly associated with other PH deficiencies (PHDs). Although previous reports have correlated multiple PHDs with severe anatomical lesions, the status of the gonadotrophic axis has not yet been thoroughly analysed. We retrospectively reviewed the medical records of 27 patients (15 males, 12 females) with GHD and PSIS defined by MRI findings. The status of the gonadotrophic axis was evaluated in children who were at least 14.5 years (boys) or 13 years (girls). Out of 27 patients, five displayed spontaneous full pubertal development with normal hormonal values at the final evaluation, whereas 22 of 27 patients (81%) had complete (n = 18) or partial pubertal deficiency. Three girls had primary amenorrhoea with normal gonadotrophin values, raising the possibility of subtle disturbances of gonadotrophin pulsatility. Of the 21 patients with TSH or ACTH deficiency, 17 (81%) had complete gonadotrophin deficiency. Two of our six patients with apparently isolated GHD during childhood had gonadotrophin deficiency. Cryptorchidism was present at birth in six boys (40%). Of these six boys, one had normal pubertal development. Ten of 11 boys with micropenis at birth had gonadotrophin deficiency. Gonadotrophin deficiency is a common finding in adolescents with PSIS and is frequently associated with other PHDs. However its severity is variable, ranging from complete gonadotrophin deficiency to normogonadotrophic amenorrhoea. The occurrence of gonadotrophin deficiency in 33% of children with apparently isolated GHD and PSIS has important implications for the counselling and follow-up of these patients.

  10. Smartphone addiction, daily interruptions and self-reported productivity

    Directory of Open Access Journals (Sweden)

    Éilish Duke

    2017-12-01

    Full Text Available The advent of the smartphone has dramatically altered how we communicate, navigate, work and entertain ourselves. While the advantages of this new technology are clear, constant use may also bring negative consequences, such as a loss of productivity due to interruptions in work life. A link between smartphone overuse and loss of productivity has often been hypothesized, but empirical evidence on this question is scarce. The present study addressed this question by collecting self-report data from N=262 participants, assessing private and work-related smartphone use, smartphone addiction and self-rated productivity. Our results indicate a moderate relationship between smartphone addiction and a self-reported decrease in productivity due to spending time on the smartphone during work, as well as with the number of work hours lost to smartphone use. Smartphone addiction was also related to a greater amount of leisure time spent on the smartphone and was strongly related to a negative impact of smartphone use on daily non-work related activities. These data support the idea that tendencies towards smartphone addiction and overt checking of the smartphone could result in less productivity both in the workplace and at home. Results are discussed in relation to productivity and technostress.

  11. Smartphone addiction, daily interruptions and self-reported productivity.

    Science.gov (United States)

    Duke, Éilish; Montag, Christian

    2017-12-01

    The advent of the smartphone has dramatically altered how we communicate, navigate, work and entertain ourselves. While the advantages of this new technology are clear, constant use may also bring negative consequences, such as a loss of productivity due to interruptions in work life. A link between smartphone overuse and loss of productivity has often been hypothesized, but empirical evidence on this question is scarce. The present study addressed this question by collecting self-report data from N  = 262 participants, assessing private and work-related smartphone use, smartphone addiction and self-rated productivity. Our results indicate a moderate relationship between smartphone addiction and a self-reported decrease in productivity due to spending time on the smartphone during work, as well as with the number of work hours lost to smartphone use. Smartphone addiction was also related to a greater amount of leisure time spent on the smartphone and was strongly related to a negative impact of smartphone use on daily non-work related activities. These data support the idea that tendencies towards smartphone addiction and overt checking of the smartphone could result in less productivity both in the workplace and at home. Results are discussed in relation to productivity and technostress.

  12. Roads, interrupted dispersal, and genetic diversity in timber rattlesnakes.

    Science.gov (United States)

    Clark, Rulon W; Brown, William S; Stechert, Randy; Zamudio, Kelly R

    2010-08-01

    Anthropogenic habitat modification often creates barriers to animal movement, transforming formerly contiguous habitat into a patchwork of habitat islands with low connectivity. Roadways are a feature of most landscapes that can act as barriers or filters to migration among local populations. Even small and recently constructed roads can have a significant impact on population genetic structure of some species, but not others. We developed a research approach that combines fine-scale molecular genetics with behavioral and ecological data to understand the impacts of roads on population structure and connectivity. We used microsatellite markers to characterize genetic variation within and among populations of timber rattlesnakes (Crotalus horridus) occupying communal hibernacula (dens) in regions bisected by roadways. We examined the impact of roads on seasonal migration, genetic diversity, and gene flow among populations. Snakes in hibernacula isolated by roads had significantly lower genetic diversity and higher genetic differentiation than snakes in hibernacula in contiguous habitat. Genetic-assignment analyses revealed that interruption to seasonal migration was the mechanism underlying these patterns. Our results underscore the sizeable impact of roads on this species, despite their relatively recent construction at our study sites (7 to 10 generations of rattlesnakes), the utility of population genetics for studies of road ecology, and the need for mitigating effects of roads.

  13. Interface requirements to couple thermal hydraulics codes to severe accident codes: ICARE/CATHARE

    Energy Technology Data Exchange (ETDEWEB)

    Camous, F.; Jacq, F.; Chatelard, P. [IPSN/DRS/SEMAR CE-Cadarache, St Paul Lez Durance (France)] [and others

    1997-07-01

    In order to describe with the same code the whole sequence of severe LWR accidents, up to the vessel failure, the Institute of Protection and Nuclear Safety has performed a coupling of the severe accident code ICARE2 to the thermalhydraulics code CATHARE2. The resulting code, ICARE/CATHARE, is designed to be as pertinent as possible in all the phases of the accident. This paper is mainly devoted to the description of the ICARE2-CATHARE2 coupling.

  14. Noncoding sequence classification based on wavelet transform analysis: part I

    Science.gov (United States)

    Paredes, O.; Strojnik, M.; Romo-Vázquez, R.; Vélez Pérez, H.; Ranta, R.; Garcia-Torales, G.; Scholl, M. K.; Morales, J. A.

    2017-09-01

    DNA sequences in human genome can be divided into the coding and noncoding ones. Coding sequences are those that are read during the transcription. The identification of coding sequences has been widely reported in literature due to its much-studied periodicity. Noncoding sequences represent the majority of the human genome. They play an important role in gene regulation and differentiation among the cells. However, noncoding sequences do not exhibit periodicities that correlate to their functions. The ENCODE (Encyclopedia of DNA elements) and Epigenomic Roadmap Project projects have cataloged the human noncoding sequences into specific functions. We study characteristics of noncoding sequences with wavelet analysis of genomic signals.

  15. Accident sequence quantification with KIRAP

    International Nuclear Information System (INIS)

    Kim, Tae Un; Han, Sang Hoon; Kim, Kil You; Yang, Jun Eon; Jeong, Won Dae; Chang, Seung Cheol; Sung, Tae Yong; Kang, Dae Il; Park, Jin Hee; Lee, Yoon Hwan; Hwang, Mi Jeong.

    1997-01-01

    The tasks of probabilistic safety assessment(PSA) consists of the identification of initiating events, the construction of event tree for each initiating event, construction of fault trees for event tree logics, the analysis of reliability data and finally the accident sequence quantification. In the PSA, the accident sequence quantification is to calculate the core damage frequency, importance analysis and uncertainty analysis. Accident sequence quantification requires to understand the whole model of the PSA because it has to combine all event tree and fault tree models, and requires the excellent computer code because it takes long computation time. Advanced Research Group of Korea Atomic Energy Research Institute(KAERI) has developed PSA workstation KIRAP(Korea Integrated Reliability Analysis Code Package) for the PSA work. This report describes the procedures to perform accident sequence quantification, the method to use KIRAP's cut set generator, and method to perform the accident sequence quantification with KIRAP. (author). 6 refs

  16. Accident sequence quantification with KIRAP

    Energy Technology Data Exchange (ETDEWEB)

    Kim, Tae Un; Han, Sang Hoon; Kim, Kil You; Yang, Jun Eon; Jeong, Won Dae; Chang, Seung Cheol; Sung, Tae Yong; Kang, Dae Il; Park, Jin Hee; Lee, Yoon Hwan; Hwang, Mi Jeong

    1997-01-01

    The tasks of probabilistic safety assessment(PSA) consists of the identification of initiating events, the construction of event tree for each initiating event, construction of fault trees for event tree logics, the analysis of reliability data and finally the accident sequence quantification. In the PSA, the accident sequence quantification is to calculate the core damage frequency, importance analysis and uncertainty analysis. Accident sequence quantification requires to understand the whole model of the PSA because it has to combine all event tree and fault tree models, and requires the excellent computer code because it takes long computation time. Advanced Research Group of Korea Atomic Energy Research Institute(KAERI) has developed PSA workstation KIRAP(Korea Integrated Reliability Analysis Code Package) for the PSA work. This report describes the procedures to perform accident sequence quantification, the method to use KIRAP`s cut set generator, and method to perform the accident sequence quantification with KIRAP. (author). 6 refs.

  17. Identifying biological pathway interrupting toxins using multi-tree ensembles

    Directory of Open Access Journals (Sweden)

    Gergo Barta

    2016-08-01

    Full Text Available The pharmaceutical industry constantly seeks new ways to improve current methods that scientists use to evaluate environmental chemicals and develop new medicines. Various automated steps are involved in the process as testing hundreds of thousands of chemicals manually would be infeasible. Our research effort and the Toxicology in the 21st Century Data Challenge focused on cost-effective automation of toxicological testing, a chemical substance screening process looking for possible toxic effects caused by interrupting biological pathways. The computational models we propose in this paper successfully combine various publicly available substance fingerprinting tools with advanced machine learning techniques. In our paper, we explore the significance and utility of assorted feature selection methods as the structural analyzers generate a plethora of features for each substance. Machine learning models were carefully selected and evaluated based on their capability to cope with the high-dimensional high-variety data with multi-tree ensemble methods coming out on top. Techniques like Random forests and Extra trees combine numerous simple tree models and proved to produce reliable predictions on toxic activity while being nearly non-parametric and insensitive to dimensionality extremes. The Tox21 Data Challenge contest offered a great platform to compare a wide range of solutions in a controlled and orderly manner. The results clearly demonstrate that the generic approach presented in this paper is comparable to advanced deep learning and domain-specific solutions. Even surpassing the competition in some nuclear receptor signaling and stress pathway assays and achieving an accuracy of up to 94 percent.

  18. Preliminary observations of gate valve flow interruption tests, Phase 2

    International Nuclear Information System (INIS)

    Steele, R. Jr.; DeWall, K.G.

    1990-01-01

    This paper presents preliminary observations from the US Nuclear Regulatory Commission/Idaho National Engineering Laboratory Flexible Wedge Gate Valve Qualification and Flow Interruption Test Program, Phase 2. The program investigated the ability of selected boiling water reactor (BWR) process line valves to perform their containment isolation function at high energy pipe break conditions and other more normal flow conditions. The fluid and valve operating responses were measured to provide information concerning valve and operator performance at various valve loadings so that the information could be used to assess typical nuclear industry motor operator sizing equations. Six valves were tested, three 6-in. isolation valves representative of those used in reactor water cleanup systems in BWRs and three 10-in. isolation valves representative of those used in BWR high pressure coolant injection (HPCI) steam lines. The concern with these normally open isolation valves is whether they will close in the event of a downstream pipe break outside of containment. The results of this testing will provide part of the technical insights for NRC efforts regarding Generic Issue 87 (GI-87), Failure of the HPCI Steam Line Without Isolation, which includes concerns about the uncertainties in gate valve motor operator sizing and torque switch settings for these BWR containment isolation valves. As of this writing, the Phase 2 test program has just been completed. Preliminary observations made in the field confirmed most of the results from the Phase 1 test program. All six valves closing in high energy water, high energy steam, and high pressure cold water require more force to close than would be calculated using the typical variables in the standard industry motor operator sizing equations

  19. Self Cleaning HEPA Filtration without Interrupting Process Flow

    International Nuclear Information System (INIS)

    Wylde, M.

    2009-01-01

    The strategy of protecting the traditional glass fibre HEPA filtration train from it's blinding contamination and the recovery of dust by the means of self cleaning, pre-filtration is a proven means in the reduction of ultimate disposal volumes and has been used within the Fuel Production Industry. However, there is an increasing demand in nuclear applications requiring elevated operating temperatures, fire resistance, moisture resistance and chemical composition that the existing glass fibre HEPA filtration cannot accommodate, which can be remedied by the use of a metallic HEPA filter media. Previous research (Bergman et al 1997, Moore et al 1992) suggests that the then costs to the DOE, based on a five year life cycle, was $29.5 million for the installation, testing, removal and disposal of glass fibre HEPA filtration trains. Within these costs, $300 was the value given to the filter and $4,450 was given to the peripheral activity. Development of a low cost, cleanable, metallic, direct replacement of the traditional filter train will the clear solution. The Bergman et al work has suggested that a 1000 ft 3 /min, cleanable, stainless HEPA could be commercially available for $5,000 each, whereas the industry has determined that the truer cost of such an item in isolation would be closer to $15,000. This results in a conflict within the requirement between 'low cost' and 'stainless HEPA'. By proposing a system that combines metallic HEPA filtration with the ability to self clean without interrupting the process flow, the need for a tradition HEPA filtration train will be eliminated and this dramatically reduces the resources required for cleaning or disposal, thus presenting a route to reducing ultimate costs. The paper will examine the performance characteristics, filtration efficiency, flow verses differential pressure and cleanability of a self cleaning HEPA grade sintered metal filter element, together with data to prove the contention. (authors)

  20. Cardiogenic shock due to coronary artery disease associated with interrupted aortic arch

    Directory of Open Access Journals (Sweden)

    Luís Alberto Oliveira Dallan

    2013-06-01

    Full Text Available Acute pulmonary edema is a serious event. Its occurrence in association with interrupted aortic arch and coronary heart disease is rare. Recently, an old patient developed cardiogenic shock and acute pulmonary edema due to acute coronary insufficiency, associated with interrupted aortic arch. The coronary angiography revealed occlusion of the right coronary artery and 95% obstruction in the left main coronary artery, associated with interruption of the descending aorta. Coronary artery bypass graft was performed, without extracorporeal circulation, to the anterior descending coronary artery. We discuss the initial management, given the seriousness of the case.

  1. The effect of interruptions and prolonged treatment time in radiotherapy for nasopharyngeal carcinoma

    International Nuclear Information System (INIS)

    Kwong, Dora L.W.; Sham, Jonathan S.T.; Chua, Daniel T.T.; Choy, Damon T.K.; Au, Gordon K.H.; Wu, P.M.

    1997-01-01

    Purpose: The effect of interruptions and prolonged overall treatment time in radiotherapy for nasopharyngeal carcinoma and the significance of timing of interruption was investigated. Methods and Materials: Treatment records of 229 patients treated with continuous course (CC) and 567 patients treated with split course (SC) radiotherapy for nonmetastatic NPC were reviewed. Overall treatment time without inclusion of time for boost was calculated. Treatment that extended 1 week beyond scheduled time was considered prolonged. Outcome in patients who completed treatment 'per schedule' were compared with those who had 'prolonged' treatment. Because of known patient selection bias between CC and SC, patients on the two schedules were analyzed separately. Multivariate analysis was performed for patients on SC. Total number of days of interruption, age, sex, T and N stage, and the use of boost were tested for the whole SC group. Analysis on the effect of timing of interruption was performed in a subgroup of 223 patients on SC who had a single unplanned interruption. Timing of interruption, either before or after the fourth week for the unplanned interruption, was tested in addition to the other variables in multivariate analysis for this subgroup of SC. Results: Twenty-seven (11.8%) patients on CC and 96 (16.9%) patients on SC had prolonged treatment. Patients on SC who had prolonged treatment had significantly poorer loco-regional control rate and disease free survival when compared with those who completed radiotherapy per schedule (p = 0.0063 and 0.001, respectively, with adjustment for stage). For CC, the effect of prolonged treatment on outcome was not significant. The small number of events for patients on CC probably account for the insignificant finding. The number of days of interruption was confirmed as prognostic factor, independent of T and N stages, for loco-regional control and disease-free survival in multivariate analysis for SC. The hazard rate for loco

  2. Algorithm Design of CPCI Backboard's Interrupts Management Based on VxWorks' Multi-Tasks

    Science.gov (United States)

    Cheng, Jingyuan; An, Qi; Yang, Junfeng

    2006-09-01

    This paper begins with a brief introduction of the embedded real-time operating system VxWorks and CompactPCI standard, then gives the programming interfaces of Peripheral Controller Interface (PCI) configuring, interrupts handling and multi-tasks programming interface under VxWorks, and then emphasis is placed on the software frameworks of CPCI interrupt management based on multi-tasks. This method is sound in design and easy to adapt, ensures that all possible interrupts are handled in time, which makes it suitable for data acquisition systems with multi-channels, a high data rate, and hard real-time high energy physics.

  3. An Assessment of Instant Messaging Interruptions on Knowledge Workers' Task Performance in E-Learning-Based Training

    Science.gov (United States)

    Mansi, Gary R.

    2011-01-01

    The modern workplace environment is filled with interruptions due to the necessity of coworkers to communicate with each other. Studies have revealed that interruptions can disrupt the ability of a knowledge worker to concentrate on a task, which can impact task performance (TP). Communication interruptions are due, in part, to the unavoidable…

  4. Comparative genomics beyond sequence-based alignments

    DEFF Research Database (Denmark)

    Þórarinsson, Elfar; Yao, Zizhen; Wiklund, Eric D.

    2008-01-01

    Recent computational scans for non-coding RNAs (ncRNAs) in multiple organisms have relied on existing multiple sequence alignments. However, as sequence similarity drops, a key signal of RNA structure--frequent compensating base changes--is increasingly likely to cause sequence-based alignment me...

  5. Cloning, sequencing and expression of a xylanase gene from the maize pathogen Helminthosporium turcicum

    DEFF Research Database (Denmark)

    Degefu, Y.; Paulin, L.; Lübeck, Peter Stephensen

    2001-01-01

    A gene encoding an endoxylanase from the phytopathogenic fungus Helminthosporium turcicum Pass. was cloned and sequenced. The entire nucleotide sequence of a 1991 bp genomic fragment containing an endoxylanase gene was determined. The xylanase gene of 795 bp, interrupted by two introns of 52 and ...

  6. Treatment interruptions and non-adherence with imatinib and associated healthcare costs: a retrospective analysis among managed care patients with chronic myelogenous leukaemia.

    Science.gov (United States)

    Darkow, Theodore; Henk, Henry J; Thomas, Simu K; Feng, Weiwei; Baladi, Jean-Francois; Goldberg, George A; Hatfield, Alan; Cortes, Jorge

    2007-01-01

    Identify treatment interruptions and non-adherence with imatinib; examine the clinical and patient characteristics related to treatment interruptions and non-adherence; and estimate the association between treatment interruptions and non-adherence with imatinib and healthcare costs for US managed care patients with chronic myeloid leukaemia (CML). This retrospective analysis utilised electronic healthcare claims data from a US managed care provider. Adult patients with CML (as determined by International Classification of Diseases, ninth revision, Clinical Modification [ICD-9-CM] diagnosis code) were identified who began treatment with imatinib from 1 June 2001 through 31 March 2004. Treatment interruptions (i.e. failure to refill imatinib within 30 days from the run-out date of the prior prescription) were identified during the 12-month follow-up period. Medication possession ratio (MPR), calculated as total days' supply of imatinib divided by 365, was also examined. Healthcare costs (i.e. paid amounts for all prescription medications and medical services received, including health plan and patient liability) were examined in three ways: (i) total healthcare costs; (ii) total healthcare costs exclusive of imatinib costs; and (iii) total medical costs. All costs were converted to US dollars (2004 values) using the medical component of the Consumer Price Index. MPR was modelled using ordinary least squares regression. Presence of treatment interruptions was modelled using logistic regression. The association between MPR and healthcare costs was estimated using a generalised linear model specified with a gamma error distribution and a log link. All models included adjustment for age, gender, number of concomitant medications, starting dose of imatinib and cancer complexity. A total of 267 patients were identified. Average age was approximately 50 years, and 43% were women. Mean MPR was 77.7%, with 31% of patients having a treatment interruption. However, all of these

  7. Automatic coding method of the ACR Code

    International Nuclear Information System (INIS)

    Park, Kwi Ae; Ihm, Jong Sool; Ahn, Woo Hyun; Baik, Seung Kook; Choi, Han Yong; Kim, Bong Gi

    1993-01-01

    The authors developed a computer program for automatic coding of ACR(American College of Radiology) code. The automatic coding of the ACR code is essential for computerization of the data in the department of radiology. This program was written in foxbase language and has been used for automatic coding of diagnosis in the Department of Radiology, Wallace Memorial Baptist since May 1992. The ACR dictionary files consisted of 11 files, one for the organ code and the others for the pathology code. The organ code was obtained by typing organ name or code number itself among the upper and lower level codes of the selected one that were simultaneous displayed on the screen. According to the first number of the selected organ code, the corresponding pathology code file was chosen automatically. By the similar fashion of organ code selection, the proper pathologic dode was obtained. An example of obtained ACR code is '131.3661'. This procedure was reproducible regardless of the number of fields of data. Because this program was written in 'User's Defined Function' from, decoding of the stored ACR code was achieved by this same program and incorporation of this program into program in to another data processing was possible. This program had merits of simple operation, accurate and detail coding, and easy adjustment for another program. Therefore, this program can be used for automation of routine work in the department of radiology

  8. Genome sequence analysis of five Canadian isolates of strawberry mottle virus reveals extensive intra-species diversity and a longer RNA2 with increased coding capacity compared to a previously characterized European isolate.

    Science.gov (United States)

    Bhagwat, Basdeo; Dickison, Virginia; Ding, Xinlun; Walker, Melanie; Bernardy, Michael; Bouthillier, Michel; Creelman, Alexa; DeYoung, Robyn; Li, Yinzi; Nie, Xianzhou; Wang, Aiming; Xiang, Yu; Sanfaçon, Hélène

    2016-06-01

    In this study, we report the genome sequence of five isolates of strawberry mottle virus (family Secoviridae, order Picornavirales) from strawberry field samples with decline symptoms collected in Eastern Canada. The Canadian isolates differed from the previously characterized European isolate 1134 in that they had a longer RNA2, resulting in a 239-amino-acid extension of the C-terminal region of the polyprotein. Sequence analysis suggests that reassortment and recombination occurred among the isolates. Phylogenetic analysis revealed that the Canadian isolates are diverse, grouping in two separate branches along with isolates from Europe and the Americas.

  9. Error-correction coding

    Science.gov (United States)

    Hinds, Erold W. (Principal Investigator)

    1996-01-01

    This report describes the progress made towards the completion of a specific task on error-correcting coding. The proposed research consisted of investigating the use of modulation block codes as the inner code of a concatenated coding system in order to improve the overall space link communications performance. The study proposed to identify and analyze candidate codes that will complement the performance of the overall coding system which uses the interleaved RS (255,223) code as the outer code.

  10. Dynamic benchmarking of simulation codes

    International Nuclear Information System (INIS)

    Henry, R.E.; Paik, C.Y.; Hauser, G.M.

    1996-01-01

    Computer simulation of nuclear power plant response can be a full-scope control room simulator, an engineering simulator to represent the general behavior of the plant under normal and abnormal conditions, or the modeling of the plant response to conditions that would eventually lead to core damage. In any of these, the underlying foundation for their use in analysing situations, training of vendor/utility personnel, etc. is how well they represent what has been known from industrial experience, large integral experiments and separate effects tests. Typically, simulation codes are benchmarked with some of these; the level of agreement necessary being dependent upon the ultimate use of the simulation tool. However, these analytical models are computer codes, and as a result, the capabilities are continually enhanced, errors are corrected, new situations are imposed on the code that are outside of the original design basis, etc. Consequently, there is a continual need to assure that the benchmarks with important transients are preserved as the computer code evolves. Retention of this benchmarking capability is essential to develop trust in the computer code. Given the evolving world of computer codes, how is this retention of benchmarking capabilities accomplished? For the MAAP4 codes this capability is accomplished through a 'dynamic benchmarking' feature embedded in the source code. In particular, a set of dynamic benchmarks are included in the source code and these are exercised every time the archive codes are upgraded and distributed to the MAAP users. Three different types of dynamic benchmarks are used: plant transients; large integral experiments; and separate effects tests. Each of these is performed in a different manner. The first is accomplished by developing a parameter file for the plant modeled and an input deck to describe the sequence; i.e. the entire MAAP4 code is exercised. The pertinent plant data is included in the source code and the computer

  11. Dynamic Shannon Coding

    OpenAIRE

    Gagie, Travis

    2005-01-01

    We present a new algorithm for dynamic prefix-free coding, based on Shannon coding. We give a simple analysis and prove a better upper bound on the length of the encoding produced than the corresponding bound for dynamic Huffman coding. We show how our algorithm can be modified for efficient length-restricted coding, alphabetic coding and coding with unequal letter costs.

  12. Fundamentals of convolutional coding

    CERN Document Server

    Johannesson, Rolf

    2015-01-01

    Fundamentals of Convolutional Coding, Second Edition, regarded as a bible of convolutional coding brings you a clear and comprehensive discussion of the basic principles of this field * Two new chapters on low-density parity-check (LDPC) convolutional codes and iterative coding * Viterbi, BCJR, BEAST, list, and sequential decoding of convolutional codes * Distance properties of convolutional codes * Includes a downloadable solutions manual

  13. Codes Over Hyperfields

    Directory of Open Access Journals (Sweden)

    Atamewoue Surdive

    2017-12-01

    Full Text Available In this paper, we define linear codes and cyclic codes over a finite Krasner hyperfield and we characterize these codes by their generator matrices and parity check matrices. We also demonstrate that codes over finite Krasner hyperfields are more interesting for code theory than codes over classical finite fields.

  14. Interruption of Onchocerca volvulus transmission in Northern Venezuela

    Science.gov (United States)

    2013-01-01

    Background Onchocerciasis is caused by Onchocerca volvulus and transmitted by Simulium species (black flies). In the Americas, the infection has been previously described in 13 discrete regional foci distributed among six countries (Brazil, Colombia, Ecuador, Guatemala, Mexico and Venezuela) where more than 370,000 people are currently considered at risk. Since 2001, disease control in Venezuela has relied on the mass drug administration to the at-risk communities. This report provides empirical evidence of interruption of Onchocerca volvulus transmission by Simulium metallicum in 510 endemic communities from two Northern foci of Venezuela, after 10–12 years of 6-monthly Mectizan® (ivermectin) treatment to all the eligible residents. Methods In-depth entomologic and epidemiologic surveys were serially conducted from 2001–2012 in selected (sentinel and extra-sentinel) communities from the North-central (NC) and North-east (NE) onchocerciasis foci of Venezuela in order to monitor the impact of ivermectin treatment. Results From 2007–2009, entomological indicators in both foci confirmed that 0 out of 112,637 S. metallicum females examined by PCR contained L3 infection in insect heads. The upper bound of the 95% confidence intervals of the infective rate of the vector reached values below 1% by 2009 (NC) and 2012 (NE). Additionally, after 14 (NC) and 22 (NE) rounds of treatment, the seasonal transmission potential (±UL CIs) of S. metallicum was under the critical threshold of 20 L3 per person per season. Serological analysis in school children < 15 years-old demonstrated that 0 out of 6,590 individuals were harboring antibodies to Ov-16. Finally, epidemiological surveys made during 2010 (NC) and 2012 (NE) showed no evidence of microfilariae in the skin and eyes of the population. Conclusions These results meet the WHO criteria for absence of parasite transmission and disease morbidity in these endemic areas which represent 91% of the population previously at

  15. Reduction of Hospital Physicians' Workflow Interruptions: A Controlled Unit-Based Intervention Study

    Directory of Open Access Journals (Sweden)

    Matthias Weigl

    2012-01-01

    Full Text Available Highly interruptive clinical environments may cause work stress and suboptimal clinical care. This study features an intervention to reduce workflow interruptions by re-designing work and organizational practices in hospital physicians providing ward coverage. A prospective, controlled intervention was conducted in two surgical and two internal wards. The intervention was based on physician quality circles - a participative technique to involve employees in the development of solutions to overcome work-related stressors. Outcome measures were the frequency of observed workflow interruptions. Workflow interruptions by fellow physicians and nursing staff were significantly lower after the intervention. However, a similar decrease was also observed in control units. Additional interviews to explore process-related factors suggested that there might have been spill-over effects in the sense that solutions were not strictly confined to the intervention group. Recommendations for further research on the effectiveness and consequences of such interventions for professional communication and patient safety are discussed.

  16. A randomized controlled trial of daily sedation interruption in critically ill children

    NARCIS (Netherlands)

    Vet, N.J.; Wildt, S.N. de; Verlaat, C.W.; Knibbe, C.A.; Mooij, M.G.; Woensel, J.B. van; Rosmalen, J. van; Tibboel, D.; Hoog, M. de

    2016-01-01

    PURPOSE: To compare daily sedation interruption plus protocolized sedation (DSI + PS) to protocolized sedation only (PS) in critically ill children. METHODS: In this multicenter randomized controlled trial in three pediatric intensive care units in the Netherlands, mechanically ventilated critically

  17. A randomized controlled trial of daily sedation interruption in critically ill children

    NARCIS (Netherlands)

    Vet, Nienke J.; de Wildt, Saskia N.; Verlaat, Carin W. M.; Knibbe, Catherijne A. J.; Mooij, Miriam G.; van Woensel, Job B. M.; van Rosmalen, Joost; Tibboel, Dick; de Hoog, Matthijs

    2016-01-01

    To compare daily sedation interruption plus protocolized sedation (DSI + PS) to protocolized sedation only (PS) in critically ill children. In this multicenter randomized controlled trial in three pediatric intensive care units in the Netherlands, mechanically ventilated critically ill children with

  18. Workflow interruptions, cognitive failure and near-accidents in health care.

    Science.gov (United States)

    Elfering, Achim; Grebner, Simone; Ebener, Corinne

    2015-01-01

    Errors are frequent in health care. A specific model was tested that affirms failure in cognitive action regulation to mediate the influence of nurses' workflow interruptions and safety conscientiousness on near-accidents in health care. One hundred and sixty-five nurses from seven Swiss hospitals participated in a questionnaire survey. Structural equation modelling confirmed the hypothesised mediation model. Cognitive failure in action regulation significantly mediated the influence of workflow interruptions on near-accidents (p accidents via cognitive failure in action regulation was also significant (p accidents; moreover, cognitive failure mediated the association between compliance and near-accidents (p < .05). Contrary to expectations, compliance with safety regulations was not related to workflow interruptions. Workflow interruptions caused by colleagues, patients and organisational constraints are likely to trigger errors in nursing. Work redesign is recommended to reduce cognitive failure and improve safety of nurses and patients.

  19. Nested Interrupt Analysis of Low Cost and High Performance Embedded Systems Using GSPN Framework

    Science.gov (United States)

    Lin, Cheng-Min

    Interrupt service routines are a key technology for embedded systems. In this paper, we introduce the standard approach for using Generalized Stochastic Petri Nets (GSPNs) as a high-level model for generating CTMC Continuous-Time Markov Chains (CTMCs) and then use Markov Reward Models (MRMs) to compute the performance for embedded systems. This framework is employed to analyze two embedded controllers with low cost and high performance, ARM7 and Cortex-M3. Cortex-M3 is designed with a tail-chaining mechanism to improve the performance of ARM7 when a nested interrupt occurs on an embedded controller. The Platform Independent Petri net Editor 2 (PIPE2) tool is used to model and evaluate the controllers in terms of power consumption and interrupt overhead performance. Using numerical results, in spite of the power consumption or interrupt overhead, Cortex-M3 performs better than ARM7.

  20. Cerebrospinal fluid signs of neuronal damage after antiretroviral treatment interruption in HIV-1 infection

    Directory of Open Access Journals (Sweden)

    Deeks Steven G

    2005-08-01

    Full Text Available Abstract Background The neurofilament is a major structural component of myelinated axons. Increased cerebrospinal fluid (CSF concentrations of the light chain of the neurofilament protein (NFL can serve as a sensitive indicator of central nervous system (CNS injury. To assess whether interrupting antiretroviral treatment of HIV infection might have a deleterious effect on the CNS, we measured NFL levels in HIV-infected subjects interrupting therapy. We identified subjects who had CSF HIV RNA concentrations below 50 copies/mL at the time combination antiretroviral therapy was interrupted, and for whom CSF samples were available before and after the interruption. Results A total of 8 subjects were studied. The median (range CSF NFL level at baseline was Conclusion These findings suggest that resurgence of active HIV replication may result in measurable, albeit subclinical, CNS injury. Further studies are needed to define the frequency and pathobiological importance of the increase in CSF NFL.

  1. The effect of training and job interruptions on logging crews' safety in ...

    African Journals Online (AJOL)

    The effect of training and job interruptions on logging crews' safety in ... method, experienced and inexperienced crews were studied before training, after ... that provision of appropriate safety gears as well as delivery of on job training are ...

  2. Sequence assembly

    DEFF Research Database (Denmark)

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

    2009-01-01

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

  3. Genome Sequencing

    DEFF Research Database (Denmark)

    Sato, Shusei; Andersen, Stig Uggerhøj

    2014-01-01

    The current Lotus japonicus reference genome sequence is based on a hybrid assembly of Sanger TAC/BAC, Sanger shotgun and Illumina shotgun sequencing data generated from the Miyakojima-MG20 accession. It covers nearly all expressed L. japonicus genes and has been annotated mainly based on transcr......The current Lotus japonicus reference genome sequence is based on a hybrid assembly of Sanger TAC/BAC, Sanger shotgun and Illumina shotgun sequencing data generated from the Miyakojima-MG20 accession. It covers nearly all expressed L. japonicus genes and has been annotated mainly based...

  4. Classifying Coding DNA with Nucleotide Statistics

    Directory of Open Access Journals (Sweden)

    Nicolas Carels

    2009-10-01

    Full Text Available In this report, we compared the success rate of classification of coding sequences (CDS vs. introns by Codon Structure Factor (CSF and by a method that we called Universal Feature Method (UFM. UFM is based on the scoring of purine bias (Rrr and stop codon frequency. We show that the success rate of CDS/intron classification by UFM is higher than by CSF. UFM classifies ORFs as coding or non-coding through a score based on (i the stop codon distribution, (ii the product of purine probabilities in the three positions of nucleotide triplets, (iii the product of Cytosine (C, Guanine (G, and Adenine (A probabilities in the 1st, 2nd, and 3rd positions of triplets, respectively, (iv the probabilities of G in 1st and 2nd position of triplets and (v the distance of their GC3 vs. GC2 levels to the regression line of the universal correlation. More than 80% of CDSs (true positives of Homo sapiens (>250 bp, Drosophila melanogaster (>250 bp and Arabidopsis thaliana (>200 bp are successfully classified with a false positive rate lower or equal to 5%. The method releases coding sequences in their coding strand and coding frame, which allows their automatic translation into protein sequences with 95% confidence. The method is a natural consequence of the compositional bias of nucleotides in coding sequences.

  5. A Study of the Effect of Interrupted Quenches on a Thermomechanically Processed High Carbon Steel.

    Science.gov (United States)

    1982-10-01

    steel . Successful martempering requires a cooling rate sufficient to avoid the nose of the C- curve and thus prevent significant bainite formation. When...STUDY OF THE EFFECT OF INTERRUPTED QUENCHES ON A THERMONECHANICALLY PROCESSED HIGH CARBON STEEL by Steven A. Barton October 1982 Thesis Advisor: T.R...unlimited. A Study of the Effect of Interrupted Quenches on a Thermomechanically Processed High Carbon Steel by Steven A. Barton Lieutenant, United

  6. Interrupted Time Series Versus Statistical Process Control in Quality Improvement Projects.

    Science.gov (United States)

    Andersson Hagiwara, Magnus; Andersson Gäre, Boel; Elg, Mattias

    2016-01-01

    To measure the effect of quality improvement interventions, it is appropriate to use analysis methods that measure data over time. Examples of such methods include statistical process control analysis and interrupted time series with segmented regression analysis. This article compares the use of statistical process control analysis and interrupted time series with segmented regression analysis for evaluating the longitudinal effects of quality improvement interventions, using an example study on an evaluation of a computerized decision support system.

  7. Interruption or congenital stenosis of the inferior vena cava: Prevalence, imaging, and clinical findings

    International Nuclear Information System (INIS)

    Koc, Zafer; Oguzkurt, Levent

    2007-01-01

    Objective: To present the prevalence, clinical, and imaging findings of interruption or congenital stenotic lesions of the inferior vena cava (IVC), associated malformations, and their clinical relevance. Materials and methods: Between March 2004 and March 2006, 7972 patients who had undergone consecutive routine abdominal multidetector row computed tomography were analyzed for interruption or stenotic lesion of the IVC. Results: Prevalence of interruption (n = 8) or congenital stenosis (n = 4) of the IVC occurred in 12 (0.15%) of 7972 patients. Four patients with interruption and four patients with congenital stenosis of the IVC were symptomatic with DVT (n = 4), leg swelling (n = 4), leg pain (n = 2), lower extremity varices (n = 2), hepatic vein thrombosis (n = 1), and hematochezia (n = 1). All four of the asymptomatic patients were from the interruption group, and these patients had interrupted IVC with well-developed azygos/hemiazygos continuation. Eight symptomatic patients did not have a well-developed azygos/hemiazygos continuation, and drainage of lower extremity was mainly from collateral veins. Additional findings in eight symptomatic patients were abdominal venous collaterals (n = 8), venous aneurysm (n = 2), lower extremity varices (n = 2), varicocele (n = 2), and pelvic varices (n = 1). Conclusion: Interruption or stenosis of the IVC are rare on routine abdominal CT examinations and may cause different clinical findings depending on the variant drainage patterns or collaterals. Interrupted IVC is commonly asymptomatic if associated with well-developed azygos/hemiazygos continuation, whereas commonly symptomatic if well-developed azygos/hemiazygos continuation is not present

  8. Brief Lags in Interrupted Sequential Performance: Evaluating a Model and Model Evaluation Method

    Science.gov (United States)

    2015-01-05

    interruption where they had left off. The experimenter remained present during this period to provide answers if necessary. A sheet of paper with the choice...the probabilities of different possible “paths” through predecessor/successor pairs. For exam - ple, the most likely path to selection of the correct...participant’s interruption durations. References Altmann, E.M., 2004. The preparation effect in task switching: Carryover of SOA . Memory & Cognition 32, 153

  9. Physicians interrupted by mobile devices in hospitals: understanding the interaction between devices, roles, and duties.

    Science.gov (United States)

    Solvoll, Terje; Scholl, Jeremiah; Hartvigsen, Gunnar

    2013-03-07

    A common denominator of modern hospitals is a variety of communication problems. In particular, interruptions from mobile communication devices are a cause of great concern for many physicians. To characterize how interruptions from mobile devices disturb physicians in their daily work. The gathered knowledge will be subsequently used as input for the design and development of a context-sensitive communication system for mobile communications suitable for hospitals. This study adheres to an ethnographic and interpretive field research approach. The data gathering consisted of participant observations, non-structured and mostly ad hoc interviews, and open-ended discussions with a selected group of physicians. Eleven physicians were observed for a total of 135 hours during May and June 2009. The study demonstrates to what degree physicians are interrupted by mobile devices in their daily work and in which situations they are interrupted, such as surgery, examinations, and during patients/relatives high-importance level conversations. The participants in the study expected, and also indicated, that wireless phones probably led to more interruptions immediately after their introduction in a clinic, when compared to a pager, but this changed after a short while. The unpleasant feeling experienced by the caller when interrupting someone by calling them differs compared to sending a page message, which leaves it up to the receiver when to return the call. Mobile devices, which frequently interrupt physicians in hospitals, are a problem for both physicians and patients. The results from this study contribute to knowledge being used as input for designing and developing a prototype for a context-sensitive communication system for mobile communication suitable for hospitals. We combined these findings with results from earlier studies and also involved actual users to develop the prototype, CallMeSmart. This system intends to reduce such interruptions and at the same time

  10. Assessment of treatment interruption among pulmonary tuberculosis patients: A cross-sectional study

    Directory of Open Access Journals (Sweden)

    Satya Bhgath Gorityala

    2015-01-01

    Full Text Available Background: Multi-drug resistant tuberculosis (TB is a rising peril of the TB control in India caused mostly by incomplete treatment. Aim: The aim was to assess the treatment interruption among pulmonary TB (PTB patients. Materials and Methods: A cross-sectional study was carried out for a period of 9 months among PTB patients. Patients admitted with active pulmonary Koch′s and history of anti-TB treatment (ATT for 1-month or more from any source and who returns to treatment after not taking ATT consecutively for 2 months or more were included in the study. The data were collected from the patients or their caretakers to obtain the source of treatment given previously before default, number of treatment interruptions, phase and reasons for treatment interruption treatment. Results: A total of 107 defaulters were identified during the study period. In the present study, 62.6% of the patients interrupted treatment only once, 55.34% of the patient′s early continuation (3-4 months treatment, and 47.66% of the patient′s only one reason for the treatment interruptions during the course of the treatment. The most common reason for the treatment interruptions were felt well with TB treatment (29.53% followed by side effects (16.06%, lack of money (8.29%, and other reasons. Conclusion: The study revealed that most of the defaulters were in the age group between 35 and 60 years, male gender, illiterates, daily wage labor, and married. The treatment interruptions were minimized by putting the efforts to improve direct supervision; pretreatment counseling and retrieve treatment interrupters were recommended.

  11. Chemoradiotherapy in patients with anal cancer: Impact of length of unplanned treatment interruption on outcome

    Energy Technology Data Exchange (ETDEWEB)

    Meyer, Andreas; Meier Zu Eissen, Juergen; Karstens, Johann H.; Bremer, Michael [Medical School Hannover (Germany). Dept. of Radiation Oncology

    2006-09-15

    The aim of this retrospective analysis was to evaluate feasibility and effectiveness of definitive chemoradiotherapy without split-course technique in anal cancer patients. From 1993 to 2003, 81 patients were treated; 13 were excluded due to various chemotherapeutic regimes, thus 68 patients were analysed. In case of acute grade 3 toxicities, treatment was halted until improvement or resolution independent of dose. Short interruption was defined as completing treatment without exceeding eight cumulative treatment days beyond scheduled plan, other patients were considered to have had prolonged interruption. Median follow-up was 46 months. Median overall treatment time was 53 days corresponding to an interruption of eight cumulative treatment days. Thirty-five patients (51%) had treatment interruption of <8 days. No acute grade 4 toxicities were observed; one fatality occurred during treatment due to ileus-like symptoms according to acute grade 5 toxicity. Comparing patients with short vs. prolonged interruption 5-year actuarial rates for local control were 85% vs. 81% (p{approx}0.605) and for colostomy-free survival 85% vs. 87% (p{approx}0.762), respectively. Chemoradiotherapy with short individualised treatment interruptions seems to be feasible with acceptable acute or late toxicities. Treatment is highly effective in terms of local control and colostomy-free survival.

  12. [Deliberate interruptions and changes of dose of inhaled corticosteroids by asthma patients: "a community pharmacy study"].

    Science.gov (United States)

    Laforest, L; Van Ganse, É; Devouassoux, G; Chatté, G; Tamberou, C; Belhassen, M; Chamba, G

    2015-01-01

    Adherence to inhaled corticosteroids (ICS) remains a major issue for asthma management, even among patients receiving a regular prescription from their doctor. The frequency of deliberate interruption of ICS, and of spontaneous changes of dose, were studied in a population of asthma patients recruited in community pharmacies. Asthma patients (aged 18-50) recruited in community pharmacies reported in self-administered questionnaires their spontaneous interruptions and changes of doses of ICS during the past 3 months. The characteristics of patients who interrupted their therapy or who modified the dose were compared with other patients. The studied population included 252 patients (mean age 35 year-old, females: 59%), of whom 62% had inadequately controlled asthma. Among these patients, 25% had interrupted ICS therapy during the past 3 months, while 21% spontaneously changed the dose. The most reported reason for interrupting ICS was the cessation of symptoms (50%). In multivariate analysis, interrupting ICS was mainly associated with inadequate asthma control (OR=3.1, 95% CI 1.5-6.4), while the strongest association with changing ICS doses was the patients' perception of asthma as a concern in their lives (OR=3.2, 95% CI 1.2-8.4). These results underline a poor understanding of the purpose of ICS therapy by patients. They also highlight the need of therapeutic education to improve the management of the disease. Copyright © 2014 SPLF. Published by Elsevier Masson SAS. All rights reserved.

  13. Control instrumentation and data handling of heavy current inductive load interrupter

    International Nuclear Information System (INIS)

    Calpin, J.E.

    1983-01-01

    The heavy duty DC interrupter is a switching system with the ability to interrupt very high inductive currents with precise timing, work in concert with an additional number of similar systems, and withstand fast recovery voltages (30 kV) after interruption. Further, it is required to be self-protecting and the high current busses isolated to 50 kV DC and subjected to 95 kV BIL test voltages. Interruption is accomplished by the separation of vacuum interrupter contacts, which prior to counterpulse arc for milliseconds, generating horrendous noise signals of frequencies from DC to ultraviolet. Neutralization of such signals on the computer interface was effected by unique BALUN filters on 25 control and status lines. The noise abatement circuitry rationale will be discussed along with triple shielding, Hall effect current level sensing and light pipe communication between high level busses and interface HTL cards. Triggering of the isolated counterpulse circuitry will be outlined. The self-protective aspects of the system employ current sensors to reclose the interrupter if current persists for two milliseconds after counterpulse

  14. Stated preferences based estimation of power interruption costs in private households: An example from Germany

    International Nuclear Information System (INIS)

    Praktiknjo, Aaron J.

    2014-01-01

    Concerns regarding supply security are increasingly raised in reaction to the transition of the German energy system toward a renewable and nuclear-free system called “Energiewende”. The goal of this work is to contribute to a measurability of supply security by quantifying the consequences of power interruptions monetarily. The focus lies within the investigation of power interruption costs in private households. An online survey with 859 participants in 2011 is used to gather the necessary data. Based on this data, a two-staged bottom-up regression model was estimated to describe interruption costs for durations of 15 min, 1 h, 4 h, 1 day and 4 days. Finally, micro-data from 55,000 households were used to perform Monte Carlo simulations to increase the representativeness of the estimations. The frequency distributions of the estimated interruption costs indicate potentials for load-shedding measures. Such measures could be an economically viable contribution to a successful integration of large shares of renewable fluctuating generation like wind or solar power. - Highlights: • Power interruption costs have been analyzed for private households in Germany. • Five different interruption durations have been analyzed. • An online survey, a regression and a bottom-up simulation model has been used. • The results indicate interesting potentials for demand response measures. • Such measures might contribute to the integration of large shares of renewables

  15. An upper bound on the number of errors corrected by a convolutional code

    DEFF Research Database (Denmark)

    Justesen, Jørn

    2000-01-01

    The number of errors that a convolutional codes can correct in a segment of the encoded sequence is upper bounded by the number of distinct syndrome sequences of the relevant length.......The number of errors that a convolutional codes can correct in a segment of the encoded sequence is upper bounded by the number of distinct syndrome sequences of the relevant length....

  16. Vector Network Coding Algorithms

    OpenAIRE

    Ebrahimi, Javad; Fragouli, Christina

    2010-01-01

    We develop new algebraic algorithms for scalar and vector network coding. In vector network coding, the source multicasts information by transmitting vectors of length L, while intermediate nodes process and combine their incoming packets by multiplying them with L x L coding matrices that play a similar role as coding c in scalar coding. Our algorithms for scalar network jointly optimize the employed field size while selecting the coding coefficients. Similarly, for vector coding, our algori...

  17. Syndrome-source-coding and its universal generalization. [error correcting codes for data compression

    Science.gov (United States)

    Ancheta, T. C., Jr.

    1976-01-01

    A method of using error-correcting codes to obtain data compression, called syndrome-source-coding, is described in which the source sequence is treated as an error pattern whose syndrome forms the compressed data. It is shown that syndrome-source-coding can achieve arbitrarily small distortion with the number of compressed digits per source digit arbitrarily close to the entropy of a binary memoryless source. A 'universal' generalization of syndrome-source-coding is formulated which provides robustly effective distortionless coding of source ensembles. Two examples are given, comparing the performance of noiseless universal syndrome-source-coding to (1) run-length coding and (2) Lynch-Davisson-Schalkwijk-Cover universal coding for an ensemble of binary memoryless sources.

  18. Homological stabilizer codes

    Energy Technology Data Exchange (ETDEWEB)

    Anderson, Jonas T., E-mail: jonastyleranderson@gmail.com

    2013-03-15

    In this paper we define homological stabilizer codes on qubits which encompass codes such as Kitaev's toric code and the topological color codes. These codes are defined solely by the graphs they reside on. This feature allows us to use properties of topological graph theory to determine the graphs which are suitable as homological stabilizer codes. We then show that all toric codes are equivalent to homological stabilizer codes on 4-valent graphs. We show that the topological color codes and toric codes correspond to two distinct classes of graphs. We define the notion of label set equivalencies and show that under a small set of constraints the only homological stabilizer codes without local logical operators are equivalent to Kitaev's toric code or to the topological color codes. - Highlights: Black-Right-Pointing-Pointer We show that Kitaev's toric codes are equivalent to homological stabilizer codes on 4-valent graphs. Black-Right-Pointing-Pointer We show that toric codes and color codes correspond to homological stabilizer codes on distinct graphs. Black-Right-Pointing-Pointer We find and classify all 2D homological stabilizer codes. Black-Right-Pointing-Pointer We find optimal codes among the homological stabilizer codes.

  19. Gray Code for Cayley Permutations

    Directory of Open Access Journals (Sweden)

    J.-L. Baril

    2003-10-01

    Full Text Available A length-n Cayley permutation p of a total ordered set S is a length-n sequence of elements from S, subject to the condition that if an element x appears in p then all elements y < x also appear in p . In this paper, we give a Gray code list for the set of length-n Cayley permutations. Two successive permutations in this list differ at most in two positions.

  20. Diagnostic Coding for Epilepsy.

    Science.gov (United States)

    Williams, Korwyn; Nuwer, Marc R; Buchhalter, Jeffrey R

    2016-02-01

    Accurate coding is an important function of neurologic practice. This contribution to Continuum is part of an ongoing series that presents helpful coding information along with examples related to the issue topic. Tips for diagnosis coding, Evaluation and Management coding, procedure coding, or a combination are presented, depending on which is most applicable to the subject area of the issue.

  1. Coding of Neuroinfectious Diseases.

    Science.gov (United States)

    Barkley, Gregory L

    2015-12-01

    Accurate coding is an important function of neurologic practice. This contribution to Continuum is part of an ongoing series that presents helpful coding information along with examples related to the issue topic. Tips for diagnosis coding, Evaluation and Management coding, procedure coding, or a combination are presented, depending on which is most applicable to the subject area of the issue.

  2. Evaluation of Gaussia luciferase and foot-and-mouth disease virus 2A translational interrupter chimeras as polycistronic reporters for transgene expression.

    Science.gov (United States)

    Puckette, Michael; Burrage, Thomas; Neilan, John G; Rasmussen, Max

    2017-06-12

    The Gaussia princeps luciferase is used as a stand-alone reporter of transgene expression for in vitro and in vivo expression systems due to the rapid and easy monitoring of luciferase activity. We sought to simultaneously quantitate production of other recombinant proteins by transcriptionally linking the Gaussia princeps luciferase gene to other genes of interest through the foot-and-mouth disease virus 2A translational interrupter sequence. We produced six plasmids, each encoding a single open reading frame, with the foot-and-mouth disease virus 2A sequence placed either N-terminal or C-terminal to the Gaussia princeps luciferase gene. Two plasmids included novel Gaussia princeps luciferase variants with the position 1 methionine deleted. Placing a foot-and-mouth disease virus 2A translational interrupter sequence on either the N- or C-terminus of the Gaussia princeps luciferase gene did not prevent the secretion or luminescence of resulting chimeric luciferase proteins. We also measured the ability of another polycistronic plasmid vector with a 2A-luciferase sequence placed downstream of the foot-and-mouth disease virus P1 and 3C protease genes to produce of foot-and-mouth disease virus-like particles and luciferase activity from transfected cells. Incorporation of the 2A-luciferase sequence into a transgene encoding foot-and-mouth disease virus structural proteins retained luciferase activity and the ability to form virus-like particles. We demonstrated a mechanism for the near real-time, sequential, non-destructive quantitative monitoring of transcriptionally-linked recombinant proteins and a valuable method for monitoring transgene expression in recombinant vaccine constructs.

  3. Effect of Radiotherapy Interruptions on Survival in Medicare Enrollees With Local and Regional Head-and-Neck Cancer

    International Nuclear Information System (INIS)

    Fesinmeyer, Megan Dann; Mehta, Vivek; Blough, David; Tock, Lauri; Ramsey, Scott D.

    2010-01-01

    Purpose: To investigate whether interruptions in radiotherapy are associated with decreased survival in a population-based sample of head-and-neck cancer patients. Methods and Materials: Using the Surveillance, Epidemiology, and End Results-Medicare linked database we identified Medicare beneficiaries aged 66 years and older diagnosed with local-regional head-and-neck cancer during the period 1997-2003. We examined claims records of 3864 patients completing radiotherapy for the presence of one or more 5-30-day interruption(s) in therapy. We then performed Cox regression analyses to estimate the association between therapy interruptions and survival. Results: Patients with laryngeal tumors who experienced an interruption in radiotherapy had a 68% (95% confidence interval, 41-200%) increased risk of death, compared with patients with no interruptions. Patients with nasal cavity, nasopharynx, oral, salivary gland, and sinus tumors had similar associations between interruptions and increased risk of death, but these did not reach statistical significance because of small sample sizes. Conclusions: Treatment interruptions seem to influence survival time among patients with laryngeal tumors completing a full course of radiotherapy. At all head-and-neck sites, the association between interruptions and survival is sensitive to confounding by stage and other treatments. Further research is needed to develop methods to identify patients most susceptible to interruption-induced mortality.

  4. Driven to distraction: The nature and apparent purpose of interruptions in critical care and implications for HIT.

    Science.gov (United States)

    Mamykina, Lena; Carter, Eileen J; Sheehan, Barbara; Stanley Hum, R; Twohig, Bridget C; Kaufman, David R

    2017-05-01

    To examine the apparent purpose of interruptions in a Pediatric Intensive Care Unit and opportunities to reduce their burden with informatics solutions. In this prospective observational study, researchers shadowed clinicians in the unit for one hour at a time, recording all interruptions participating clinicians experienced or initiated, their starting time, duration, and a short description that could help to infer their apparent purpose. All captured interruptions were classified inductively on their source and apparent purpose and on the optimal representational media for fulfilling their apparent purpose. The researchers observed thirty-four one-hour sessions with clinicians in the unit, including 21 nurses and 13 residents and house physicians. The physicians were interrupted on average 11.9 times per hour and interrupted others 8.8 times per hour. Nurses were interrupted 8.6 times per hour and interrupted others 5.1 times per hour. The apparent purpose of interruptions included Information Seeking and Sharing (n=259, 46.3%), Directives and Requests (n=70, 12%), Shared Decision-Making (n=49, 8.8%), Direct Patient Care (n=36, 6.4%), Social (n=71, 12.7%), Device Alarms (n=28, 5%), and Non-Clinical (n=10, 1.8%); 6.6% were not classified due to insufficient description. Of all captured interruptions, 29.5% were classified as being better served with informational displays or computer-mediated communication. Deeper understanding of the purpose of interruptions in critical care can help to distinguish between interruptions that require face-to-face conversation and those that can be eliminated with informatics solutions. The proposed taxonomy of interruptions and representational analysis can be used to further advance the science of interruptions in clinical care. Copyright © 2017 Elsevier Inc. All rights reserved.

  5. Computer codes in particle transport physics

    International Nuclear Information System (INIS)

    Pesic, M.

    2004-01-01

    is given. Importance of validation and verification of data and computer codes is underlined briefly. Examples of applications of the MCNPX, FLUKA and SHIELD codes to simulation of some of processes in nature, from reactor physics, ion medical therapy, cross section calculations, design of accelerator driven sub-critical systems to astrophysics and shielding of spaceships, are shown. More reliable and more frequent cross sections data in intermediate and high- energy range for particles transport and interactions with mater are expected in near future, as a result of new experimental investigations that are under way with the aim to validate theoretical models applied currently in the codes. These new data libraries are expected to be much larger and more comprehensive than existing ones requiring more computer memory and faster CPUs. Updated versions of the codes to be developed in future, beside sequential computation versions, will also include the MPI or PVM options to allow faster ru: ming of the code at acceptable cost for an end-user. A new option to be implemented in the codes is expected too - an end-user written application for particular problem could be added relatively simple to the general source code script. Initial works on full implementation of graphic user interface for preparing input and analysing output of codes and ability to interrupt and/or continue code running should be upgraded to user-friendly level. (author)

  6. INTERRUPTED IN-SITU COMPRESSIVE DEFORMATION EXPERIMENTS ON MMC FOAMS IN AN XCT: EXPERIMENTS AND ESTIMATION OF DISPLACEMENT FIELDS

    Directory of Open Access Journals (Sweden)

    Katharina Losch

    2014-05-01

    Full Text Available The mechanical properties of a metal-matrix composite foam are investigated by interrupted in-situ compressive deformation experiments within an X-ray computed tomography device (XCT. Each in-situ experiment generates a sequence of reconstructed 3D images of the foam microstructure. From these data, the deformation field is estimated by registring the images corresponding to three consecutive steps. To this end, the generic registration framework of the itk software suite is exploited and combined with several image preprocessing steps. Both segmented (binary images having just two grey values for foreground (strut structure and background (pore space and the result of the Euclidean distance transform (EDT on pore space and solid phase are used. The estimation quality is evaluated based on a sequence of synthetic data sets, where the foam’s microstructure is modelled by a random Laguerre tessellation. For large deformations, a combination of non-rigid registration for the EDT images and partwise-rigid registration on strongly deformed regions of the binary images, yields surprisingly small estimation errors.

  7. Vector Network Coding

    OpenAIRE

    Ebrahimi, Javad; Fragouli, Christina

    2010-01-01

    We develop new algebraic algorithms for scalar and vector network coding. In vector network coding, the source multicasts information by transmitting vectors of length L, while intermediate nodes process and combine their incoming packets by multiplying them with L X L coding matrices that play a similar role as coding coefficients in scalar coding. Our algorithms for scalar network jointly optimize the employed field size while selecting the coding coefficients. Similarly, for vector co...

  8. Entropy Coding in HEVC

    OpenAIRE

    Sze, Vivienne; Marpe, Detlev

    2014-01-01

    Context-Based Adaptive Binary Arithmetic Coding (CABAC) is a method of entropy coding first introduced in H.264/AVC and now used in the latest High Efficiency Video Coding (HEVC) standard. While it provides high coding efficiency, the data dependencies in H.264/AVC CABAC make it challenging to parallelize and thus limit its throughput. Accordingly, during the standardization of entropy coding for HEVC, both aspects of coding efficiency and throughput were considered. This chapter describes th...

  9. Generalized concatenated quantum codes

    International Nuclear Information System (INIS)

    Grassl, Markus; Shor, Peter; Smith, Graeme; Smolin, John; Zeng Bei

    2009-01-01

    We discuss the concept of generalized concatenated quantum codes. This generalized concatenation method provides a systematical way for constructing good quantum codes, both stabilizer codes and nonadditive codes. Using this method, we construct families of single-error-correcting nonadditive quantum codes, in both binary and nonbinary cases, which not only outperform any stabilizer codes for finite block length but also asymptotically meet the quantum Hamming bound for large block length.

  10. Rateless feedback codes

    DEFF Research Database (Denmark)

    Sørensen, Jesper Hemming; Koike-Akino, Toshiaki; Orlik, Philip

    2012-01-01

    This paper proposes a concept called rateless feedback coding. We redesign the existing LT and Raptor codes, by introducing new degree distributions for the case when a few feedback opportunities are available. We show that incorporating feedback to LT codes can significantly decrease both...... the coding overhead and the encoding/decoding complexity. Moreover, we show that, at the price of a slight increase in the coding overhead, linear complexity is achieved with Raptor feedback coding....

  11. When daily planning improves employee performance: The importance of planning type, engagement, and interruptions.

    Science.gov (United States)

    Parke, Michael R; Weinhardt, Justin M; Brodsky, Andrew; Tangirala, Subrahmaniam; DeVoe, Sanford E

    2018-03-01

    Does planning for a particular workday help employees perform better than on other days they fail to plan? We investigate this question by identifying 2 distinct types of daily work planning to explain why and when planning improves employees' daily performance. The first type is time management planning (TMP)-creating task lists, prioritizing tasks, and determining how and when to perform them. We propose that TMP enhances employees' performance by increasing their work engagement, but that these positive effects are weakened when employees face many interruptions in their day. The second type is contingent planning (CP) in which employees anticipate possible interruptions in their work and plan for them. We propose that CP helps employees stay engaged and perform well despite frequent interruptions. We investigate these hypotheses using a 2-week experience-sampling study. Our findings indicate that TMP's positive effects are conditioned upon the amount of interruptions, but CP has positive effects that are not influenced by the level of interruptions. Through this study, we help inform workers of the different planning methods they can use to increase their daily motivation and performance in dynamic work environments. (PsycINFO Database Record (c) 2018 APA, all rights reserved).

  12. HIV reservoirs and immune surveillance evasion cause the failure of structured treatment interruptions: a computational study.

    Directory of Open Access Journals (Sweden)

    Emiliano Mancini

    Full Text Available Continuous antiretroviral therapy is currently the most effective way to treat HIV infection. Unstructured interruptions are quite common due to side effects and toxicity, among others, and cannot be prevented. Several attempts to structure these interruptions failed due to an increased morbidity compared to continuous treatment. The cause of this failure is poorly understood and often attributed to drug resistance. Here we show that structured treatment interruptions would fail regardless of the emergence of drug resistance. Our computational model of the HIV infection dynamics in lymphoid tissue inside lymph nodes, demonstrates that HIV reservoirs and evasion from immune surveillance themselves are sufficient to cause the failure of structured interruptions. We validate our model with data from a clinical trial and show that it is possible to optimize the schedule of interruptions to perform as well as the continuous treatment in the absence of drug resistance. Our methodology enables studying the problem of treatment optimization without having impact on human beings. We anticipate that it is feasible to steer new clinical trials using computational models.

  13. Interrupted time series analysis in drug utilization research is increasing: systematic review and recommendations.

    Science.gov (United States)

    Jandoc, Racquel; Burden, Andrea M; Mamdani, Muhammad; Lévesque, Linda E; Cadarette, Suzanne M

    2015-08-01

    To describe the use and reporting of interrupted time series methods in drug utilization research. We completed a systematic search of MEDLINE, Web of Science, and reference lists to identify English language articles through to December 2013 that used interrupted time series methods in drug utilization research. We tabulated the number of studies by publication year and summarized methodological detail. We identified 220 eligible empirical applications since 1984. Only 17 (8%) were published before 2000, and 90 (41%) were published since 2010. Segmented regression was the most commonly applied interrupted time series method (67%). Most studies assessed drug policy changes (51%, n = 112); 22% (n = 48) examined the impact of new evidence, 18% (n = 39) examined safety advisories, and 16% (n = 35) examined quality improvement interventions. Autocorrelation was considered in 66% of studies, 31% reported adjusting for seasonality, and 15% accounted for nonstationarity. Use of interrupted time series methods in drug utilization research has increased, particularly in recent years. Despite methodological recommendations, there is large variation in reporting of analytic methods. Developing methodological and reporting standards for interrupted time series analysis is important to improve its application in drug utilization research, and we provide recommendations for consideration. Copyright © 2015 The Authors. Published by Elsevier Inc. All rights reserved.

  14. Power Supply Interruption Costs: Models and Methods Incorporating Time Dependent Patterns

    International Nuclear Information System (INIS)

    Kjoelle, G.H.

    1996-12-01

    This doctoral thesis develops models and methods for estimation of annual interruption costs for delivery points, emphasizing the handling of time dependent patterns and uncertainties in the variables determining the annual costs. It presents an analytical method for calculation of annual expected interruption costs for delivery points in radial systems, based on a radial reliability model, with time dependent variables. And a similar method for meshed systems, based on a list of outage events, assuming that these events are found in advance from load flow and contingency analyses. A Monte Carlo simulation model is given which handles both time variations and stochastic variations in the input variables and is based on the same list of outage events. This general procedure for radial and meshed systems provides expectation values and probability distributions for interruption costs from delivery points. There is also a procedure for handling uncertainties in input variables by a fuzzy description, giving annual interruption costs as a fuzzy membership function. The methods are developed for practical applications in radial and meshed systems, based on available data from failure statistics, load registrations and customer surveys. Traditional reliability indices such as annual interruption time, power- and energy not supplied, are calculated as by-products. The methods are presented as algorithms and/or procedures which are available as prototypes. 97 refs., 114 figs., 62 tabs

  15. Prediction of SFL Interruption Performance from the Results of Arc Simulation during High-Current Phase

    Science.gov (United States)

    Lee, Jong-Chul; Lee, Won-Ho; Kim, Woun-Jea

    2015-09-01

    The design and development procedures of SF6 gas circuit breakers are still largely based on trial and error through testing although the development costs go higher every year. The computation cannot cover the testing satisfactorily because all the real processes arc not taken into account. But the knowledge of the arc behavior and the prediction of the thermal-flow inside the interrupters by numerical simulations are more useful than those by experiments due to the difficulties to obtain physical quantities experimentally and the reduction of computational costs in recent years. In this paper, in order to get further information into the interruption process of a SF6 self-blast interrupter, which is based on a combination of thermal expansion and the arc rotation principle, gas flow simulations with a CFD-arc modeling are performed during the whole switching process such as high-current period, pre-current zero period, and current-zero period. Through the complete work, the pressure-rise and the ramp of the pressure inside the chamber before current zero as well as the post-arc current after current zero should be a good criterion to predict the short-line fault interruption performance of interrupters.

  16. Workflow interruptions, social stressors from supervisor(s) and attention failure in surgery personnel.

    Science.gov (United States)

    Pereira, Diana; Müller, Patrick; Elfering, Achim

    2015-01-01

    Workflow interruptions and social stressors among surgery personnel may cause attention failure at work that may increase rumination about work issues during leisure time. The test of these assumptions should contribute to the understanding of exhaustion in surgery personnel and patient safety. Workflow interruptions and supervisor-related social stressors were tested to predict attention failure that predicts work-related rumination during leisure time. One hundred ninety-four theatre nurses, anaesthetists and surgeons from a Swiss University hospital participated in a cross-sectional survey. The participation rate was 58%. Structural equation modelling confirmed both indirect paths from workflow interruptions and social stressors via attention failure on rumination (both pworkflow interruptions and social stressors on rumination-could not be empirically supported. Workflow interruptions and social stressors at work are likely to trigger attention failure in surgery personnel. Work redesign and team intervention could help surgery personnel to maintain a high level of quality and patient safety and detach from work related issues to recover during leisure time.

  17. Power Supply Interruption Costs: Models and Methods Incorporating Time Dependent Patterns

    Energy Technology Data Exchange (ETDEWEB)

    Kjoelle, G.H.

    1996-12-01

    This doctoral thesis develops models and methods for estimation of annual interruption costs for delivery points, emphasizing the handling of time dependent patterns and uncertainties in the variables determining the annual costs. It presents an analytical method for calculation of annual expected interruption costs for delivery points in radial systems, based on a radial reliability model, with time dependent variables. And a similar method for meshed systems, based on a list of outage events, assuming that these events are found in advance from load flow and contingency analyses. A Monte Carlo simulation model is given which handles both time variations and stochastic variations in the input variables and is based on the same list of outage events. This general procedure for radial and meshed systems provides expectation values and probability distributions for interruption costs from delivery points. There is also a procedure for handling uncertainties in input variables by a fuzzy description, giving annual interruption costs as a fuzzy membership function. The methods are developed for practical applications in radial and meshed systems, based on available data from failure statistics, load registrations and customer surveys. Traditional reliability indices such as annual interruption time, power- and energy not supplied, are calculated as by-products. The methods are presented as algorithms and/or procedures which are available as prototypes. 97 refs., 114 figs., 62 tabs.

  18. Photodiode-based cutting interruption sensor for near-infrared lasers.

    Science.gov (United States)

    Adelmann, B; Schleier, M; Neumeier, B; Hellmann, R

    2016-03-01

    We report on a photodiode-based sensor system to detect cutting interruptions during laser cutting with a fiber laser. An InGaAs diode records the thermal radiation from the process zone with a ring mirror and optical filter arrangement mounted between a collimation unit and a cutting head. The photodiode current is digitalized with a sample rate of 20 kHz and filtered with a Chebyshev Type I filter. From the measured signal during the piercing, a threshold value is calculated. When the diode signal exceeds this threshold during cutting, a cutting interruption is indicated. This method is applied to sensor signals from cutting mild steel, stainless steel, and aluminum, as well as different material thicknesses and also laser flame cutting, showing the possibility to detect cutting interruptions in a broad variety of applications. In a series of 83 incomplete cuts, every cutting interruption is successfully detected (alpha error of 0%), while no cutting interruption is reported in 266 complete cuts (beta error of 0%). With this remarkable high detection rate and low error rate, the possibility to work with different materials and thicknesses in combination with the easy mounting of the sensor unit also to existing cutting machines highlight the enormous potential for this sensor system in industrial applications.

  19. Advanced video coding systems

    CERN Document Server

    Gao, Wen

    2015-01-01

    This comprehensive and accessible text/reference presents an overview of the state of the art in video coding technology. Specifically, the book introduces the tools of the AVS2 standard, describing how AVS2 can help to achieve a significant improvement in coding efficiency for future video networks and applications by incorporating smarter coding tools such as scene video coding. Topics and features: introduces the basic concepts in video coding, and presents a short history of video coding technology and standards; reviews the coding framework, main coding tools, and syntax structure of AV

  20. Coding for dummies

    CERN Document Server

    Abraham, Nikhil

    2015-01-01

    Hands-on exercises help you learn to code like a pro No coding experience is required for Coding For Dummies,your one-stop guide to building a foundation of knowledge inwriting computer code for web, application, and softwaredevelopment. It doesn't matter if you've dabbled in coding or neverwritten a line of code, this book guides you through the basics.Using foundational web development languages like HTML, CSS, andJavaScript, it explains in plain English how coding works and whyit's needed. Online exercises developed by Codecademy, a leading online codetraining site, help hone coding skill

  1. New tools to analyze overlapping coding regions.

    Science.gov (United States)

    Bayegan, Amir H; Garcia-Martin, Juan Antonio; Clote, Peter

    2016-12-13

    Retroviruses transcribe messenger RNA for the overlapping Gag and Gag-Pol polyproteins, by using a programmed -1 ribosomal frameshift which requires a slippery sequence and an immediate downstream stem-loop secondary structure, together called frameshift stimulating signal (FSS). It follows that the molecular evolution of this genomic region of HIV-1 is highly constrained, since the retroviral genome must contain a slippery sequence (sequence constraint), code appropriate peptides in reading frames 0 and 1 (coding requirements), and form a thermodynamically stable stem-loop secondary structure (structure requirement). We describe a unique computational tool, RNAsampleCDS, designed to compute the number of RNA sequences that code two (or more) peptides p,q in overlapping reading frames, that are identical (or have BLOSUM/PAM similarity that exceeds a user-specified value) to the input peptides p,q. RNAsampleCDS then samples a user-specified number of messenger RNAs that code such peptides; alternatively, RNAsampleCDS can exactly compute the position-specific scoring matrix and codon usage bias for all such RNA sequences. Our software allows the user to stipulate overlapping coding requirements for all 6 possible reading frames simultaneously, even allowing IUPAC constraints on RNA sequences and fixing GC-content. We generalize the notion of codon preference index (CPI) to overlapping reading frames, and use RNAsampleCDS to generate control sequences required in the computation of CPI. Moreover, by applying RNAsampleCDS, we are able to quantify the extent to which the overlapping coding requirement in HIV-1 [resp. HCV] contribute to the formation of the stem-loop [resp. double stem-loop] secondary structure known as the frameshift stimulating signal. Using our software, we confirm that certain experimentally determined deleterious HCV mutations occur in positions for which our software RNAsampleCDS and RNAiFold both indicate a single possible nucleotide. We

  2. DNA Barcoding through Quaternary LDPC Codes.

    Science.gov (United States)

    Tapia, Elizabeth; Spetale, Flavio; Krsticevic, Flavia; Angelone, Laura; Bulacio, Pilar

    2015-01-01

    For many parallel applications of Next-Generation Sequencing (NGS) technologies short barcodes able to accurately multiplex a large number of samples are demanded. To address these competitive requirements, the use of error-correcting codes is advised. Current barcoding systems are mostly built from short random error-correcting codes, a feature that strongly limits their multiplexing accuracy and experimental scalability. To overcome these problems on sequencing systems impaired by mismatch errors, the alternative use of binary BCH and pseudo-quaternary Hamming codes has been proposed. However, these codes either fail to provide a fine-scale with regard to size of barcodes (BCH) or have intrinsic poor error correcting abilities (Hamming). Here, the design of barcodes from shortened binary BCH codes and quaternary Low Density Parity Check (LDPC) codes is introduced. Simulation results show that although accurate barcoding systems of high multiplexing capacity can be obtained with any of these codes, using quaternary LDPC codes may be particularly advantageous due to the lower rates of read losses and undetected sample misidentification errors. Even at mismatch error rates of 10(-2) per base, 24-nt LDPC barcodes can be used to multiplex roughly 2000 samples with a sample misidentification error rate in the order of 10(-9) at the expense of a rate of read losses just in the order of 10(-6).

  3. DNA Barcoding through Quaternary LDPC Codes.

    Directory of Open Access Journals (Sweden)

    Elizabeth Tapia

    Full Text Available For many parallel applications of Next-Generation Sequencing (NGS technologies short barcodes able to accurately multiplex a large number of samples are demanded. To address these competitive requirements, the use of error-correcting codes is advised. Current barcoding systems are mostly built from short random error-correcting codes, a feature that strongly limits their multiplexing accuracy and experimental scalability. To overcome these problems on sequencing systems impaired by mismatch errors, the alternative use of binary BCH and pseudo-quaternary Hamming codes has been proposed. However, these codes either fail to provide a fine-scale with regard to size of barcodes (BCH or have intrinsic poor error correcting abilities (Hamming. Here, the design of barcodes from shortened binary BCH codes and quaternary Low Density Parity Check (LDPC codes is introduced. Simulation results show that although accurate barcoding systems of high multiplexing capacity can be obtained with any of these codes, using quaternary LDPC codes may be particularly advantageous due to the lower rates of read losses and undetected sample misidentification errors. Even at mismatch error rates of 10(-2 per base, 24-nt LDPC barcodes can be used to multiplex roughly 2000 samples with a sample misidentification error rate in the order of 10(-9 at the expense of a rate of read losses just in the order of 10(-6.

  4. Full-length sequencing and identification of novel polymorphisms in ...

    Indian Academy of Sciences (India)

    The aim of this work was to sequence the entirecoding region of ACACA gene in Valle del Belice sheep breed to identify polymorphic sites. A total of 51 coding exons of ACACA gene were sequenced in 32 individuals of Valle del Belice sheep breed. Sequencing analysis and alignment of obtained sequences showed the ...

  5. The nucleotide sequences of two leghemoglobin genes from soybean

    DEFF Research Database (Denmark)

    Wiborg, O; Hyldig-Nielsen, J J; Jensen, E O

    1982-01-01

    We present the complete nucleotide sequences of two leghemoglobin genes isolated from soybean DNA. Both genes contain three intervening sequences in identical positions. Comparison of the coding sequences with known amino-acid sequences of soybean leghemoglobins suggest that the two genes...

  6. An automated annotation tool for genomic DNA sequences using

    Indian Academy of Sciences (India)

    Genomic sequence data are often available well before the annotated sequence is published. We present a method for analysis of genomic DNA to identify coding sequences using the GeneScan algorithm and characterize these resultant sequences by BLAST. The routines are used to develop a system for automated ...

  7. Rapid resumption of interrupted visual search. New insights on the interaction between vision and memory.

    Science.gov (United States)

    Lleras, Alejandro; Rensink, Ronald A; Enns, James T

    2005-09-01

    A modified visual search task demonstrates that humans are very good at resuming a search after it has been momentarily interrupted. This is shown by exceptionally rapid response time to a display that reappears after a brief interruption, even when an entirely different visual display is seen during the interruption and two different visual searches are performed simultaneously. This rapid resumption depends on the stability of the visual scene and is not due to display or response anticipations. These results are consistent with the existence of an iterative hypothesis-testing mechanism that compares information stored in short-term memory (the perceptual hypothesis) with information about the display (the sensory pattern). In this view, rapid resumption occurs because a hypothesis based on a previous glance of the scene can be tested very rapidly in a subsequent glance, given that the initial hypothesis-generation step has already been performed.

  8. Electric circuit breaker comprising a plurality of vacuum interrupters simultaneously operated by a common operator

    Science.gov (United States)

    Barkan, Philip; Imam, Imdad

    1980-01-01

    This circuit breaker comprises a plurality of a vacuum-type circuit interrupters, each having a movable contact rod. A common operating device for the interrupters comprises a linearly-movable operating member. The interrupters are mounted at one side of the operating member with their movable contact rods extending in a direction generally toward the operating member. Means is provided for mechanically coupling the operating member to the contact rods, and this means comprises a plurality of insulating operating rods, each connected at one end to the operating member and at its opposite end to one of the movable contact rods. The operating rods are of substantially equal length and have longitudinal axes that converge and intersect at substantially a common point.

  9. Finite element analyses of a heater-interruption in the HAW test field

    International Nuclear Information System (INIS)

    Horn, B.A. van den.

    1991-09-01

    In this report the results of two finite element analyses of the HAW field are presented. The determination of the influence of a heater-interruption on the tube load as well as the differences in the evaluation of the tube load for both types of boreholes (type A and type B) are the main objectives of this report. Axisymmetric models are made for both type of boreholes in order to simulate this heater-interruption. It appeared that a heater-interruption of 4 hours leads to a temperature drop of 17.2deg C at the borehole wall and to a maximum reduction of the tube load of 1.76 MPa. About 20 days after reparation of the heaters of the heaters the evolution of the maximum temperature and the maximum tube load will be rehabilitated; the difference with the corresponding evolutions due to an uninterrupted heat-production are negligible. (author). 9 refs.; 25 figs.; 5 tabs

  10. How much should customers be compensated for interruptions in the drinking water supply?

    Science.gov (United States)

    Molinos-Senante, María; Sala-Garrido, Ramon

    2017-05-15

    Water supply interruptions directly affect customers, and customers should be compensated accordingly. However, few water regulators have applied compensation policies given the difficulty of estimating the economic value of compensation to customers. In this study, a pioneering approach based on the concept of shadow prices is proposed to determine the compensation that customers should receive for unplanned water interruptions. The Chilean water industry was selected as a case study because there is an ongoing policy discussion between the use of penalties or compensation as an incentive to prevent water supply interruptions. The estimated results indicate that for 2014, the value of compensation ranges between 2.4% and 35.4% of the fixed charge of the water tariff. The methodology and findings of this study are of great relevance to water regulators in defining incentives to prompt water companies to provide reliable water service. Copyright © 2017 Elsevier B.V. All rights reserved.

  11. Growth-interruption-induced low-density InAs quantum dots on GaAs

    International Nuclear Information System (INIS)

    Li, L. H.; Alloing, B.; Chauvin, N.; Fiore, A.; Patriarche, G.

    2008-01-01

    We investigate the use of growth interruption to obtain low-density InAs quantum dots (QDs) on GaAs. The process was realized by Ostwald-type ripening of a thin InAs layer. It was found that the optical properties of the QDs as a function of growth interruption strongly depend on InAs growth rate. By using this approach, a low density of QDs (4 dots/μm 2 ) with uniform size distribution was achieved. As compared to QDs grown without growth interruption, a larger energy separation between the QD confined levels was observed, suggesting a situation closer to the ideal zero-dimensional system. Combining with an InGaAs capping layer such as In-rich QDs enable 1.3 μm emission at 4 K

  12. Mediated interruptions of anaesthesia providers using predictions of workload from anaesthesia information management system data.

    Science.gov (United States)

    Epstein, R H; Dexter, F

    2012-09-01

    Perioperative interruptions generated electronically from anaesthesia information management systems (AIMS) can provide useful feedback, but may adversely affect task performance if distractions occur at inopportune moments. Ideally such interruptions would occur only at times when their impact would be minimal. In this study of AIMS data, we evaluated the times of comments, drugs, fluids and periodic assessments (e.g. electrocardiogram diagnosis and train-of-four) to develop recommendations for the timing of interruptions during the intraoperative period. The 39,707 cases studied were divided into intervals between: 1) enter operating room; 2) induction; 3) intubation; 4) surgical incision; and 5) end surgery. Five-minute intervals of no documentation were determined for each case. The offsets from the start of each interval when >50% of ongoing cases had completed initial documentation were calculated (MIN50). The primary endpoint for each interval was the percentage of all cases still ongoing at MIN50. Results were that the intervals from entering the operating room to induction and from induction to intubation were unsuitable for interruptions confirming prior observational studies of anaesthesia workload. At least 13 minutes after surgical incision was the most suitable time for interruptions with 92% of cases still ongoing. Timing was minimally affected by the type of anaesthesia, surgical facility, surgical service, prone positioning or scheduled case duration. The implication of our results is that for mediated interruptions, waiting at least 13 minutes after the start of surgery is appropriate. Although we used AIMS data, operating room information system data is also suitable.

  13. Greater physiological and behavioral effects of interrupted stress pattern compared to daily restraint stress in rats.

    Directory of Open Access Journals (Sweden)

    Wei Zhang

    Full Text Available Repeated stress can trigger a range of psychiatric disorders, including anxiety. The propensity to develop abnormal behaviors after repeated stress is related to the severity, frequency and number of stressors. However, the pattern of stress exposure may contribute to the impact of stress. In addition, the anxiogenic nature of repeated stress exposure can be moderated by the degree of coping that occurs, and can be reflected in homotypic habituation to the repeated stress. However, expectations are not clear when a pattern of stress presentation is utilized that diminishes habituation. The purpose of these experiments is to test whether interrupted stress exposure decreases homotypic habituation and leads to greater effects on anxiety-like behavior in adult male rats. We found that repeated interrupted restraint stress resulted in less overall homotypic habituation compared to repeated daily restraint stress. This was demonstrated by greater production of fecal boli and greater corticosterone response to restraint. Furthermore, interrupted restraint stress resulted in a lower body weight and greater adrenal gland weight than daily restraint stress, and greater anxiety-like behavior in the elevated plus maze. Control experiments demonstrated that these effects of the interrupted pattern could not be explained by differences in the total number of stress exposures, differences in the total number of days that the stress periods encompased, nor could it be explained as a result of only the stress exposures after an interruption from stress. These experiments demonstrate that the pattern of stress exposure is a significant determinant of the effects of repeated stress, and that interrupted stress exposure that decreases habituation can have larger effects than a greater number of daily stress exposures. Differences in the pattern of stress exposure are therefore an important factor to consider when predicting the severity of the effects of repeated

  14. Discussion on LDPC Codes and Uplink Coding

    Science.gov (United States)

    Andrews, Ken; Divsalar, Dariush; Dolinar, Sam; Moision, Bruce; Hamkins, Jon; Pollara, Fabrizio

    2007-01-01

    This slide presentation reviews the progress that the workgroup on Low-Density Parity-Check (LDPC) for space link coding. The workgroup is tasked with developing and recommending new error correcting codes for near-Earth, Lunar, and deep space applications. Included in the presentation is a summary of the technical progress of the workgroup. Charts that show the LDPC decoder sensitivity to symbol scaling errors are reviewed, as well as a chart showing the performance of several frame synchronizer algorithms compared to that of some good codes and LDPC decoder tests at ESTL. Also reviewed is a study on Coding, Modulation, and Link Protocol (CMLP), and the recommended codes. A design for the Pseudo-Randomizer with LDPC Decoder and CRC is also reviewed. A chart that summarizes the three proposed coding systems is also presented.

  15. Molecular phylogenetics of the family Cyprinidae (Actinopterygii: Cypriniformes) as evidenced by sequence variation in the first intron of S7 ribosomal protein-coding gene: further evidence from a nuclear gene of the systematic chaos in the family.

    Science.gov (United States)

    He, Shunping; Mayden, Richard L; Wang, Xuzheng; Wang, Wei; Tang, Kevin L; Chen, Wei-Jen; Chen, Yiyu

    2008-03-01

    The family Cyprinidae is the largest freshwater fish group in the world, including over 200 genera and 2100 species. The phylogenetic relationships of major clades within this family are simply poorly understood, largely because of the overwhelming diversity of the group; however, several investigators have advanced different hypotheses of relationships that pre- and post-date the use of shared-derived characters as advocated through phylogenetic systematics. As expected, most previous investigations used morphological characters. Recently, mitochondrial DNA (mtDNA) sequences and combined morphological and mtDNA investigations have been used to explore and advance our understanding of species relationships and test monophyletic groupings. Limitations of these studies include limited taxon sampling and a strict reliance upon maternally inherited mtDNA variation. The present study is the first endeavor to recover the phylogenetic relationships of the 12 previously recognized monophyletic subfamilies within the Cyprinidae using newly sequenced nuclear DNA (nDNA) for over 50 species representing members of the different previously hypothesized subfamily and family groupings within the Cyprinidae and from other cypriniform families as outgroup taxa. Hypothesized phylogenetic relationships are constructed using maximum parsimony and Basyesian analyses of 1042 sites, of which 971 sites were variable and 790 were phylogenetically informative. Using other appropriate cypriniform taxa of the families Catostomidae (Myxocyprinus asiaticus), Gyrinocheilidae (Gyrinocheilus aymonieri), and Balitoridae (Nemacheilus sp. and Beaufortia kweichowensis) as outgroups, the Cyprinidae is resolved as a monophyletic group. Within the family the genera Raiamas, Barilius, Danio, and Rasbora, representing many of the tropical cyprinids, represent basal members of the family. All other species can be classified into variably supported and resolved monophyletic lineages, depending upon analysis

  16. Arch reconstruction with autologous pulmonary artery patch in interrupted aortic arch.

    Science.gov (United States)

    Lee, Won-Young; Park, Jeong-Jun

    2014-04-01

    Various surgical techniques have been developed for the repair of an interrupted aortic arch. However, tension and Gothic arch formation at the anastomotic site have remained major problems for these techniques: Excessive tension causes arch stenosis and left main bronchus compression, and Gothic arch configuration is related to cardiovascular complications. To resolve these problems, we adopted a modified surgical technique of distal aortic arch augmentation using an autologous main pulmonary artery patch. The descending aorta was then anastomosed to the augmented aortic arch in an end-to-side manner. Here, we report two cases of interrupted aortic arch that were repaired using this technique.

  17. Optimal Allocation of Smart Substations in a Distribution System Considering Interruption Costs of Customers

    DEFF Research Database (Denmark)

    Sun, Lei; You, Shi; Hu, Junjie

    2016-01-01

    number and allocation of smart substations in a given distribution system is presented, with the upgrade costs of substations and the interruption costs of customers taken into account. Besides, the reliability criterion is also properly considered in the model. By linearization strategies, the SSAM......One of the major functions of a smart substation (SS) is to restore power supply to interrupted customers as quickly as possible after an outage. The high cost of a smart substation limits its widespread utilization. In this paper, a smart substation allocation model (SSAM) to determine the optimal...

  18. Deciphering the genetic regulatory code using an inverse error control coding framework.

    Energy Technology Data Exchange (ETDEWEB)

    Rintoul, Mark Daniel; May, Elebeoba Eni; Brown, William Michael; Johnston, Anna Marie; Watson, Jean-Paul

    2005-03-01

    We have found that developing a computational framework for reconstructing error control codes for engineered data and ultimately for deciphering genetic regulatory coding sequences is a challenging and uncharted area that will require advances in computational technology for exact solutions. Although exact solutions are desired, computational approaches that yield plausible solutions would be considered sufficient as a proof of concept to the feasibility of reverse engineering error control codes and the possibility of developing a quantitative model for understanding and engineering genetic regulation. Such evidence would help move the idea of reconstructing error control codes for engineered and biological systems from the high risk high payoff realm into the highly probable high payoff domain. Additionally this work will impact biological sensor development and the ability to model and ultimately develop defense mechanisms against bioagents that can be engineered to cause catastrophic damage. Understanding how biological organisms are able to communicate their genetic message efficiently in the presence of noise can improve our current communication protocols, a continuing research interest. Towards this end, project goals include: (1) Develop parameter estimation methods for n for block codes and for n, k, and m for convolutional codes. Use methods to determine error control (EC) code parameters for gene regulatory sequence. (2) Develop an evolutionary computing computational framework for near-optimal solutions to the algebraic code reconstruction problem. Method will be tested on engineered and biological sequences.

  19. Locally orderless registration code

    DEFF Research Database (Denmark)

    2012-01-01

    This is code for the TPAMI paper "Locally Orderless Registration". The code requires intel threadding building blocks installed and is provided for 64 bit on mac, linux and windows.......This is code for the TPAMI paper "Locally Orderless Registration". The code requires intel threadding building blocks installed and is provided for 64 bit on mac, linux and windows....

  20. Decoding Codes on Graphs

    Indian Academy of Sciences (India)

    Shannon limit of the channel. Among the earliest discovered codes that approach the. Shannon limit were the low density parity check (LDPC) codes. The term low density arises from the property of the parity check matrix defining the code. We will now define this matrix and the role that it plays in decoding. 2. Linear Codes.

  1. Manually operated coded switch

    International Nuclear Information System (INIS)

    Barnette, J.H.

    1978-01-01

    The disclosure related to a manually operated recodable coded switch in which a code may be inserted, tried and used to actuate a lever controlling an external device. After attempting a code, the switch's code wheels must be returned to their zero positions before another try is made

  2. Genetically-barcoded SIV facilitates enumeration of rebound variants and estimation of reactivation rates in nonhuman primates following interruption of suppressive antiretroviral therapy.

    Directory of Open Access Journals (Sweden)

    Christine M Fennessey

    2017-05-01

    Full Text Available HIV and SIV infection dynamics are commonly investigated by measuring plasma viral loads. However, this total viral load value represents the sum of many individual infection events, which are difficult to independently track using conventional sequencing approaches. To overcome this challenge, we generated a genetically tagged virus stock (SIVmac239M with a 34-base genetic barcode inserted between the vpx and vpr accessory genes of the infectious molecular clone SIVmac239. Next-generation sequencing of the virus stock identified at least 9,336 individual barcodes, or clonotypes, with an average genetic distance of 7 bases between any two barcodes. In vitro infection of rhesus CD4+ T cells and in vivo infection of rhesus macaques revealed levels of viral replication of SIVmac239M comparable to parental SIVmac239. After intravenous inoculation of 2.2x105 infectious units of SIVmac239M, an average of 1,247 barcodes were identified during acute infection in 26 infected rhesus macaques. Of the barcodes identified in the stock, at least 85.6% actively replicated in at least one animal, and on average each barcode was found in 5 monkeys. Four infected animals were treated with combination antiretroviral therapy (cART for 82 days starting on day 6 post-infection (study 1. Plasma viremia was reduced from >106 to <15 vRNA copies/mL by the time treatment was interrupted. Virus rapidly rebounded following treatment interruption and between 87 and 136 distinct clonotypes were detected in plasma at peak rebound viremia. This study confirmed that SIVmac239M viremia could be successfully curtailed with cART, and that upon cART discontinuation, rebounding viral variants could be identified and quantified. An additional 6 animals infected with SIVmac239M were treated with cART beginning on day 4 post-infection for 305, 374, or 482 days (study 2. Upon treatment interruption, between 4 and 8 distinct viral clonotypes were detected in each animal at peak rebound

  3. Coding in Muscle Disease.

    Science.gov (United States)

    Jones, Lyell K; Ney, John P

    2016-12-01

    Accurate coding is critically important for clinical practice and research. Ongoing changes to diagnostic and billing codes require the clinician to stay abreast of coding updates. Payment for health care services, data sets for health services research, and reporting for medical quality improvement all require accurate administrative coding. This article provides an overview of administrative coding for patients with muscle disease and includes a case-based review of diagnostic and Evaluation and Management (E/M) coding principles in patients with myopathy. Procedural coding for electrodiagnostic studies and neuromuscular ultrasound is also reviewed.

  4. Flexible manipulation of terahertz wave reflection using polarization insensitive coding metasurfaces.

    Science.gov (United States)

    Jiu-Sheng, Li; Ze-Jiang, Zhao; Jian-Quan, Yao

    2017-11-27

    In order to extend to 3-bit encoding, we propose notched-wheel structures as polarization insensitive coding metasurfaces to control terahertz wave reflection and suppress backward scattering. By using a coding sequence of "00110011…" along x-axis direction and 16 × 16 random coding sequence, we investigate the polarization insensitive properties of the coding metasurfaces. By designing the coding sequences of the basic coding elements, the terahertz wave reflection can be flexibly manipulated. Additionally, radar cross section (RCS) reduction in the backward direction is less than -10dB in a wide band. The present approach can offer application for novel terahertz manipulation devices.

  5. QR Codes 101

    Science.gov (United States)

    Crompton, Helen; LaFrance, Jason; van 't Hooft, Mark

    2012-01-01

    A QR (quick-response) code is a two-dimensional scannable code, similar in function to a traditional bar code that one might find on a product at the supermarket. The main difference between the two is that, while a traditional bar code can hold a maximum of only 20 digits, a QR code can hold up to 7,089 characters, so it can contain much more…

  6. A bar coding system for environmental projects

    International Nuclear Information System (INIS)

    Barber, R.B.; Hunt, B.J.; Burgess, G.M.

    1988-01-01

    This paper presents BeCode systems, a bar coding system which provides both nuclear and commercial clients with a data capture and custody management program that is accurate, timely, and beneficial to all levels of project operations. Using bar code identifiers is an essentially paperless and error-free method which provides more efficient delivery of data through its menu card-driven structure, which speeds collection of essential data for uploading to a compatible device. The effects of this sequence include real-time information for operator analysis, management review, audits, planning, scheduling, and cost control

  7. Utility of QR codes in biological collections.

    Science.gov (United States)

    Diazgranados, Mauricio; Funk, Vicki A

    2013-01-01

    The popularity of QR codes for encoding information such as URIs has increased exponentially in step with the technological advances and availability of smartphones, digital tablets, and other electronic devices. We propose using QR codes on specimens in biological collections to facilitate linking vouchers' electronic information with their associated collections. QR codes can efficiently provide such links for connecting collections, photographs, maps, ecosystem notes, citations, and even GenBank sequences. QR codes have numerous advantages over barcodes, including their small size, superior security mechanisms, increased complexity and quantity of information, and low implementation cost. The scope of this paper is to initiate an academic discussion about using QR codes on specimens in biological collections.

  8. Utility of QR codes in biological collections

    Directory of Open Access Journals (Sweden)

    Mauricio Diazgranados

    2013-07-01

    Full Text Available The popularity of QR codes for encoding information such as URIs has increased exponentially in step with the technological advances and availability of smartphones, digital tablets, and other electronic devices. We propose using QR codes on specimens in biological collections to facilitate linking vouchers’ electronic information with their associated collections. QR codes can efficiently provide such links for connecting collections, photographs, maps, ecosystem notes, citations, and even GenBank sequences. QR codes have numerous advantages over barcodes, including their small size, superior security mechanisms, increased complexity and quantity of information, and low implementation cost. The scope of this paper is to initiate an academic discussion about using QR codes on specimens in biological collections.

  9. On Coding Non-Contiguous Letter Combinations

    Directory of Open Access Journals (Sweden)

    Frédéric eDandurand

    2011-06-01

    Full Text Available Starting from the hypothesis that printed word identification initially involves the parallel mapping of visual features onto location-specific letter identities, we analyze the type of information that would be involved in optimally mapping this location-specific orthographic code onto a location-invariant lexical code. We assume that some intermediate level of coding exists between individual letters and whole words, and that this involves the representation of letter combinations. We then investigate the nature of this intermediate level of coding given the constraints of optimality. This intermediate level of coding is expected to compress data while retaining as much information as possible about word identity. Information conveyed by letters is a function of how much they constrain word identity and how visible they are. Optimization of this coding is a combination of minimizing resources (using the most compact representations and maximizing information. We show that in a large proportion of cases, non-contiguous letter sequences contain more information than contiguous sequences, while at the same time requiring less precise coding. Moreover, we found that the best predictor of human performance in orthographic priming experiments was within-word ranking of conditional probabilities, rather than average conditional probabilities. We conclude that from an optimality perspective, readers learn to select certain contiguous and non-contiguous letter combinations as information that provides the best cue to word identity.

  10. Design of Long Period Pseudo-Random Sequences from the Addition of -Sequences over

    Directory of Open Access Journals (Sweden)

    Ren Jian

    2004-01-01

    Full Text Available Pseudo-random sequence with good correlation property and large linear span is widely used in code division multiple access (CDMA communication systems and cryptology for reliable and secure information transmission. In this paper, sequences with long period, large complexity, balance statistics, and low cross-correlation property are constructed from the addition of -sequences with pairwise-prime linear spans (AMPLS. Using -sequences as building blocks, the proposed method proved to be an efficient and flexible approach to construct long period pseudo-random sequences with desirable properties from short period sequences. Applying the proposed method to , a signal set is constructed.

  11. Rapid Resumption of Interrupted Search Is Independent of Age-Related Improvements in Visual Search

    Science.gov (United States)

    Lleras, Alejandro; Porporino, Mafalda; Burack, Jacob A.; Enns, James T.

    2011-01-01

    In this study, 7-19-year-olds performed an interrupted visual search task in two experiments. Our question was whether the tendency to respond within 500 ms after a second glimpse of a display (the "rapid resumption" effect ["Psychological Science", 16 (2005) 684-688]) would increase with age in the same way as overall search efficiency. The…

  12. Planning of continuity of service: The nuisance index, a measurement of the impact of interruptions

    International Nuclear Information System (INIS)

    Naggar, R.

    1992-01-01

    An improved approach has been developed by Hydro-Quebec to integrate its customers' needs into the planning for service continuity. A nuisance index has been developed to measure the impact of service interruptions and is currently being tested with a pilot project in the Richelieu service area. The analytic framework used differentiates three categories of customers for which a normative cost of interrptions is calculated. The classification of networks according to load density and use characteristics allows the utility to define appropriate service continuity objectives. Service continuity is measured using an indicator which is directly deduced from the cost of interruptions. The index takes into account the circumstances surrounding each interruption and an individual nuisance index is calculated for each customer. Then an average individual nuisance index is computed for customers within each category. Finally, an aggregated nuisance index is calculated for all categories as a whole. The cost of interruptions may then be derived through multiplying the nuisance indexes by the energy consumption of the corresponding set of customers and by a constant. It is possible to check whether a customer is receiving acceptable service continuity. An indicator determines the share of energy consumption for which a tolerance threshold has been exceeded. Once integrated into the planning process, these concepts enable optimal distribution network design and operation. Adjustments of network classes that match both the evolution of customers and load contribute to the permanent improvement of networks and their operation. 4 figs

  13. Three-dimensional printing in surgical planning: A case of aortopulmonary window with interrupted aortic arch

    Directory of Open Access Journals (Sweden)

    Ryan A Moore

    2018-01-01

    Full Text Available Better anatomical understanding and conceptualization of complex congenital heart defects using three-dimensional (3D printing may improve surgical planning, especially in rare defects. In this report, we utilized 3D printing to delineate the exact cardiac anatomy of a neonate with an aortopulmonary window associated with interrupted aortic arch to devise a novel approach to the repair.

  14. Analysis of Data Interruption in an LTE Highway Scenario with Dual Connectivity

    DEFF Research Database (Denmark)

    Gimenez, Lucas Chavarria; Michaelsen, Per-Henrik; Pedersen, Klaus I.

    2016-01-01

    This study evaluates whether last versions of Long Term Evolution with dual connectivity are able to support the latency and reliability requirements for the upcoming vehicular use-cases and time-critical applications. Data interruption times during handovers and cell management operations are ev...

  15. Airway resistance measurements in pre-school children with asthmatic symptoms : The interrupter technique

    NARCIS (Netherlands)

    Kooi, EMW; Schokker, S; van der Molen, T; Duiverman, EJ

    Measuring airway resistance in pre-school children with the interrupter technique has proven to be feasible and reliable in daily clinical practice and research settings. Whether it contributes to diagnosing asthma in pre-schoot children still remains uncertain. From the results of previous studies

  16. Brain activity patterns induced by interrupting the cognitive processes with online advertising.

    Science.gov (United States)

    Rejer, Izabela; Jankowski, Jarosław

    2017-11-01

    As a result of the increasing role of online advertising and strong competition among advertisers, intrusive techniques are commonly used to attract web users' attention. Moreover, since marketing content is usually delivered to the target audience when they are performing typical online tasks, like searching for information or reading online content, its delivery interrupts the web user's current cognitive process. The question posed by many researchers in the field of online advertising is: how should we measure the influence of interruption of cognitive processes on human behavior and emotional state? Much research has been conducted in this field; however, most of this research has focused on monitoring activity in the simulated environment, or processing declarative responses given by users in prepared questionnaires. In this paper, a more direct real-time approach is taken, and the effect of the interruption on a web user is analyzed directly by studying the activity of his brain. This paper presents the results of an experiment that was conducted to find the brain activity patterns associated with interruptions of the cognitive process by showing internet advertisements during a text-reading task. Three specific aspects were addressed in the experiment: individual patterns, the consistency of these patterns across trials, and the intra-subject correlation of the individual patterns. Two main effects were observed for most subjects: a drop in activity in the frontal and prefrontal cortical areas across all frequency bands, and significant changes in the frontal/prefrontal asymmetry index.

  17. Influence of Gap Distance on Vacuum Arc Characteristics of Cup Type AMF Electrode in Vacuum Interrupters

    International Nuclear Information System (INIS)

    Cheng Shaoyong; Xiu Shixin; Wang Jimei; Shen Zhengchao

    2006-01-01

    The greenhouse effect of SF 6 is a great concern today. The development of high voltage vacuum circuit breakers becomes more important. The vacuum circuit breaker has minimum pollution to the environment. The vacuum interrupter is the key part of a vacuum circuit breaker. The interrupting characteristics in vacuum and arc-controlling technique are the main problems to be solved for a longer gap distance in developing high voltage vacuum interrupters. To understand the vacuum arc characteristics and provide effective technique to control vacuum arc in a long gap distance, the arc mode transition of a cup-type axial magnetic field electrode is observed by a high-speed charge coupled device (CCD) video camera under different gap distances while the arc voltage and arc current are recorded. The controlling ability of the axial magnetic field on vacuum arc obviously decreases when the gap distance is longer than 40 mm. The noise components and mean value of the arc voltage significantly increase. The effective method for controlling the vacuum arc characteristics is provided by long gap distances based on the test results. The test results can be used as a reference to develop high voltage and large capacity vacuum interrupters

  18. A Unified Framework for Estimating Minimum Detectable Effects for Comparative Short Interrupted Time Series Designs

    Science.gov (United States)

    Price, Cristofer; Unlu, Fatih

    2014-01-01

    The Comparative Short Interrupted Time Series (C-SITS) design is a frequently employed quasi-experimental method, in which the pre- and post-intervention changes observed in the outcome levels of a treatment group is compared with those of a comparison group where the difference between the former and the latter is attributed to the treatment. The…

  19. Comparison Groups in Short Interrupted Time-Series: An Illustration Evaluating No Child Left Behind

    Science.gov (United States)

    Wong, Manyee; Cook, Thomas D.; Steiner, Peter M.

    2009-01-01

    Interrupted time-series (ITS) are often used to assess the causal effect of a planned or even unplanned shock introduced into an on-going process. The pre-intervention slope is supposed to index the causal counterfactual, and deviations from it in mean, slope or variance are used to indicate an effect. However, a secure causal inference is only…

  20. The costs of power interruptions in Germany. An assessment in the light of the Energiewende

    Energy Technology Data Exchange (ETDEWEB)

    Growitsch, Christian; Malischek, Raimund; Nick, Sebastian; Wetzel, Heike

    2013-04-15

    The German Energiewende's potential effects on the reliability of electricity supply as well as the corresponding economic consequences have recently entered both the political and scientific debate. However, empirical evidence of power outage costs in Germany is rather scarce. Following a macroeconomic approach, we analyse the economic costs imposed by potential power interruptions in Germany. Investigating a rich data set on industry and households we estimate both Values of Lost Load (VoLLs) and associated costs of power interruptions for different German regions and sectors and every hour of the year. This disaggregated approach allows for conclusions for optimal load shedding in case of technical necessity and the economic efficiency of measures to improve security of supply. We find that interruption costs vary significantly over time, between sectors and regions. Peaking on midday of a Monday in December at 750 Mio Euro per hour, the average of total national outage costs amount to approximately 430 Mio Euro per hour. The industrial sectors facing the highest outage costs are the machinery and transport equipment sectors. Their aggregated hourly outage costs average out at approximately 20 Mio Euro. Our results emphasize the prominent regional aspect of the German Energiewende as the regions with the highest estimated cost of interruptions in South and West Germany coincide with the areas which face nuclear power plant shut downs in the near future.

  1. A randomized controlled trial of daily sedation interruption in critically ill children

    NARCIS (Netherlands)

    N.J. Vet (Nienke); S.N. de Wildt (Saskia); C.W.M. Verlaat (Carin); C.A.J. Knibbe (Catherijne); M.G. Mooij (Miriam); J.B. van Woensel (Job); J.M. van Rosmalen (Joost); D. Tibboel (Dick); M. de Hoog (Matthijs)

    2016-01-01

    textabstractPurpose: To compare daily sedation interruption plus protocolized sedation (DSI + PS) to protocolized sedation only (PS) in critically ill children. Methods: In this multicenter randomized controlled trial in three pediatric intensive care units in the Netherlands, mechanically

  2. Immunological Analysis of Treatment Interruption After Early Highly Active Antiretroviral Therapy

    NARCIS (Netherlands)

    Schellens, Ingrid M. M.; Pogany, Katalin; Westerlaken, Geertje H. A.; Borghans, José A. M.; Miedema, Frank; van Valkengoed, Irene G. M.; Kroon, Frank P.; Lange, Joep M. A.; Brinkman, Kees; Prins, Jan M.; van Baarle, Debbie

    2010-01-01

    We longitudinally evaluated HIV-specific T-cell immunity after discontinuation of highly active antiretroviral therapy (HAART). After treatment interruption (TI), some individuals could maintain a low plasma viral load ( <15,000 copies/mL), whereas others could not (>50,000 copies/mL). Before HAART

  3. Eventual Suicide in Interrupted and Uninterrupted Attempters: A Challenge to the Cry-for-Help Hypothesis.

    Science.gov (United States)

    Steer, Robert A.; And Others

    1988-01-01

    Followed patients (N=499) hospitalized for suicide attempts (attempters) between 1970 and 1975 until 1982. Found under six percent eventually committed suicide. Found the interrupted attempters were approximately three times more likely to commit suicide than were the uninterrupted attempters. (Author/ABL)

  4. Role of working memory and lexical knowledge in perceptual restoration of interrupted speech.

    Science.gov (United States)

    Nagaraj, Naveen K; Magimairaj, Beula M

    2017-12-01

    The role of working memory (WM) capacity and lexical knowledge in perceptual restoration (PR) of missing speech was investigated using the interrupted speech perception paradigm. Speech identification ability, which indexed PR, was measured using low-context sentences periodically interrupted at 1.5 Hz. PR was measured for silent gated, low-frequency speech noise filled, and low-frequency fine-structure and envelope filled interrupted conditions. WM capacity was measured using verbal and visuospatial span tasks. Lexical knowledge was assessed using both receptive vocabulary and meaning from context tests. Results showed that PR was better for speech noise filled condition than other conditions tested. Both receptive vocabulary and verbal WM capacity explained unique variance in PR for the speech noise filled condition, but were unrelated to performance in the silent gated condition. It was only receptive vocabulary that uniquely predicted PR for fine-structure and envelope filled conditions. These findings suggest that the contribution of lexical knowledge and verbal WM during PR depends crucially on the information content that replaced the silent intervals. When perceptual continuity was partially restored by filler speech noise, both lexical knowledge and verbal WM capacity facilitated PR. Importantly, for fine-structure and envelope filled interrupted conditions, lexical knowledge was crucial for PR.

  5. Current-zero measurements of vacuum circuit breakers interrupting short-line faults

    NARCIS (Netherlands)

    Smeets, R.P.P.; Linden, van der W.A.

    2003-01-01

    Current zero measurements are performed during short-line fault interruption tests of vacuum circuit breakers. This switching cycle is characterized by a very steep transient recovery voltage. High-resolution measurements of near current-zero arc current and voltage were carried out. Various

  6. Do Work Beliefs Moderate the Relationship Between Work Interruptions, Wellbeing and Psychosomatic Symptoms?

    Science.gov (United States)

    Zoupanou, Zoi(e); Rydstedt, Leif W.

    2017-01-01

    The purpose of this study was to explore the moderating effects of work beliefs in the relationship between work interruptions and general health, wellbeing and reports of psychosomatic symptoms. Self-report data were gathered from 310 employees from different occupational sectors. Results revealed that beliefs in hard work and morality ethic moderated the positive appraisal of work interruptions and acted as protective factors on impaired general health and wellbeing. The relationship was stronger among employees who endorsed strong beliefs in hard work and did not have regard for morality/ethics as a value. Likewise, beliefs in delay of gratification and morality/ethics moderated positive appraisal of work interruptions and reduced psychosomatic complaints. More specifically, the relationship was stronger among employees who had strong belief in the values of delayed gratification and weaker morality/ethics. These findings indicate that organisations should adopt work ideology or practices focused on work values particularly of hard work, delay of gratification and conformity to morality as protective factors that reduce the impact of work interruptions on employees’ general health and wellbeing. PMID:28580023

  7. RTtxGap: An android radiobiological tool for compensation of radiotherapy treatment interruption

    International Nuclear Information System (INIS)

    Yusoff, A L; Mohamad, M; Bhavaraju, V M K; Idris, N R Nik; Abdullah, R

    2016-01-01

    Treatment interruption is not uncommon in radiotherapy. Common reasons for treatment interruption include machine breakdown, holidays and patient severe radiation reactions. Here RTtxGap, an Android application to assist calculations of compensation for treatment gap, is reported. It uses linear quadratic (LQ) model to calculate the biological effective dose (BED) that is used to solve for treatment gap compensations. Solutions are calculated using BED equation, with consideration for tissue proliferation. The accuracy of results has been verified using LQL Equiv software to be accurate within 1%. Five treatment interruption examples were used to illustrate the capability of the software to calculate the treatment compensation schedules. Solving these examples also illustrates the general consensus regarding compensating for unscheduled treatment interruptions, which ultimately involves balancing the BEDs of tumour and organ at risk. In addition to compensation for treatment gap, RTtxGap can also be used to calculate equivalent total dose in 2-Gy fraction (EQD2), to modify treatment schedule and to calculate alternative dose prescriptions having the same isoeffect. (paper)

  8. The costs of electricity interruptions in Spain. Are we sending the right signals?

    International Nuclear Information System (INIS)

    Linares, Pedro; Rey, Luis

    2013-01-01

    One of the objectives of energy security is the uninterrupted physical availability of energy. However, there is limited information about how much is the cost of energy supply interruptions. This information is essential to optimize investment and operating decisions to prevent energy shortages, or, alternatively, to determine the strength of the signals to be sent to the agents so that they may invest accordingly. In this paper, we estimate the economic impact of an electricity interruption in different sectors and regions of Spain. Although there are several caveats in our analysis, we find that in 2008 the cost for the Spanish economy of one kWh of electricity not supplied was above €4 even in a conservative scenario, which is higher than the signals currently being sent as incentives to avoid these interruptions. This might result in an underinvestment in short-term energy security, particularly when we add the usual risk aversion of most consumers. - Highlights: • We calculate the costs of electricity interruptions in Spain. • We find that in 2008 the cost for the Spanish economy of one kWh of electricity not supplied was around €6. • The results imply that Spain is underinvesting in short-term energy security

  9. Preparing School Leaders to Interrupt Racism at Various Levels in Educational Systems

    Science.gov (United States)

    Boske, Christa

    2015-01-01

    This narrative inquiry seeks to advance the field of educational leadership preparation by exploring ways to interrupt personal, interpersonal, and institutional racism through the senses--ways in which people perceive their experiences and relation to others. Findings suggest that participants engage in actions aligned with revelations from their…

  10. The Impact of the Hotel Room Tax: An Interrupted Time Series Approach

    OpenAIRE

    Bonham, Carl; Fujii, Edwin; Im, Eric; Mak, James

    1992-01-01

    Employs interrupted time series analysis to estimate ex post the impact of a hotel room tax on real net hotel revenues by analyzing that time series before and after the imposition of the tax. Finds that the tax had a negligible effect on real hotel revenues.

  11. Further Evaluation of Response Interruption and Redirection as Treatment for Stereotypy

    Science.gov (United States)

    Ahrens, Erin N.; Lerman, Dorothea C.; Kodak, Tiffany; Worsdell, April S.; Keegan, Courtney

    2011-01-01

    The effects of 2 forms of response interruption and redirection (RIRD)--motor RIRD and vocal RIRD--were examined with 4 boys with autism to evaluate further the effects of this intervention and its potential underlying mechanisms. In Experiment 1, the effects of motor RIRD and vocal RIRD on vocal stereotypy and appropriate vocalizations were…

  12. PERFORMANCE COMPARISON OF USART COMMUNICATION BETWEEN REAL TIME OPERATING SYSTEM (RTOS AND NATIVE INTERRUPT

    Directory of Open Access Journals (Sweden)

    Novian Habibie

    2016-02-01

    Full Text Available Comunication between microcontrollers is one of the crucial point in embedded sytems. On the other hand, embedded system must be able to run many parallel task simultaneously. To handle this, we need a reliabe system that can do a multitasking without decreasing every task’s performance. The most widely used methods for multitasking in embedded systems are using Interrupt Service Routine (ISR or using Real Time Operating System (RTOS. This research compared perfomance of USART communication on system with RTOS to a system that use interrupt. Experiments run on two identical development board XMega A3BU-Xplained which used intenal sensor (light and temperature and used servo as external component. Perfomance comparison done by counting ping time (elapsing time to transmit data and get a reply as a mark that data has been received and compare it. This experiments divided into two scenarios: (1 system loaded with many tasks, (2 system loaded with few tasks. Result of the experiments show that communication will be faster if system only loaded with few tasks. System with RTOS has won from interrupt in case (1, but lose to interrupt in case (2.

  13. 77 FR 11591 - Certain Ground Fault Circuit Interrupters and Products Containing Same, Investigations...

    Science.gov (United States)

    2012-02-27

    ... INTERNATIONAL TRADE COMMISSION [Investigation No. 337-TA-739] Certain Ground Fault Circuit Interrupters and Products Containing Same, Investigations: Terminations, Modifications and Rulings AGENCY: U.S... importation, and the sale within the United States after importation of certain ground fault circuit...

  14. Women’s work interruptions and career prospects in Germany and Sweden

    NARCIS (Netherlands)

    Evertsson, M.; Grunow, D.

    2012-01-01

    Purpose - The purpose of this paper is to focus on two welfare state regimes with differing degrees of de-familialisation strategies, Germany and Sweden, to study whether and how women's career interruptions influence their labour market prospects. By comparing women with continuous careers to those

  15. Interrupting Gendered Discursive Practices in Classroom Talk About Texts: Easy To Think About, Difficult To Do.

    Science.gov (United States)

    Alvermann, Donna E.; Commeyras, Michelle; Young, Josephine P.; Randall, Sally; Hinson, David

    1997-01-01

    Focuses on university- and school-based teacher researchers attempting to alter or interrupt certain gendered discursive practices that threatened to reproduce some of the same inequities in classroom talk about texts that were noted in the past, but were not challenged. Finds four types of interactions: self-deprecating, discriminatory, and…

  16. Bronchial histamine challenge. A combined interrupter-dosimeter method compared with a standard method

    DEFF Research Database (Denmark)

    Pavlovic, M; Holstein-Rathlou, N H; Madsen, F

    1985-01-01

    We compared the provocative concentration (PC) values obtained by two different methods of performing bronchial histamine challenge. One test was done on an APTA, an apparatus which allows simultaneous provocation with histamine and measurement of airway resistance (Rtot) by the interrupter metho...

  17. Direct-Current Forced Interruption and Breaking Performance of Spiral-Type Contacts in Aero Applications

    Directory of Open Access Journals (Sweden)

    Wenlei Huo

    2017-05-01

    Full Text Available This paper analyses the transient characteristics and breaking performance of direct-current (DC forced-interruption vacuum interrupters in 270 V power-supply systems. Three stages are identified in forced interruption: the DC-arcing stage, current-commutation stage, and voltage-recovery stage. During the current-commutation stage, the reverse peak-current coefficient k, which is a key design factor, is used to calculate the rate of current at zero-crossing (di/dt. MATLAB/Simulink simulation models are established to obtain the transient characteristics influenced by the forced-commutation branch parameters and the coefficient k. To study the breaking performance of spiral-type contacts, experiments are conducted for different contact materials and arcing times for currents less than 3.5 kA. During the DC-arcing stage, a locally intensive burning arc is observed in the CuW80 contact; however, it is not observed in the CuCr50 contact. On examining the re-ignition interruption results of the CuW80 contact, the intensive burning arc is found to be positioned within a possible re-ignition region. When the arcing time is longer than 1 ms, the intensive burning arc occurs and affects the breaking performance of the spiral-type contacts. If the DC-arcing stage is prolonged, the total arcing energy increases, which leads to a lower breaking capacity.

  18. Multiple tag labeling method for DNA sequencing

    Science.gov (United States)

    Mathies, R.A.; Huang, X.C.; Quesada, M.A.

    1995-07-25

    A DNA sequencing method is described which uses single lane or channel electrophoresis. Sequencing fragments are separated in the lane and detected using a laser-excited, confocal fluorescence scanner. Each set of DNA sequencing fragments is separated in the same lane and then distinguished using a binary coding scheme employing only two different fluorescent labels. Also described is a method of using radioisotope labels. 5 figs.

  19. Computer simulation of replacement sequences in copper

    International Nuclear Information System (INIS)

    Schiffgens, J.O.; Schwartz, D.W.; Ariyasu, R.G.; Cascadden, S.E.

    1978-01-01

    Results of computer simulations of , , and replacement sequences in copper are presented, including displacement thresholds, focusing energies, energy losses per replacement, and replacement sequence lengths. These parameters are tabulated for six interatomic potentials and shown to vary in a systematic way with potential stiffness and range. Comparisons of results from calculations made with ADDES, a quasi-dynamical code, and COMENT, a dynamical code, show excellent agreement, demonstrating that the former can be calibrated and used satisfactorily in the analysis of low energy displacement cascades. Upper limits on , , and replacement sequences were found to be approximately 10, approximately 30, and approximately 14 replacements, respectively. (author)

  20. The accuracy evaluation according to dose delivery interruption and restart for volumetric modulated arc therapy

    Energy Technology Data Exchange (ETDEWEB)

    Lee, Dong Hyung; Bae, Sun Myung; Kwak, Jung Won; Kang, Tae Young; Bck, Geum Mun [Dept. of Radiation Oncology, Asan Medical Center, Seoul(Korea, Republic of)

    2013-03-15

    The accurate movement of gantry rotation, collimator and correct application of dose rate are very important to approach the successful performance of Volumetric Modulated Arc Therapy (VMAT), because it is tightly interlocked with a complex treatment plan. The interruption and restart of dose delivery, however, are able to occur on treatment by various factors of a treatment machine and treatment plan. If unexpected problems of a treat machine or a patient interrupt the VMAT, the movement of treatment machine for delivering the remaining dose will be restarted at the start point. In this investigation, We would like to know the effect of interruptions and restart regarding dose delivery at VMAT. Treatment plans of 10 patients who had been treated at our center were used to measure and compare the dose distribution of each VMAT after converting to a form of digital image and communications in Medicine (DICOM) with treatment planning system (Eclipse V 10.0, Varian, USA). We selected the 6 MV photon energy of Trilogy (Varian, USA) and used OmniPro I'mRT system (V 1.7b, IBA dosimetry, Germany) to analyze the data that were acquired through this measurement with two types of interruptions four times for each case. The door interlock and the beam-off were used to stop and then to restart the dose delivery of VMAT. The gamma index in OmniPro I'mRT system and T-test in Microsoft Excel 2007 were used to evaluate the result of this investigation. The deviations of average gamma index in cases with door interlock, beam-off and without interruption on VMAT are 0.141, 0.128 and 0.1. The standard deviations of acquired gamma values are 0.099, 0.091, 0.071 and The maximum gamma value in each case is 0.413, 0.379, 0.286, respectively. This analysis has a 95-percent confidence level and the P-value of T-test is under 0.05. Gamma pass rate (3%, 3 mm) is acceptable in all of measurements. As a result, We could make sure that the interruption of this investgation are not