WorldWideScience

Sample records for autonomously replicating sequences

  1. Characterization of human chromosomal DNA sequences which replicate autonomously in Saccharomyces cerevisiae.

    Science.gov (United States)

    Montiel, J F; Norbury, C J; Tuite, M F; Dobson, M J; Mills, J S; Kingsman, A J; Kingsman, S M

    1984-01-01

    We have characterised two restriction fragments, isolated from a "shotgun" collection of human DNA, which function as autonomously replicating sequences (ARSs) in Saccharomyces cerevisiae. Functional domains of these fragments have been defined by subcloning and exonuclease (BAL 31) deletion analysis. Both fragments contain two spatially distinct domains. One is essential for high frequency transformation and is termed the Replication Sequence (RS) domain, the other, termed the Replication Enhancer (RE) domain, has no inherent replication competence but is essential for ensuring maximum function of the RS domain. The nucleotide sequence of these domains reveals several conserved sequences one of which is strikingly similar to the yeast ARS consensus sequence. PMID:6320114

  2. Characterization of human chromosomal DNA sequences which replicate autonomously in Saccharomyces cerevisiae.

    OpenAIRE

    Montiel, J F; Norbury, C. J.; Tuite, M F; Dobson, M J; Mills, J S; Kingsman, A J; Kingsman, S M

    1984-01-01

    We have characterised two restriction fragments, isolated from a "shotgun" collection of human DNA, which function as autonomously replicating sequences (ARSs) in Saccharomyces cerevisiae. Functional domains of these fragments have been defined by subcloning and exonuclease (BAL 31) deletion analysis. Both fragments contain two spatially distinct domains. One is essential for high frequency transformation and is termed the Replication Sequence (RS) domain, the other, termed the Replication En...

  3. Mechanism of Gene Amplification via Yeast Autonomously Replicating Sequences

    Directory of Open Access Journals (Sweden)

    Shelly Sehgal

    2015-01-01

    Full Text Available The present investigation was aimed at understanding the molecular mechanism of gene amplification. Interplay of fragile sites in promoting gene amplification was also elucidated. The amplification promoting sequences were chosen from the Saccharomyces cerevisiae ARS, 5S rRNA regions of Plantago ovata and P. lagopus, proposed sites of replication pausing at Ste20 gene locus of S. cerevisiae, and the bend DNA sequences within fragile site FRA11A in humans. The gene amplification assays showed that plasmid bearing APS from yeast and human beings led to enhanced protein concentration as compared to the wild type. Both the in silico and in vitro analyses were pointed out at the strong bending potential of these APS. In addition, high mitotic stability and presence of TTTT repeats and SAR amongst these sequences encourage gene amplification. Phylogenetic analysis of S. cerevisiae ARS was also conducted. The combinatorial power of different aspects of APS analyzed in the present investigation was harnessed to reach a consensus about the factors which stimulate gene expression, in presence of these sequences. It was concluded that the mechanism of gene amplification was that AT rich tracts present in fragile sites of yeast serve as binding sites for MAR/SAR and DNA unwinding elements. The DNA protein interactions necessary for ORC activation are facilitated by DNA bending. These specific bindings at ORC promote repeated rounds of DNA replication leading to gene amplification.

  4. Mapping autonomously replicating sequence elements in a 73-kb region of chromosome II of the fission yeast, Schizosaccharomyces pombe

    Indian Academy of Sciences (India)

    Vinay Kumar Srivastava; Dharani Dhar Dubey

    2007-08-01

    Autonomously replicating sequence (ARS) elements are the genetic determinants of replication origin function in yeasts. They can be easily identified as the plasmids containing them transform yeast cells at a high frequency. As the first step towards identifying all potential replication origins in a 73-kb region of the long arm of fission yeast chromosome II, we have mapped five new ARS elements using systematic subcloning and transformation assay. 2D analysis of one of the ARS plasmids that showed highest transformation frequency localized the replication origin activity within the cloned genomic DNA. All the new ARS elements are localized in two clusters in centromere proximal 40 kb of the region. The presence of at least six ARS elements, including the previously reported ars727, is suggestive of a higher origin density in this region than that predicted earlier using a computer based search.

  5. In Vivo Accumulation of Cyclin A and Cellular Replication Factors in Autonomous Parvovirus Minute Virus of Mice-Associated Replication Bodies

    OpenAIRE

    Bashir, Tarig; Rommelaere, Jean; Cziepluch, Celina

    2001-01-01

    Autonomous parvovirus minute virus of mice (MVM) DNA replication is strictly dependent on cellular factors expressed during the S phase of the cell cycle. Here we report that MVM DNA replication proceeds in specific nuclear structures termed autonomous parvovirus-associated replication bodies, where components of the basic cellular replication machinery accumulate. The presence of DNA polymerases α and δ in these bodies suggests that MVM utilizes partially preformed cellular replication compl...

  6. Replication of cloned DNA containing the Alu family sequence during cell extract-promoting simian virus 40 DNA synthesis.

    OpenAIRE

    Ariga, H

    1984-01-01

    The replicating activity of several cloned DNAs containing putative origin sequences was examined in a cell-free extract that absolutely depends on simian virus 40 (SV40) T antigen promoting initiation of SV40 DNA replication in vitro. Of the three DNAs containing the human Alu family sequence (BLUR8), the origin of (Saccharomyces cerevisiae plasmid 2 micron DNA (pJD29), and the yeast autonomous replicating sequence (YRp7), only BLUR8 was active as a template. Replication in a reaction mixtur...

  7. Can human autonomic classical conditioning occur without contingency awareness? The critical importance of the trial sequence.

    Science.gov (United States)

    Singh, Kulwinder; Dawson, Michael E; Schell, Anne M; Courtney, Christopher G; Payne, Andrew F H

    2013-04-01

    Most evidence suggests that awareness of the CS-US contingency is necessary for human autonomic conditioning. However, Schultz and Helmstetter (2010) reported unaware skin conductance conditioning using difficult-to-discriminate visual CSs. We sought to replicate these findings with procedures nearly identical to Schultz and Helmstetter among 66 participants. Results replicated the findings of significantly greater autonomic responding to CS+ than CS-; however, participants also demonstrated greater expectancy of shock to CS+ than CS- despite being classified as unaware. The differential expectancy and conditioning occurred only on trials that followed a CS+/CS- alternating sequence. On non-alternating trials, there was significantly higher expectancy and skin conductance responding to CS- compared to CS+. These results indicate that what initially appeared to be unaware differential conditioning was likely due to differential expectancy arising from a predictable trial sequence. These results underscore the critical importance of controlling for trial sequence effects in the study of learning.

  8. Drosophila ARSs contain the yeast ARS consensus sequence and a replication enhancer.

    OpenAIRE

    Mills, J S; Kingsman, A J; Kingsman, S M

    1986-01-01

    A number of restriction fragments that function as autonomously replicating sequences (ARSs) in yeast have been isolated from Drosophila melanogaster DNA. The behaviour in yeast of plasmids containing Drosophila ARS elements was studied and compared to that exhibited by the archetypal yeast ARS-1 plasmid. ARS functions were localised by subcloning and BAL-31 deletion analysis. These studies demonstrated the structural and functional complexity of Drosophila ARSs. Each Drosophila ARS element h...

  9. High-frequency transformation of a methylotrophic yeast, Candida boidinii, with autonomously replicating plasmids which are also functional in Saccharomyces cerevisiae.

    OpenAIRE

    Sakai, Y.; Goh, T K; Tani, Y

    1993-01-01

    We have developed a transformation system which uses autonomous replicating plasmids for a methylotrophic yeast, Candida boidinii. Two autonomous replication sequences, CARS1 and CARS2, were newly cloned from the genome of C. boidinii. Plasmids having both a CARS fragment and the C. boidinii URA3 gene transformed C. boidinii ura3 cells to Ura+ phenotype at frequencies of up to 10(4) CFU/micrograms of DNA. From Southern blot analysis, CARS plasmids seemed to exist in polymeric forms as well as...

  10. Sequence and recombination analyses of the geminivirus replication initiator protein

    Indian Academy of Sciences (India)

    T Vadivukarasi; K R Girish; R Usha

    2007-01-01

    The sequence motifs present in the replication initiator protein (Rep) of geminiviruses have been compared with those present in all known rolling circle replication initiators. The predicted secondary structures of Rep representing each group of organisms have been compared and found to be conserved. Regions of recombination in the Rep gene and the adjoining 5′ intergenic region (IR) of representative species of Geminiviridae have been identified using Recombination Detection Programs. The possible implications of such recombinations on the increasing host range of geminivirus infections are discussed.

  11. Learning Sequences of Actions in Collectives of Autonomous Agents

    Science.gov (United States)

    Turner, Kagan; Agogino, Adrian K.; Wolpert, David H.; Clancy, Daniel (Technical Monitor)

    2001-01-01

    In this paper we focus on the problem of designing a collective of autonomous agents that individually learn sequences of actions such that the resultant sequence of joint actions achieves a predetermined global objective. We are particularly interested in instances of this problem where centralized control is either impossible or impractical. For single agent systems in similar domains, machine learning methods (e.g., reinforcement learners) have been successfully used. However, applying such solutions directly to multi-agent systems often proves problematic, as agents may work at cross-purposes, or have difficulty in evaluating their contribution to achievement of the global objective, or both. Accordingly, the crucial design step in multiagent systems centers on determining the private objectives of each agent so that as the agents strive for those objectives, the system reaches a good global solution. In this work we consider a version of this problem involving multiple autonomous agents in a grid world. We use concepts from collective intelligence to design goals for the agents that are 'aligned' with the global goal, and are 'learnable' in that agents can readily see how their behavior affects their utility. We show that reinforcement learning agents using those goals outperform both 'natural' extensions of single agent algorithms and global reinforcement, learning solutions based on 'team games'.

  12. Perinatally Influenced Autonomic System Fluctuations Drive Infant Vocal Sequences.

    Science.gov (United States)

    Zhang, Yisi S; Ghazanfar, Asif A

    2016-05-23

    The variable vocal behavior of human infants is the scaffolding upon which speech and social interactions develop. It is important to know what factors drive this developmentally critical behavioral output. Using marmoset monkeys as a model system, we first addressed whether the initial conditions for vocal output and its sequential structure are perinatally influenced. Using dizygotic twins and Markov analyses of their vocal sequences, we found that in the first postnatal week, twins had more similar vocal sequences to each other than to their non-twin siblings. Moreover, both twins and their siblings had more vocal sequence similarity with each other than with non-sibling infants. Using electromyography, we then investigated the physiological basis of vocal sequence structure by measuring respiration and arousal levels (via changes in heart rate). We tested the hypothesis that early-life influences on vocal output are via fluctuations of the autonomic nervous system (ANS) mediated by vocal biomechanics. We found that arousal levels fluctuate at ∼0.1 Hz (the Mayer wave) and that this slow oscillation modulates the amplitude of the faster, ∼1.0 Hz respiratory rhythm. The systematic changes in respiratory amplitude result in the different vocalizations that comprise infant vocal sequences. Among twins, the temporal structure of arousal level changes was similar and therefore indicates why their vocal sequences were similar. Our study shows that vocal sequences are tightly linked to respiratory patterns that are modulated by ANS fluctuations and that the temporal structure of ANS fluctuations is perinatally influenced. PMID:27068420

  13. Nucleotide sequence analysis of regions of adenovirus 5 DNA containing the origins of DNA replication

    International Nuclear Information System (INIS)

    The purpose of the investigations described is the determination of nucleotide sequences at the molecular ends of the linear adenovirus type 5 DNA. Knowledge of the primary structure at the termini of this DNA molecule is of particular interest in the study of the mechanism of replication of adenovirus DNA. The initiation- and termination sites of adenovirus DNA replication are located at the ends of the DNA molecule. (Auth.)

  14. Autonomic Management of Object Replication for FT-CORBA Based Intelligent Transportation Systems

    Science.gov (United States)

    Suh, Woonsuk; Lee, Eunseok

    Intelligent Transportation Systems (ITS) comprises the electronics, communications or information processing used singly or integrated to improve the efficiency or safety of surface transportation. Accordingly, the ITS has to perform collection, management, and provision of real time transport information reliably. It can be deployed based on the Common Object Request Broker Architecture (CORBA) of the Object Management Group (OMG) because it consists of many interconnected heterogeneous systems deployed by independent organizations. Fault Tolerant CORBA (FT-CORBA) supports real time requirement of transport information stably through redundancy by replication of server objects. However, object replication, management, and related protocols of FT-CORBA require extra system resources of CPU and memory, and can degrade the system performance both locally and as a whole. This paper proposes an architecture to enhance performance of FT-CORBA based ITS in terms of CPU and memory by managing object replication adaptively during system operation with an agent. The application of the agent is expected to support fault tolerance of real ITS efficiently.

  15. Open chromatin encoded in DNA sequence is the signature of 'master' replication origins in human cells.

    Science.gov (United States)

    Audit, Benjamin; Zaghloul, Lamia; Vaillant, Cédric; Chevereau, Guillaume; d'Aubenton-Carafa, Yves; Thermes, Claude; Arneodo, Alain

    2009-10-01

    For years, progress in elucidating the mechanisms underlying replication initiation and its coupling to transcriptional activities and to local chromatin structure has been hampered by the small number (approximately 30) of well-established origins in the human genome and more generally in mammalian genomes. Recent in silico studies of compositional strand asymmetries revealed a high level of organization of human genes around 1000 putative replication origins. Here, by comparing with recently experimentally identified replication origins, we provide further support that these putative origins are active in vivo. We show that regions approximately 300-kb wide surrounding most of these putative replication origins that replicate early in the S phase are hypersensitive to DNase I cleavage, hypomethylated and present a significant enrichment in genomic energy barriers that impair nucleosome formation (nucleosome-free regions). This suggests that these putative replication origins are specified by an open chromatin structure favored by the DNA sequence. We discuss how this distinctive attribute makes these origins, further qualified as 'master' replication origins, priviledged loci for future research to decipher the human spatio-temporal replication program. Finally, we argue that these 'master' origins are likely to play a key role in genome dynamics during evolution and in pathological situations.

  16. Calorie Restriction-Mediated Replicative Lifespan Extension in Yeast Is Non-Cell Autonomous

    OpenAIRE

    Szu-Chieh Mei; Charles Brenner

    2015-01-01

    In laboratory yeast strains with Sir2 and Fob1 function, wild-type NAD+ salvage is required for calorie restriction (CR) to extend replicative lifespan. CR does not significantly alter steady state levels of intracellular NAD+ metabolites. However, levels of Sir2 and Pnc1, two enzymes that sequentially convert NAD+ to nicotinic acid (NA), are up-regulated during CR. To test whether factors such as NA might be exported by glucose-restricted mother cells to survive later generations, we develop...

  17. Universal Sequence Replication, Reversible Polymerization and Early Functional Biopolymers: A Model for the Initiation of Prebiotic Sequence Evolution

    Science.gov (United States)

    Walker, Sara Imari; Grover, Martha A.; Hud, Nicholas V.

    2012-01-01

    Many models for the origin of life have focused on understanding how evolution can drive the refinement of a preexisting enzyme, such as the evolution of efficient replicase activity. Here we present a model for what was, arguably, an even earlier stage of chemical evolution, when polymer sequence diversity was generated and sustained before, and during, the onset of functional selection. The model includes regular environmental cycles (e.g. hydration-dehydration cycles) that drive polymers between times of replication and functional activity, which coincide with times of different monomer and polymer diffusivity. Template-directed replication of informational polymers, which takes place during the dehydration stage of each cycle, is considered to be sequence-independent. New sequences are generated by spontaneous polymer formation, and all sequences compete for a finite monomer resource that is recycled via reversible polymerization. Kinetic Monte Carlo simulations demonstrate that this proposed prebiotic scenario provides a robust mechanism for the exploration of sequence space. Introduction of a polymer sequence with monomer synthetase activity illustrates that functional sequences can become established in a preexisting pool of otherwise non-functional sequences. Functional selection does not dominate system dynamics and sequence diversity remains high, permitting the emergence and spread of more than one functional sequence. It is also observed that polymers spontaneously form clusters in simulations where polymers diffuse more slowly than monomers, a feature that is reminiscent of a previous proposal that the earliest stages of life could have been defined by the collective evolution of a system-wide cooperation of polymer aggregates. Overall, the results presented demonstrate the merits of considering plausible prebiotic polymer chemistries and environments that would have allowed for the rapid turnover of monomer resources and for regularly varying monomer

  18. Universal sequence replication, reversible polymerization and early functional biopolymers: a model for the initiation of prebiotic sequence evolution.

    Directory of Open Access Journals (Sweden)

    Sara Imari Walker

    Full Text Available Many models for the origin of life have focused on understanding how evolution can drive the refinement of a preexisting enzyme, such as the evolution of efficient replicase activity. Here we present a model for what was, arguably, an even earlier stage of chemical evolution, when polymer sequence diversity was generated and sustained before, and during, the onset of functional selection. The model includes regular environmental cycles (e.g. hydration-dehydration cycles that drive polymers between times of replication and functional activity, which coincide with times of different monomer and polymer diffusivity. Template-directed replication of informational polymers, which takes place during the dehydration stage of each cycle, is considered to be sequence-independent. New sequences are generated by spontaneous polymer formation, and all sequences compete for a finite monomer resource that is recycled via reversible polymerization. Kinetic Monte Carlo simulations demonstrate that this proposed prebiotic scenario provides a robust mechanism for the exploration of sequence space. Introduction of a polymer sequence with monomer synthetase activity illustrates that functional sequences can become established in a preexisting pool of otherwise non-functional sequences. Functional selection does not dominate system dynamics and sequence diversity remains high, permitting the emergence and spread of more than one functional sequence. It is also observed that polymers spontaneously form clusters in simulations where polymers diffuse more slowly than monomers, a feature that is reminiscent of a previous proposal that the earliest stages of life could have been defined by the collective evolution of a system-wide cooperation of polymer aggregates. Overall, the results presented demonstrate the merits of considering plausible prebiotic polymer chemistries and environments that would have allowed for the rapid turnover of monomer resources and for

  19. DNAskew: Statistical Analysis of Base Compositional Asymmetry and Prediction of Replication Boundaries in the Genome Sequences

    Institute of Scientific and Technical Information of China (English)

    Xiang-RuMA; Shao-BoXIAO; Ai-ZhenGUO; Jian-QiangLUE; Huan-ChunCHEN

    2004-01-01

    Sueoka and Lobry declared respectively that, in the absence of bias between the two DNA strands for mutation and selection, the base composition within each strand should be A=T and C=G (this state is called Parity Rule type 2, PR2). However, the genome sequences of many bacteria, vertebrates and viruses showed asymmetries in base composition and gene direction. To determine the relationship of base composition skews with replication orientation, gene function, codon usage biases and phylogenetic evolution,in this paper a program called DNAskew was developed for the statistical analysis of strand asymmetry and codon composition bias in the DNA sequence. In addition, the program can also be used to predict the replication boundaries of genome sequences. The method builds on the fact that there are compositional asymmetries between the leading and the lagging strand for replication. DNAskew was written in Perl script language and implemented on the LINUX operating system. It works quickly with annotated or unannotated sequences in GBFF (GenBank flatfile) or fasta format. The source code is freely available for academic use at http://www.epizooty.com/pub/stat/DNAskew.

  20. Parvovirus B19 promoter at map unit 6 confers autonomous replication competence and erythroid specificity to adeno-associated virus 2 in primary human hematopoietic progenitor cells.

    OpenAIRE

    Wang, X S; Yoder, M C; Zhou, S. Z.; A Srivastava

    1995-01-01

    The pathogenic human parvovirus B19 is an autonomously replicating virus with a remarkable tropism for human erythroid progenitor cells. Although the target cell specificity for B19 infection has been suggested to be mediated by the erythrocyte P-antigen receptor (globoside), a number of nonerythroid cells that express this receptor are nonpermissive for B19 replication. To directly test the role of expression from the B19 promoter at map unit 6 (B19p6) in the erythroid cell specificity of B1...

  1. Replication error deficient and proficient colorectal cancer gene expression differences caused by 3'UTR polyT sequence deletions

    DEFF Research Database (Denmark)

    Wilding, Jennifer L; McGowan, Simon; Liu, Ying;

    2010-01-01

    Replication error deficient (RER+) colorectal cancers are a distinct subset of colorectal cancers, characterized by inactivation of the DNA mismatch repair system. These cancers are typically pseudodiploid, accumulate mutations in repetitive sequences as a result of their mismatch repair deficiency...

  2. Inhibition of hepatitis B virus replication with linear DNA sequences expressing antiviral micro-RNA shuttles

    Energy Technology Data Exchange (ETDEWEB)

    Chattopadhyay, Saket; Ely, Abdullah; Bloom, Kristie; Weinberg, Marc S. [Antiviral Gene Therapy Research Unit, University of the Witwatersrand (South Africa); Arbuthnot, Patrick, E-mail: Patrick.Arbuthnot@wits.ac.za [Antiviral Gene Therapy Research Unit, University of the Witwatersrand (South Africa)

    2009-11-20

    RNA interference (RNAi) may be harnessed to inhibit viral gene expression and this approach is being developed to counter chronic infection with hepatitis B virus (HBV). Compared to synthetic RNAi activators, DNA expression cassettes that generate silencing sequences have advantages of sustained efficacy and ease of propagation in plasmid DNA (pDNA). However, the large size of pDNAs and inclusion of sequences conferring antibiotic resistance and immunostimulation limit delivery efficiency and safety. To develop use of alternative DNA templates that may be applied for therapeutic gene silencing, we assessed the usefulness of PCR-generated linear expression cassettes that produce anti-HBV micro-RNA (miR) shuttles. We found that silencing of HBV markers of replication was efficient (>75%) in cell culture and in vivo. miR shuttles were processed to form anti-HBV guide strands and there was no evidence of induction of the interferon response. Modification of terminal sequences to include flanking human adenoviral type-5 inverted terminal repeats was easily achieved and did not compromise silencing efficacy. These linear DNA sequences should have utility in the development of gene silencing applications where modifications of terminal elements with elimination of potentially harmful and non-essential sequences are required.

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

    Science.gov (United States)

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

    2016-08-01

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

  4. RNA Replication from the Simian Virus 5 Antigenomic Promoter Requires Three Sequence-Dependent Elements Separated by Sequence-Independent Spacer Regions

    Science.gov (United States)

    Keller, Michael A.; Murphy, Susan K.; Parks, Griffith D.

    2001-01-01

    We have previously shown for the paramyxovirus simian virus 5 (SV5) that a functional promoter for RNA replication requires proper spacing between two discontinuous elements: a 19-base segment at the 3′ terminus (conserved region I [CRI]) and an 18-base internal region (CRII) that is contained within the coding region of the L protein gene. In the work described here, we have used a reverse-genetics system to determine if the 53-base segment between CRI and CRII contains additional sequence-specific signals required for optimal replication or if this segment functions solely as a sequence-independent spacer region. A series of copyback defective interfering minigenome analogs were constructed to contain substitutions of nonviral sequences in place of bases 21 to 72 of the antigenomic promoter, and the relative level of RNA replication was measured by Northern blot analysis. The results from our mutational analysis indicate that in addition to CRI and CRII, optimal replication from the SV5 antigenomic promoter requires a third sequence-dependent element located 51 to 66 bases from the 3′ end of the RNA. Minigenome RNA replication was not affected by changes in the either the position of this element in relation to CRI and CRII or the predicted hexamer phase of NP encapsidation. Thus, optimal RNA replication from the SV5 antigenomic promoter requires three sequence-dependent elements, CRI, CRII and bases 51 to 66. PMID:11264390

  5. The Replication Focus Targeting Sequence (RFTS) Domain Is a DNA-competitive Inhibitor of Dnmt1

    Energy Technology Data Exchange (ETDEWEB)

    Syeda, Farisa; Fagan, Rebecca L.; Wean, Matthew; Avvakumov, George V.; Walker, John R.; Xue, Sheng; Dhe-Paganon, Sirano; Brenner, Charles (Iowa); (Toronto)

    2015-11-30

    Dnmt1 (DNA methyltransferase 1) is the principal enzyme responsible for maintenance of cytosine methylation at CpG dinucleotides in the mammalian genome. The N-terminal replication focus targeting sequence (RFTS) domain of Dnmt1 has been implicated in subcellular localization, protein association, and catalytic function. However, progress in understanding its function has been limited by the lack of assays for and a structure of this domain. Here, we show that the naked DNA- and polynucleosome-binding activities of Dnmt1 are inhibited by the RFTS domain, which functions by virtue of binding the catalytic domain to the exclusion of DNA. Kinetic analysis with a fluorogenic DNA substrate established the RFTS domain as a 600-fold inhibitor of Dnmt1 enzymatic activity. The crystal structure of the RFTS domain reveals a novel fold and supports a mechanism in which an RFTS-targeted Dnmt1-binding protein, such as Uhrf1, may activate Dnmt1 for DNA binding.

  6. Localization of Non-Linearly Modeled Autonomous Mobile Robots Using Out-of-Sequence Measurements

    Directory of Open Access Journals (Sweden)

    Jesus M. de la Cruz

    2012-02-01

    Full Text Available This paper presents a state of the art of the estimation algorithms dealing with Out-of-Sequence (OOS measurements for non-linearly modeled systems. The state of the art includes a critical analysis of the algorithm properties that takes into account the applicability of these techniques to autonomous mobile robot navigation based on the fusion of the measurements provided, delayed and OOS, by multiple sensors. Besides, it shows a representative example of the use of one of the most computationally efficient approaches in the localization module of the control software of a real robot (which has non-linear dynamics, and linear and non-linear sensors and compares its performance against other approaches. The simulated results obtained with the selected OOS algorithm shows the computational requirements that each sensor of the robot imposes to it. The real experiments show how the inclusion of the selected OOS algorithm in the control software lets the robot successfully navigate in spite of receiving many OOS measurements. Finally, the comparison highlights that not only is the selected OOS algorithm among the best performing ones of the comparison, but it also has the lowest computational and memory cost.

  7. Localization of non-linearly modeled autonomous mobile robots using out-of-sequence measurements.

    Science.gov (United States)

    Besada-Portas, Eva; Lopez-Orozco, Jose A; Lanillos, Pablo; de la Cruz, Jesus M

    2012-01-01

    This paper presents a state of the art of the estimation algorithms dealing with Out-of-Sequence (OOS) measurements for non-linearly modeled systems. The state of the art includes a critical analysis of the algorithm properties that takes into account the applicability of these techniques to autonomous mobile robot navigation based on the fusion of the measurements provided, delayed and OOS, by multiple sensors. Besides, it shows a representative example of the use of one of the most computationally efficient approaches in the localization module of the control software of a real robot (which has non-linear dynamics, and linear and non-linear sensors) and compares its performance against other approaches. The simulated results obtained with the selected OOS algorithm shows the computational requirements that each sensor of the robot imposes to it. The real experiments show how the inclusion of the selected OOS algorithm in the control software lets the robot successfully navigate in spite of receiving many OOS measurements. Finally, the comparison highlights that not only is the selected OOS algorithm among the best performing ones of the comparison, but it also has the lowest computational and memory cost.

  8. Genes and sequences involved in the replication of cowpea mosaic virus RNAs.

    NARCIS (Netherlands)

    Eggen, R.

    1989-01-01

    The aim of the studies described in this thesis was to gain more insight in the complex molecular mechanisms underlying the RNA replication of the cowpea mosaic virus genome. Previously the replication of CPMV RNA has been examined extensively with crude membrane fractions prepared from CPMV inf

  9. DNAskew:Statistical Analysis of Base Compositional Asymmetry and Prediction of Replication Boundaries in the Genome Sequences

    Institute of Scientific and Technical Information of China (English)

    Xiang-Ru MA; Shao-Bo XIAO; Ai-Zhen GUO; Jian-Qiang L(U); Huan-Chun CHEN

    2004-01-01

    Sueoka and Lobry declared respectively that, in the absence of bias between the two DNA strands for mutation and selection, the base composition within each strand should be A=T and C=G (this state is called Parity Rule type 2, PR2). However, the genome sequences of many bacteria, vertebrates and viruses showed asymmetries in base composition and gene direction. To determine the relationship of base composition skews with replication orientation, gene function, codon usage biases and phylogenetic evolution,in this paper a program called DNAskew was developed for the statistical analysis of strand asymmetry and codon composition bias in the DNA sequence. In addition, the program can also be used to predict the replication boundaries of genome sequences. The method builds on the fact that there are compositional asymmetries between the leading and the lagging strand for replication. DNAskew was written in Perl script language and implemented on the LINUX operating system. It works quickly with annotated or unannotated sequences in GBFF (GenBank flatfile) or fasta format. The source code is freely available for academic use at http://www.epizooty.com/pub/stat/DNAskew.

  10. Homology-independent discovery of replicating pathogenic circular RNAs by deep sequencing and a new computational algorithm.

    Science.gov (United States)

    Wu, Qingfa; Wang, Ying; Cao, Mengji; Pantaleo, Vitantonio; Burgyan, Joszef; Li, Wan-Xiang; Ding, Shou-Wei

    2012-03-01

    A common challenge in pathogen discovery by deep sequencing approaches is to recognize viral or subviral pathogens in samples of diseased tissue that share no significant homology with a known pathogen. Here we report a homology-independent approach for discovering viroids, a distinct class of free circular RNA subviral pathogens that encode no protein and are known to infect plants only. Our approach involves analyzing the sequences of the total small RNAs of the infected plants obtained by deep sequencing with a unique computational algorithm, progressive filtering of overlapping small RNAs (PFOR). Viroid infection triggers production of viroid-derived overlapping siRNAs that cover the entire genome with high densities. PFOR retains viroid-specific siRNAs for genome assembly by progressively eliminating nonoverlapping small RNAs and those that overlap but cannot be assembled into a direct repeat RNA, which is synthesized from circular or multimeric repeated-sequence templates during viroid replication. We show that viroids from the two known families are readily identified and their full-length sequences assembled by PFOR from small RNAs sequenced from infected plants. PFOR analysis of a grapevine library further identified a viroid-like circular RNA 375 nt long that shared no significant sequence homology with known molecules and encoded active hammerhead ribozymes in RNAs of both plus and minus polarities, which presumably self-cleave to release monomer from multimeric replicative intermediates. A potential application of the homology-independent approach for viroid discovery in plant and animal species where RNA replication triggers the biogenesis of siRNAs is discussed. PMID:22345560

  11. Genome sequences of SAT 2 foot-and-mouth disease viruses from Egypt and Palestinian Autonomous Territories (Gaza Strip).

    Science.gov (United States)

    Valdazo-González, Begoña; Knowles, Nick J; Hammond, Jef; King, Donald P

    2012-08-01

    Two foot-and-mouth disease virus (FMDV) genome sequences have been determined for isolates collected from recent field outbreaks in North Africa (Egypt) and the Middle East (Palestinian Autonomous Territories). These data represent the first examples of complete genomic sequences for the FMDV SAT 2 topotype VII, which is thought to be endemic in countries immediately to the south of the Sahara desert. Further studies are now urgently required to provide insights into the epidemiological links between these outbreaks and to define the pathogenicity of this emerging lineage. PMID:22843860

  12. Molecular cloning and DNA sequence analysis of Escherichia coli priA, the gene encoding the primosomal protein replication factor Y.

    OpenAIRE

    Nurse, P; DiGate, R J; Zavitz, K H; Marians, K J

    1990-01-01

    Escherichia coli replication factor Y (protein n') functions in the assembly of a mobile multiprotein replication-priming complex called the primosome. Although the role of factor Y in primosome assembly during replication in vitro of bacteriophage phi X174 and plasmid pBR322 DNA is clear, its role in E. coli chromosomal replication is not. To address this issue, the gene for factor Y has been cloned molecularly and its DNA sequence has been determined. The cloned fragment of DNA contained an...

  13. Sequence analysis and characterization of rolling-circle replicating plasmid pVCM01 from Salmonella enterica

    Directory of Open Access Journals (Sweden)

    Penido, A. F. B.

    2013-12-01

    Full Text Available Aims: Characterization of cryptic plasmid pVCM01 (accession number JX133088 isolated from Salmonella enterica Enteritidis. Methodology and results: The complete sequence of pVCM01 was obtained. This plasmid possesses 1981 bp, with G+C content of 57% in agreement of the range of Salmonella genomic DNA. pVCM01 has a high degree of similarity to pB and pJ plasmids. It possesses six main open reading frames, only one have a very high degree of amino acid identity with protein involved in the rolling-circle-like replication (RCR. Based on the sequence similarities, pVCM01 plasmid belonged to the pC194/pUB110 rolling-circle replicating plasmid family. The Rep pVCM01 possesses the motifs: FLTLTVRN, HPHFHTL, SGDGYVKHERW, which were present in all Rep proteins. Conclusion, significance and impact of study: The small size of pVCM01 plasmid and its stability in E. coli cells, make it an attractive candidate to develop new vectors, such as cloning and/or expression vector.

  14. SOVEREIGN: An autonomous neural system for incrementally learning planned action sequences to navigate towards a rewarded goal.

    Science.gov (United States)

    Gnadt, William; Grossberg, Stephen

    2008-06-01

    How do reactive and planned behaviors interact in real time? How are sequences of such behaviors released at appropriate times during autonomous navigation to realize valued goals? Controllers for both animals and mobile robots, or animats, need reactive mechanisms for exploration, and learned plans to reach goal objects once an environment becomes familiar. The SOVEREIGN (Self-Organizing, Vision, Expectation, Recognition, Emotion, Intelligent, Goal-oriented Navigation) animat model embodies these capabilities, and is tested in a 3D virtual reality environment. SOVEREIGN includes several interacting subsystems which model complementary properties of cortical What and Where processing streams and which clarify similarities between mechanisms for navigation and arm movement control. As the animat explores an environment, visual inputs are processed by networks that are sensitive to visual form and motion in the What and Where streams, respectively. Position-invariant and size-invariant recognition categories are learned by real-time incremental learning in the What stream. Estimates of target position relative to the animat are computed in the Where stream, and can activate approach movements toward the target. Motion cues from animat locomotion can elicit head-orienting movements to bring a new target into view. Approach and orienting movements are alternately performed during animat navigation. Cumulative estimates of each movement are derived from interacting proprioceptive and visual cues. Movement sequences are stored within a motor working memory. Sequences of visual categories are stored in a sensory working memory. These working memories trigger learning of sensory and motor sequence categories, or plans, which together control planned movements. Predictively effective chunk combinations are selectively enhanced via reinforcement learning when the animat is rewarded. Selected planning chunks effect a gradual transition from variable reactive exploratory

  15. Autonomously generating operations sequences for a Mars Rover using AI-based planning

    Science.gov (United States)

    Sherwood, Rob; Mishkin, Andrew; Estlin, Tara; Chien, Steve; Backes, Paul; Cooper, Brian; Maxwell, Scott; Rabideau, Gregg

    2001-01-01

    This paper discusses a proof-of-concept prototype for ground-based automatic generation of validated rover command sequences from highlevel science and engineering activities. This prototype is based on ASPEN, the Automated Scheduling and Planning Environment. This Artificial Intelligence (AI) based planning and scheduling system will automatically generate a command sequence that will execute within resource constraints and satisfy flight rules.

  16. On Optimal Control of Non-Autonomous Switched Systems with a Fixed Mode Sequence

    Science.gov (United States)

    Kamgarpour, Maryam; Tomlin, Claire

    2012-01-01

    We consider differentiability with respect to the switch times of the value function of an optimal control problem for a non-autonomous switched system. The control variables are the switch times between the modes and the input in each mode. We provide a method to compute the derivative of the cost function given a nominal input. Then, we view the optimal control problem as a parametrized optimization problem in which the switch times are the parameters and the optimization is over the set of feasible inputs of each mode. From this point of view, we provide conditions under which the continuity and differentiability of the optimal value function, that is the cost function optimized over the inputs, can be guaranteed.

  17. Residue profile in predivergence sequences as a guide to the origin of DNA replication

    CERN Document Server

    Davis, B K

    1999-01-01

    DNA dependent RNA polymerase core subunits abb' conserved residues at frequencies most closely matched with codons at stage 10.4-11.1 in code evolution. An excess of acidic residues (stage 2 additions) lowered this estimate, but not by more than 2.3 stages. With 1 tryptophan (stage 14 addition) in 529 conserved residues, abb' significantly under-represented this amino acid, consistent with a cut-off in its residue profile before completion of the genetic code. Residue profiles in FEN-1 homologs and DNA topoisomerase I-5' placed their origin at stage 11-13. Prokaryote septation protein, FtsZ, arose earlier, between stage 8-11. Proteolipid in an ATP-driven proton pump served as a marker for cell membrane formation. It indicated this event took place near stage 7. Cell division, DNA replication and transcription were inferred to have originated in a protocell antecedent of the last common ancestor. Late-forming residue profiles characterized RNA dependent RNA replicase, DNA polymerase, reverse transcriptase and ...

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

    Science.gov (United States)

    Genilloud, O; Moreno, F; Kolter, R

    1989-02-01

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

  19. Possible antiviral effect of ciprofloxacin treatment on polyomavirus BK replication and analysis of non-coding control region sequences.

    Science.gov (United States)

    Umbro, Ilaria; Anzivino, Elena; Tinti, Francesca; Zavatto, Assunta; Bellizzi, Anna; Rodio, Donatella Maria; Mancini, Carlo; Pietropaolo, Valeria; Mitterhofer, Anna Paola

    2013-01-01

    Acute renal dysfunction (ARD) is a common complication in renal transplant recipients. Multiple factors contribute to ARD development, including acute rejection and microbial infections. Many viral infections after kidney transplantation result from reactivation of "latent" viruses in the host or from the graft, such as the human Polyomavirus BK (BKV). We report the case of a 39 year-old recipient of a 2nd kidney graft who experienced BKV reactivation after a second episode of acute humoral rejection. A 10-day treatment with the quinolone antibiotic ciprofloxacin was administered with an increase of immunosuppressive therapy despite the active BKV replication. Real Time PCR analysis performed after treatment with ciprofloxacin, unexpectedly showed clearance of BK viremia and regression of BK viruria. During the follow-up, BK viremia persisted undetectable while viruria decreased further and disappeared after 3 months.BKV non-coding control region sequence analysis from all positive samples always showed the presence of archetypal sequences, with two single-nucleotide substitutions and one nucleotide deletion that, interestingly, were all representative of the subtype/subgroup I/b-1 we identified by the viral protein 1 sequencing analysis.We report the potential effect of the quinolone antibiotic ciprofloxacin in the decrease of the BKV load in both blood and urine.

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

    KAUST Repository

    Bagchi, Samik

    2014-10-19

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

  1. Autonomously Generating Operations Sequences for a Mars Rover Using Artificial Intelligence-Based Planning

    Science.gov (United States)

    Sherwood, R.; Mutz, D.; Estlin, T.; Chien, S.; Backes, P.; Norris, J.; Tran, D.; Cooper, B.; Rabideau, G.; Mishkin, A.; Maxwell, S.

    2001-07-01

    This article discusses a proof-of-concept prototype for ground-based automatic generation of validated rover command sequences from high-level science and engineering activities. This prototype is based on ASPEN, the Automated Scheduling and Planning Environment. This artificial intelligence (AI)-based planning and scheduling system will automatically generate a command sequence that will execute within resource constraints and satisfy flight rules. An automated planning and scheduling system encodes rover design knowledge and uses search and reasoning techniques to automatically generate low-level command sequences while respecting rover operability constraints, science and engineering preferences, environmental predictions, and also adhering to hard temporal constraints. This prototype planning system has been field-tested using the Rocky 7 rover at JPL and will be field-tested on more complex rovers to prove its effectiveness before transferring the technology to flight operations for an upcoming NASA mission. Enabling goal-driven commanding of planetary rovers greatly reduces the requirements for highly skilled rover engineering personnel. This in turn greatly reduces mission operations costs. In addition, goal-driven commanding permits a faster response to changes in rover state (e.g., faults) or science discoveries by removing the time-consuming manual sequence validation process, allowing rapid "what-if" analyses, and thus reducing overall cycle times.

  2. Control regions for chromosome replication are conserved with respect to both sequence and location between Escherichia coli strains

    DEFF Research Database (Denmark)

    Frimodt-Møller, Jakob; Charbon, Godefroid; Krogfelt, Karen Angeliki;

    2015-01-01

    In Escherichia coli, chromosome replication is initiated from oriC by the DnaA initiator protein associated with ATP. Three non-coding regions contribute to the activity of DnaA. The datA locus is instrumental in conversion of DnaAATP to DnaAADP (DDAH; datA dependent DnaAATP hydrolysis) whereas Dna......A rejuvenation sequences 1 and 2 (DARS1 and DARS2) reactivate DnaAADP to DnaAATP. The structural organization of oriC, datA, DARS1 and DARS2 were found conserved between 59 fully sequenced E. coli genomes, with differences primarily in the non-functional spacer regions between key protein binding sites....... Competition experiments during balanced growth in rich medium and during mouse colonization indicated roles of datA, DARS1 and DARS2 for bacterial fitness although the relative contribution of each region differed between growth conditions. We suggest that this fitness cost contribute to conservation of both...

  3. Identification and characterization of a novel type of replication terminator with bidirectional activity on the Bacillus subtilis theta plasmid pLS20

    NARCIS (Netherlands)

    Meijer, WJJ; Smith, M; Wake, RG; deBoer, AL; Venema, G; Bron, S

    1996-01-01

    We have sequenced and analysed a 3.1 kb fragment of the 55 kb endogenous Bacillus subtilis plasmid pLS20 containing its replication functions, Just outside the region required for autonomous replication, a segment of 18 bp was identified as being almost identical to part of the major B. subtilis chr

  4. An Autonomous System for Grouping Events in a Developing Aftershock Sequence

    Energy Technology Data Exchange (ETDEWEB)

    Harris, D. B. [Lawrence Livermore National Lab. (LLNL), Livermore, CA (United States); Dodge, D. A. [Lawrence Livermore National Lab. (LLNL), Livermore, CA (United States)

    2011-03-22

    We describe a prototype detection framework that automatically clusters events in real time from a rapidly unfolding aftershock sequence. We use the fact that many aftershocks are repetitive, producing similar waveforms. By clustering events based on correlation measures of waveform similarity, the number of independent event instances that must be examined in detail by analysts may be reduced. Our system processes array data and acquires waveform templates with a short-term average (STA)/long-term average (LTA) detector operating on a beam directed at the P phases of the aftershock sequence. The templates are used to create correlation-type (subspace) detectors that sweep the subsequent data stream for occurrences of the same waveform pattern. Events are clustered by association with a particular detector. Hundreds of subspace detectors can run in this framework a hundred times faster than in real time. Nonetheless, to check the growth in the number of detectors, the framework pauses periodically and reclusters detections to reduce the number of event groups. These groups define new subspace detectors that replace the older generation of detectors. Because low-magnitude occurrences of a particular signal template may be missed by the STA/LTA detector, we advocate restarting the framework from the beginning of the sequence periodically to reprocess the entire data stream with the existing detectors. We tested the framework on 10 days of data from the Nevada Seismic Array (NVAR) covering the 2003 San Simeon earthquake. One hundred eighty-four automatically generated detectors produced 676 detections resulting in a potential reduction in analyst workload of up to 73%.

  5. Translesion replication by DNA polymerase beta is modulated by sequence context and stimulated by fork-like flap structures in DNA.

    Science.gov (United States)

    Daube, S S; Arad, G; Livneh, Z

    2000-01-18

    Mutations in the human genome are clustered in hot-spot regions, suggesting that some sequences are more prone to accumulate mutations than others. These regions are therefore more likely to lead to the development of cancer. Several pathways leading to the creation of mutations may be influenced by the DNA sequence, including sensitivity to DNA damaging agents, and repair mechanisms. We have analyzed sequence context effects on translesion replication, the error-prone repair of single-stranded DNA regions carrying lesions. By using synthetic oligonucleotides containing systematic variations of sequences flanking a synthetic abasic site, we show that translesion replication by the repair polymerase DNA polymerase beta is stimulated to a moderate extent by low stacking levels of the template nucleotides downstream of the lesion, combined with homopolymeric runs flanking the lesion both upstream and downstream. A strong stimulation of translesion replication by DNA polymerase beta was seen when fork-like flap structures were introduced into the DNA substrate downstream of the lesion. Unlike for gapped substrates, this stimulation was independent of the presence of a phosphate group at the 5' terminus of the flap. These results suggest that DNA polymerase beta may participate in cellular DNA transactions involving higher order structures. The significance of these results for in vivo translesion replication is discussed. PMID:10631001

  6. AMID: autonomous modeler of intragenic duplication.

    Science.gov (United States)

    Kummerfeld, Sarah K; Weiss, Anthony S; Fekete, Alan; Jermiin, Lars S

    2003-01-01

    Intragenic duplication is an evolutionary process where segments of a gene become duplicated. While there has been much research into whole-gene or domain duplication, there have been very few studies of non-tandem intragenic duplication. The identification of intragenically replicated sequences may provide insight into the evolution of proteins, helping to link sequence data with structure and function. This paper describes a tool for autonomously modelling intragenic duplication. AMID provides: identification of modularly repetitive genes; an algorithm for identifying repeated modules; and a scoring system for evaluating the modules' similarity. An evaluation of the algorithms and use cases are presented.

  7. Immunodetection and N-terminal sequencing of DNA replication proteins of bacteriophage BFK20 - lytic phage of Brevibacterium flavum.

    Science.gov (United States)

    Bukovská, G; Halgašová, N; Hromadová, L; Koščová, H; Bukovský, M

    2014-01-01

    Phages are excellent models for studying the mechanism of DNA replication in prokaryotes. Identification of phage proteins involved in phage DNA replication is the first prerequisite for elucidation of the phage replication module. We focused on replication proteins gp41 (a putative helicase from SF2 superfamily), gp43 (a RepA-like protein), and gp44 (a putative DNA polymerase A) of phage BFK20 grown in Brevibacterium flavum. To identify them in the phage-host system, we prepared antibodies to these proteins which were cloned and expressed in Escherichia coli as his-tagged recombinant proteins. After purification to homogeneity the recombinant proteins served for raising specific polyclonal antibodies in mice. Using these antibodies in Western blot analysis the phage proteins gp41, gp43 and gp44 were detected during the phage growth cycle. The proteins gp41 and gp43, prepared from cell lysate by ammonium sulphate precipitation, were N-terminally sequenced and found to contain the sequences N-SVKPRELR-C and N-MLGSTML-C, respectively. This means that gp41 starts with serine but not with common methionine. We consider these findings an initial but important step towards more thorough characterization of replication proteins of phage BFK20. PMID:24957720

  8. The minimal sequence essential for replication and movement of Cotton leaf curl Multan betasatellite DNA by a helper virus in plant cells.

    Science.gov (United States)

    Eini, Omid; Behjatnia, S A Akbar

    2016-10-01

    Betasatellites are single-stranded circular DNAs associated with a number of monopartite begomoviruses. Betasatellites rely on the helper begomoviruses for replication and movement in plant tissues and plant-to-plant transmission by vectors. Their genomes are approximately half the size of the helper viruses and consist of three main regions including the βC1 gene, an adenine-rich (A-rich) region, and the satellite conserved region (SCR). In this study, we investigated the minimal sequences required for Cotton leaf curl Multan betasatellite (CLCuMB) replication and movement. Mutational analysis of CLCuMB DNA genome indicated that βC1 gene and A-rich region were not required for trans-replication and movement of CLCuMB in host plants by a helper virus. Deletion of βC1 gene and a fragment (135 nt in length) upstream of this gene impaired CLCuMB replication. However, CLCuMB mutant with deletion of βC1 gene and a further 163 nucleotides replicated at a lower level as compared to the wild-type betasatellite. This suggests that there are essential elements in the fragment upstream of βC1 gene, which are required for the replication of CLCuMB rather than the size limitation of CLCuMB DNA. PMID:27193570

  9. Ubiquitous human ‘master’ origins of replication are encoded in the DNA sequence via a local enrichment in nucleosome excluding energy barriers

    Science.gov (United States)

    Drillon, Guénola; Audit, Benjamin; Argoul, Françoise; Arneodo, Alain

    2015-02-01

    As the elementary building block of eukaryotic chromatin, the nucleosome is at the heart of the compromise between the necessity of compacting DNA in the cell nucleus and the required accessibility to regulatory proteins. The recent availability of genome-wide experimental maps of nucleosome positions for many different organisms and cell types has provided an unprecedented opportunity to elucidate to what extent the DNA sequence conditions the primary structure of chromatin and in turn participates in the chromatin-mediated regulation of nuclear functions, such as gene expression and DNA replication. In this study, we use in vivo and in vitro genome-wide nucleosome occupancy data together with the set of nucleosome-free regions (NFRs) predicted by a physical model of nucleosome formation based on sequence-dependent bending properties of the DNA double-helix, to investigate the role of intrinsic nucleosome occupancy in the regulation of the replication spatio-temporal programme in human. We focus our analysis on the so-called replication U/N-domains that were shown to cover about half of the human genome in the germline (skew-N domains) as well as in embryonic stem cells, somatic and HeLa cells (mean replication timing U-domains). The ‘master’ origins of replication (MaOris) that border these megabase-sized U/N-domains were found to be specified by a few hundred kb wide regions that are hyper-sensitive to DNase I cleavage, hypomethylated, and enriched in epigenetic marks involved in transcription regulation, the hallmarks of localized open chromatin structures. Here we show that replication U/N-domain borders that are conserved in all considered cell lines have an environment highly enriched in nucleosome-excluding-energy barriers, suggesting that these ubiquitous MaOris have been selected during evolution. In contrast, MaOris that are cell-type-specific are mainly regulated epigenetically and are no longer favoured by a local abundance of intrinsic NFRs

  10. Ubiquitous human 'master' origins of replication are encoded in the DNA sequence via a local enrichment in nucleosome excluding energy barriers.

    Science.gov (United States)

    Drillon, Guénola; Audit, Benjamin; Argoul, Françoise; Arneodo, Alain

    2015-02-18

    As the elementary building block of eukaryotic chromatin, the nucleosome is at the heart of the compromise between the necessity of compacting DNA in the cell nucleus and the required accessibility to regulatory proteins. The recent availability of genome-wide experimental maps of nucleosome positions for many different organisms and cell types has provided an unprecedented opportunity to elucidate to what extent the DNA sequence conditions the primary structure of chromatin and in turn participates in the chromatin-mediated regulation of nuclear functions, such as gene expression and DNA replication. In this study, we use in vivo and in vitro genome-wide nucleosome occupancy data together with the set of nucleosome-free regions (NFRs) predicted by a physical model of nucleosome formation based on sequence-dependent bending properties of the DNA double-helix, to investigate the role of intrinsic nucleosome occupancy in the regulation of the replication spatio-temporal programme in human. We focus our analysis on the so-called replication U/N-domains that were shown to cover about half of the human genome in the germline (skew-N domains) as well as in embryonic stem cells, somatic and HeLa cells (mean replication timing U-domains). The 'master' origins of replication (MaOris) that border these megabase-sized U/N-domains were found to be specified by a few hundred kb wide regions that are hyper-sensitive to DNase I cleavage, hypomethylated, and enriched in epigenetic marks involved in transcription regulation, the hallmarks of localized open chromatin structures. Here we show that replication U/N-domain borders that are conserved in all considered cell lines have an environment highly enriched in nucleosome-excluding-energy barriers, suggesting that these ubiquitous MaOris have been selected during evolution. In contrast, MaOris that are cell-type-specific are mainly regulated epigenetically and are no longer favoured by a local abundance of intrinsic NFRs encoded in

  11. Characterizing and controlling intrinsic biases of lambda exonuclease in nascent strand sequencing reveals phasing between nucleosomes and G-quadruplex motifs around a subset of human replication origins

    DEFF Research Database (Denmark)

    Foulk, M. S.; Urban, J. M.; Casella, Cinzia;

    2015-01-01

    Nascent strand sequencing (NS-seq) is used to discover DNA replication origins genome-wide, allowing identification of features for their specification. NS-seq depends on the ability of lambda exonuclease (lambda-exo) to efficiently digest parental DNA while leaving RNA-primer protected nascent...... are not general determinants for origin specification but may play a role for a subset. Interestingly, we observed a periodic spacing of G4 motifs and nucleosomes around the peak summits, suggesting that G4s may position nucleosomes at this subset of origins. Finally, we demonstrate that use of Na+ instead of K...

  12. Transmission of human enterovirus 85 recombinants containing new unknown serotype HEV-B donor sequences in Xinjiang Uighur autonomous region, China.

    Directory of Open Access Journals (Sweden)

    Qiang Sun

    Full Text Available BACKGROUND: Human enterovirus 85 (HEV85, whose prototype strain (Strain BAN00-10353/BAN/2000 was isolated in Bangladesh in 2000, is a recently identified serotype within the human enterovirus B (HEV-B species. At present, only one nucleotide sequence of HEV85 (the complete genome sequence of the prototype strain is available in the GenBank database. PRINCIPAL FINDINGS: In this study, we report the genetic characteristics of 33 HEV85 isolates that circulated in the Xinjiang Uighur autonomous region of China in 2011. Sequence analysis revealed that all these Chinese HEV85 isolates belong to 2 transmission chains, and intertypic recombination was found with the new unknown serotype HEV-B donor sequences. Two HEV85 isolates recovered from a patient presenting acute flaccid paralysis and one of his contacts were temperature-insensitive strains, and some nucleotide substitutions in the non-coding regions and in the 2C or 3D coding regions may have affected the temperature sensitivity of HEV85 strains. CONCLUSIONS: The Chinese HEV85 recombinant described in this study trapped a new unknown serotype HEV-B donor sequence, indicating that new unknown HEV-B serotypes exist or circulate in Xinjiang of China. Our study also indicated that HEV85 is a prevalent and common enterovirus serotype in Xinjiang.

  13. A Crystallographic Study of the Role of Sequence Context in Thymine Glycol Bypass by a Replicative DNA Polymerase Serendipitously Sheds Light on the Exonuclease Complex

    Energy Technology Data Exchange (ETDEWEB)

    Aller, Pierre; Duclos, Stéphanie; Wallace, Susan S.; Doublié, Sylvie (Vermont)

    2012-06-27

    Thymine glycol (Tg) is the most common oxidation product of thymine and is known to be a strong block to replicative DNA polymerases. A previously solved structure of the bacteriophage RB69 DNA polymerase (RB69 gp43) in complex with Tg in the sequence context 5'-G-Tg-G shed light on how Tg blocks primer elongation: The protruding methyl group of the oxidized thymine displaces the adjacent 5'-G, which can no longer serve as a template for primer elongation [Aller, P., Rould, M. A., Hogg, M, Wallace, S. S. and Doublie S. (2007). A structural rationale for stalling of a replicative DNA polymerase at the most common oxidative thymine lesion, thymine glycol. Proc. Natl. Acad. Sci. USA, 104, 814-818.]. Several studies showed that in the sequence context 5'-C-Tg-purine, Tg is more likely to be bypassed by Klenow fragment, an A-family DNA polymerase. We set out to investigate the role of sequence context in Tg bypass in a B-family polymerase and to solve the crystal structures of the bacteriophage RB69 DNA polymerase in complex with Tg-containing DNA in the three remaining sequence contexts: 5'-A-Tg-G, 5'-T-Tg-G, and 5'-C-Tg-G. A combination of several factors - including the associated exonuclease activity, the nature of the 3' and 5' bases surrounding Tg, and the cis-trans interconversion of Tg - influences Tg bypass. We also visualized for the first time the structure of a well-ordered exonuclease complex, allowing us to identify and confirm the role of key residues (Phe123, Met256, and Tyr257) in strand separation and in the stabilization of the primer strand in the exonuclease site.

  14. [Autonomic neuropathies].

    Science.gov (United States)

    Siepmann, T; Penzlin, A I; Illigens, B M W

    2013-07-01

    Autonomic neuropathies are a heterogeneous group of diseases that involve damage of small peripheral autonomic Aδ- and C-fibers. Causes of autonomic nerve fiber damage are disorders such as diabetes mellitus and HIV-infection. Predominant symptoms of autonomic neuropathy are orthostatic hypotension, gastro-intestinal problems, urogenital dysfunction, and cardiac arrhythmia, which can severely impair the quality of life in affected patients. Furthermore, autonomic neuropathies can be induced by autoimmune diseases such as acute inflammatory demyelinating polyneuropathy, hereditary disorders such as the lysosomal storage disorder Fabry disease and hereditary sensory and autonomic neuropathies, as well as certain toxins and drugs.

  15. Genome sequence of foot-and-mouth disease virus outside the 3A region is also responsible for virus replication in bovine cells.

    Science.gov (United States)

    Ma, Xueqing; Li, Pinghua; Sun, Pu; Lu, Zengjun; Bao, Huifang; Bai, Xingwen; Fu, Yuanfang; Cao, Yimei; Li, Dong; Chen, Yingli; Qiao, Zilin; Liu, Zaixin

    2016-07-15

    The deletion of residues 93-102 in non-structure protein 3A of foot-and-mouth disease virus (FMDV) is associated with the inability of FMDV to grow in bovine cells and attenuated virulence in cattle.Whereas, a previously reported FMDV strain O/HKN/21/70 harboring 93-102 deletion in 3A protein grew equally well in bovine and swine cells. This suggests that changes inFMDV genome sequence, in addition to 93-102 deletion in 3A, may also affectthe viral growth phenotype in bovine cellsduring infection and replication.However, it is nuclear that changes in which region (inside or outside of 3A region) influences FMDV growth phenotype in bovine cells.In this study, to determine the region in FMDV genomeaffecting viral growth phenotype in bovine cells, we constructed chimeric FMDVs, rvGZSB-HKN3A and rvHN-HKN3A, by introducing the 3A coding region of O/HKN/21/70 into the context of O/SEA/Mya-98 strain O/GZSB/2011 and O Cathay topotype strain O/HN/CHA/93, respectively, since O/GZSB/2011 containing full-length 3A protein replicated well in bovine and swine cells, and O/HN/CHA/93 harboring 93-102 deletion in 3A protein grew poorly in bovine cells.The chimeric virusesrvGZSB-HKN3A and rvHN-HKN3A displayed growth properties and plaque phenotypes similar to those of the parental virus rvGZSB and rv-HN in BHK-21 and primary fetal porcine kidney (FPK) cells. However, rvHN-HKN3A and rv-HN replicated poorly in primary fetal bovine kidney (FBK) cells with no visible plaques, and rvGZSB-HKN3A exhibited lower growth rate and smaller plaque size phenotypes than those of the parental virus in FBK cells, but similar growth properties and plaque phenotypes to those of the recombinant viruses harboring 93-102 deletion in 3A. These results demonstrate that the difference present in FMDV genome sequence outside the 3A coding region also have influence on FMDV replication ability in bovine cells. PMID:27094491

  16. Nucleotide sequence and transcript organization of a region of the vaccinia virus genome which encodes a constitutively expressed gene required for DNA replication.

    Science.gov (United States)

    Roseman, N A; Hruby, D E

    1987-05-01

    A vaccinia virus (VV) gene required for DNA replication has been mapped to the left side of the 16-kilobase (kb) VV HindIII D DNA fragment by marker rescue of a DNA- temperature-sensitive mutant, ts17, using cloned fragments of the viral genome. The region of VV DNA containing the ts17 locus (3.6 kb) was sequenced. This nucleotide sequence contains one complete open reading frame (ORF) and two incomplete ORFs reading from left to right. Analysis of this region at early times revealed that transcription from the incomplete upstream ORF terminates coincidentally with the complete ORF encoding the ts17 gene product, which is directly downstream. The predicted proteins encoded by this region correlate well with polypeptides mapped by in vitro translation of hybrid-selected early mRNA. The nucleotide sequences of a 1.3-kb BglII fragment derived from ts17 and from two ts17 revertants were also determined, and the nature of the ts17 mutation was identified. S1 nuclease protection studies were carried out to determine the 5' and 3' ends of the transcripts and to examine the kinetics of expression of the ts17 gene during viral infection. The ts17 transcript is present at both early and late times postinfection, indicating that this gene is constitutively expressed. Surprisingly, the transcriptional start throughout infection occurs at the proposed late regulatory element TAA, which immediately precedes the putative initiation codon ATG. Although the biological activity of the ts17-encoded polypeptide was not identified, it was noted that in ts17-infected cells, expression of a nonlinked VV immediate-early gene (thymidine kinase) was deregulated at the nonpermissive temperature. This result may indicate that the ts17 gene product is functionally required at an early step of the VV replicative cycle.

  17. Agent, autonomous

    OpenAIRE

    Luciani, Annie

    2007-01-01

    The expression autonomous agents, widely used in virtual reality, computer graphics, artificial intelligence and artificial life, corresponds to the simulation of autonomous creatures, virtual (i.e. totally computed by a program), or embodied in a physical envelope, as done in autonomous robots.

  18. Inhibition of human immunodeficiency virus type 1 transcription and replication by DNA sequence-selective plant lignans.

    Science.gov (United States)

    Gnabre, J N; Brady, J N; Clanton, D J; Ito, Y; Dittmer, J; Bates, R B; Huang, R C

    1995-11-21

    A plant lignan, 3'-O-methyl nordihydroguaiaretic acid (3'-O-methyl NDGA, denoted Malachi 4:5-6 or Mal.4; molecular weigth 316), was isolated from Larrea tridentata and found to be able to inhibit human immunodeficiency virus (HIV) Tat-regulated transactivation in vivo, induce protection of lymphoblastoid CEM-SS cells from HIV (strain IIIB) killing, and suppress the replication of five HIV-1 strains (WM, MN, VS, JR-CSF, and IIIB) in mitogen-stimulated peripheral blood mononuclear cells, all in a dose-dependent manner. Mal.4 inhibits both basal transcription and Tat-regulated transactivation in vitro. The target of Mal.4 has been localized to nucleotides -87 to -40 of the HIV long terminal repeat. Mal.4 directly and specifically interferes with the binding of Sp1 to Sp1 sites in the HIV long terminal repeat. By inhibiting proviral expression, Mal.4 may be able to interrupt the life cycles of both wild-type and reverse transcriptase or protease mutant viruses in HIV-infected patients. PMID:7479972

  19. Early monitoring of the human polyomavirus BK replication and sequencing analysis in a cohort of adult kidney transplant patients treated with basiliximab

    Directory of Open Access Journals (Sweden)

    Mischitelli Monica

    2011-08-01

    Full Text Available Abstract Background Nowadays, better immunosuppressors have decreased the rates of acute rejection in kidney transplantation, but have also led to the emergence of BKV-associated nephropathy (BKVAN. Therefore, we prospectively investigated BKV load in plasma and urine samples in a cohort of kidney transplants, receiving basiliximab combined with a mycophenolate mofetil-based triple immunotherapy, to evaluate the difference between BKV replication during the first 3 months post-transplantation, characterized by the non-depleting action of basiliximab, versus the second 3 months, in which the maintenance therapy acts alone. We also performed sequencing analysis to assess whether a particular BKV subtype/subgroup or transcriptional control region (TCR variants were present. Methods We monitored BK viruria and viremia by quantitative polymerase chain reaction (Q-PCR at 12 hours (Tx, 1 (T1, 3 (T2 and 6 (T3 months post-transplantation among 60 kidney transplant patients. Sequencing analysis was performed by nested-PCR with specific primers for TCR and VP1 regions. Data were statistically analyzed using χ2 test and Student's t-test. Results BKV was detected at Tx in 4/60 urine and in 16/60 plasma, with median viral loads of 3,70 log GEq/mL and 3,79 log GEq/mL, respectively, followed by a significant increase of both BKV-positive transplants (32/60 and median values of viruria (5,78 log GEq/mL and viremia (4,52 log GEq/mL at T2. Conversely, a significantly decrease of patients with viruria and viremia (17/60 was observed at T3, together with a reduction of the median urinary and plasma viral loads (4,09 log GEq/mL and 4,00 log GEq/mL, respectively. BKV TCR sequence analysis always showed the presence of archetypal sequences, with a few single-nucleotide substitutions and one nucleotide insertion that, interestingly, were all representative of the particular subtypes/subgroups we identified by VP1 sequencing analysis: I/b-2 and IV/c-2. Conclusions Our

  20. Conserved sequences in the carboxyl terminus of integrase that are essential for human immunodeficiency virus type 1 replication.

    OpenAIRE

    Cannon, P M; Byles, E D; Kingsman, S M; Kingsman, A J

    1996-01-01

    We have previously identified a residue in the carboxyl terminus of human immunodeficiency virus type 1 integrase (HIV-1 IN), W-235, the requirement for which is only revealed in viral assays for integrase function (P. M. Cannon, W. Wilson, E. Byles, S. M. Kingsman, and A. J. Kingsman, J. Virol. 68:4768-4775, 1994). Our further analysis of this region of retroviral IN has now identified several sequence motifs which are conserved in all the retroviruses we examined, apart from human spumaretr...

  1. Chromosomal context and replication properties of ARS plasmids in Schizosaccharomyces pombe

    Indian Academy of Sciences (India)

    Aditya S Pratihar; Vishnu P Tripathi; Mukesh P Yadav; Dharani D Dubey

    2015-12-01

    Short, specific DNA sequences called as Autonomously Replicating Sequence (ARS) elements function as plasmid as well as chromosomal replication origins in yeasts. As compared to ARSs, different chromosomal origins vary greatly in their efficiency and timing of replication probably due to their wider chromosomal context. The two Schizosaccharomyces pombe ARS elements, ars727 and ars2OO4, represent two extremities in their chromosomal origin activity - ars727 is inactive and late replicating, while ars2OO4 is a highly active, early-firing origin. To determine the effect of chromosomal context on the activity of these ARS elements, we have cloned them with their extended chromosomal context as well as in the context of each other in both orientations and analysed their replication efficiency by ARS and plasmid stability assays. We found that these ARS elements retain their origin activity in their extended/altered context. However, deletion of a 133-bp region of the previously reported ars727-associated late replication enforcing element (LRE) caused advancement in replication timing of the resulting plasmid. These results confirm the role of LRE in directing plasmid replication timing and suggest that the plasmid origin efficiency of ars2OO4 or ars727 remains unaltered by the extended chromosomal context.

  2. Autonomic disturbances in narcolepsy.

    Science.gov (United States)

    Plazzi, Giuseppe; Moghadam, Keivan Kaveh; Maggi, Leonardo Serra; Donadio, Vincenzo; Vetrugno, Roberto; Liguori, Rocco; Zoccoli, Giovanna; Poli, Francesca; Pizza, Fabio; Pagotto, Uberto; Ferri, Raffaele

    2011-06-01

    Narcolepsy is a clinical condition characterized mainly by excessive sleepiness and cataplexy. Hypnagogic hallucinations and sleep paralysis complete the narcoleptic tetrad; disrupted night sleep, automatic behaviors and weight gain are also usual complaints. Different studies focus on autonomic changes or dysfunctions among narcoleptic patients, such as pupillary abnormalities, fainting spells, erectile dysfunction, night sweats, gastric problems, low body temperature, systemic hypotension, dry mouth, heart palpitations, headache and extremities dysthermia. Even if many studies lack sufficient standardization or their results have not been replicated, a non-secondary involvement of the autonomic nervous system in narcolepsy is strongly suggested, mainly by metabolic and cardiovascular findings. Furthermore, the recent discovery of a high risk for overweight and for metabolic syndrome in narcoleptic patients represents an important warning for clinicians in order to monitor and follow them up for their autonomic functions. We review here studies on autonomic functions and clinical disturbances in narcoleptic patients, trying to shed light on the possible contribute of alterations of the hypocretin system in autonomic pathophysiology.

  3. Characterization of the replication and stability regions of Agrobacterium tumefaciens plasmid pTAR.

    OpenAIRE

    Gallie, D R; Zaitlin, D; Perry, K L; Kado, C I

    1984-01-01

    A 5.4-kilobase region containing the origin of replication and stability maintenance of the 44-kilobase Agrobacterium tumefaciens plasmid pTAR has been mapped and characterized. Within this region is a 1.3-kilobase segment that is capable of directing autonomous replication. The remaining segment contains the stability locus for maintenance of pTAR during nonselective growth. Approximately 35% of pTAR shares sequence homology with pAg119, a 44-kilobase cryptic plasmid in grapevine strain 1D11...

  4. Conserved sequences in the carboxyl terminus of integrase that are essential for human immunodeficiency virus type 1 replication.

    Science.gov (United States)

    Cannon, P M; Byles, E D; Kingsman, S M; Kingsman, A J

    1996-01-01

    We have previously identified a residue in the carboxyl terminus of human immunodeficiency virus type 1 integrase (HIV-1 IN), W-235, the requirement for which is only revealed in viral assays for integrase function (P. M. Cannon, W. Wilson, E. Byles, S. M. Kingsman, and A. J. Kingsman, J. Virol. 68:4768-4775, 1994). Our further analysis of this region of retroviral IN has now identified several sequence motifs which are conserved in all the retroviruses we examined, apart from human spumaretrovirus. We have made mutations within these motifs in HIV-1 IN and examined their phenotypes when reintroduced into an infectious proviral clone. The deleterious effects of several of these mutations demonstrate the importance of these regions for IN function in vivo. We observed a further discrepancy, at a motif that is only conserved in the lentiviruses, in the ability of mutants to function in in vitro and in vivo assays. Substitutions both in this region and at W-235 abolish HIV-1 infectivity but do not affect particle production, morphology, reverse transcription, or nuclear import in T-cell lines. Taken together with the in vitro data suggesting that neither of these residues is directly involved in the catalytic reactions of IN, it seems likely that we have identified regions of IN that are essential for interactions with other components of the integration machinery. PMID:8523588

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

    Science.gov (United States)

    Arneodo, Alain

    2011-03-01

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

  6. Autonomic neuropathy

    DEFF Research Database (Denmark)

    Hilsted, J

    1983-01-01

    The diagnosis of autonomic neuropathy is often difficult to establish, since clinical symptoms generally appear late in the course of the disease, and may be non-specific. A number of recently developed quantifiable and reproducible autonomic nerve function tests are reviewed, with emphasis on th...

  7. Autonomic neuropathy

    DEFF Research Database (Denmark)

    Hilsted, J

    1980-01-01

    In order to elucidate the physiological significance of autonomic neuropathy in juvenile diabetics, cardiovascular, hormonal and metabolic functions have been investigated in three groups of juvenile diabetics: One group had no signs of neuropathy, one group had presumably slight autonomic...... neuropathy (reduced beat-to-beat variation in heart rate during hyperventilation) and one group had clinically severe autonomic neuropathy, defined by presence of orthostatic hypotension. In all three experimental situations we found sympathetic dysfunction causing cardiovascular and/or hormonal...... maladjustments in patients with autonomic neuropathy. Regarding metabolic functions we found normal responses to graded exercise and insulin-induced hypoglycemia in patients with autonomic neuropathy in spite of blunted catecholamine responses, suggesting increased sensitivity of glycogen stores and adipose...

  8. Characterizing and controlling intrinsic biases of lambda exonuclease in nascent strand sequencing reveals phasing between nucleosomes and G-quadruplex motifs around a subset of human replication origins.

    Science.gov (United States)

    Foulk, Michael S; Urban, John M; Casella, Cinzia; Gerbi, Susan A

    2015-05-01

    Nascent strand sequencing (NS-seq) is used to discover DNA replication origins genome-wide, allowing identification of features for their specification. NS-seq depends on the ability of lambda exonuclease (λ-exo) to efficiently digest parental DNA while leaving RNA-primer protected nascent strands intact. We used genomics and biochemical approaches to determine if λ-exo digests all parental DNA sequences equally. We report that λ-exo does not efficiently digest G-quadruplex (G4) structures in a plasmid. Moreover, λ-exo digestion of nonreplicating genomic DNA (LexoG0) enriches GC-rich DNA and G4 motifs genome-wide. We used LexoG0 data to control for nascent strand-independent λ-exo biases in NS-seq and validated this approach at the rDNA locus. The λ-exo-controlled NS-seq peaks are not GC-rich, and only 35.5% overlap with 6.8% of all G4s, suggesting that G4s are not general determinants for origin specification but may play a role for a subset. Interestingly, we observed a periodic spacing of G4 motifs and nucleosomes around the peak summits, suggesting that G4s may position nucleosomes at this subset of origins. Finally, we demonstrate that use of Na(+) instead of K(+) in the λ-exo digestion buffer reduced the effect of G4s on λ-exo digestion and discuss ways to increase both the sensitivity and specificity of NS-seq.

  9. Sequence characteristics required for cooperative binding and efficient in vivo titration of the replication initiator protein DnaA in E. coli

    DEFF Research Database (Denmark)

    Hansen, Flemming G.; Christensen, Bjarke Bak; Atlung, Tove

    2007-01-01

    Plasmids carrying the mioC promoter region, which contains two DnaA boxes, R5 and R6 with one misfit to the consensus TT(A)/(T)TNCACA, are as efficient in in vivo titration of the DnaA protein as plasmids carrying a replication-inactivated oriC region with its eight DnaA boxes. Three additional Dna......A boxes around the promoter proximal R5 DnaA box were identified and shown by mutational analysis to be necessary for the cooperative binding of DnaA required for titration. These four DnaA boxes are located in the same orientation and with a spacing of two or three base-pairs. The cooperative binding...... was eliminated by insertion of half a helical turn between any of the DnaA boxes. Titration strongly depends on the presence and orientation of the promoter distal R6 DnaA box located 104 bp upstream of the R5 box as well as neighbouring sequences downstream of R6. Titration depends on the integrity of a 43 bp...

  10. The Caulobacter crescentus chromosome replication origin evolved two classes of weak DnaA binding sites.

    Science.gov (United States)

    Taylor, James A; Ouimet, Marie-Claude; Wargachuk, Richard; Marczynski, Gregory T

    2011-10-01

    The Caulobacter crescentus replication initiator DnaA and essential response regulator CtrA compete to control chromosome replication. The C. crescentus replication origin (Cori) contains five strong CtrA binding sites but only two apparent DnaA boxes, termed G-boxes (with a conserved second position G, TGATCCACA). Since clusters of DnaA boxes typify bacterial replication origins, this discrepancy suggested that C. crescentus DnaA recognizes different DNA sequences or compensates with novel DNA-binding proteins. We searched for novel DNA sites by scanning mutagenesis of the most conserved Cori DNA. Autonomous replication assays showed that G-boxes and novel W-boxes (TCCCCA) are essential for replication. Further analyses showed that C. crescentus DnaA binds G-boxes with moderate and W-boxes with very weak affinities significantly below DnaA's capacity for high-affinity Escherichia coli-boxes (TTATCCACA). Cori has five conserved W-boxes. Increasing W-box affinities increases or decreases autonomous replication depending on their strategic positions between the G-boxes. In vitro, CtrA binding displaces DnaA from proximal G-boxes and from distal W-boxes implying CtrA-DnaA competition and DnaA-DnaA cooperation between G-boxes and W-boxes. Similarly, during cell cycle progression, CtrA proteolysis coincides with DnaA binding to Cori. We also observe highly conserved W-boxes in other replication origins lacking E. coli-boxes. Therefore, strategically weak DnaA binding can be a general means of replication control.

  11. Database Replication

    CERN Document Server

    Kemme, Bettina

    2010-01-01

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

  12. Analysis of a new strain of Euphorbia mosaic virus with distinct replication specificity unveils a lineage of begomoviruses with short Rep sequences in the DNA-B intergenic region

    Directory of Open Access Journals (Sweden)

    Argüello-Astorga Gerardo R

    2010-10-01

    Full Text Available Abstract Background Euphorbia mosaic virus (EuMV is a member of the SLCV clade, a lineage of New World begomoviruses that display distinctive features in their replication-associated protein (Rep and virion-strand replication origin. The first entirely characterized EuMV isolate is native from Yucatan Peninsula, Mexico; subsequently, EuMV was detected in weeds and pepper plants from another region of Mexico, and partial DNA-A sequences revealed significant differences in their putative replication specificity determinants with respect to EuMV-YP. This study was aimed to investigate the replication compatibility between two EuMV isolates from the same country. Results A new isolate of EuMV was obtained from pepper plants collected at Jalisco, Mexico. Full-length clones of both genomic components of EuMV-Jal were biolistically inoculated into plants of three different species, which developed symptoms indistinguishable from those induced by EuMV-YP. Pseudorecombination experiments with EuMV-Jal and EuMV-YP genomic components demonstrated that these viruses do not form infectious reassortants in Nicotiana benthamiana, presumably because of Rep-iteron incompatibility. Sequence analysis of the EuMV-Jal DNA-B intergenic region (IR led to the unexpected discovery of a 35-nt-long sequence that is identical to a segment of the rep gene in the cognate viral DNA-A. Similar short rep sequences ranging from 35- to 51-nt in length were identified in all EuMV isolates and in three distinct viruses from South America related to EuMV. These short rep sequences in the DNA-B IR are positioned downstream to a ~160-nt non-coding domain highly similar to the CP promoter of begomoviruses belonging to the SLCV clade. Conclusions EuMV strains are not compatible in replication, indicating that this begomovirus species probably is not a replicating lineage in nature. The genomic analysis of EuMV-Jal led to the discovery of a subgroup of SLCV clade viruses that contain in

  13. Comparative analysis of seven viral nuclear export signals (NESs reveals the crucial role of nuclear export mediated by the third NES consensus sequence of nucleoprotein (NP in influenza A virus replication.

    Directory of Open Access Journals (Sweden)

    Nopporn Chutiwitoonchai

    Full Text Available The assembly of influenza virus progeny virions requires machinery that exports viral genomic ribonucleoproteins from the cell nucleus. Currently, seven nuclear export signal (NES consensus sequences have been identified in different viral proteins, including NS1, NS2, M1, and NP. The present study examined the roles of viral NES consensus sequences and their significance in terms of viral replication and nuclear export. Mutation of the NP-NES3 consensus sequence resulted in a failure to rescue viruses using a reverse genetics approach, whereas mutation of the NS2-NES1 and NS2-NES2 sequences led to a strong reduction in viral replication kinetics compared with the wild-type sequence. While the viral replication kinetics for other NES mutant viruses were also lower than those of the wild-type, the difference was not so marked. Immunofluorescence analysis after transient expression of NP-NES3, NS2-NES1, or NS2-NES2 proteins in host cells showed that they accumulated in the cell nucleus. These results suggest that the NP-NES3 consensus sequence is mostly required for viral replication. Therefore, each of the hydrophobic (Φ residues within this NES consensus sequence (Φ1, Φ2, Φ3, or Φ4 was mutated, and its viral replication and nuclear export function were analyzed. No viruses harboring NP-NES3 Φ2 or Φ3 mutants could be rescued. Consistent with this, the NP-NES3 Φ2 and Φ3 mutants showed reduced binding affinity with CRM1 in a pull-down assay, and both accumulated in the cell nucleus. Indeed, a nuclear export assay revealed that these mutant proteins showed lower nuclear export activity than the wild-type protein. Moreover, the Φ2 and Φ3 residues (along with other Φ residues within the NP-NES3 consensus were highly conserved among different influenza A viruses, including human, avian, and swine. Taken together, these results suggest that the Φ2 and Φ3 residues within the NP-NES3 protein are important for its nuclear export function

  14. Involvement of the 5'-leader sequence in coupling the stability of a human H3 histone mRNA with DNA replication

    International Nuclear Information System (INIS)

    Two lines of evidence derived from fusion gene constructs indicate that sequences residing in the 5'-nontranslated region of a cell cycle-dependent human H3 histone mRNA are involved in the selective destabilization that occurs when DNA synthesis is terminated. The experimental approach was to construct chimeric genes in which fragments of the mRNA coding regions of the H3 histone gene were fused with fragments of genes not expressed in a cell cycle-dependent manner. After transfection in HeLa S3 cells with the recombinant plasmids, levels of fusion mRNAs were determined by S1 nuclease analysis prior to and following DNA synthesis inhibition. When the first 20 nucleotides of an H3 histone mRNA leader were replaced with 89 nucleotides of the leader from a Drosophila heat-shock (hsp70) mRNA, the fusion transcript remained stable during inhibition of DNA synthesis, in contrast to the rapid destabilization of the endogenous histone mRNA in these cells. In a reciprocal experiment, a histone-globin fusion gene was constructed that produced a transcript with the initial 20 nucleotides of the H3 histone mRNA substituted for the human β-globin mRNA leader. In HeLa cells treated with inhibitors of DNA synthesis and/or protein synthesis, cellular levels of this histone-globin fusion mRNA appeared to be regulated in a manner similar to endogenous histone mRNA levels. These results suggest that the first 20 nucleotides of the leader are sufficient to couple histone mRNA stability with DNA replication

  15. Replicating vaccines

    Science.gov (United States)

    Early work on fish immunology and disease resistance demonstrated fish (like animals and humans) that survived infection were typically resistant to re-infection with the same pathogen. The concepts of resistance upon reinfection lead to the research and development of replicating (live) vaccines in...

  16. Susceptibility to superhelically driven DNA duplex destabilization: a highly conserved property of yeast replication origins.

    Directory of Open Access Journals (Sweden)

    2005-06-01

    Full Text Available Strand separation is obligatory for several DNA functions, including replication. However, local DNA properties such as A+T content or thermodynamic stability alone do not determine the susceptibility to this transition in vivo. Rather, superhelical stresses provide long-range coupling among the transition behaviors of all base pairs within a topologically constrained domain. We have developed methods to analyze superhelically induced duplex destabilization (SIDD in genomic DNA that take into account both this long-range stress-induced coupling and sequence-dependent local thermodynamic stability. Here we apply this approach to examine the SIDD properties of 39 experimentally well-characterized autonomously replicating DNA sequences (ARS elements, which function as replication origins in the yeast Saccharomyces cerevisiae. We find that these ARS elements have a strikingly increased susceptibility to SIDD relative to their surrounding sequences. On average, these ARS elements require 4.78 kcal/mol less free energy to separate than do their immediately surrounding sequences, making them more than 2,000 times easier to open. Statistical analysis shows that the probability of this strong an association between SIDD sites and ARS elements arising by chance is approximately 4 x 10. This local enhancement of the propensity to separate to single strands under superhelical stress has obvious implications for origin function. SIDD properties also could be used, in conjunction with other known origin attributes, to identify putative replication origins in yeast, and possibly in other metazoan genomes.

  17. In search of the holy replicator

    OpenAIRE

    Gilbert, David M.

    2004-01-01

    After 40 years of searching for the eukaryotic replicator sequence, it is time to abandon the concept of ‘the’ replicator as a single genetic entity. Here I propose a ‘relaxed replicon model’ in which a positive initiator–replicator interaction is facilitated by a combination of several complex features of chromatin. An important question for the future is whether the positions of replication origins are simply a passive result of local chromatin structure or are actively localized to coordin...

  18. Mutator phenotypes due to DNA replication infidelity

    OpenAIRE

    Arana, Mercedes E.; Kunkel, Thomas A.

    2010-01-01

    This article considers the fidelity of DNA replication performed by eukaryotic DNA polymerases involved in replicating the nuclear genome. DNA replication fidelity can vary widely depending on the DNA polymerase, the composition of the error, the flanking sequence, the presence of DNA damage and the ability to correct errors. As a consequence, defects in processes that determine DNA replication fidelity can confer strong mutator phenotypes whose specificity can help determine the molecular na...

  19. Selection of functional tRNA primers and primer binding site sequences from a retroviral combinatorial library: identification of new functional tRNA primers in murine leukemia virus replication

    DEFF Research Database (Denmark)

    Lund, Anders Henrik; Duch, M; Pedersen, F S

    2000-01-01

    Retroviral reverse transcription is initiated from a cellular tRNA molecule and all known exogenous isolates of murine leukemia virus utilise a tRNA(Pro)molecule. While several studies suggest flexibility in murine leukemia virus primer utilisation, studies on human immunodeficiency virus and avian...... retro-viruses have revealed evidence of molecular adapt-ation towards the specific tRNA isoacceptor used as replication primer. In this study, murine leukemia virus tRNA utilisation is investigated by in vivo screening of a retroviral vector combinatorial library with randomised primer binding sites....... While most of the selected primer binding sites are complementary to the 3'-end of tRNA((Pro)), we also retrieved PBS sequences matching four other tRNA molecules and demonstrate that Akv murine leukemia virus vectors may efficiently replicate using tRNA(Arg(CCU)), tRNA(Phe(GAA))and a hitherto unknown...

  20. Identification of a Single Strand Origin of Replication in the Integrative and Conjugative Element ICEBs1 of Bacillus subtilis.

    Directory of Open Access Journals (Sweden)

    Laurel D Wright

    2015-10-01

    Full Text Available We identified a functional single strand origin of replication (sso in the integrative and conjugative element ICEBs1 of Bacillus subtilis. Integrative and conjugative elements (ICEs, also known as conjugative transposons are DNA elements typically found integrated into a bacterial chromosome where they are transmitted to daughter cells by chromosomal replication and cell division. Under certain conditions, ICEs become activated and excise from the host chromosome and can transfer to neighboring cells via the element-encoded conjugation machinery. Activated ICEBs1 undergoes autonomous rolling circle replication that is needed for the maintenance of the excised element in growing and dividing cells. Rolling circle replication, used by many plasmids and phages, generates single-stranded DNA (ssDNA. In many cases, the presence of an sso enhances the conversion of the ssDNA to double-stranded DNA (dsDNA by enabling priming of synthesis of the second DNA strand. We initially identified sso1 in ICEBs1 based on sequence similarity to the sso of an RCR plasmid. Several functional assays confirmed Sso activity. Genetic analyses indicated that ICEBs1 uses sso1 and at least one other region for second strand DNA synthesis. We found that Sso activity was important for two key aspects of the ICEBs1 lifecycle: 1 maintenance of the plasmid form of ICEBs1 in cells after excision from the chromosome, and 2 stable acquisition of ICEBs1 following transfer to a new host. We identified sequences similar to known plasmid sso's in several other ICEs. Together, our results indicate that many other ICEs contain at least one single strand origin of replication, that these ICEs likely undergo autonomous replication, and that replication contributes to the stability and spread of these elements.

  1. Do transcriptional enhancers also augment DNA replication?

    OpenAIRE

    O'Connor, D T; Subramani, S

    1988-01-01

    Enhancers are DNA elements that augment transcription in cis, independent of distance and orientation. Evidence such as hormone dependent neoplastic cell growth and the stimulation of viral replication by sequences present in enhancers suggests that enhancers may also directly affect DNA replication. We tested this hypothesis in recombinant plasmids by asking whether sequences that stimulated DNA replication shared the properties of transcriptional enhancers. The homologous simian virus 40 (S...

  2. Autonomous Search

    CERN Document Server

    Hamadi, Youssef; Saubion, Frédéric

    2012-01-01

    Decades of innovations in combinatorial problem solving have produced better and more complex algorithms. These new methods are better since they can solve larger problems and address new application domains. They are also more complex which means that they are hard to reproduce and often harder to fine-tune to the peculiarities of a given problem. This last point has created a paradox where efficient tools are out of reach of practitioners. Autonomous search (AS) represents a new research field defined to precisely address the above challenge. Its major strength and originality consist in the

  3. Pure Autonomic Failure

    Science.gov (United States)

    ... Drugs GARD Information Navigator FAQs About Rare Diseases Pure autonomic failure Title Other Names: Bradbury Eggleston syndrome; ... Categories: Nervous System Diseases ; RDCRN Summary Summary Listen Pure autonomic failure is characterized by generalized autonomic failure ...

  4. Diabetic autonomic neuropathy.

    Science.gov (United States)

    Freeman, Roy

    2014-01-01

    Diabetes mellitus is the commonest cause of an autonomic neuropathy in the developed world. Diabetic autonomic neuropathy causes a constellation of symptoms and signs affecting cardiovascular, urogenital, gastrointestinal, pupillomotor, thermoregulatory, and sudomotor systems. Several discrete syndromes associated with diabetes cause autonomic dysfunction. The most prevalent of these are: generalized diabetic autonomic neuropathy, autonomic neuropathy associated with the prediabetic state, treatment-induced painful and autonomic neuropathy, and transient hypoglycemia-associated autonomic neuropathy. These autonomic manifestations of diabetes are responsible for the most troublesome and disabling features of diabetic peripheral neuropathy and result in a significant proportion of the mortality and morbidity associated with the disease.

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

    NARCIS (Netherlands)

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

    1979-01-01

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

  6. Transmission of Human Enterovirus 85 Recombinants Containing New Unknown Serotype HEV-B Donor Sequences in Xinjiang Uighur Autonomous Region, China

    OpenAIRE

    Qiang Sun; Yong Zhang; Shuangli Zhu; Huifang Tian; Guohong Huang; Hui Cui; Xiaolei Li; Dongmei Yan; Zhen Zhu; Jing Li; Peng Zheng; Huafang Jiang; Bo Zhang; Xiaojuan Tan; Hui Zhu

    2013-01-01

    BACKGROUND: Human enterovirus 85 (HEV85), whose prototype strain (Strain BAN00-10353/BAN/2000) was isolated in Bangladesh in 2000, is a recently identified serotype within the human enterovirus B (HEV-B) species. At present, only one nucleotide sequence of HEV85 (the complete genome sequence of the prototype strain) is available in the GenBank database. PRINCIPAL FINDINGS: In this study, we report the genetic characteristics of 33 HEV85 isolates that circulated in the Xinjiang Uighur autonomo...

  7. Replication in Economics

    OpenAIRE

    Hamermesh, Daniel S.

    2007-01-01

    This examination of the role and potential for replication in economics points out the paucity of both pure replication -- checking on others' published papers using their data -- and scientific replication -- using data representing different populations in one's own work or in a Comment. Several controversies in empirical economics illustrate how and how not to behave when replicating others' work. The incentives for replication facing editors, authors and potential replicators are examined...

  8. A highly conserved DNA replication module from Streptococcus thermophilus phages is similar in sequence and topology to a module from Lactococcus lactis phages.

    Science.gov (United States)

    Desiere, F; Lucchini, S; Bruttin, A; Zwahlen, M C; Brüssow, H

    1997-08-01

    A highly conserved DNA region extending over 5 kb was observed in Streptococcus thermophilus bacteriophages. Comparative sequencing of one temperate and 26 virulent phages demonstrated in the most extreme case an 18% aa difference for a predicted protein, while the majority of the phages showed fewer, if any aa changes. The relative degree of aa conservation was not homogeneous over the DNA segment investigated. Sequence analysis of the conserved segment revealed genes possibly involved in DNA transactions. Three predicted proteins (orf 233, 443, and 382 gene product (gp)) showed nucleoside triphosphate binding motifs. Orf 443 gp showed in addition a DEAH box motif, characteristically found in a subgroup of helicases, and a variant zinc finger motif known from a phage T7 helicase/primase. Tree analysis classified orf 443 gp as a distant member of the helicase superfamily. Orf 382 gp showed similarity to putative plasmid DNA primases. Downstream of orf 382 a noncoding repeat region was identified that showed similarity to a putative minus origin from a cryptic S. thermophilus plasmid. Four predicted proteins showed not only high degrees of aa identity (34 to 63%) with proteins from Lactococcus lactis phages, but their genes showed a similar topological organization. We interpret this as evidence for a horizontal gene transfer event between phages of the two bacterial genera in the distant past. PMID:9268169

  9. Mrc1 is a replication fork component whose phosphorylation in response to DNA replication stress activates Rad53

    OpenAIRE

    Osborn, Alexander J.; Elledge, Stephen J.

    2003-01-01

    When DNA replication is stalled, a signal transduction pathway is activated that promotes the stability of stalled forks and resumption of DNA synthesis. In budding yeast, this pathway includes the kinases Mec1 and Rad53. Here we report that the Mediator protein Mrc1, which is required for normal DNA replication and for activation of Rad53, is present at replication forks. Mrc1 initially binds early-replicating sequences and moves along chromatin with the replication f...

  10. Autonomic Nervous System Disorders

    Science.gov (United States)

    Your autonomic nervous system is the part of your nervous system that controls involuntary actions, such as the beating of your heart ... breathing and swallowing Erectile dysfunction in men Autonomic nervous system disorders can occur alone or as the result ...

  11. Autoimmune Autonomic Ganglionopathy

    Science.gov (United States)

    ... Accessed 9/2/2015. Autoimmune Autonomic Ganglionopathy Summary. Dysautonomia International . http://www.dysautonomiainternational.org/page.php?ID= ... page Basic Information In Depth Information Basic Information Dysautonomia International offers an information page on Autoimmune autonomic ...

  12. [Trigeminal autonomic cephalgias].

    Science.gov (United States)

    Maximova, M Yu; Piradov, M A; Suanova, E T; Sineva, N A

    2015-01-01

    Review of literature on the trigeminal autonomic cephalgias are presented. Trigeminal autonomic cephalgias are primary headaches with phenotype consisting of trigeminal pain with autonomic sign including lacrimation, rhinorrhea and miosis. Discussed are issues of classification, pathogenesis, clinical picture, diagnosis, differential diagnosis and treatment of this headache. Special attention is paid to cluster headache, paroxysmal hemicrania, SUNCT syndrome, hemicrania continua.

  13. DLESE Teaching Box Pilot Project: Developing a Replicable Model for Collaboratively Creating Innovative Instructional Sequences Using Exemplary Resources in the Digital Library for Earth System Education (DLESE)

    Science.gov (United States)

    Weingroff, M.

    2004-12-01

    Before the advent of digital libraries, it was difficult for teachers to find suitable high-quality resources to use in their teaching. Digital libraries such as DLESE have eased the task by making high quality resources more easily accessible and providing search mechanisms that allow teachers to 'fine tune' the criteria over which they search. Searches tend to return lists of resources with some contextualizing information. However, teachers who are teaching 'out of discipline' or who have minimal training in science often need additional support to know how to use and sequence them. The Teaching Box Pilot Project was developed to address these concerns, bringing together educators, scientists, and instructional designers in a partnership to build an online framework to fully support innovative units of instruction about the Earth system. Each box integrates DLESE resources and activities, teaching tips, standards, concepts, teaching outcomes, reviews, and assessment information. Online templates and best practice guidelines are being developed that will enable teachers to create their own boxes or customize existing ones. Two boxes have been developed so far, one on weather for high school students, and one on the evidence for plate tectonics for middle schoolers. The project has met with significant enthusiasm and interest, and we hope to expand it by involving individual teachers, school systems, pre-service programs, and universities in the development and use of teaching boxes. A key ingredient in the project's success has been the close collaboration between the partners, each of whom has brought unique experiences, perspectives, knowledge, and skills to the project. This first effort involved teachers in the San Francisco Bay area, the University of California Museum of Paleontology, San Francisco State University, U.S. Geological Survey, and DLESE. This poster will allow participants to explore one of the teaching boxes. We will discuss how the boxes were

  14. Replicability of Experiment

    Directory of Open Access Journals (Sweden)

    John D. Norton

    2015-06-01

    Full Text Available The replicability of experiment is routinely offered as the gold standard of evidence. I argue that it is not supported by a universal principle of replicability in inductive logic. A failure of replication may not impugn a credible experimental result; and a successful replication can fail to vindicate an incredible experimental result. Rather, employing a material approach to inductive inference, the evidential import of successful replication of an experiment is determined by the prevailing background facts. Commonly, these background facts do support successful replication as a good evidential guide and this has fostered the illusion of a deeper, exceptionless principle.

  15. Archaeal DNA replication.

    Science.gov (United States)

    Kelman, Lori M; Kelman, Zvi

    2014-01-01

    DNA replication is essential for all life forms. Although the process is fundamentally conserved in the three domains of life, bioinformatic, biochemical, structural, and genetic studies have demonstrated that the process and the proteins involved in archaeal DNA replication are more similar to those in eukaryal DNA replication than in bacterial DNA replication, but have some archaeal-specific features. The archaeal replication system, however, is not monolithic, and there are some differences in the replication process between different species. In this review, the current knowledge of the mechanisms governing DNA replication in Archaea is summarized. The general features of the replication process as well as some of the differences are discussed. PMID:25421597

  16. DNA replication and cancer

    DEFF Research Database (Denmark)

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

    2016-01-01

    A dividing cell has to duplicate its DNA precisely once during the cell cycle to preserve genome integrity avoiding the accumulation of genetic aberrations that promote diseases such as cancer. A large number of endogenous impacts can challenge DNA replication and cells harbor a battery of pathways...... to promote genome integrity during DNA replication. This includes suppressing new replication origin firing, stabilization of replicating forks, and the safe restart of forks to prevent any loss of genetic information. Here, we describe mechanisms by which oncogenes can interfere with DNA replication thereby...... causing DNA replication stress and genome instability. Further, we describe cellular and systemic responses to these insults with a focus on DNA replication restart pathways. Finally, we discuss the therapeutic potential of exploiting intrinsic replicative stress in cancer cells for targeted therapy....

  17. Comparison of three replication strategies in complex multicellular organisms: Asexual replication, sexual replication with identical gametes, and sexual replication with distinct sperm and egg gametes

    Science.gov (United States)

    Tannenbaum, Emmanuel

    2008-01-01

    This paper studies the mutation-selection balance in three simplified replication models. The first model considers a population of organisms replicating via the production of asexual spores. The second model considers a sexually replicating population that produces identical gametes. The third model considers a sexually replicating population that produces distinct sperm and egg gametes. All models assume diploid organisms whose genomes consist of two chromosomes, each of which is taken to be functional if equal to some master sequence, and defective otherwise. In the asexual population, the asexual diploid spores develop directly into adult organisms. In the sexual populations, the haploid gametes enter a haploid pool, where they may fuse with other haploids. The resulting immature diploid organisms then proceed to develop into mature organisms. Based on an analysis of all three models, we find that, as organism size increases, a sexually replicating population can only outcompete an asexually replicating population if the adult organisms produce distinct sperm and egg gametes. A sexual replication strategy that is based on the production of large numbers of sperm cells to fertilize a small number of eggs is found to be necessary in order to maintain a sufficiently low cost for sex for the strategy to be selected for over a purely asexual strategy. We discuss the usefulness of this model in understanding the evolution and maintenance of sexual replication as the preferred replication strategy in complex, multicellular organisms.

  18. Context based computational analysis and characterization of ARS consensus sequences (ACS) of Saccharomyces cerevisiae genome.

    Science.gov (United States)

    Singh, Vinod Kumar; Krishnamachari, Annangarachari

    2016-09-01

    Genome-wide experimental studies in Saccharomyces cerevisiae reveal that autonomous replicating sequence (ARS) requires an essential consensus sequence (ACS) for replication activity. Computational studies identified thousands of ACS like patterns in the genome. However, only a few hundreds of these sites act as replicating sites and the rest are considered as dormant or evolving sites. In a bid to understand the sequence makeup of replication sites, a content and context-based analysis was performed on a set of replicating ACS sequences that binds to origin-recognition complex (ORC) denoted as ORC-ACS and non-replicating ACS sequences (nrACS), that are not bound by ORC. In this study, DNA properties such as base composition, correlation, sequence dependent thermodynamic and DNA structural profiles, and their positions have been considered for characterizing ORC-ACS and nrACS. Analysis reveals that ORC-ACS depict marked differences in nucleotide composition and context features in its vicinity compared to nrACS. Interestingly, an A-rich motif was also discovered in ORC-ACS sequences within its nucleosome-free region. Profound changes in the conformational features, such as DNA helical twist, inclination angle and stacking energy between ORC-ACS and nrACS were observed. Distribution of ACS motifs in the non-coding segments points to the locations of ORC-ACS which are found far away from the adjacent gene start position compared to nrACS thereby enabling an accessible environment for ORC-proteins. Our attempt is novel in considering the contextual view of ACS and its flanking region along with nucleosome positioning in the S. cerevisiae genome and may be useful for any computational prediction scheme. PMID:27508123

  19. Context based computational analysis and characterization of ARS consensus sequences (ACS of Saccharomyces cerevisiae genome

    Directory of Open Access Journals (Sweden)

    Vinod Kumar Singh

    2016-09-01

    Full Text Available Genome-wide experimental studies in Saccharomyces cerevisiae reveal that autonomous replicating sequence (ARS requires an essential consensus sequence (ACS for replication activity. Computational studies identified thousands of ACS like patterns in the genome. However, only a few hundreds of these sites act as replicating sites and the rest are considered as dormant or evolving sites. In a bid to understand the sequence makeup of replication sites, a content and context-based analysis was performed on a set of replicating ACS sequences that binds to origin-recognition complex (ORC denoted as ORC-ACS and non-replicating ACS sequences (nrACS, that are not bound by ORC. In this study, DNA properties such as base composition, correlation, sequence dependent thermodynamic and DNA structural profiles, and their positions have been considered for characterizing ORC-ACS and nrACS. Analysis reveals that ORC-ACS depict marked differences in nucleotide composition and context features in its vicinity compared to nrACS. Interestingly, an A-rich motif was also discovered in ORC-ACS sequences within its nucleosome-free region. Profound changes in the conformational features, such as DNA helical twist, inclination angle and stacking energy between ORC-ACS and nrACS were observed. Distribution of ACS motifs in the non-coding segments points to the locations of ORC-ACS which are found far away from the adjacent gene start position compared to nrACS thereby enabling an accessible environment for ORC-proteins. Our attempt is novel in considering the contextual view of ACS and its flanking region along with nucleosome positioning in the S. cerevisiae genome and may be useful for any computational prediction scheme.

  20. Replicating chromatin: a tale of histones

    DEFF Research Database (Denmark)

    Groth, Anja

    2009-01-01

    Chromatin serves structural and functional roles crucial for genome stability and correct gene expression. This organization must be reproduced on daughter strands during replication to maintain proper overlay of epigenetic fabric onto genetic sequence. Nucleosomes constitute the structural...... reassembly on nascent DNA strands. The aim of this review is to discuss how histones - new and old - are handled at the replication fork, highlighting new mechanistic insights and revisiting old paradigms....

  1. MOLECULAR REPLICATOR DYNAMICS

    OpenAIRE

    BÄRBEL M. R. STADLER; Stadler, Peter F

    2003-01-01

    Template-dependent replication at the molecular level is the basis of reproduction in nature. A detailed understanding of the peculiarities of the chemical reaction kinetics associated with replication processes is therefore an indispensible prerequisite for any understanding of evolution at the molecular level. Networks of interacting self-replicating species can give rise to a wealth of different dynamical phenomena, from competitive exclusion to permanent coexistence, from global stability...

  2. Stimulating autonomous motivation in the classroom: The role of interpersonal teacher agency and communion

    NARCIS (Netherlands)

    Wijsman, Lindy; Mainhard, Tim; Brekelmans, Mieke

    2014-01-01

    Self Determination Theory (SDT) distinguishes the quality of motivation from its quantity or intensity (Vansteenkiste, Sierens, Soetens, Luyckx, & Lens, 2009). A sequence from controlled to autonomous motivation is adopted; autonomous motivation is seen as the best quality type. Being autonomously m

  3. Self-replicating systems.

    Science.gov (United States)

    Clixby, Gregory; Twyman, Lance

    2016-05-01

    Over the past 25 years, there has been a surge of development in research towards self-replication and self-replicating systems. The interest in these systems relates to one of the most fundamental questions posed in all fields of science - How did life on earth begin? Investigating how the self-replication process evolved may hold the key to understanding the emergence and evolution of living systems and, ultimately, gain a clear insight into the origin of life on earth. This introductory review aims to highlight the fundamental prerequisites of self-replication along with the important research that has been conducted over the past few decades. PMID:27086507

  4. Trigeminal autonomic cephalgias

    OpenAIRE

    Benoliel, Rafael

    2012-01-01

    1. Trigeminal autonomic cephalgias (TACs) are headaches/facial pains classified together based on:a suspected common pathophysiology involving the trigeminovascular system, the trigeminoparasympathetic reflex and centres controlling circadian rhythms;a similar clinical presentation of trigeminal pain, and autonomic activation.

  5. Testing for autonomic neuropathy

    DEFF Research Database (Denmark)

    Hilsted, J

    1984-01-01

    Autonomic neuropathy is a common complication in long-term diabetes, about 30% of the patients showing measurable signs of autonomic dysfunction after 10 years duration of disease. The diagnosis is often difficult to establish because clinical symptoms generally occur late in the course...

  6. Replicating animal mitochondrial DNA

    Directory of Open Access Journals (Sweden)

    Emily A. McKinney

    2013-01-01

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

  7. Meiotic transmission of an in vitro-assembled autonomous maize minichromosome.

    Directory of Open Access Journals (Sweden)

    Shawn R Carlson

    2007-10-01

    Full Text Available Autonomous chromosomes are generated in yeast (yeast artificial chromosomes and human fibrosarcoma cells (human artificial chromosomes by introducing purified DNA fragments that nucleate a kinetochore, replicate, and segregate to daughter cells. These autonomous minichromosomes are convenient for manipulating and delivering DNA segments containing multiple genes. In contrast, commercial production of transgenic crops relies on methods that integrate one or a few genes into host chromosomes; extensive screening to identify insertions with the desired expression level, copy number, structure, and genomic location; and long breeding programs to produce varieties that carry multiple transgenes. As a step toward improving transgenic crop production, we report the development of autonomous maize minichromosomes (MMCs. We constructed circular MMCs by combining DsRed and nptII marker genes with 7-190 kb of genomic maize DNA fragments containing satellites, retroelements, and/or other repeats commonly found in centromeres and using particle bombardment to deliver these constructs into embryogenic maize tissue. We selected transformed cells, regenerated plants, and propagated their progeny for multiple generations in the absence of selection. Fluorescent in situ hybridization and segregation analysis demonstrated that autonomous MMCs can be mitotically and meiotically maintained. The MMC described here showed meiotic segregation ratios approaching Mendelian inheritance: 93% transmission as a disome (100% expected, 39% transmission as a monosome crossed to wild type (50% expected, and 59% transmission in self crosses (75% expected. The fluorescent DsRed reporter gene on the MMC was expressed through four generations, and Southern blot analysis indicated the encoded genes were intact. This novel approach for plant transformation can facilitate crop biotechnology by (i combining several trait genes on a single DNA fragment, (ii arranging genes in a defined

  8. Wireless autonomous device data transmission

    Science.gov (United States)

    Sammel, Jr., David W. (Inventor); Cain, James T. (Inventor); Mickle, Marlin H. (Inventor); Mi, Minhong (Inventor)

    2013-01-01

    A method of communicating information from a wireless autonomous device (WAD) to a base station. The WAD has a data element having a predetermined profile having a total number of sequenced possible data element combinations. The method includes receiving at the WAD an RF profile transmitted by the base station that includes a triggering portion having a number of pulses, wherein the number is at least equal to the total number of possible data element combinations. The method further includes keeping a count of received pulses and wirelessly transmitting a piece of data, preferably one bit, to the base station when the count reaches a value equal to the stored data element's particular number in the sequence. Finally, the method includes receiving the piece of data at the base station and using the receipt thereof to determine which of the possible data element combinations the stored data element is.

  9. Therapeutic targeting of replicative immortality.

    Science.gov (United States)

    Yaswen, Paul; MacKenzie, Karen L; Keith, W Nicol; Hentosh, Patricia; Rodier, Francis; Zhu, Jiyue; Firestone, Gary L; Matheu, Ander; Carnero, Amancio; Bilsland, Alan; Sundin, Tabetha; Honoki, Kanya; Fujii, Hiromasa; Georgakilas, Alexandros G; Amedei, Amedeo; Amin, Amr; Helferich, Bill; Boosani, Chandra S; Guha, Gunjan; Ciriolo, Maria Rosa; Chen, Sophie; Mohammed, Sulma I; Azmi, Asfar S; Bhakta, Dipita; Halicka, Dorota; Niccolai, Elena; Aquilano, Katia; Ashraf, S Salman; Nowsheen, Somaira; Yang, Xujuan

    2015-12-01

    One of the hallmarks of malignant cell populations is the ability to undergo continuous proliferation. This property allows clonal lineages to acquire sequential aberrations that can fuel increasingly autonomous growth, invasiveness, and therapeutic resistance. Innate cellular mechanisms have evolved to regulate replicative potential as a hedge against malignant progression. When activated in the absence of normal terminal differentiation cues, these mechanisms can result in a state of persistent cytostasis. This state, termed "senescence," can be triggered by intrinsic cellular processes such as telomere dysfunction and oncogene expression, and by exogenous factors such as DNA damaging agents or oxidative environments. Despite differences in upstream signaling, senescence often involves convergent interdependent activation of tumor suppressors p53 and p16/pRB, but can be induced, albeit with reduced sensitivity, when these suppressors are compromised. Doses of conventional genotoxic drugs required to achieve cancer cell senescence are often much lower than doses required to achieve outright cell death. Additional therapies, such as those targeting cyclin dependent kinases or components of the PI3K signaling pathway, may induce senescence specifically in cancer cells by circumventing defects in tumor suppressor pathways or exploiting cancer cells' heightened requirements for telomerase. Such treatments sufficient to induce cancer cell senescence could provide increased patient survival with fewer and less severe side effects than conventional cytotoxic regimens. This positive aspect is countered by important caveats regarding senescence reversibility, genomic instability, and paracrine effects that may increase heterogeneity and adaptive resistance of surviving cancer cells. Nevertheless, agents that effectively disrupt replicative immortality will likely be valuable components of new combinatorial approaches to cancer therapy. PMID:25869441

  10. Replication landscape of the human genome.

    Science.gov (United States)

    Petryk, Nataliya; Kahli, Malik; d'Aubenton-Carafa, Yves; Jaszczyszyn, Yan; Shen, Yimin; Silvain, Maud; Thermes, Claude; Chen, Chun-Long; Hyrien, Olivier

    2016-01-01

    Despite intense investigation, human replication origins and termini remain elusive. Existing data have shown strong discrepancies. Here we sequenced highly purified Okazaki fragments from two cell types and, for the first time, quantitated replication fork directionality and delineated initiation and termination zones genome-wide. Replication initiates stochastically, primarily within non-transcribed, broad (up to 150 kb) zones that often abut transcribed genes, and terminates dispersively between them. Replication fork progression is significantly co-oriented with the transcription. Initiation and termination zones are frequently contiguous, sometimes separated by regions of unidirectional replication. Initiation zones are enriched in open chromatin and enhancer marks, even when not flanked by genes, and often border 'topologically associating domains' (TADs). Initiation zones are enriched in origin recognition complex (ORC)-binding sites and better align to origins previously mapped using bubble-trap than λ-exonuclease. This novel panorama of replication reveals how chromatin and transcription modulate the initiation process to create cell-type-specific replication programs. PMID:26751768

  11. Autonomous linear lossless systems

    OpenAIRE

    Rao, Shodhan; Rapisarda, Paolo

    2008-01-01

    We define a lossless autonomous system as one having a quadratic differential form associated with it called an energy function, which is positive and which is conserved. We define an oscillatory system as one which has all its trajectories bounded on the entire time axis. In this paper, we show that an autonomous system is lossless if and only if it is oscillatory. Next we discuss a few properties of energy functions of autonomous lossless systems and a suitable way of splitting a given ener...

  12. Autonomous surveillance for biosecurity.

    Science.gov (United States)

    Jurdak, Raja; Elfes, Alberto; Kusy, Branislav; Tews, Ashley; Hu, Wen; Hernandez, Emili; Kottege, Navinda; Sikka, Pavan

    2015-04-01

    The global movement of people and goods has increased the risk of biosecurity threats and their potential to incur large economic, social, and environmental costs. Conventional manual biosecurity surveillance methods are limited by their scalability in space and time. This article focuses on autonomous surveillance systems, comprising sensor networks, robots, and intelligent algorithms, and their applicability to biosecurity threats. We discuss the spatial and temporal attributes of autonomous surveillance technologies and map them to three broad categories of biosecurity threat: (i) vector-borne diseases; (ii) plant pests; and (iii) aquatic pests. Our discussion reveals a broad range of opportunities to serve biosecurity needs through autonomous surveillance. PMID:25744760

  13. Synchronization of DNA array replication kinetics

    Science.gov (United States)

    Manturov, Alexey O.; Grigoryev, Anton V.

    2016-04-01

    In the present work we discuss the features of the DNA replication kinetics at the case of multiplicity of simultaneously elongated DNA fragments. The interaction between replicated DNA fragments is carried out by free protons that appears at the every nucleotide attachment at the free end of elongated DNA fragment. So there is feedback between free protons concentration and DNA-polymerase activity that appears as elongation rate dependence. We develop the numerical model based on a cellular automaton, which can simulate the elongation stage (growth of DNA strands) for DNA elongation process with conditions pointed above and we study the possibility of the DNA polymerases movement synchronization. The results obtained numerically can be useful for DNA polymerase movement detection and visualization of the elongation process in the case of massive DNA replication, eg, under PCR condition or for DNA "sequencing by synthesis" sequencing devices evaluation.

  14. Initial amplification of the HPV18 genome proceeds via two distinct replication mechanisms

    Science.gov (United States)

    Orav, Marit; Geimanen, Jelizaveta; Sepp, Eva-Maria; Henno, Liisi; Ustav, Ene; Ustav, Mart

    2015-01-01

    Determining the mechanism of HPV18 replication is paramount for identifying possible drug targets against HPV infection. We used two-dimensional and three-dimensional gel electrophoresis techniques to identify replication intermediates arising during the initial amplification of HPV18 episomal genomes. We determined that the first rounds of HPV18 replication proceed via bidirectional theta structures; however, a notable accumulation of almost fully replicated HPV18 genomes indicates difficulties with the completion of theta replication. We also observed intermediates that were created by a second replication mechanism during the initial amplification of HPV18 genomes. The second replication mechanism does not utilize specific initiation or termination sequences and proceeds via a unidirectional replication fork. We suggest a significant role for the second replication mechanism during the initial replication of the HPV18 genome and propose that the second replication mechanism is recombination-dependent replication. PMID:26522968

  15. Initial amplification of the HPV18 genome proceeds via two distinct replication mechanisms.

    Science.gov (United States)

    Orav, Marit; Geimanen, Jelizaveta; Sepp, Eva-Maria; Henno, Liisi; Ustav, Ene; Ustav, Mart

    2015-01-01

    Determining the mechanism of HPV18 replication is paramount for identifying possible drug targets against HPV infection. We used two-dimensional and three-dimensional gel electrophoresis techniques to identify replication intermediates arising during the initial amplification of HPV18 episomal genomes. We determined that the first rounds of HPV18 replication proceed via bidirectional theta structures; however, a notable accumulation of almost fully replicated HPV18 genomes indicates difficulties with the completion of theta replication. We also observed intermediates that were created by a second replication mechanism during the initial amplification of HPV18 genomes. The second replication mechanism does not utilize specific initiation or termination sequences and proceeds via a unidirectional replication fork. We suggest a significant role for the second replication mechanism during the initial replication of the HPV18 genome and propose that the second replication mechanism is recombination-dependent replication. PMID:26522968

  16. Highly Autonomous Systems Workshop

    Science.gov (United States)

    Doyle, R.; Rasmussen, R.; Man, G.; Patel, K.

    1998-01-01

    It is our aim by launching a series of workshops on the topic of highly autonomous systems to reach out to the larger community interested in technology development for remotely deployed systems, particularly those for exploration.

  17. Autonomic Nervous System Disorders

    Science.gov (United States)

    ... with breathing and swallowing Erectile dysfunction in men Autonomic nervous system disorders can occur alone or as the result of another disease, such as Parkinson's disease, alcoholism and diabetes. Problems can affect either part ...

  18. Chromatin Immunoprecipitation of Replication Factors Moving with the Replication Fork

    OpenAIRE

    Rapp, Jordan B.; Ansbach, Alison B.; Noguchi, Chiaki; Noguchi, Eishi

    2009-01-01

    Replication of chromosomes involves a variety of replication proteins including DNA polymerases, DNA helicases, and other accessory factors. Many of these proteins are known to localize at replication forks and travel with them as components of the replisome complex. Other proteins do not move with replication forks but still play an essential role in DNA replication. Therefore, in order to understand the mechanisms of DNA replication and its controls, it is important to examine localization ...

  19. Autonomous Star Tracker Algorithms

    DEFF Research Database (Denmark)

    Betto, Maurizio; Jørgensen, John Leif; Kilsgaard, Søren;

    1998-01-01

    Proposal, in response to an ESA R.f.P., to design algorithms for autonomous star tracker operations.The proposal also included the development of a star tracker breadboard to test the algorithms performances.......Proposal, in response to an ESA R.f.P., to design algorithms for autonomous star tracker operations.The proposal also included the development of a star tracker breadboard to test the algorithms performances....

  20. Modeling DNA Replication.

    Science.gov (United States)

    Bennett, Joan

    1998-01-01

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

  1. Abiotic self-replication.

    Science.gov (United States)

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

    2012-12-18

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

  2. Checkpoint responses to replication stalling: inducing tolerance and preventing mutagenesis

    Energy Technology Data Exchange (ETDEWEB)

    Kai, Mihoko; Wang, Teresa S.-F

    2003-11-27

    Replication mutants often exhibit a mutator phenotype characterized by point mutations, single base frameshifts, and the deletion or duplication of sequences flanked by homologous repeats. Mutation in genes encoding checkpoint proteins can significantly affect the mutator phenotype. Here, we use fission yeast (Schizosaccharomyces pombe) as a model system to discuss the checkpoint responses to replication perturbations induced by replication mutants. Checkpoint activation induced by a DNA polymerase mutant, aside from delay of mitotic entry, up-regulates the translesion polymerase DinB (Pol{kappa}). Checkpoint Rad9-Rad1-Hus1 (9-1-1) complex, which is loaded onto chromatin by the Rad17-Rfc2-5 checkpoint complex in response to replication perturbation, recruits DinB onto chromatin to generate the point mutations and single nucleotide frameshifts in the replication mutator. This chain of events reveals a novel checkpoint-induced tolerance mechanism that allows cells to cope with replication perturbation, presumably to make possible restarting stalled replication forks. Fission yeast Cds1 kinase plays an essential role in maintaining DNA replication fork stability in the face of DNA damage and replication fork stalling. Cds1 kinase is known to regulate three proteins that are implicated in maintaining replication fork stability: Mus81-Eme1, a hetero-dimeric structure-specific endonuclease complex; Rqh1, a RecQ-family helicase involved in suppressing inappropriate recombination during replication; and Rad60, a protein required for recombinational repair during replication. These Cds1-regulated proteins are thought to cooperatively prevent mutagenesis and maintain replication fork stability in cells under replication stress. These checkpoint-regulated processes allow cells to survive replication perturbation by preventing stalled replication forks from degenerating into deleterious DNA structures resulting in genomic instability and cancer development.

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

    NARCIS (Netherlands)

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

    2014-01-01

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

  4. Hepatitis B virus replication

    Institute of Scientific and Technical Information of China (English)

    2007-01-01

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

  5. DNA Sequences Proximal to Human Mitochondrial DNA Deletion Breakpoints Prevalent in Human Disease Form G-quadruplexes, a Class of DNA Structures Inefficiently Unwound by the Mitochondrial Replicative Twinkle Helicase

    NARCIS (Netherlands)

    Bharti, S.K.; Sommers, J.A.; Zhou, J.; Kaplan, D.L.; Spelbrink, J.N.; Mergny, J.L.; Brosh, R.M., Jr.

    2014-01-01

    Mitochondrial DNA deletions are prominent in human genetic disorders, cancer, and aging. It is thought that stalling of the mitochondrial replication machinery during DNA synthesis is a prominent source of mitochondrial genome instability; however, the precise molecular determinants of defective mit

  6. Architecture of autonomous systems

    Science.gov (United States)

    Dikshit, Piyush; Guimaraes, Katia; Ramamurthy, Maya; Agrawala, Ashok; Larsen, Ronald L.

    1989-01-01

    Automation of Space Station functions and activities, particularly those involving robotic capabilities with interactive or supervisory human control, is a complex, multi-disciplinary systems design problem. A wide variety of applications using autonomous control can be found in the literature, but none of them seem to address the problem in general. All of them are designed with a specific application in mind. In this report, an abstract model is described which unifies the key concepts underlying the design of automated systems such as those studied by the aerospace contractors. The model has been kept as general as possible. The attempt is to capture all the key components of autonomous systems. With a little effort, it should be possible to map the functions of any specific autonomous system application to the model presented here.

  7. Exercise and autonomic function.

    Science.gov (United States)

    Goldsmith, R L; Bloomfield, D M; Rosenwinkel, E T

    2000-03-01

    The complex interplay between the dichotomous subdivisions of the autonomic nervous system establishes and maintains a delicately tuned homeostasis in spite of an ever-changing environment. Aerobic exercise training can increase activity of the parasympathetic nervous system and decrease sympathetic activity. Conversely, it is well-documented that cardiac disease is often characterized by attenuated parasympathetic activity and heightened sympathetic tone. A correlation between autonomic disequilibrium and disease has led to the hypothesis that exercise training, as a therapy that restores the autonomic nervous system towards normal function, may be associated with, and possibly responsible for, outcome improvements in various populations. This is merely one of the many benefits that is conferred by chronic exercise training and reviewed in this issue. PMID:10758814

  8. Growing Through Innovation Replicability

    DEFF Research Database (Denmark)

    Hsuan, Juliana; Lévesque, Moren

    2012-01-01

    We propose a formal model of firm growth through replication that considers the extent of the investment to adapt routines as replication unfolds and the portion of this investment that goes toward innovation in the routines. The use of these two investment constructs brings about four types...... of growth policies. We use a utility function that considers proxies for both growth and failure potential to uncover the role played in selecting these policies by the economic environment of the targeted market for expansion. Our analysis further reveals the importance of the innovation...

  9. Autonomous electrochromic assembly

    Science.gov (United States)

    Berland, Brian Spencer; Lanning, Bruce Roy; Stowell, Jr., Michael Wayne

    2015-03-10

    This disclosure describes system and methods for creating an autonomous electrochromic assembly, and systems and methods for use of the autonomous electrochromic assembly in combination with a window. Embodiments described herein include an electrochromic assembly that has an electrochromic device, an energy storage device, an energy collection device, and an electrochromic controller device. These devices may be combined into a unitary electrochromic insert assembly. The electrochromic assembly may have the capability of generating power sufficient to operate and control an electrochromic device. This control may occur through the application of a voltage to an electrochromic device to change its opacity state. The electrochromic assembly may be used in combination with a window.

  10. Overview of the Autonomic Nervous System

    Science.gov (United States)

    ... reversible or progressive. Anatomy of the autonomic nervous system The autonomic nervous system is the part of ... they connect with. Function of the autonomic nervous system The autonomic nervous system controls internal body processes ...

  11. Mobility and generation of mosaic non-autonomous transposons by Tn3-derived inverted-repeat miniature elements (TIMEs.

    Directory of Open Access Journals (Sweden)

    Magdalena Szuplewska

    Full Text Available Functional transposable elements (TEs of several Pseudomonas spp. strains isolated from black shale ore of Lubin mine and from post-flotation tailings of Zelazny Most in Poland, were identified using a positive selection trap plasmid strategy. This approach led to the capture and characterization of (i 13 insertion sequences from 5 IS families (IS3, IS5, ISL3, IS30 and IS1380, (ii isoforms of two Tn3-family transposons--Tn5563a and Tn4662a (the latter contains a toxin-antitoxin system, as well as (iii non-autonomous TEs of diverse structure, ranging in size from 262 to 3892 bp. The non-autonomous elements transposed into AT-rich DNA regions and generated 5- or 6-bp sequence duplications at the target site of transposition. Although these TEs lack a transposase gene, they contain homologous 38-bp-long terminal inverted repeat sequences (IRs, highly conserved in Tn5563a and many other Tn3-family transposons. The simplest elements of this type, designated TIMEs (Tn3 family-derived Inverted-repeat Miniature Elements (262 bp, were identified within two natural plasmids (pZM1P1 and pLM8P2 of Pseudomonas spp. It was demonstrated that TIMEs are able to mobilize segments of plasmid DNA for transposition, which results in the generation of more complex non-autonomous elements, resembling IS-driven composite transposons in structure. Such transposon-like elements may contain different functional genetic modules in their core regions, including plasmid replication systems. Another non-autonomous element "captured" with a trap plasmid was a TIME derivative containing a predicted resolvase gene and a res site typical for many Tn3-family transposons. The identification of a portable site-specific recombination system is another intriguing example confirming the important role of non-autonomous TEs of the TIME family in shuffling genetic information in bacterial genomes. Transposition of such mosaic elements may have a significant impact on diversity and

  12. ADAM: ADaptive Autonomous Machine

    NARCIS (Netherlands)

    Oosten, van Daan C.; Nijenhuis, Lucas F.J.; Bakkers, André W.P.; Vervoort, Wiek A.

    1996-01-01

    This paper describes a part of the development of an adaptive autonomous machine that is able to move in an unknown world extract knowledge out of the perceived data, has the possibility to reason, and finally has the capability to exchange experiences and knowledge with other agents. The agent is n

  13. Autonomous data transmission apparatus

    Science.gov (United States)

    Kotlyar, Oleg M.

    1997-01-01

    A autonomous borehole data transmission apparatus for transmitting measurement data from measuring instruments at the downhole end of a drill string by generating pressure pulses utilizing a transducer longitudinally responsive to magnetic field pulses caused by electrical pulses corresponding to the measured downhole parameters.

  14. Autonomous parvovirus LuIII encapsidates equal amounts of plus and minus DNA strands

    Energy Technology Data Exchange (ETDEWEB)

    Bates, R.C.; Snyder, C.E.; Banerjee, P.T.; Mitra, S.

    1984-02-01

    Autonomous parvoviruses are thought to uniquely encapsidate single-stranded DNA of minus polarity. In contrast, the defective adeno-associated viruses separately encapsidate equal amounts of plus and minus DNA strands. The uniqueness of minus strand encapsidation is reexamined for the autonomous parvoviruses. Although it was found that Kilham rat virus and H-1 virus encapsidate varying but small amounts of complementary-strand DNA, it was unexpected to find that LuIII virus encapsidated equal amounts of plus and minus DNA. The extracted LuIII DNA possessed properties of double-stranded replicative-form DNA, including insensitivity to S1 endonuclease, cleavage by restriction enzymes, and conversion to unit-length, single-stranded DNA when electrophoresed under denaturing conditions. However, the inability of this DNA to form single-stranded DNA circles when denatured and then renatured in the presence of formamide and the lack of double-stranded DNA circle formation after treatment with exonuclease III and reannealing shows a lack of sequence homology of the 3' and 5' termini of LuIII DNA, in contrast to adeno-associated virus DNA. Digestion of LuIII double-stranded DNA with EcoRI and HincII and separation of plus and minus DNA strands on composite agarose-acrylamide gels identified a heterogeneity present only in the plus DNA strand. These results suggest that strand specificity of viral DNA encapsidation is not a useful property for differentiation between the autonomous and defective parvoviruses. Furthermore, encapsidation by LuIII of equal amounts of complementary DNA strands in contrast to encapsidation of minus strands by H-1 virus, when propagated in the same host cell type, suggests that selection of strands for encapsidation is a virus-coded rather than host-controlled event.

  15. Software Architecture for Autonomous Spacecraft

    Science.gov (United States)

    Shih, Jimmy S.

    1997-01-01

    The thesis objective is to design an autonomous spacecraft architecture to perform both deliberative and reactive behaviors. The Autonomous Small Planet In-Situ Reaction to Events (ASPIRE) project uses the architecture to integrate several autonomous technologies for a comet orbiter mission.

  16. A Straightening Theorem for non-Autonomous Iteration

    OpenAIRE

    Comerford, Mark

    2011-01-01

    The classical straightening theorem as proved by Douady and Hubbard shows that a polynomial-like sequence is hybrid equivalent to a polynomial. We generalize this result to non-autonomous iteration where one considers composition sequences arising from a varying sequence of functions. In order to do this, new techniques are required to control the distortion and quasiconformal dilatation of the hybrid equivalence. In particular, the Caratheodory topology for pointed domains allows us to speci...

  17. Catecholamines and diabetic autonomic neuropathy

    DEFF Research Database (Denmark)

    Hilsted, J

    1995-01-01

    In diabetic patients with autonomic neuropathy plasma noradrenaline concentration, used as an index of sympathetic nervous activity, is low. This decrease is, however, only found in patients with a long duration of diabetes with clinically severe autonomic neuropathy. This apparent insensitivity...... of plasma catecholamine measurements is not due to changes in the clearance of catecholamines in diabetic autonomic neuropathy. The physiological responses to infused adrenaline and to noradrenaline are enhanced, for noradrenaline mainly cardiovascular responses. Adrenoceptors (alpha and beta adrenoceptors......) are not altered in circulating blood cells in diabetic autonomic neuropathy. Thus, a generalized up-regulation of adrenoceptors does not occur in diabetic autonomic neuropathy....

  18. The Lysine Residues within the Human Ribosomal Protein S17 Sequence Naturally Inserted into the Viral Nonstructural Protein of a Unique Strain of Hepatitis E Virus Are Important for Enhanced Virus Replication

    OpenAIRE

    Kenney, Scott P.; Meng, Xiang-Jin

    2015-01-01

    Hepatitis E virus (HEV) is an important but extremely understudied human pathogen. Due largely to the lack of an efficient cell culture system for HEV, the molecular mechanisms of HEV replication and pathogenesis are poorly understood. Recently, a unique genotype 3 strain of HEV recovered from a chronically infected patient was adapted for growth in HepG2C3A human hepatoma cells. The adaptation of the Kernow C-1 P6 HEV to propagate in HepG2C3A cells selected for a rare virus recombinant that ...

  19. Chromatin replication and epigenome maintenance

    DEFF Research Database (Denmark)

    Alabert, Constance; Groth, Anja

    2012-01-01

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

  20. Mobile Autonomous Humanoid Assistant

    Science.gov (United States)

    Diftler, M. A.; Ambrose, R. O.; Tyree, K. S.; Goza, S. M.; Huber, E. L.

    2004-01-01

    A mobile autonomous humanoid robot is assisting human co-workers at the Johnson Space Center with tool handling tasks. This robot combines the upper body of the National Aeronautics and Space Administration (NASA)/Defense Advanced Research Projects Agency (DARPA) Robonaut system with a Segway(TradeMark) Robotic Mobility Platform yielding a dexterous, maneuverable humanoid perfect for aiding human co-workers in a range of environments. This system uses stereo vision to locate human team mates and tools and a navigation system that uses laser range and vision data to follow humans while avoiding obstacles. Tactile sensors provide information to grasping algorithms for efficient tool exchanges. The autonomous architecture utilizes these pre-programmed skills to form human assistant behaviors. The initial behavior demonstrates a robust capability to assist a human by acquiring a tool from a remotely located individual and then following the human in a cluttered environment with the tool for future use.

  1. Mobile Intelligent Autonomous Systems

    OpenAIRE

    Jitendra R. Raol; Ajith Gopal

    2010-01-01

    Mobile intelligent autonomous systems (MIAS) is a fast emerging research area. Although it can be regarded as a general R&D area, it is mainly directed towards robotics. Several important subtopics within MIAS research are:(i) perception and reasoning, (ii) mobility and navigation,(iii) haptics and teleoperation, (iv) image fusion/computervision, (v) modelling of manipulators, (vi) hardware/software architectures for planning and behaviour learning leadingto robotic architecture, (vii) ve...

  2. Nature's Autonomous Oscillators

    Science.gov (United States)

    Mayr, H. G.; Yee, J.-H.; Mayr, M.; Schnetzler, R.

    2012-01-01

    Nonlinearity is required to produce autonomous oscillations without external time dependent source, and an example is the pendulum clock. The escapement mechanism of the clock imparts an impulse for each swing direction, which keeps the pendulum oscillating at the resonance frequency. Among nature's observed autonomous oscillators, examples are the quasi-biennial oscillation and bimonthly oscillation of the Earth atmosphere, and the 22-year solar oscillation. The oscillations have been simulated in numerical models without external time dependent source, and in Section 2 we summarize the results. Specifically, we shall discuss the nonlinearities that are involved in generating the oscillations, and the processes that produce the periodicities. In biology, insects have flight muscles, which function autonomously with wing frequencies that far exceed the animals' neural capacity; Stretch-activation of muscle contraction is the mechanism that produces the high frequency oscillation of insect flight, discussed in Section 3. The same mechanism is also invoked to explain the functioning of the cardiac muscle. In Section 4, we present a tutorial review of the cardio-vascular system, heart anatomy, and muscle cell physiology, leading up to Starling's Law of the Heart, which supports our notion that the human heart is also a nonlinear oscillator. In Section 5, we offer a broad perspective of the tenuous links between the fluid dynamical oscillators and the human heart physiology.

  3. Trigeminal autonomic cephalalgias.

    Science.gov (United States)

    Eller, M; Goadsby, P J

    2016-01-01

    The trigeminal autonomic cephalalgias (TACs) are a group of primary headache disorders characterised by lateralized symptoms: prominent headache and ipsilateral cranial autonomic features, such as conjunctival injection, lacrimation and rhinorrhea. The TACs are: cluster headache (CH), paroxysmal hemicrania (PH), short-lasting unilateral neuralgiform headache attacks with conjunctival injection and tearing (SUNCT)/short-lasting neuralgiform headache attacks with cranial autonomic features (SUNA) and hemicrania continua (HC). Their diagnostic criteria are outlined in the International Classification of Headache Disorders, third edition-beta (ICHD-IIIb). These conditions are distinguished by their attack duration and frequency, as well as response to treatment. HC is continuous and by definition responsive to indomethacin. The main differential when considering this headache is chronic migraine. Other TACs are remarkable for their short duration and must be distinguished from other short-lasting painful conditions, such as trigeminal neuralgia and primary stabbing headache. Cluster headache is characterised by exquisitely painful attacks that occur in discrete episodes lasting 15-180 min a few times a day. In comparison, PH occurs more frequently and is of shorter duration, and like HC is responsive to indomethacin. SUNCT/SUNA is the shortest duration and highest frequency TAC; attacks can occur over a hundred times every day. PMID:24888770

  4. Trigeminal autonomic cephalalgias.

    Science.gov (United States)

    Eller, M; Goadsby, P J

    2016-01-01

    The trigeminal autonomic cephalalgias (TACs) are a group of primary headache disorders characterised by lateralized symptoms: prominent headache and ipsilateral cranial autonomic features, such as conjunctival injection, lacrimation and rhinorrhea. The TACs are: cluster headache (CH), paroxysmal hemicrania (PH), short-lasting unilateral neuralgiform headache attacks with conjunctival injection and tearing (SUNCT)/short-lasting neuralgiform headache attacks with cranial autonomic features (SUNA) and hemicrania continua (HC). Their diagnostic criteria are outlined in the International Classification of Headache Disorders, third edition-beta (ICHD-IIIb). These conditions are distinguished by their attack duration and frequency, as well as response to treatment. HC is continuous and by definition responsive to indomethacin. The main differential when considering this headache is chronic migraine. Other TACs are remarkable for their short duration and must be distinguished from other short-lasting painful conditions, such as trigeminal neuralgia and primary stabbing headache. Cluster headache is characterised by exquisitely painful attacks that occur in discrete episodes lasting 15-180 min a few times a day. In comparison, PH occurs more frequently and is of shorter duration, and like HC is responsive to indomethacin. SUNCT/SUNA is the shortest duration and highest frequency TAC; attacks can occur over a hundred times every day.

  5. Replication Research and Special Education

    Science.gov (United States)

    Travers, Jason C.; Cook, Bryan G.; Therrien, William J.; Coyne, Michael D.

    2016-01-01

    Replicating previously reported empirical research is a necessary aspect of an evidence-based field of special education, but little formal investigation into the prevalence of replication research in the special education research literature has been conducted. Various factors may explain the lack of attention to replication of special education…

  6. Inhibition of retroviral replication by anti-sense RNA.

    OpenAIRE

    To, R Y; Booth, S C; Neiman, P E

    1986-01-01

    We tested the effect of anti-sense RNA on the replication of avian retroviruses in cultured cells. The replication of a recombinant retrovirus carrying a neomycin resistance gene (neor) in the anti-sense orientation was blocked when the cells expressed high steady-state levels of RNA molecules with neor in sequence in the sense was blocked when the cells expressed high steady-state levels of RNA molecules with neor sequences in the sense orientation, i.e., complementary to the viral sequence....

  7. Replication fork progression is paused in two large chromosomal zones flanking the DNA replication origin in Escherichia coli.

    Science.gov (United States)

    Akiyama, Masahiro Tatsumi; Oshima, Taku; Chumsakul, Onuma; Ishikawa, Shu; Maki, Hisaji

    2016-08-01

    Although the speed of nascent DNA synthesis at individual replication forks is relatively uniform in bacterial cells, the dynamics of replication fork progression on the chromosome are hampered by a variety of natural impediments. Genome replication dynamics can be directly measured from an exponentially growing cell population by sequencing newly synthesized DNA strands that were specifically pulse-labeled with the thymidine analogue 5-bromo-2'-deoxyuridine (BrdU). However, a short pulse labeling with BrdU is impracticable for bacteria because of poor incorporation of BrdU into the cells, and thus, the genomewide dynamics of bacterial DNA replication remain undetermined. Using a new thymidine-requiring Escherichia coli strain, eCOMB, and high-throughput sequencing, we succeeded in determining the genomewide replication profile in bacterial cells. We also found that fork progression is paused in two ~200-kb chromosomal zones that flank the replication origin in the growing cells. This origin-proximal obstruction to fork progression was overcome by an increased thymidine concentration in the culture medium and enhanced by inhibition of transcription. These indicate that DNA replication near the origin is sensitive to the impediments to fork progression, namely a scarcity of the DNA precursor deoxythymidine triphosphate and probable conflicts between replication and transcription machineries. PMID:27353572

  8. The X gene of adeno-associated virus 2 (AAV2 is involved in viral DNA replication.

    Directory of Open Access Journals (Sweden)

    Maohua Cao

    Full Text Available Adeno-associated virus (AAV (type 2 is a popular human gene therapy vector with a long active transgene expression period and no reported vector-induced adverse reactions. Yet the basic molecular biology of this virus has not been fully addressed. One potential gene at the far 3' end of the AAV2 genome, previously referred to as X (nt 3929 to 4393, overlapping the 3' end of the cap gene, has never been characterized, although we did previously identify a promoter just up-stream (p81. Computer analysis suggested that X was involved in replication and transcription. The X protein was identified during active AAV2 replication using a polyclonal antibody against a peptide starting at amino acid 98. Reagents for the study of X included an AAV2 deletion mutant (dl78-91, a triple nucleotide substitution mutant that destroys all three 5' AUG-initiation products of X, with no effect on the cap coding sequence, and X-positive-293 cell lines. Here, we found that X up-regulated AAV2 DNA replication in differentiating keratinocytes (without helper virus, autonomous replication and in various forms of 293 cell-based assays with help from wild type adenovirus type 5 (wt Ad5 or Ad5 helper plasmid (pHelper. The strongest contribution by X was seen in increasing wt AAV2 DNA replication in keratinocytes and dl78-91 in Ad5-infected X-positive-293 cell lines (both having multi-fold effects. Mutating the X gene in pAAV-RC (pAAV-RC-3Xneg yielded approximately a ∼33% reduction in recombinant AAV vector DNA replication and virion production, but a larger effect was seen when using this same X-knockout AAV helper plasmid in X-positive-293 cell lines versus normal 293 cells (again, multi-fold. Taken together these data strongly suggest that AAV2 X encodes a protein involved in the AAV life cycle, particularly in increasing AAV2 DNA replication, and suggests that further studies are warranted.

  9. Replication studies in longevity

    DEFF Research Database (Denmark)

    Varcasia, O; Garasto, S; Rizza, T;

    2001-01-01

    In Danes we replicated the 3'APOB-VNTR gene/longevity association study previously carried out in Italians, by which the Small alleles (less than 35 repeats) had been identified as frailty alleles for longevity. In Danes, neither genotype nor allele frequencies differed between centenarians and 20......-sex interaction relevant to Long alleles (more than 37 repeats). The different findings in Denmark and Italy suggest that gene/longevity associations are population-specific, and heavily affected by the population-specific genetic and environmental history....

  10. Modeling inhomogeneous DNA replication kinetics.

    Directory of Open Access Journals (Sweden)

    Michel G Gauthier

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

  11. Jam avoidance with autonomous systems

    OpenAIRE

    Tordeux, Antoine; Lassarre, Sylvain

    2015-01-01

    Many car-following models are developed for jam avoidance in highways. Two mechanisms are used to improve the stability: feedback control with autonomous models and increasing of the interaction within cooperative ones. In this paper, we compare the linear autonomous and collective optimal velocity (OV) models. We observe that the stability is significantly increased by adding predecessors in interaction with collective models. Yet autonomous and collective approaches are close when the speed...

  12. Chemical Specification of Autonomic Systems

    OpenAIRE

    Banâtre, Jean-Pierre; Fradet, Pascal; Radenac, Yann

    2004-01-01

    Autonomic computing provides a vision of information systems allowing self-management of many predefined properties. Such systems take care of their own behavior and of their interactions with other components without any external intervention. One of the major challenges concerns the expression of properties and constraints of autonomic systems. We believe that the {\\em chemical programming paradigm} (represented here by the Gamma formalism) is well-suited to the specification of autonomic s...

  13. Timeline based autonomous mission planning system for deep space exploration

    Institute of Scientific and Technical Information of China (English)

    徐瑞; 崔平远; 徐晓飞; 崔祜涛; 栾恩杰

    2004-01-01

    In order to realize the explorer autonomy, the software architecture of autonomous mission management system (AMMS) is given for the deep space explorer, and the autonomous mission planning system, the kernel part of this architecture, is designed in detail. In order to describe the parallel activity, the state timeline is introduced to build the formal model of the planning system and based on this model, the temporal constraint satisfaction planning algorithm is proposed to produce the explorer's activity sequence. With some key subsystems of the deep space explorer as examples, the autonomous mission planning simulation system is designed.The results show that this system can calculate the executable activity sequence with the given mission goals and initial state of the explorer.

  14. Jam avoidance with autonomous systems

    CERN Document Server

    Tordeux, Antoine

    2016-01-01

    Many car-following models are developed for jam avoidance in highways. Two mechanisms are used to improve the stability: feedback control with autonomous models and increasing of the interaction within cooperative ones. In this paper, we compare the linear autonomous and collective optimal velocity (OV) models. We observe that the stability is significantly increased by adding predecessors in interaction with collective models. Yet autonomous and collective approaches are close when the speed difference term is taking into account. Within the linear OV models tested, the autonomous models including speed difference are sufficient to maximise the stability.

  15. Robotics and Autonomous Systems Laboratory

    Data.gov (United States)

    Federal Laboratory Consortium — FUNCTION: Provides an environment for developing and evaluating intelligent software for both actual and simulated autonomous vehicles. Laboratory computers provide...

  16. Autonomous packaging robot

    OpenAIRE

    Vo, Van Thanh

    2010-01-01

    The objective of the autonomous packaging robot application is to replace manual product packaging in food industry with a fully automatic robot. The objective is achieved by using the combination of machine vision, central computer, sensors, microcontroller and a typical ABB robot. The method is to equip the robot with different sensors: camera as “eyes” of robot, distance sensor and microcontroller as “sense of touch” of the robot, central computer as “brain” of the robot. Because the ro...

  17. Experimental Autonomous Vehicle Systems

    DEFF Research Database (Denmark)

    Ravn, Ole; Andersen, Nils Axel

    1998-01-01

    The paper describes the requirements for and a prototype configuration of a software architecture for control of an experimental autonomous vehicle. The test bed nature of the system is emphasised in the choice of architecture making re-configurability, data logging and extendability simple....... The central element of the architecture is the ‘global database’ that serves several purposes, such as storing system parameters, making signals available for data logging and inter-process communication. Standard software components are used to a large extent, OS-9 as real-time operating system, a custom...

  18. Roles for Dam methylation in bacterial chromosome replication

    DEFF Research Database (Denmark)

    Charbon, Godefroid; Koch, Birgit; Skovgaard, Ole;

    GATC sequences in the DNA of Escherichia coli and related species are methylated at the adenine residue by DNA adenine methyltransferase (DamMT). These methylated residues and/or the level of DamMT influence initiation of chromosome replication from the replication origin, oriC, which contain...... an over-representation of GATC sites, in at least two ways. First, full methylation of oriC promotes duplex opening and hence certain oriC mutants are dependent on Dam methylation for initiation. Second, newly replicated and hemimethylated origins, are bound by SeqA (‘sequestered’) and remain inactive...

  19. Replicated Spectrographs in Astronomy

    CERN Document Server

    Hill, Gary J

    2014-01-01

    As telescope apertures increase, the challenge of scaling spectrographic astronomical instruments becomes acute. The next generation of extremely large telescopes (ELTs) strain the availability of glass blanks for optics and engineering to provide sufficient mechanical stability. While breaking the relationship between telescope diameter and instrument pupil size by adaptive optics is a clear path for small fields of view, survey instruments exploiting multiplex advantages will be pressed to find cost-effective solutions. In this review we argue that exploiting the full potential of ELTs will require the barrier of the cost and engineering difficulty of monolithic instruments to be broken by the use of large-scale replication of spectrographs. The first steps in this direction have already been taken with the soon to be commissioned MUSE and VIRUS instruments for the Very Large Telescope and the Hobby-Eberly Telescope, respectively. MUSE employs 24 spectrograph channels, while VIRUS has 150 channels. We compa...

  20. SUMO and KSHV Replication

    Energy Technology Data Exchange (ETDEWEB)

    Chang, Pei-Ching [Institute of Microbiology and Immunology, National Yang-Ming University, Taipei 112, Taiwan (China); Kung, Hsing-Jien, E-mail: hkung@nhri.org.tw [Institute for Translational Medicine, College of Medical Science and Technology, Taipei Medical University, Taipei 110, Taiwan (China); Department of Biochemistry and Molecular Medicine, University of California, Davis, CA 95616 (United States); UC Davis Cancer Center, University of California, Davis, CA 95616 (United States); Division of Molecular and Genomic Medicine, National Health Research Institutes, 35 Keyan Road, Zhunan, Miaoli County 35053, Taiwan (China)

    2014-09-29

    Small Ubiquitin-related MOdifier (SUMO) modification was initially identified as a reversible post-translational modification that affects the regulation of diverse cellular processes, including signal transduction, protein trafficking, chromosome segregation, and DNA repair. Increasing evidence suggests that the SUMO system also plays an important role in regulating chromatin organization and transcription. It is thus not surprising that double-stranded DNA viruses, such as Kaposi’s sarcoma-associated herpesvirus (KSHV), have exploited SUMO modification as a means of modulating viral chromatin remodeling during the latent-lytic switch. In addition, SUMO regulation allows the disassembly and assembly of promyelocytic leukemia protein-nuclear bodies (PML-NBs), an intrinsic antiviral host defense, during the viral replication cycle. Overcoming PML-NB-mediated cellular intrinsic immunity is essential to allow the initial transcription and replication of the herpesvirus genome after de novo infection. As a consequence, KSHV has evolved a way as to produce multiple SUMO regulatory viral proteins to modulate the cellular SUMO environment in a dynamic way during its life cycle. Remarkably, KSHV encodes one gene product (K-bZIP) with SUMO-ligase activities and one gene product (K-Rta) that exhibits SUMO-targeting ubiquitin ligase (STUbL) activity. In addition, at least two viral products are sumoylated that have functional importance. Furthermore, sumoylation can be modulated by other viral gene products, such as the viral protein kinase Orf36. Interference with the sumoylation of specific viral targets represents a potential therapeutic strategy when treating KSHV, as well as other oncogenic herpesviruses. Here, we summarize the different ways KSHV exploits and manipulates the cellular SUMO system and explore the multi-faceted functions of SUMO during KSHV’s life cycle and pathogenesis.

  1. Molecular analysis of the replication region of the theta-replicating plasmid pUCL287 from Tetragenococcus (Pediococcus) halophilus ATCC33315.

    Science.gov (United States)

    Benachour, A; Frère, J; Flahaut, S; Novel, G; Auffray, Y

    1997-08-01

    The complete nucleotide sequence of the 8.7-kb theta-replicating plasmid pUCL287 from Tetragenococcus halophilus (formerly Pediococcus halophilus) ATCC33315 has been determined. The replication region was identified and analyzed. Its nucleotide sequence contains an untranslated region, the replication origin, followed by two open reading frames (ORFs) encoding two proteins of 311 (RepA287) and 168 (RepB287) amino acids, respectively. Evidence is presented to show that RepA287 represents the plasmid replication protein. RepB287, which is non-essential for replication, is involved in the plasmid copy-number control and segregational stability. The roles of lactococcal proteins homologous to RepB287 have not been defined so far. Nevertheless, the structural organization of the pUCL287 replication region is remarkably similar to those of well known theta-replicating lactococcal plasmids despite the absence of homology of the replication origin and of the replication protein, and this suggests that pUCL287 uses the same mechanism of replication. Nucleotide sequence comparisons show that pSMB74, a pediococcal plasmid encoding bacteriocin production, is a member of the pUCL287 replicon family. PMID:9294035

  2. Nemesis Autonomous Test System

    Science.gov (United States)

    Barltrop, Kevin J.; Lee, Cin-Young; Horvath, Gregory A,; Clement, Bradley J.

    2012-01-01

    A generalized framework has been developed for systems validation that can be applied to both traditional and autonomous systems. The framework consists of an automated test case generation and execution system called Nemesis that rapidly and thoroughly identifies flaws or vulnerabilities within a system. By applying genetic optimization and goal-seeking algorithms on the test equipment side, a "war game" is conducted between a system and its complementary nemesis. The end result of the war games is a collection of scenarios that reveals any undesirable behaviors of the system under test. The software provides a reusable framework to evolve test scenarios using genetic algorithms using an operation model of the system under test. It can automatically generate and execute test cases that reveal flaws in behaviorally complex systems. Genetic algorithms focus the exploration of tests on the set of test cases that most effectively reveals the flaws and vulnerabilities of the system under test. It leverages advances in state- and model-based engineering, which are essential in defining the behavior of autonomous systems. It also uses goal networks to describe test scenarios.

  3. Towards autonomous vehicular clouds

    Directory of Open Access Journals (Sweden)

    Stephan Olariu

    2011-09-01

    Full Text Available The dawn of the 21st century has seen a growing interest in vehicular networking and its myriad potential applications. The initial view of practitioners and researchers was that radio-equipped vehicles could keep the drivers informed about potential safety risks and increase their awareness of road conditions. The view then expanded to include access to the Internet and associated services. This position paper proposes and promotes a novel and more comprehensive vision namely, that advances in vehicular networks, embedded devices and cloud computing will enable the formation of autonomous clouds of vehicular computing, communication, sensing, power and physical resources. Hence, we coin the term, autonomous vehicular clouds (AVCs. A key feature distinguishing AVCs from conventional cloud computing is that mobile AVC resources can be pooled dynamically to serve authorized users and to enable autonomy in real-time service sharing and management on terrestrial, aerial, or aquatic pathways or theaters of operations. In addition to general-purpose AVCs, we also envision the emergence of specialized AVCs such as mobile analytics laboratories. Furthermore, we envision that the integration of AVCs with ubiquitous smart infrastructures including intelligent transportation systems, smart cities and smart electric power grids will have an enormous societal impact enabling ubiquitous utility cyber-physical services at the right place, right time and with right-sized resources.

  4. Learning for Autonomous Navigation

    Science.gov (United States)

    Angelova, Anelia; Howard, Andrew; Matthies, Larry; Tang, Benyang; Turmon, Michael; Mjolsness, Eric

    2005-01-01

    Robotic ground vehicles for outdoor applications have achieved some remarkable successes, notably in autonomous highway following (Dickmanns, 1987), planetary exploration (1), and off-road navigation on Earth (1). Nevertheless, major challenges remain to enable reliable, high-speed, autonomous navigation in a wide variety of complex, off-road terrain. 3-D perception of terrain geometry with imaging range sensors is the mainstay of off-road driving systems. However, the stopping distance at high speed exceeds the effective lookahead distance of existing range sensors. Prospects for extending the range of 3-D sensors is strongly limited by sensor physics, eye safety of lasers, and related issues. Range sensor limitations also allow vehicles to enter large cul-de-sacs even at low speed, leading to long detours. Moreover, sensing only terrain geometry fails to reveal mechanical properties of terrain that are critical to assessing its traversability, such as potential for slippage, sinkage, and the degree of compliance of potential obstacles. Rovers in the Mars Exploration Rover (MER) mission have got stuck in sand dunes and experienced significant downhill slippage in the vicinity of large rock hazards. Earth-based off-road robots today have very limited ability to discriminate traversable vegetation from non-traversable vegetation or rough ground. It is impossible today to preprogram a system with knowledge of these properties for all types of terrain and weather conditions that might be encountered.

  5. Chromatin Dynamics During DNA Replication and Uncharacterized Replication Factors determined by Nascent Chromatin Capture (NCC) Proteomics

    Science.gov (United States)

    Alabert, Constance; Bukowski-Wills, Jimi-Carlo; Lee, Sung-Bau; Kustatscher, Georg; Nakamura, Kyosuke; de Lima Alves, Flavia; Menard, Patrice; Mejlvang, Jakob; Rappsilber, Juri; Groth, Anja

    2014-01-01

    SUMMARY To maintain genome function and stability, DNA sequence and its organization into chromatin must be duplicated during cell division. Understanding how entire chromosomes are copied remains a major challenge. Here, we use Nascent Chromatin Capture (NCC) to profile chromatin proteome dynamics during replication in human cells. NCC relies on biotin-dUTP labelling of replicating DNA, affinity-purification and quantitative proteomics. Comparing nascent chromatin with mature post-replicative chromatin, we provide association dynamics for 3995 proteins. The replication machinery and 485 chromatin factors like CAF-1, DNMT1, SUV39h1 are enriched in nascent chromatin, whereas 170 factors including histone H1, DNMT3, MBD1-3 and PRC1 show delayed association. This correlates with H4K5K12diAc removal and H3K9me1 accumulation, while H3K27me3 and H3K9me3 remain unchanged. Finally, we combine NCC enrichment with experimentally derived chromatin probabilities to predict a function in nascent chromatin for 93 uncharacterized proteins and identify FAM111A as a replication factor required for PCNA loading. Together, this provides an extensive resource to understand genome and epigenome maintenance. PMID:24561620

  6. Novel parvoviruses in reptiles and genome sequence of a lizard parvovirus shed light on Dependoparvovirus genus evolution.

    Science.gov (United States)

    Pénzes, Judit J; Pham, Hanh T; Benkö, Mária; Tijssen, Peter

    2015-09-01

    Here, we report the detection and partial genome characterization of two novel reptilian parvoviruses derived from a short-tailed pygmy chameleon (Rampholeon brevicaudatus) and a corn snake (Pantherophis guttatus) along with the complete genome analysis of the first lizard parvovirus, obtained from four bearded dragons (Pogona vitticeps). Both homology searches and phylogenetic tree reconstructions demonstrated that all are members of the genus Dependoparvovirus. Even though most dependoparvoviruses replicate efficiently only in co-infections with large DNA viruses, no such agents could be detected in one of the bearded dragon samples, hence the possibility of autonomous replication was explored. The alternative ORF encoding the full assembly activating protein (AAP), typical for the genus, could be obtained from reptilian parvoviruses for the first time, with a structure that appears to be more ancient than that of avian and mammalian parvoviruses. All three viruses were found to harbour short introns as previously observed for snake adeno-associated virus, shorter than that of any non-reptilian dependoparvovirus. According to the phylogenetic calculations based on full non-structural protein (Rep) and AAP sequences, the monophyletic cluster of reptilian parvoviruses seems to be the most basal out of all lineages of genus Dependoparvovirus. The suspected ability for autonomous replication, results of phylogenetic tree reconstruction, intron lengths and the structure of the AAP suggested that a single Squamata origin instead of the earlier assumed diapsid (common avian-reptilian) origin is more likely for the genus Dependoparvovirus of the family Parvoviridae.

  7. Novel parvoviruses in reptiles and genome sequence of a lizard parvovirus shed light on Dependoparvovirus genus evolution.

    Science.gov (United States)

    Pénzes, Judit J; Pham, Hanh T; Benkö, Mária; Tijssen, Peter

    2015-09-01

    Here, we report the detection and partial genome characterization of two novel reptilian parvoviruses derived from a short-tailed pygmy chameleon (Rampholeon brevicaudatus) and a corn snake (Pantherophis guttatus) along with the complete genome analysis of the first lizard parvovirus, obtained from four bearded dragons (Pogona vitticeps). Both homology searches and phylogenetic tree reconstructions demonstrated that all are members of the genus Dependoparvovirus. Even though most dependoparvoviruses replicate efficiently only in co-infections with large DNA viruses, no such agents could be detected in one of the bearded dragon samples, hence the possibility of autonomous replication was explored. The alternative ORF encoding the full assembly activating protein (AAP), typical for the genus, could be obtained from reptilian parvoviruses for the first time, with a structure that appears to be more ancient than that of avian and mammalian parvoviruses. All three viruses were found to harbour short introns as previously observed for snake adeno-associated virus, shorter than that of any non-reptilian dependoparvovirus. According to the phylogenetic calculations based on full non-structural protein (Rep) and AAP sequences, the monophyletic cluster of reptilian parvoviruses seems to be the most basal out of all lineages of genus Dependoparvovirus. The suspected ability for autonomous replication, results of phylogenetic tree reconstruction, intron lengths and the structure of the AAP suggested that a single Squamata origin instead of the earlier assumed diapsid (common avian-reptilian) origin is more likely for the genus Dependoparvovirus of the family Parvoviridae. PMID:26067293

  8. The Escherichia coli Tus-Ter replication fork barrier causes site-specific DNA replication perturbation in yeast

    DEFF Research Database (Denmark)

    Larsen, Nicolai B; Sass, Ehud; Suski, Catherine;

    2014-01-01

    Replication fork (RF) pausing occurs at both 'programmed' sites and non-physiological barriers (for example, DNA adducts). Programmed RF pausing is required for site-specific DNA replication termination in Escherichia coli, and this process requires the binding of the polar terminator protein, Tus...... utilized as a versatile, site-specific, heterologous DNA replication-perturbing system, with a variety of potential applications......., to specific DNA sequences called Ter. Here, we demonstrate that Tus-Ter modules also induce polar RF pausing when engineered into the Saccharomyces cerevisiae genome. This heterologous RF barrier is distinct from a number of previously characterized, protein-mediated, RF pause sites in yeast, as it...

  9. An autonomous molecular assembler for programmable chemical synthesis

    Science.gov (United States)

    Meng, Wenjing; Muscat, Richard A.; McKee, Mireya L.; Milnes, Phillip J.; El-Sagheer, Afaf H.; Bath, Jonathan; Davis, Benjamin G.; Brown, Tom; O'Reilly, Rachel K.; Turberfield, Andrew J.

    2016-06-01

    Molecular machines that assemble polymers in a programmed sequence are fundamental to life. They are also an achievable goal of nanotechnology. Here, we report synthetic molecular machinery made from DNA that controls and records the formation of covalent bonds. We show that an autonomous cascade of DNA hybridization reactions can create oligomers, from building blocks linked by olefin or peptide bonds, with a sequence defined by a reconfigurable molecular program. The system can also be programmed to achieve combinatorial assembly. The sequence of assembly reactions and thus the structure of each oligomer synthesized is recorded in a DNA molecule, which enables this information to be recovered by PCR amplification followed by DNA sequencing.

  10. Chromatin Assembly at Kinetochores Is Uncoupled from DNA Replication

    Science.gov (United States)

    Shelby, Richard D.; Monier, Karine; Sullivan, Kevin F.

    2000-01-01

    The specification of metazoan centromeres does not depend strictly on centromeric DNA sequences, but also requires epigenetic factors. The mechanistic basis for establishing a centromeric “state” on the DNA remains unclear. In this work, we have directly examined replication timing of the prekinetochore domain of human chromosomes. Kinetochores were labeled by expression of epitope-tagged CENP-A, which stably marks prekinetochore domains in human cells. By immunoprecipitating CENP-A mononucleosomes from synchronized cells pulsed with [3H]thymidine we demonstrate that CENP-A–associated DNA is replicated in mid-to-late S phase. Cytological analysis of DNA replication further demonstrated that centromeres replicate asynchronously in parallel with numerous other genomic regions. In contrast, quantitative Western blot analysis demonstrates that CENP-A protein synthesis occurs later, in G2. Quantitative fluorescence microscopy and transient transfection in the presence of aphidicolin, an inhibitor of DNA replication, show that CENP-A can assemble into centromeres in the absence of DNA replication. Thus, unlike most genomic chromatin, histone synthesis and assembly are uncoupled from DNA replication at the kinetochore. Uncoupling DNA replication from CENP-A synthesis suggests that regulated chromatin assembly or remodeling could play a role in epigenetic centromere propagation. PMID:11086012

  11. Murine leukemia virus (MLV replication monitored with fluorescent proteins

    Directory of Open Access Journals (Sweden)

    Bittner Alexandra

    2004-12-01

    Full Text Available Abstract Background Cancer gene therapy will benefit from vectors that are able to replicate in tumor tissue and cause a bystander effect. Replication-competent murine leukemia virus (MLV has been described to have potential as cancer therapeutics, however, MLV infection does not cause a cytopathic effect in the infected cell and viral replication can only be studied by immunostaining or measurement of reverse transcriptase activity. Results We inserted the coding sequences for green fluorescent protein (GFP into the proline-rich region (PRR of the ecotropic envelope protein (Env and were able to fluorescently label MLV. This allowed us to directly monitor viral replication and attachment to target cells by flow cytometry. We used this method to study viral replication of recombinant MLVs and split viral genomes, which were generated by replacement of the MLV env gene with the red fluorescent protein (RFP and separately cloning GFP-Env into a retroviral vector. Co-transfection of both plasmids into target cells resulted in the generation of semi-replicative vectors, and the two color labeling allowed to determine the distribution of the individual genomes in the target cells and was indicative for the occurrence of recombination events. Conclusions Fluorescently labeled MLVs are excellent tools for the study of factors that influence viral replication and can be used to optimize MLV-based replication-competent viruses or vectors for gene therapy.

  12. Expanded Perspectives on Autonomous Learners

    Science.gov (United States)

    Oxford, Rebecca L.

    2015-01-01

    This paper explores two general perspectives on autonomous learners: psychological and sociocultural. These perspectives introduce a range of theoretically grounded facets of autonomous learners, facets such as the self-regulated learner, the emotionally intelligent learner, the self-determined learner, the mediated learner, the socioculturally…

  13. Efficient usage of Adabas replication

    CERN Document Server

    Storr, Dieter W

    2011-01-01

    In today's IT organization replication becomes more and more an essential technology. This makes Software AG's Event Replicator for Adabas an important part of your data processing. Setting the right parameters and establishing the best network communication, as well as selecting efficient target components, is essential for successfully implementing replication. This book provides comprehensive information and unique best-practice experience in the field of Event Replicator for Adabas. It also includes sample codes and configurations making your start very easy. It describes all components ne

  14. Autonomic and Neuroendocrine Responses to a Psychosocial Stressor in Adults with Autistic Spectrum

    Science.gov (United States)

    Jansen, Lucres M. C.; Gispen-de Wied, Christine C.; Wiegant, Victor M.; Westenberg, Herman G. M.; Lahuis, Bertine E.; van Engeland, Herman

    2006-01-01

    Objective of the study was to replicate in adults our previous findings of decreased heart rate and normal endocrine responses to stress in autistic children and to elucidate the discrepancy between autonomic and endocrine stress responses by including epinephrine, norepinephrine, oxytocin and vasopressin measurements. Ten autistic spectrum…

  15. Evolutionary Autonomous Health Monitoring System (EAHMS) Project

    Data.gov (United States)

    National Aeronautics and Space Administration — For supporting NASA's Robotics, Tele-Robotics and Autonomous Systems Roadmap, we are proposing the "Evolutionary Autonomous Health Monitoring System" (EAHMS) for...

  16. Autonomous component carrier selection

    DEFF Research Database (Denmark)

    Garcia, Luis Guilherme Uzeda; Pedersen, Klaus; Mogensen, Preben

    2009-01-01

    in local areas, basing our study case on LTE-Advanced. We present extensive network simulation results to demonstrate that a simple and robust interference management scheme, called autonomous component carrier selection allows each cell to select the most attractive frequency configuration; improving......Low-power base stations such as e.g. Femto-cells are one of the candidates for high data rate provisioning in local areas, such as residences, apartment complexes, business offices and outdoor hotspot scenarios. Unfortunately, the benefits are not without new challenges in terms of interference...... management and efficient system operation. Due to the expected large number of user-deployed cells, centralized network planning becomes unpractical and new scalable alternatives must be sought. In this article, we propose a fully distributed and scalable solution to the interference management problem...

  17. Autonomous Gaussian Decomposition

    CERN Document Server

    Lindner, Robert R; Murray, Claire E; Stanimirović, Snežana; Babler, Brian L; Heiles, Carl; Hennebelle, Patrick; Goss, W M; Dickey, John

    2014-01-01

    We present a new algorithm, named Autonomous Gaussian Decomposition (AGD), for automatically decomposing spectra into Gaussian components. AGD uses derivative spectroscopy and machine learning to provide optimized guesses for the number of Gaussian components in the data, and also their locations, widths, and amplitudes. We test AGD and find that it produces results comparable to human-derived solutions on 21cm absorption spectra from the 21cm SPectral line Observations of Neutral Gas with the EVLA (21-SPONGE) survey. We use AGD with Monte Carlo methods to derive the HI line completeness as a function of peak optical depth and velocity width for the 21-SPONGE data, and also show that the results of AGD are stable against varying observational noise intensity. The autonomy and computational efficiency of the method over traditional manual Gaussian fits allow for truly unbiased comparisons between observations and simulations, and for the ability to scale up and interpret the very large data volumes from the up...

  18. Autonomous Flying Controls Testbed

    Science.gov (United States)

    Motter, Mark A.

    2005-01-01

    The Flying Controls Testbed (FLiC) is a relatively small and inexpensive unmanned aerial vehicle developed specifically to test highly experimental flight control approaches. The most recent version of the FLiC is configured with 16 independent aileron segments, supports the implementation of C-coded experimental controllers, and is capable of fully autonomous flight from takeoff roll to landing, including flight test maneuvers. The test vehicle is basically a modified Army target drone, AN/FQM-117B, developed as part of a collaboration between the Aviation Applied Technology Directorate (AATD) at Fort Eustis,Virginia and NASA Langley Research Center. Several vehicles have been constructed and collectively have flown over 600 successful test flights.

  19. Mobile Intelligent Autonomous Systems

    Directory of Open Access Journals (Sweden)

    Jitendra R. Raol

    2010-01-01

    Full Text Available Mobile intelligent autonomous systems (MIAS is a fast emerging research area. Although it can be regarded as a general R&D area, it is mainly directed towards robotics. Several important subtopics within MIAS research are:(i perception and reasoning, (ii mobility and navigation,(iii haptics and teleoperation, (iv image fusion/computervision, (v modelling of manipulators, (vi hardware/software architectures for planning and behaviour learning leadingto robotic architecture, (vii vehicle-robot path and motionplanning/control, (viii human-machine interfaces for interaction between humans and robots, and (ix application of artificial neural networks (ANNs, fuzzy logic/systems (FLS,probabilistic/approximate reasoning (PAR, Bayesian networks(BN and genetic algorithms (GA to the above-mentioned problems. Also, multi-sensor data fusion (MSDF playsvery crucial role at many levels of the data fusion process:(i kinematic fusion (position/bearing tracking, (ii imagefusion (for scene recognition, (iii information fusion (forbuilding world models, and (iv decision fusion (for tracking,control actions. The MIAS as a technology is useful for automation of complex tasks, surveillance in a hazardousand hostile environment, human-assistance in very difficultmanual works, medical robotics, hospital systems, autodiagnosticsystems, and many other related civil and military systems. Also, other important research areas for MIAScomprise sensor/actuator modelling, failure management/reconfiguration, scene understanding, knowledge representation, learning and decision-making. Examples ofdynamic systems considered within the MIAS would be:autonomous systems (unmanned ground vehicles, unmannedaerial vehicles, micro/mini air vehicles, and autonomousunder water vehicles, mobile/fixed robotic systems, dexterousmanipulator robots, mining robots, surveillance systems,and networked/multi-robot systems, to name a few.Defence Science Journal, 2010, 60(1, pp.3-4,

  20. Charter School Replication. Policy Guide

    Science.gov (United States)

    Rhim, Lauren Morando

    2009-01-01

    "Replication" is the practice of a single charter school board or management organization opening several more schools that are each based on the same school model. The most rapid strategy to increase the number of new high-quality charter schools available to children is to encourage the replication of existing quality schools. This policy guide…

  1. Kinodynamic Motion Planning for Autonomous Vehicles

    Directory of Open Access Journals (Sweden)

    Jiwung Choi

    2014-06-01

    Full Text Available This article proposes a computationally effective motion planning algorithm for autonomous ground vehicles operating in a semi-structured environment with a mission specified by waypoints, corridor widths and obstacles. The algorithm switches between two kinds of planners, (i static planners and (ii moving obstacle avoidance manoeuvre planners, depending on the mobility of any detected obstacles. While the first is broken down into a path planner and a controller, the second generates a sequence of controls without global path planning. Each subsystem is implemented as follows. The path planner produces an optimal piecewise linear path by applying a variant of cell decomposition and dynamic programming. The piecewise linear path is smoothed by Bézier curves such that the maximum curvatures of the curves are minimized. The controller calculates the highest allowable velocity profile along the path, consistent with the limits on both tangential and radial acceleration and the steering command for the vehicle to track the trajectory using a pure pursuit method. The moving obstacle avoidance manoeuvre produces a sequence of time-optimal local velocities, by minimizing the cost as determined by the safety of the current velocity against obstacles in the velocity obstacle paradigm and the deviation of the current velocity relative to the desired velocity, to satisfy the waypoint constraint. The algorithms are shown to be robust and computationally efficient, and to demonstrate a viable methodology for autonomous vehicle control in the presence of unknown obstacles.

  2. DATABASE REPLICATION IN HETEROGENOUS PLATFORM

    Directory of Open Access Journals (Sweden)

    Hendro Nindito

    2014-01-01

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

  3. Cybersecurity for aerospace autonomous systems

    Science.gov (United States)

    Straub, Jeremy

    2015-05-01

    High profile breaches have occurred across numerous information systems. One area where attacks are particularly problematic is autonomous control systems. This paper considers the aerospace information system, focusing on elements that interact with autonomous control systems (e.g., onboard UAVs). It discusses the trust placed in the autonomous systems and supporting systems (e.g., navigational aids) and how this trust can be validated. Approaches to remotely detect the UAV compromise, without relying on the onboard software (on a potentially compromised system) as part of the process are discussed. How different levels of autonomy (task-based, goal-based, mission-based) impact this remote characterization is considered.

  4. Autonomous Image Analysis for Future Mars Missions

    Science.gov (United States)

    Gulick, V. C.; Morris, R. L.; Ruzon, M. A.; Bandari, E.; Roush, T. L.

    1999-01-01

    To explore high priority landing sites and to prepare for eventual human exploration, future Mars missions will involve rovers capable of traversing tens of kilometers. However, the current process by which scientists interact with a rover does not scale to such distances. Specifically, numerous command cycles are required to complete even simple tasks, such as, pointing the spectrometer at a variety of nearby rocks. In addition, the time required by scientists to interpret image data before new commands can be given and the limited amount of data that can be downlinked during a given command cycle constrain rover mobility and achievement of science goals. Experience with rover tests on Earth supports these concerns. As a result, traverses to science sites as identified in orbital images would require numerous science command cycles over a period of many weeks, months or even years, perhaps exceeding rover design life and other constraints. Autonomous onboard science analysis can address these problems in two ways. First, it will allow the rover to preferentially transmit "interesting" images, defined as those likely to have higher science content. Second, the rover will be able to anticipate future commands. For example, a rover might autonomously acquire and return spectra of "interesting" rocks along with a high-resolution image of those rocks in addition to returning the context images in which they were detected. Such approaches, coupled with appropriate navigational software, help to address both the data volume and command cycle bottlenecks that limit both rover mobility and science yield. We are developing fast, autonomous algorithms to enable such intelligent on-board decision making by spacecraft. Autonomous algorithms developed to date have the ability to identify rocks and layers in a scene, locate the horizon, and compress multi-spectral image data. We are currently investigating the possibility of reconstructing a 3D surface from a sequence of images

  5. Framework for Autonomous Optimization Project

    Data.gov (United States)

    National Aeronautics and Space Administration — Phoenix Integration and MIT propose to create a novel autonomous optimization tool and application programming interface (API). The API will demonstrate the ability...

  6. Autonomic Function in Neurodegenerative Diseases

    DEFF Research Database (Denmark)

    Sørensen, Gertrud Laura; Jennum, Poul Jørgen

    2013-01-01

    Neurodegenerative diseases are highly debilitating and often lead to severe morbidity and even death. Parkinson’s disease (PD) is the second most common neurodegenerative disease after Alzheimer’s disease. According to the Braak staging study, the progressionof PD starts in the medulla oblongata......, which includes the cardiac centre and controls autonomic functions, and therefore autonomic dysfunction may be experienced early in the disease course. Sleep disturbances are also common non-motor complications of PD, and therefore PD patients undergo polysomnography at the Danish Center for Sleep...... Medicine to assess the sleep disturbances. The aim of this PhD dissertation was to: 1) Develop a method to investigate autonomic changes during sleep in neurodegenerative diseases, and apply this method on PD, iRBD and narcolepsy patients to evaluate the autonomic function in these diseases. 2) Validate...

  7. AUTONOMOUS GAUSSIAN DECOMPOSITION

    Energy Technology Data Exchange (ETDEWEB)

    Lindner, Robert R.; Vera-Ciro, Carlos; Murray, Claire E.; Stanimirović, Snežana; Babler, Brian [Department of Astronomy, University of Wisconsin, 475 North Charter Street, Madison, WI 53706 (United States); Heiles, Carl [Radio Astronomy Lab, UC Berkeley, 601 Campbell Hall, Berkeley, CA 94720 (United States); Hennebelle, Patrick [Laboratoire AIM, Paris-Saclay, CEA/IRFU/SAp-CNRS-Université Paris Diderot, F-91191 Gif-sur Yvette Cedex (France); Goss, W. M. [National Radio Astronomy Observatory, P.O. Box O, 1003 Lopezville, Socorro, NM 87801 (United States); Dickey, John, E-mail: rlindner@astro.wisc.edu [University of Tasmania, School of Maths and Physics, Private Bag 37, Hobart, TAS 7001 (Australia)

    2015-04-15

    We present a new algorithm, named Autonomous Gaussian Decomposition (AGD), for automatically decomposing spectra into Gaussian components. AGD uses derivative spectroscopy and machine learning to provide optimized guesses for the number of Gaussian components in the data, and also their locations, widths, and amplitudes. We test AGD and find that it produces results comparable to human-derived solutions on 21 cm absorption spectra from the 21 cm SPectral line Observations of Neutral Gas with the EVLA (21-SPONGE) survey. We use AGD with Monte Carlo methods to derive the H i line completeness as a function of peak optical depth and velocity width for the 21-SPONGE data, and also show that the results of AGD are stable against varying observational noise intensity. The autonomy and computational efficiency of the method over traditional manual Gaussian fits allow for truly unbiased comparisons between observations and simulations, and for the ability to scale up and interpret the very large data volumes from the upcoming Square Kilometer Array and pathfinder telescopes.

  8. Autonomous Mission Operations Roadmap

    Science.gov (United States)

    Frank, Jeremy David

    2014-01-01

    As light time delays increase, the number of such situations in which crew autonomy is the best way to conduct the mission is expected to increase. However, there are significant open questions regarding which functions to allocate to ground and crew as the time delays increase. In situations where the ideal solution is to allocate responsibility to the crew and the vehicle, a second question arises: should the activity be the responsibility of the crew or an automated vehicle function? More specifically, we must answer the following questions: What aspects of mission operation responsibilities (Plan, Train, Fly) should be allocated to ground based or vehicle based planning, monitoring, and control in the presence of significant light-time delay between the vehicle and the Earth?How should the allocated ground based planning, monitoring, and control be distributed across the flight control team and ground system automation? How should the allocated vehicle based planning, monitoring, and control be distributed between the flight crew and onboard system automation?When during the mission should responsibility shift from flight control team to crew or from crew to vehicle, and what should the process of shifting responsibility be as the mission progresses? NASA is developing a roadmap of capabilities for Autonomous Mission Operations for human spaceflight. This presentation will describe the current state of development of this roadmap, with specific attention to in-space inspection tasks that crews might perform with minimum assistance from the ground.

  9. Regulation of Replication Recovery and Genome Integrity

    DEFF Research Database (Denmark)

    Colding, Camilla Skettrup

    Preserving genome integrity is essential for cell survival. To this end, mechanisms that supervise DNA replication and respond to replication perturbations have evolved. One such mechanism is the replication checkpoint, which responds to DNA replication stress and acts to ensure replication pausing...

  10. Build Autonomic Agents with ABLE

    Institute of Scientific and Technical Information of China (English)

    吴吉义

    2007-01-01

    The IBM Agent Building and Learning Environment(ABLE) provides a lightweight Java~(TM) agent frame- work,a comprehensive JavaBeansTM library of intelligent software components,a set of development and test tools, and an agent platform.After the introduction to ABLE,classes and interfaces in the ABLE agent framework were put forward.At last an autonomic agent that is an ABLE-based architecture for incrementally building autonomic systems was discussed.

  11. The hunt for origins of DNA replication in multicellular eukaryotes

    DEFF Research Database (Denmark)

    Urban, J. M.; Foulk, M. S.; Casella, Cinzia;

    2015-01-01

    Origins of DNA replication (ORIs) occur at defined regions in the genome. Although DNA sequence defines the position of ORIs in budding yeast, the factors for ORI specification remain elusive in metazoa. Several methods have been used recently to map ORIs in metazoan genomes with the hope...

  12. Modification of a loop sequence between α-helices 6 and 7 of virus capsid (CA protein in a human immunodeficiency virus type 1 (HIV-1 derivative that has simian immunodeficiency virus (SIVmac239 vif and CA α-helices 4 and 5 loop improves replication in cynomolgus monkey cells

    Directory of Open Access Journals (Sweden)

    Adachi Akio

    2009-08-01

    Full Text Available Abstract Background Human immunodeficiency virus type 1 (HIV-1 productively infects only humans and chimpanzees but not cynomolgus or rhesus monkeys while simian immunodeficiency virus isolated from macaque (SIVmac readily establishes infection in those monkeys. Several HIV-1 and SIVmac chimeric viruses have been constructed in order to develop an animal model for HIV-1 infection. Construction of an HIV-1 derivative which contains sequences of a SIVmac239 loop between α-helices 4 and 5 (L4/5 of capsid protein (CA and the entire SIVmac239 vif gene was previously reported. Although this chimeric virus could grow in cynomolgus monkey cells, it did so much more slowly than did SIVmac. It was also reported that intrinsic TRIM5α restricts the post-entry step of HIV-1 replication in rhesus and cynomolgus monkey cells, and we previously demonstrated that a single amino acid in a loop between α-helices 6 and 7 (L6/7 of HIV type 2 (HIV-2 CA determines the susceptibility of HIV-2 to cynomolgus monkey TRIM5α. Results In the study presented here, we replaced L6/7 of HIV-1 CA in addition to L4/5 and vif with the corresponding segments of SIVmac. The resultant HIV-1 derivatives showed enhanced replication capability in established T cell lines as well as in CD8+ cell-depleted primary peripheral blood mononuclear cells from cynomolgus monkey. Compared with the wild type HIV-1 particles, the viral particles produced from a chimeric HIV-1 genome with those two SIVmac loops were less able to saturate the intrinsic restriction in rhesus monkey cells. Conclusion We have succeeded in making the replication of simian-tropic HIV-1 in cynomolgus monkey cells more efficient by introducing into HIV-1 the L6/7 CA loop from SIVmac. It would be of interest to determine whether HIV-1 derivatives with SIVmac CA L4/5 and L6/7 can establish infection of cynomolgus monkeys in vivo.

  13. International Expansion through Flexible Replication

    DEFF Research Database (Denmark)

    Jonsson, Anna; Foss, Nicolai Juul

    2011-01-01

    Business organizations may expand internationally by replicating a part of their value chain, such as a sales and marketing format, in other countries. However, little is known regarding how such “international replicators” build a format for replication, or how they can adjust it in order to adapt...... to local environments and under the impact of new learning. To illuminate these issues, we draw on a longitudinal in-depth study of Swedish home furnishing giant IKEA, involving more than 70 interviews. We find that IKEA has developed organizational mechanisms that support an ongoing learning process aimed...... at frequent modification of the format for replication. Another finding is that IKEA treats replication as hierarchical: lower-level features (marketing efforts, pricing, etc.) are allowed to vary across IKEA stores in response to market-based learning, while higher-level features (fundamental values, vision...

  14. Where does DNA replication start in archaea?

    OpenAIRE

    Vas, Amit; Leatherwood, Janet

    2000-01-01

    Genome-wide measures of DNA strand composition have been used to find archaeal DNA replication origins. Archaea seem to replicate using a single origin (as do eubacteria) even though archaeal replication factors are more like those of eukaryotes.

  15. Distance from cohesive end site cos determines the replication requirement for recombination in phage lambda.

    OpenAIRE

    Stahl, F. W.; KOBAYASHI, I.; Stahl, M M

    1982-01-01

    Previous work showed that crossing-over in the middle of the chromosome of phage lambda requires more DNA replication than does crossing-over near the termini. Relocation of cos, the sequence that determines the lambda termini, alters the requirements for replication in a given marked interval, demonstrating that distance from cos determines the amount of DNA replication that is required for genetic exchange. This result supports a break and copy mechanism for recombination mediated by the re...

  16. Identification of imprinted genes using a novel screening method based on asynchronous DNA replication

    Energy Technology Data Exchange (ETDEWEB)

    Kawame, H.; Hansen, R.S.; Gartler, S.M. [Univ. of Washington, Seattle, WA (United States)

    1994-09-01

    Genomic imprinting refers to the process of epigenetic change that occurs during germ cell development that results in either maternal- or paternal-specific gene expression. Identification of imprinted genes is of primary importance to the understanding of imprinting mechanisms and the role of specific imprinted genes in human disease. Recently, it has been established that chromosomal regions known to contain imprinted genes replicate asynchronously. We propose a novel screening method to identify imprinted genes based on replication asynchrony as a marker for imprinted domains. Dividing human cells were pulse-labeled with BrdU and separated into different fractions of S-phase by flow cytometry. A library of late-replicating inter-Alu sequences should be enriched in gene-associated sequences that replicate early on one chromosome and late on the other homologue. Clones were analyzed for replication timing by hybridization to inter-Alu replication profiles. Candidates for replication asynchrony exhibited broad or biphasic replication timing, and these were analyzed for chromosomal location by hybridizations to inter-Alu products from a hybrid mapping panel. Initial screening of 123 clones resulted in 3 asynchronously-replicating clones that localized to single chromosomes. Chromosome 17 and chromosome 19 candidates might be located in regions thought to be imprinted by synteny with mouse chromosomes. A chromosome 15 clone was further characterized because of its possible localization to the Prader-Willi/Angelman locus. This sequence was localized outside the region deleted in Prader-Willi patients, and was found to be expressed in human cell lines. Replication asynchrony for this sequence appears to be polymorphic because cells derived from some individuals indicated synchronous replication. This appears to be the first example of a polymorphism in replication asynchrony.

  17. File Transfer Algorithm for Autonomous Decentralized System

    Institute of Scientific and Technical Information of China (English)

    GUI Xun; TAN Yong-dong; Qian Qing-quan

    2008-01-01

    A file transfer algorithm based on ADP (autonomous decentralized protocol) was proposed to solve the problem that the ADS (autonomous decentralized system) middleware (NeXUS/Dlink) lacks of file transfer functions for Windows. The algorithm realizes the peer-to-peer file transfer, one-to-N inquiry/multi-response file transfer and one-to-N file distribution in the same data field based on communication patterns provided by the ADP. The peer-to-peer file transfer is implemented through a peer-to-peer communication path, one-to-N inquiry/multi-response file transfer and one-to-N file distribution are implemented through multicast commtmieation. In this algorithm, a file to be transferred is named with a GUID ( global unique identification), every data packet is marked with a sequence number, and file-receiving in parallel is implemented by caching DPOs (data processing objects) and multithread technologies. The algorithm is applied in a simulation system of the decentralized control platform, and the test results and long time stable mrming prove the feasibility of the algorithm.

  18. Identifying Cancer Driver Genes Using Replication-Incompetent Retroviral Vectors

    Directory of Open Access Journals (Sweden)

    Victor M. Bii

    2016-10-01

    Full Text Available Identifying novel genes that drive tumor metastasis and drug resistance has significant potential to improve patient outcomes. High-throughput sequencing approaches have identified cancer genes, but distinguishing driver genes from passengers remains challenging. Insertional mutagenesis screens using replication-incompetent retroviral vectors have emerged as a powerful tool to identify cancer genes. Unlike replicating retroviruses and transposons, replication-incompetent retroviral vectors lack additional mutagenesis events that can complicate the identification of driver mutations from passenger mutations. They can also be used for almost any human cancer due to the broad tropism of the vectors. Replication-incompetent retroviral vectors have the ability to dysregulate nearby cancer genes via several mechanisms including enhancer-mediated activation of gene promoters. The integrated provirus acts as a unique molecular tag for nearby candidate driver genes which can be rapidly identified using well established methods that utilize next generation sequencing and bioinformatics programs. Recently, retroviral vector screens have been used to efficiently identify candidate driver genes in prostate, breast, liver and pancreatic cancers. Validated driver genes can be potential therapeutic targets and biomarkers. In this review, we describe the emergence of retroviral insertional mutagenesis screens using replication-incompetent retroviral vectors as a novel tool to identify cancer driver genes in different cancer types.

  19. Integrated Motion Planning and Autonomous Control Technology for Autonomous ISR Project

    Data.gov (United States)

    National Aeronautics and Space Administration — SSCI and MIT propose to design, implement and test a comprehensive Integrated Mission Planning & Autonomous Control Technology (IMPACT) for Autonomous ISR...

  20. Autonomous Landing on Moving Platforms

    KAUST Repository

    Mendoza Chavez, Gilberto

    2016-08-01

    This thesis investigates autonomous landing of a micro air vehicle (MAV) on a nonstationary ground platform. Unmanned aerial vehicles (UAVs) and micro air vehicles (MAVs) are becoming every day more ubiquitous. Nonetheless, many applications still require specialized human pilots or supervisors. Current research is focusing on augmenting the scope of tasks that these vehicles are able to accomplish autonomously. Precise autonomous landing on moving platforms is essential for self-deployment and recovery of MAVs, but it remains a challenging task for both autonomous and piloted vehicles. Model Predictive Control (MPC) is a widely used and effective scheme to control constrained systems. One of its variants, output-feedback tube-based MPC, ensures robust stability for systems with bounded disturbances under system state reconstruction. This thesis proposes a MAV control strategy based on this variant of MPC to perform rapid and precise autonomous landing on moving targets whose nominal (uncommitted) trajectory and velocity are slowly varying. The proposed approach is demonstrated on an experimental setup.

  1. Autonomous mobile robots: Vehicles with cognitive control

    Energy Technology Data Exchange (ETDEWEB)

    Meystel, A.

    1987-01-01

    This book explores a new rapidly developing area of robotics. It describes the state-of-the-art intelligence control, applied machine intelligence, and research and initial stages of manufacturing of autonomous mobile robots. A complete account of the theoretical and experimental results obtained during the last two decades together with some generalizations on Autonomous Mobile Systems are included in this book. Contents: Introduction; Requirements and Specifications; State-of-the-art in Autonomous Mobile Robots Area; Structure of Intelligent Mobile Autonomous System; Planner, Navigator; Pilot; Cartographer; Actuation Control; Computer Simulation of Autonomous Operation; Testing the Autonomous Mobile Robot; Conclusions; Bibliography.

  2. RNA interference-mediated inhibition of Hepatitis B Virus replication

    Institute of Scientific and Technical Information of China (English)

    TANG Ni; ZHANG Bingqiang; YAN Ge; PU Dan; GAO Xiaolin; Tong-Chuan He; HUANG Ailong

    2004-01-01

    Persistent and recurrent infection of hepatitis B virus (HBV) represents one of the most common and severe viral infections of humans, and has caused a formidable health problem in the affected countries. Currently used antiviral drugs have a very limited success on controlling HBV replication and infection. RNA interference (RNAi), a process by which double-stranded RNA (dsRNA) directs sequence-specific degradation of target mRNA in mammalian and plant cells, has recently been used to knockdown gene expression in various species. In this study, we sought to determine whether RNAi-mediated silencing of HBV viral gene expression could lead to the effective inhibition of HBV replication. We first developed RNAi vectors that expressed small interfering RNA (siRNA) and targeted the HBV core or surface gene sequence. Our results demonstrated that these specific siRNAs efficiently reduced the levels of corresponding viral RNAs and proteins, and thus suppressed viral replication. Treatment with siRNA gave the greatest reduction in the levels of HBsAg (92%) and in HBeAg (85%) respectively in the cultured cell medium. Our findings further demonstrated that the RNAi-mediated antiviral effect was sequence-specific and dose-dependent. Therefore, our findings strongly suggest that RNAi-mediated silencing of HBV viral genes could effectively inhibit the replication of HBV, hence RNAi-based strategy should be further explored as a more efficacious antiviral therapy of HBV infection.

  3. Autonomous Industrial Mobile Manipulation (AIMM)

    DEFF Research Database (Denmark)

    Hvilshøj, Mads; Bøgh, Simon; Nielsen, Oluf Skov;

    2012-01-01

    Purpose - The purpose of this paper is to provide a review of the interdisciplinary research field Autonomous Industrial Mobile Manipulation (AIMM), with an emphasis on physical implementations and applications. Design/methodology/approach - Following an introduction to AIMM, this paper investiga......Purpose - The purpose of this paper is to provide a review of the interdisciplinary research field Autonomous Industrial Mobile Manipulation (AIMM), with an emphasis on physical implementations and applications. Design/methodology/approach - Following an introduction to AIMM, this paper......; sustainability, configuration, adaptation, autonomy, positioning, manipulation and grasping, robot-robot interaction, human-robot interaction, process quality, dependability, and physical properties. Findings - The concise yet comprehensive review provides both researchers (academia) and practitioners (industry......) with a quick and gentle overview of AIMM. Furthermore, the paper identifies key open issues and promising research directions to realize real-world integration and maturation of the AIMM technology. Originality/value - This paper reviews the interdisciplinary research field Autonomous Industrial Mobile...

  4. Autonomous underwater riser inspection tool

    Energy Technology Data Exchange (ETDEWEB)

    Camerini, Claudio; Marnet, Robson [Petrobras SA, (Brazil); Freitas, Miguel; Von der Weid, Jean Pierre [CPTI/PUC-Rio, Rio de Janeiro, (Brazil); Artigas Lander, Ricardo [EngeMOVI, Curitiba, (Brazil)

    2010-07-01

    The detection of damage on the riser is a serious concern for pipeline companies. Visual examinations by remotely operated vehicle (ROV) are presently carried out to detect the defects but this process has limitations and is expensive. This paper presents the development of a new tool to ensure autonomous underwater riser inspection (AURI) that uses the riser itself for guidance. The AURI, which is autonomous in terms of control and power supply, is equipped with several cameras that perform a complete visual inspection of the riser with 100 % coverage of the external surface of the riser. The paper presents the detailed characteristics of the first AURI prototype, describes its launching procedure and provides the preliminary test results from pool testing. The results showed that the AURI is a viable system for autonomous riser inspection. Offshore tests on riser pipelines are scheduled to be performed shortly.

  5. Hereditary sensory and autonomic neuropathies.

    Science.gov (United States)

    Auer-Grumbach, Michaela

    2013-01-01

    Hereditary sensory and autonomic neuropathies (HSN/HSAN) are clinically and genetically heterogeneous disorders of the peripheral nervous system that predominantly affect the sensory and autonomic neurons. Hallmark features comprise not only prominent sensory signs and symptoms and ulcerative mutilations but also variable autonomic and motor disturbances. Autosomal dominant and autosomal recessive inheritance has been reported. Molecular genetics studies have identified disease-causing mutations in 11 genes. Some of the affected proteins have nerve-specific roles but underlying mechanisms have also been shown to involve sphingolipid metabolism, vesicular transport, structural integrity, and transcription regulation. Genetic and functional studies have substantially improved the understanding of the pathogenesis of the HSN/HSAN and will help to find preventive and causative therapies in the future.

  6. The Autonomous Glycosylation of Large DNA Viruses

    Directory of Open Access Journals (Sweden)

    Francesco Piacente

    2015-12-01

    Full Text Available Glycosylation of surface molecules is a key feature of several eukaryotic viruses, which use the host endoplasmic reticulum/Golgi apparatus to add carbohydrates to their nascent glycoproteins. In recent years, a newly discovered group of eukaryotic viruses, belonging to the Nucleo-Cytoplasmic Large DNA Virus (NCLDV group, was shown to have several features that are typical of cellular organisms, including the presence of components of the glycosylation machinery. Starting from initial observations with the chlorovirus PBCV-1, enzymes for glycan biosynthesis have been later identified in other viruses; in particular in members of the Mimiviridae family. They include both the glycosyltransferases and other carbohydrate-modifying enzymes and the pathways for the biosynthesis of the rare monosaccharides that are found in the viral glycan structures. These findings, together with genome analysis of the newly-identified giant DNA viruses, indicate that the presence of glycogenes is widespread in several NCLDV families. The identification of autonomous viral glycosylation machinery leads to many questions about the origin of these pathways, the mechanisms of glycan production, and eventually their function in the viral replication cycle. The scope of this review is to highlight some of the recent results that have been obtained on the glycosylation systems of the large DNA viruses, with a special focus on the enzymes involved in nucleotide-sugar production.

  7. Regulation of beta cell replication

    DEFF Research Database (Denmark)

    Lee, Ying C; Nielsen, Jens Høiriis

    2008-01-01

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

  8. Defects of mitochondrial DNA replication.

    Science.gov (United States)

    Copeland, William C

    2014-09-01

    Mitochondrial DNA is replicated by DNA polymerase γ in concert with accessory proteins such as the mitochondrial DNA helicase, single-stranded DNA binding protein, topoisomerase, and initiating factors. Defects in mitochondrial DNA replication or nucleotide metabolism can cause mitochondrial genetic diseases due to mitochondrial DNA deletions, point mutations, or depletion, which ultimately cause loss of oxidative phosphorylation. These genetic diseases include mitochondrial DNA depletion syndromes such as Alpers or early infantile hepatocerebral syndromes, and mitochondrial DNA deletion disorders, such as progressive external ophthalmoplegia, ataxia-neuropathy, or mitochondrial neurogastrointestinal encephalomyopathy. This review focuses on our current knowledge of genetic defects of mitochondrial DNA replication (POLG, POLG2, C10orf2, and MGME1) that cause instability of mitochondrial DNA and mitochondrial disease.

  9. Mimiviruses: Replication, Purification, and Quantification.

    Science.gov (United States)

    Abrahão, Jônatas Santos; Oliveira, Graziele Pereira; Ferreira da Silva, Lorena Christine; Dos Santos Silva, Ludmila Karen; Kroon, Erna Geessien; La Scola, Bernard

    2016-01-01

    The aim of this protocol is to describe the replication, purification, and titration of mimiviruses. These viruses belong to the Mimiviridae family, the first member of which was isolated in 1992 from a cooling tower water sample collected during an outbreak of pneumonia in a hospital in Bradford, England. In recent years, several new mimiviruses have been isolated from different environmental conditions. These giant viruses are easily replicated in amoeba of the Acanthamoeba genus, its natural host. Mimiviruses present peculiar features that make them unique viruses, such as the particle and genome size and the genome's complexity. The discovery of these viruses rekindled discussions about their origin and evolution, and the genetic and structural complexity opened up a new field of study. Here, we describe some methods utilized for mimiviruses replication, purification, and titration. © 2016 by John Wiley & Sons, Inc. PMID:27153385

  10. Lymphatic endothelial cells are a replicative niche for Mycobacterium tuberculosis

    Science.gov (United States)

    Lerner, Thomas R.; de Souza Carvalho-Wodarz, Cristiane; Repnik, Urska; Russell, Matthew R.G.; Borel, Sophie; Diedrich, Collin R.; Rohde, Manfred; Wainwright, Helen; Collinson, Lucy M.; Wilkinson, Robert J.; Griffiths, Gareth; Gutierrez, Maximiliano G.

    2016-01-01

    In extrapulmonary tuberculosis, the most common site of infection is within the lymphatic system, and there is growing recognition that lymphatic endothelial cells (LECs) are involved in immune function. Here, we identified LECs, which line the lymphatic vessels, as a niche for Mycobacterium tuberculosis in the lymph nodes of patients with tuberculosis. In cultured primary human LECs (hLECs), we determined that M. tuberculosis replicates both in the cytosol and within autophagosomes, but the bacteria failed to replicate when the virulence locus RD1 was deleted. Activation by IFN-γ induced a cell-autonomous response in hLECs via autophagy and NO production that restricted M. tuberculosis growth. Thus, depending on the activation status of LECs, autophagy can both promote and restrict replication. Together, these findings reveal a previously unrecognized role for hLECs and autophagy in tuberculosis pathogenesis and suggest that hLECs are a potential niche for M. tuberculosis that allows establishment of persistent infection in lymph nodes. PMID:26901813

  11. Progress towards autonomous, intelligent systems

    Science.gov (United States)

    Lum, Henry; Heer, Ewald

    1987-01-01

    An aggressive program has been initiated to develop, integrate, and implement autonomous systems technologies starting with today's expert systems and evolving to autonomous, intelligent systems by the end of the 1990s. This program includes core technology developments and demonstration projects for technology evaluation and validation. This paper discusses key operational frameworks in the content of systems autonomy applications and then identifies major technological challenges, primarily in artificial intelligence areas. Program content and progress made towards critical technologies and demonstrations that have been initiated to achieve the required future capabilities in the year 2000 era are discussed.

  12. Discerning non-autonomous dynamics

    International Nuclear Information System (INIS)

    Structure and function go hand in hand. However, while a complex structure can be relatively safely broken down into the minutest parts, and technology is now delving into nanoscales, the function of complex systems requires a completely different approach. Here the complexity clearly arises from nonlinear interactions, which prevents us from obtaining a realistic description of a system by dissecting it into its structural component parts. At best, the result of such investigations does not substantially add to our understanding or at worst it can even be misleading. Not surprisingly, the dynamics of complex systems, facilitated by increasing computational efficiency, is now readily tackled in the case of measured time series. Moreover, time series can now be collected in practically every branch of science and in any structural scale—from protein dynamics in a living cell to data collected in astrophysics or even via social networks. In searching for deterministic patterns in such data we are limited by the fact that no complex system in the real world is autonomous. Hence, as an alternative to the stochastic approach that is predominantly applied to data from inherently non-autonomous complex systems, theory and methods specifically tailored to non-autonomous systems are needed. Indeed, in the last decade we have faced a huge advance in mathematical methods, including the introduction of pullback attractors, as well as time series methods that cope with the most important characteristic of non-autonomous systems—their time-dependent behaviour. Here we review current methods for the analysis of non-autonomous dynamics including those for extracting properties of interactions and the direction of couplings. We illustrate each method by applying it to three sets of systems typical for chaotic, stochastic and non-autonomous behaviour. For the chaotic class we select the Lorenz system, for the stochastic the noise-forced Duffing system and for the non-autonomous

  13. Intelligent, autonomous systems in space

    Science.gov (United States)

    Lum, H.; Heer, E.

    1988-01-01

    The Space Station is expected to be equipped with intelligent, autonomous capabilities; to achieve and incorporate these capabilities, the required technologies need to be identitifed, developed and validated within realistic application scenarios. The critical technologies for the development of intelligent, autonomous systems are discussed in the context of a generalized functional architecture. The present state of this technology implies that it be introduced and applied in an evolutionary process which must start during the Space Station design phase. An approach is proposed to accomplish design information acquisition and management for knowledge-base development.

  14. Contingency Software in Autonomous Systems

    Science.gov (United States)

    Lutz, Robyn; Patterson-Hine, Ann

    2006-01-01

    This viewgraph presentation reviews the development of contingency software for autonomous systems. Autonomous vehicles currently have a limited capacity to diagnose and mitigate failures. There is a need to be able to handle a broader range of contingencies. The goals of the project are: 1. Speed up diagnosis and mitigation of anomalous situations.2.Automatically handle contingencies, not just failures.3.Enable projects to select a degree of autonomy consistent with their needs and to incrementally introduce more autonomy.4.Augment on-board fault protection with verified contingency scripts

  15. Discerning non-autonomous dynamics

    Energy Technology Data Exchange (ETDEWEB)

    Clemson, Philip T.; Stefanovska, Aneta, E-mail: aneta@lancaster.ac.uk

    2014-09-30

    Structure and function go hand in hand. However, while a complex structure can be relatively safely broken down into the minutest parts, and technology is now delving into nanoscales, the function of complex systems requires a completely different approach. Here the complexity clearly arises from nonlinear interactions, which prevents us from obtaining a realistic description of a system by dissecting it into its structural component parts. At best, the result of such investigations does not substantially add to our understanding or at worst it can even be misleading. Not surprisingly, the dynamics of complex systems, facilitated by increasing computational efficiency, is now readily tackled in the case of measured time series. Moreover, time series can now be collected in practically every branch of science and in any structural scale—from protein dynamics in a living cell to data collected in astrophysics or even via social networks. In searching for deterministic patterns in such data we are limited by the fact that no complex system in the real world is autonomous. Hence, as an alternative to the stochastic approach that is predominantly applied to data from inherently non-autonomous complex systems, theory and methods specifically tailored to non-autonomous systems are needed. Indeed, in the last decade we have faced a huge advance in mathematical methods, including the introduction of pullback attractors, as well as time series methods that cope with the most important characteristic of non-autonomous systems—their time-dependent behaviour. Here we review current methods for the analysis of non-autonomous dynamics including those for extracting properties of interactions and the direction of couplings. We illustrate each method by applying it to three sets of systems typical for chaotic, stochastic and non-autonomous behaviour. For the chaotic class we select the Lorenz system, for the stochastic the noise-forced Duffing system and for the non-autonomous

  16. Gas House Autonomous System Monitoring

    Science.gov (United States)

    Miller, Luke; Edsall, Ashley

    2015-01-01

    Gas House Autonomous System Monitoring (GHASM) will employ Integrated System Health Monitoring (ISHM) of cryogenic fluids in the High Pressure Gas Facility at Stennis Space Center. The preliminary focus of development incorporates the passive monitoring and eventual commanding of the Nitrogen System. ISHM offers generic system awareness, adept at using concepts rather than specific error cases. As an enabler for autonomy, ISHM provides capabilities inclusive of anomaly detection, diagnosis, and abnormality prediction. Advancing ISHM and Autonomous Operation functional capabilities enhances quality of data, optimizes safety, improves cost effectiveness, and has direct benefits to a wide spectrum of aerospace applications.

  17. Genome-wide alterations of the DNA replication program during tumor progression

    Science.gov (United States)

    Arneodo, A.; Goldar, A.; Argoul, F.; Hyrien, O.; Audit, B.

    2016-08-01

    Oncogenic stress is a major driving force in the early stages of cancer development. Recent experimental findings reveal that, in precancerous lesions and cancers, activated oncogenes may induce stalling and dissociation of DNA replication forks resulting in DNA damage. Replication timing is emerging as an important epigenetic feature that recapitulates several genomic, epigenetic and functional specificities of even closely related cell types. There is increasing evidence that chromosome rearrangements, the hallmark of many cancer genomes, are intimately associated with the DNA replication program and that epigenetic replication timing changes often precede chromosomic rearrangements. The recent development of a novel methodology to map replication fork polarity using deep sequencing of Okazaki fragments has provided new and complementary genome-wide replication profiling data. We review the results of a wavelet-based multi-scale analysis of genomic and epigenetic data including replication profiles along human chromosomes. These results provide new insight into the spatio-temporal replication program and its dynamics during differentiation. Here our goal is to bring to cancer research, the experimental protocols and computational methodologies for replication program profiling, and also the modeling of the spatio-temporal replication program. To illustrate our purpose, we report very preliminary results obtained for the chronic myelogeneous leukemia, the archetype model of cancer. Finally, we discuss promising perspectives on using genome-wide DNA replication profiling as a novel efficient tool for cancer diagnosis, prognosis and personalized treatment.

  18. Autonomic regulation predicts performance on Wisconsin Card Sorting Test (WCST) in adults with schizophrenia.

    Science.gov (United States)

    Mathewson, Karen J; Jetha, Michelle K; Goldberg, Joel O; Schmidt, Louis A

    2012-12-01

    Although executive functions have been associated with autonomic regulatory capacity in healthy adults, there appear to be no reports of these relations in adults with schizophrenia to date. We tested whether baseline autonomic regulation was associated with performance on the Wisconsin Card Sorting Test (WCST) in a group of 42 stable community outpatients with schizophrenia. Patients exhibited faster resting heart rates and lower respiratory sinus arrhythmia (RSA) than age-matched controls, consistent with previous research. Patients also completed relatively few WCST categories and made many perseverative errors, replicating prior studies. Within the patient group, relatively better WCST performance was associated with slower resting heart rate and higher RSA, suggesting that inefficient executive and autonomic functioning in schizophrenia may be linked. WCST performance and autonomic regulatory capacity were further reduced in a subset of patients receiving clozapine, but relations between WCST performance and autonomic regulatory parameters did not differ from those of other patients. Findings extend the neurovisceral integration model of autonomic regulation to adults with schizophrenia and attest to the reliability of the model.

  19. A Robust Compositional Architecture for Autonomous Systems

    Science.gov (United States)

    Brat, Guillaume; Deney, Ewen; Farrell, Kimberley; Giannakopoulos, Dimitra; Jonsson, Ari; Frank, Jeremy; Bobby, Mark; Carpenter, Todd; Estlin, Tara

    2006-01-01

    Space exploration applications can benefit greatly from autonomous systems. Great distances, limited communications and high costs make direct operations impossible while mandating operations reliability and efficiency beyond what traditional commanding can provide. Autonomous systems can improve reliability and enhance spacecraft capability significantly. However, there is reluctance to utilizing autonomous systems. In part this is due to general hesitation about new technologies, but a more tangible concern is that of reliability of predictability of autonomous software. In this paper, we describe ongoing work aimed at increasing robustness and predictability of autonomous software, with the ultimate goal of building trust in such systems. The work combines state-of-the-art technologies and capabilities in autonomous systems with advanced validation and synthesis techniques. The focus of this paper is on the autonomous system architecture that has been defined, and on how it enables the application of validation techniques for resulting autonomous systems.

  20. Result Analysis and Benefits of Detecting Replicate Documents Using MD5 Hash Function

    Directory of Open Access Journals (Sweden)

    Pushpendra Singh Tomar

    2011-12-01

    Full Text Available The definition of what constitutes a replicate has somewhat different interpretations. For instance, some define a replicate as having the exact syntactic terms and sequence, whether having formatting differences or not. In effect, there are either no difference or only formatting differences and the contents of the data are exactly the same. In any case, data replication happens all the time. In large data warehouses, data replication is an inevitable phenomenon as millions of data are gathered at very short intervals. In this paper we provide a detail result analysis on the basis of our approach and the previous one.

  1. Result Analysis and Benefits of Detecting Replicate Documents Using MD5 Hash Function

    Directory of Open Access Journals (Sweden)

    Mr. Pushpendra Singh Tomar

    2011-09-01

    Full Text Available The definition of what constitutes a replicate has somewhat different interpretations. For instance, some define a replicate as having the exact syntactic terms and sequence, whether having formatting differences or not. In effect, there are either no difference or only formatting differences and the contents of the data are exactly the same. In any case, data replication happens all the time. In large data warehouses, data replication is an inevitable phenomenon as millions of data are gathered at very short intervals. In this paper we provide a detail result analysis on the basis of our approach and the previous one.

  2. Cellular factors required for papillomavirus DNA replication.

    OpenAIRE

    Melendy, T; Sedman, J; Stenlund, A

    1995-01-01

    In vitro replication of papillomavirus DNA has been carried out with a combination of purified proteins and partially purified extracts made from human cells. DNA synthesis requires the viral E1 protein and the papillomavirus origin of replication. The E2 protein stimulates DNA synthesis in a binding site-independent manner. Papillomavirus DNA replication is also dependent on the cellular factors replication protein A, replication factor C, and proliferating-cell nuclear antigen as well as a ...

  3. Optimal Placement of Origins for DNA Replication

    OpenAIRE

    Karschau, Jens; Blow, J. Julian; de Moura, Alessandro P. S.

    2012-01-01

    DNA replication is an essential process in biology and its timing must be robust so that cells can divide properly. Random fluctuations in the formation of replication starting points, called origins, and the subsequent activation of proteins lead to variations in the replication time. We analyse these stochastic properties of DNA and derive the positions of origins corresponding to the minimum replication time. We show that under some conditions the minimization of replication time leads to ...

  4. The replication-transcription conflict

    OpenAIRE

    Soultanas, Panos

    2011-01-01

    In response to environmental and nutritional stimuli, a whole array of proteins remodel genome architecture, activate or transcribe genes, suppress genes, repair lesions and base-modifications, faithfully replicate and safely separate the parental and daughter genomes during cell division. Negotiating and resolving conflicts of genome trafficking is essential for genome stability.

  5. Covert Reinforcement: A Partial Replication.

    Science.gov (United States)

    Ripstra, Constance C.; And Others

    A partial replication of an investigation of the effect of covert reinforcement on a perceptual estimation task is described. The study was extended to include an extinction phase. There were five treatment groups: covert reinforcement, neutral scene reinforcement, noncontingent covert reinforcement, and two control groups. Each subject estimated…

  6. Cellular Responses to Replication Problems

    NARCIS (Netherlands)

    M. Budzowska (Magdalena)

    2008-01-01

    textabstractDuring every S-phase cells need to duplicate their genomes so that both daughter cells inherit complete copies of genetic information. It is a tremendous task, given the large sizes of mammalian genomes and the required precision of DNA replication. A major threat to the accuracy and eff

  7. Hyperthermia stimulates HIV-1 replication.

    Directory of Open Access Journals (Sweden)

    Ferdinand Roesch

    Full Text Available HIV-infected individuals may experience fever episodes. Fever is an elevation of the body temperature accompanied by inflammation. It is usually beneficial for the host through enhancement of immunological defenses. In cultures, transient non-physiological heat shock (42-45°C and Heat Shock Proteins (HSPs modulate HIV-1 replication, through poorly defined mechanisms. The effect of physiological hyperthermia (38-40°C on HIV-1 infection has not been extensively investigated. Here, we show that culturing primary CD4+ T lymphocytes and cell lines at a fever-like temperature (39.5°C increased the efficiency of HIV-1 replication by 2 to 7 fold. Hyperthermia did not facilitate viral entry nor reverse transcription, but increased Tat transactivation of the LTR viral promoter. Hyperthermia also boosted HIV-1 reactivation in a model of latently-infected cells. By imaging HIV-1 transcription, we further show that Hsp90 co-localized with actively transcribing provirus, and this phenomenon was enhanced at 39.5°C. The Hsp90 inhibitor 17-AAG abrogated the increase of HIV-1 replication in hyperthermic cells. Altogether, our results indicate that fever may directly stimulate HIV-1 replication, in a process involving Hsp90 and facilitation of Tat-mediated LTR activity.

  8. Biomarkers of replicative senescence revisited

    DEFF Research Database (Denmark)

    Nehlin, Jan

    2016-01-01

    of telomere length and associated damage, and the accompanying changes that take place elicit signals that have an impact on a number of molecules and downstream events. Precise measurements of replicative senescence biomarkers in biological samples from individuals could be clinically associated...

  9. The autonomic phenotype of rumination.

    Science.gov (United States)

    Ottaviani, Cristina; Shapiro, David; Davydov, Dmitry M; Goldstein, Iris B; Mills, Paul J

    2009-06-01

    Recent studies suggest that ruminative thoughts may be mediators of the prolonged physiological effects of stress. We hypothesized that autonomic dysregulation plays a role in the relation between rumination and health. Rumination was induced by an anger-recall task in 45 healthy subjects. Heart rate variability (HRV), baroreflex sensitivity (BRS), and baroreflex effectiveness index (BEI) change scores were evaluated to obtain the autonomic phenotype of rumination. Personality traits and endothelial activation were examined for their relation to autonomic responses during rumination. Degree of endothelial activation was assessed by circulating soluble intercellular adhesion molecule-1 (sICAM-1). Vagal withdrawal during rumination was greater for women than men. Larger decreases in the high frequency component of HRV were associated with higher levels of anger-in, depression, and sICAM-1 levels. BRS reactivity was negatively related to trait anxiety. BEI reactivity was positively related to anger-in, hostility, anxiety, and depression. Lower BEI and BRS recovery were associated with lower social desirability and higher anger-out, anxiety, and depression. Findings suggest that the autonomic dysregulation that characterizes rumination plays a role in the relationships between personality and cardiovascular health. PMID:19272312

  10. Hazard Map for Autonomous Navigation

    DEFF Research Database (Denmark)

    Riis, Troels

    This dissertation describes the work performed in the area of using image analysis in the process of landing a spacecraft autonomously and safely on the surface of the Moon. This is suggested to be done using a Hazard Map. The correspondence problem between several Hazard Maps are investigated...

  11. Computing architecture for autonomous microgrids

    Science.gov (United States)

    Goldsmith, Steven Y.

    2015-09-29

    A computing architecture that facilitates autonomously controlling operations of a microgrid is described herein. A microgrid network includes numerous computing devices that execute intelligent agents, each of which is assigned to a particular entity (load, source, storage device, or switch) in the microgrid. The intelligent agents can execute in accordance with predefined protocols to collectively perform computations that facilitate uninterrupted control of the .

  12. The Bering Autonomous Target Detection

    DEFF Research Database (Denmark)

    Jørgensen, John Leif; Denver, Troelz; Betto, Maurizio;

    2003-01-01

    autonomous star tracker the Advanced Stellar Compass (ASC). One feature of this instrument is that potential targets are registered directly in terms of date, right ascension, declination, and intensity, which greatly facilitates both tracking search and registering. Results from ground and inflight tests...... are encouraging, both with respect to robustness, speed and accuracy, and demonstrates the span and range of applications of this technology....

  13. Autonomous navigation for artificial satellites

    Science.gov (United States)

    Desai, P. S.

    1975-01-01

    An autonomous navigation system is considered that provides a satellite with sufficient numbers and types of sensors, as well as computational hardware and software, to enable it to track itself. Considered are attitude type sensors, meteorological cameras and scanners, one way Doppler, and image correlator.

  14. New histone supply regulates replication fork speed and PCNA unloading

    DEFF Research Database (Denmark)

    Mejlvang, Jakob; Feng, Yunpeng; Alabert, Constance;

    2014-01-01

    Correct duplication of DNA sequence and its organization into chromatin is central to genome function and stability. However, it remains unclear how cells coordinate DNA synthesis with provision of new histones for chromatin assembly to ensure chromosomal stability. In this paper, we show...... that replication fork speed is dependent on new histone supply and efficient nucleosome assembly. Inhibition of canonical histone biosynthesis impaired replication fork progression and reduced nucleosome occupancy on newly synthesized DNA. Replication forks initially remained stable without activation...... of conventional checkpoints, although prolonged histone deficiency generated DNA damage. PCNA accumulated on newly synthesized DNA in cells lacking new histones, possibly to maintain opportunity for CAF-1 recruitment and nucleosome assembly. Consistent with this, in vitro and in vivo analysis showed that PCNA...

  15. Crinivirus replication and host interactions

    Directory of Open Access Journals (Sweden)

    Zsofia A Kiss

    2013-05-01

    Full Text Available Criniviruses comprise one of the genera within the family Closteroviridae. Members in this family are restricted to the phloem and rely on whitefly vectors of the genera Bemisia and/or Trialeurodes for plant-to-plant transmission. All criniviruses have bipartite, positive-sense ssRNA genomes, although there is an unconfirmed report of one having a tripartite genome. Lettuce infectious yellows virus (LIYV is the type species of the genus, the best studied so far of the criniviruses and the first for which a reverse genetics system was available. LIYV RNA 1 encodes for proteins predicted to be involved in replication, and alone is competent for replication in protoplasts. Replication results in accumulation of cytoplasmic vesiculated membranous structures which are characteristic of most studied members of the Closteroviridae. These membranous structures, often referred to as BYV-type vesicles, are likely sites of RNA replication. LIYV RNA 2 is replicated in trans when co-infecting cells with RNA 1, but is temporally delayed relative to RNA1. Efficient RNA 2 replication also is dependent on the RNA 1-encoded RNA binding protein, P34. No LIYV RNA 2-encoded proteins have been shown to affect RNA replication, but at least four, CP, CPm, Hsp70h, and p59 are virion structural components and CPm is a determinant of whitefly transmissibility. Roles of other LIYV RNA 2-encoded proteins are largely as yet unknown, but P26 is a non-virion protein that accumulates in cells as characteristic plasmalemma deposits which in plants are localized within phloem parenchyma and companion cells over plasmodesmata connections to sieve elements. The two remaining crinivirus-conserved RNA 2-encoded proteins are P5 and P9. P5 is 39 amino acid protein and is encoded at the 5’ end of RNA 2 as ORF1 and is part of the hallmark closterovirus gene array. The orthologous gene in BYV has been shown to play a role in cell-to-cell movement and indicated to be localized to the

  16. Autonomous Duffing-Holmes Type Chaotic Oscillator

    DEFF Research Database (Denmark)

    Tamaševičius, A.; Bumelienė, S.; Kirvaitis, R.;

    2009-01-01

    We have designed and built a novel Duffing type autonomous 3rd-order chaotic oscillator. In comparison with the common non-autonomous DuffingHolmes type oscillator the autonomous circuit has an internal positive feedback loop instead of an external periodic drive source. In addition...

  17. Indoor Autonomous Airship Control and Navigation System

    OpenAIRE

    Fedorenko Roman; Krukhmalev Victor

    2016-01-01

    The paper presents an automatic control system for autonomous airship. The system is designed to organize autonomous flight of the mini-airship performing flight mission defined from ground control station. Structure, hardware and software implementation of indoor autonomous airship and its navigation and control system as well as experiment results are described.

  18. Indoor Autonomous Airship Control and Navigation System

    Directory of Open Access Journals (Sweden)

    Fedorenko Roman

    2016-01-01

    Full Text Available The paper presents an automatic control system for autonomous airship. The system is designed to organize autonomous flight of the mini-airship performing flight mission defined from ground control station. Structure, hardware and software implementation of indoor autonomous airship and its navigation and control system as well as experiment results are described.

  19. Trapping DNA replication origins from the human genome.

    Science.gov (United States)

    Eki, Toshihiko; Murakami, Yasufumi; Hanaoka, Fumio

    2013-04-17

    Synthesis of chromosomal DNA is initiated from multiple origins of replication in higher eukaryotes; however, little is known about these origins' structures. We isolated the origin-derived nascent DNAs from a human repair-deficient cell line by blocking the replication forks near the origins using two different origin-trapping methods (i.e., UV- or chemical crosslinker-treatment and cell synchronization in early S phase using DNA replication inhibitors). Single-stranded DNAs (of 0.5-3 kb) that accumulated after such treatments were labeled with bromodeoxyuridine (BrdU). BrdU-labeled DNA was immunopurified after fractionation by alkaline sucrose density gradient centrifugation and cloned by complementary-strand synthesis and PCR amplification. Competitive PCR revealed an increased abundance of DNA derived from known replication origins (c-myc and lamin B2 genes) in the nascent DNA fractions from the UV-treated or crosslinked cells. Nucleotide sequences of 85 and 208 kb were obtained from the two libraries (I and II) prepared from the UV-treated log-phase cells and early S phase arrested cells, respectively. The libraries differed from each other in their G+C composition and replication-related motif contents, suggesting that differences existed between the origin fragments isolated by the two different origin-trapping methods. The replication activities for seven out of 12 putative origin loci from the early-S phase cells were shown by competitive PCR. We mapped 117 (library I) and 172 (library II) putative origin loci to the human genome; approximately 60% and 50% of these loci were assigned to the G-band and intragenic regions, respectively. Analyses of the flanking sequences of the mapped loci suggested that the putative origin loci tended to associate with genes (including conserved sites) and DNase I hypersensitive sites; however, poor correlations were found between such loci and the CpG islands, transcription start sites, and K27-acetylated histone H3 peaks.

  20. A real-time distributed software infrastructure for cooperating mobile autonomous robots

    OpenAIRE

    Frederico Santos; Luis Almeida; Paulo Pedreiras; Luis Seabra Lopes

    2009-01-01

    Cooperating mobile autonomous robots have been generating a growing interest in fields such as rescue, demining and security. These applications require a real time middleware and wireless communication protocol that can effecient and timely support the fusion of the distributed perception and the development of coordinated behaviors. This paper proposes an affordable middleware, based on low-cost and open-source COTS technologies, which relies on a real-time database partially replicated in ...

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

    Directory of Open Access Journals (Sweden)

    Majid Eshaghi

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

  2. Priming DNA Replication from Triple Helix Oligonucleotides: Possible Threestranded DNA in DNA Polymerases

    OpenAIRE

    Lestienne, Patrick P.

    2011-01-01

    Triplex associate with a duplex DNA presenting the same polypurine or polypyrimidine-rich sequence in an antiparallel orientation. So far, triplex forming oligonucleotides (TFOs) are known to inhibit transcription, replication, and to induce mutations. A new property of TFO is reviewed here upon analysis of DNA breakpoint yielding DNA rearrangements; the synthesized sequence of the first direct repeat displays a skewed polypurine- rich sequence. This synthesized sequence can bind the second h...

  3. Autonomic computing enabled cooperative networked design

    CERN Document Server

    Wodczak, Michal

    2014-01-01

    This book introduces the concept of autonomic computing driven cooperative networked system design from an architectural perspective. As such it leverages and capitalises on the relevant advancements in both the realms of autonomic computing and networking by welding them closely together. In particular, a multi-faceted Autonomic Cooperative System Architectural Model is defined which incorporates the notion of Autonomic Cooperative Behaviour being orchestrated by the Autonomic Cooperative Networking Protocol of a cross-layer nature. The overall proposed solution not only advocates for the inc

  4. Autonomous Cryogenics Loading Operations Simulation Software: Knowledgebase Autonomous Test Engineer

    Science.gov (United States)

    Wehner, Walter S., Jr.

    2013-01-01

    Working on the ACLO (Autonomous Cryogenics Loading Operations) project I have had the opportunity to add functionality to the physics simulation software known as KATE (Knowledgebase Autonomous Test Engineer), create a new application allowing WYSIWYG (what-you-see-is-what-you-get) creation of KATE schematic files and begin a preliminary design and implementation of a new subsystem that will provide vision services on the IHM (Integrated Health Management) bus. The functionality I added to KATE over the past few months includes a dynamic visual representation of the fluid height in a pipe based on number of gallons of fluid in the pipe and implementing the IHM bus connection within KATE. I also fixed a broken feature in the system called the Browser Display, implemented many bug fixes and made changes to the GUI (Graphical User Interface).

  5. Analysis of JC virus DNA replication using a quantitative and high-throughput assay

    International Nuclear Information System (INIS)

    Progressive Multifocal Leukoencephalopathy (PML) is caused by lytic replication of JC virus (JCV) in specific cells of the central nervous system. Like other polyomaviruses, JCV encodes a large T-antigen helicase needed for replication of the viral DNA. Here, we report the development of a luciferase-based, quantitative and high-throughput assay of JCV DNA replication in C33A cells, which, unlike the glial cell lines Hs 683 and U87, accumulate high levels of nuclear T-ag needed for robust replication. Using this assay, we investigated the requirement for different domains of T-ag, and for specific sequences within and flanking the viral origin, in JCV DNA replication. Beyond providing validation of the assay, these studies revealed an important stimulatory role of the transcription factor NF1 in JCV DNA replication. Finally, we show that the assay can be used for inhibitor testing, highlighting its value for the identification of antiviral drugs targeting JCV DNA replication. - Highlights: • Development of a high-throughput screening assay for JCV DNA replication using C33A cells. • Evidence that T-ag fails to accumulate in the nuclei of established glioma cell lines. • Evidence that NF-1 directly promotes JCV DNA replication in C33A cells. • Proof-of-concept that the HTS assay can be used to identify pharmacological inhibitor of JCV DNA replication

  6. Analysis of JC virus DNA replication using a quantitative and high-throughput assay

    Energy Technology Data Exchange (ETDEWEB)

    Shin, Jong; Phelan, Paul J.; Chhum, Panharith; Bashkenova, Nazym; Yim, Sung; Parker, Robert [Department of Developmental, Molecular and Chemical Biology, Tufts University School of Medicine, Boston, MA 02111 (United States); Gagnon, David [Institut de Recherches Cliniques de Montreal (IRCM), 110 Pine Avenue West, Montreal, Quebec, Canada H2W 1R7 (Canada); Department of Biochemistry and Molecular Medicine, Université de Montréal, Montréal, Quebec (Canada); Gjoerup, Ole [Molecular Oncology Research Institute, Tufts Medical Center, Boston, MA 02111 (United States); Archambault, Jacques [Institut de Recherches Cliniques de Montreal (IRCM), 110 Pine Avenue West, Montreal, Quebec, Canada H2W 1R7 (Canada); Department of Biochemistry and Molecular Medicine, Université de Montréal, Montréal, Quebec (Canada); Bullock, Peter A., E-mail: Peter.Bullock@tufts.edu [Department of Developmental, Molecular and Chemical Biology, Tufts University School of Medicine, Boston, MA 02111 (United States)

    2014-11-15

    Progressive Multifocal Leukoencephalopathy (PML) is caused by lytic replication of JC virus (JCV) in specific cells of the central nervous system. Like other polyomaviruses, JCV encodes a large T-antigen helicase needed for replication of the viral DNA. Here, we report the development of a luciferase-based, quantitative and high-throughput assay of JCV DNA replication in C33A cells, which, unlike the glial cell lines Hs 683 and U87, accumulate high levels of nuclear T-ag needed for robust replication. Using this assay, we investigated the requirement for different domains of T-ag, and for specific sequences within and flanking the viral origin, in JCV DNA replication. Beyond providing validation of the assay, these studies revealed an important stimulatory role of the transcription factor NF1 in JCV DNA replication. Finally, we show that the assay can be used for inhibitor testing, highlighting its value for the identification of antiviral drugs targeting JCV DNA replication. - Highlights: • Development of a high-throughput screening assay for JCV DNA replication using C33A cells. • Evidence that T-ag fails to accumulate in the nuclei of established glioma cell lines. • Evidence that NF-1 directly promotes JCV DNA replication in C33A cells. • Proof-of-concept that the HTS assay can be used to identify pharmacological inhibitor of JCV DNA replication.

  7. Morphologic Changes in Autonomic Nerves in Diabetic Autonomic Neuropathy

    Directory of Open Access Journals (Sweden)

    Heung Yong Jin

    2015-12-01

    Full Text Available Diabetic neuropathy is one of the major complications of diabetes, and it increases morbidity and mortality in patients with both type 1 diabetes mellitus (T1DM and type 2 diabetes mellitus (T2DM. Because the autonomic nervous system, for example, parasympathetic axons, has a diffuse and wide distribution, we do not know the morphological changes that occur in autonomic neural control and their exact mechanisms in diabetic patients with diabetic autonomic neuropathy (DAN. Although the prevalence of sympathetic and parasympathetic neuropathy is similar in T1DM versus T2DM patients, sympathetic nerve function correlates with parasympathetic neuropathy only in T1DM patients. The explanation for these discrepancies might be that parasympathetic nerve function was more severely affected among T2DM patients. As parasympathetic nerve damage seems to be more advanced than sympathetic nerve damage, it might be that parasympathetic neuropathy precedes sympathetic neuropathy in T2DM, which was Ewing's concept. This could be explained by the intrinsic morphologic difference. Therefore, the morphological changes in the sympathetic and parasympathetic nerves of involved organs in T1DM and T2DM patients who have DAN should be evaluated. In this review, evaluation methods for morphological changes in the epidermal nerves of skin, and the intrinsic nerves of the stomach will be discussed.

  8. Hyperthermia stimulates HIV-1 replication.

    OpenAIRE

    Ferdinand Roesch; Oussama Meziane; Anna Kula; Sébastien Nisole; Françoise Porrot; Ian Anderson; Fabrizio Mammano; Ariberto Fassati; Alessandro Marcello; Monsef Benkirane; Olivier Schwartz

    2012-01-01

    International audience HIV-infected individuals may experience fever episodes. Fever is an elevation of the body temperature accompanied by inflammation. It is usually beneficial for the host through enhancement of immunological defenses. In cultures, transient non-physiological heat shock (42-45°C) and Heat Shock Proteins (HSPs) modulate HIV-1 replication, through poorly defined mechanisms. The effect of physiological hyperthermia (38-40°C) on HIV-1 infection has not been extensively inve...

  9. Cardiac autonomic nerve distribution and arrhythmia

    Institute of Scientific and Technical Information of China (English)

    Quan Liu; Dongmei Chen; Yonggang Wang; Xin Zhao; Yang Zheng

    2012-01-01

    OBJECTIVE: To analyze the distribution characteristics of cardiac autonomic nerves and to explore the correlation between cardiac autonomic nerve distribution and arrhythmia.DATA RETRIEVAL: A computer-based retrieval was performed for papers examining the distribution of cardiac autonomic nerves, using "heart, autonomic nerve, sympathetic nerve, vagus nerve, nerve distribution, rhythm and atrial fibrillation" as the key words.SELECTION CRITERIA: A total of 165 studies examining the distribution of cardiac autonomic nerve were screened, and 46 of them were eventually included.MAIN OUTCOME MEASURES: The distribution and characteristics of cardiac autonomic nerves were observed, and immunohistochemical staining was applied to determine the levels of tyrosine hydroxylase and acetylcholine transferase (main markers of cardiac autonomic nerve distribution). In addition, the correlation between cardiac autonomic nerve distribution and cardiac arrhythmia was investigated.RESULTS: Cardiac autonomic nerves were reported to exhibit a disordered distribution in different sites, mainly at the surface of the cardiac atrium and pulmonary vein, forming a ganglia plexus. The distribution of the pulmonary vein autonomic nerve was prominent at the proximal end rather than the distal end, at the upper left rather than the lower right, at the epicardial membrane rather than the endocardial membrane, at the left atrium rather than the right atrium, and at the posterior wall rather than the anterior wall. The main markers used for cardiac autonomic nerves were tyrosine hydroxylase and acetylcholine transferase. Protein gene product 9.5 was used to label the immunoreactive nerve distribution, and the distribution density of autonomic nerves was determined using a computer-aided morphometric analysis system.CONCLUSION: The uneven distribution of the cardiac autonomic nerves is the leading cause of the occurrence of arrhythmia, and the cardiac autonomic nerves play an important role in the

  10. Dynamic replication of Web contents

    Institute of Scientific and Technical Information of China (English)

    2007-01-01

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

  11. An Autonomously Reciprocating Transmembrane Nanoactuator.

    Science.gov (United States)

    Watson, Matthew A; Cockroft, Scott L

    2016-01-22

    Biological molecular machines operate far from equilibrium by coupling chemical potential to repeated cycles of dissipative nanomechanical motion. This principle has been exploited in supramolecular systems that exhibit true machine behavior in solution and on surfaces. However, designed membrane-spanning assemblies developed to date have been limited to simple switches or stochastic shuttles, and true machine behavior has remained elusive. Herein, we present a transmembrane nanoactuator that turns over chemical fuel to drive autonomous reciprocating (back-and-forth) nanomechanical motion. Ratcheted reciprocating motion of a DNA/PEG copolymer threaded through a single α-hemolysin pore was induced by a combination of DNA strand displacement processes and enzyme-catalyzed reactions. Ion-current recordings revealed saw-tooth patterns, indicating that the assemblies operated in autonomous, asymmetric cycles of conformational change at rates of up to one cycle per minute. PMID:26661295

  12. Cardiovascular autonomic neuropathy in diabetes

    DEFF Research Database (Denmark)

    Spallone, Vincenza; Ziegler, Dan; Freeman, Roy;

    2011-01-01

    Cardiovascular Autonomic Neuropathy (CAN) Subcommittee of Toronto Consensus Panel on Diabetic Neuropathy worked to update CAN guidelines, with regard to epidemiology, clinical impact, diagnosis, usefulness of CAN testing, and management. CAN is the impairment of cardiovascular autonomic control...... in the setting of diabetes after exclusion of other causes. The prevalence of confirmed CAN is around 20%, and increases up to 65% with age and diabetes duration. Established risk factors for CAN are glycaemic control in type 1 and a combination of hypertension, dyslipidemia, obesity and glycaemic control...... in type 2 diabetes. CAN is a risk marker of mortality and cardiovascular morbidity, and possibly a progression promoter of diabetic nephropathy. Criteria for CAN diagnosis and staging are: 1. one abnormal cardio-vagal test identifies possible or early CAN; 2. at least two abnormal cardio-vagal tests...

  13. Treatment of gastrointestinal autonomic neuropathy.

    Science.gov (United States)

    Törnblom, Hans

    2016-03-01

    The symptoms caused by gastrointestinal autonomic neuropathy in diabetes mellitus is important to highlight since it affects a large proportion of people with diabetes, regardless of whether this is type 1 or type 2. Gastroparesis and general signs of bowel dysfunction, such as constipation, diarrhoea and abdominal pain are most often encountered and involve both pharmacological and non-pharmacological treatment options. This mini-review summarises a presentation given at the 'Diagnosis and treatment of autonomic diabetic neuropathy in the gut' symposium at the 2015 annual meeting of the EASD. It is accompanied by another mini-review on a topic from this symposium (by Azpiroz and Malagelada, DOI: 10.1007/s00125-015-3831-1 ) and a commentary by the Session Chair, Péter Kempler (DOI: 10.1007/s00125-015-3826-y ). PMID:26634570

  14. Insurance for autonomous underwater vehicles

    OpenAIRE

    Griffiths, G; N Bose; Ferguson, J.; Blidberg, D.R.

    2007-01-01

    The background and practice of insurance for autonomous underwater vehicles (AUVs) are examined. Key topics include: relationships between clients, brokers and underwriters; contract wording to provide appropriate coverage; and actions to take when an incident occurs. Factors that affect cost of insurance are discussed, including level of autonomy, team experience and operating environment. Four case studies from industry and academia illustrate how AUV insurance has worked in practice. The p...

  15. Prototype design for autonomous vehicle

    OpenAIRE

    Lehander, Jacob; Persson, Joel

    2015-01-01

    This thesis describes the mechanical design of a prototype vehicle developed for a company located in California. The project was based on an earlier vehicle located at KTH, Transport Labs, and investigated if the existing concept for the vehicle would work as a concept for an autonomous prototype, with focus on component layout and increased forces. The design of the vehicle is based on a concept with a carbon fiber bottom plate, two separate suspension modules with electric hub motors and s...

  16. [Autonomic nervous system in diabetes].

    Science.gov (United States)

    Emdin, M

    2001-08-01

    Hyperglycemia and hyperinsulinemia have a primary role in determining the early functional and later anatomic changes at the level of the autonomic pathways controlling the circulation, and besides in directly influencing cardiac and vascular cellular targets and feed-back baroreceptor system sensitivity to neurohumoral modulation in patients with diabetes mellitus. The basic mechanisms of dysfunction and damage, and the clinical and prognostic value of diabetic cardiovascular dysautonomia are discussed together with the diagnostic apparatus and the possible therapeutic approaches.

  17. Design of Autonomous Underwater Vehicle

    OpenAIRE

    Tadahiro Hyakudome

    2011-01-01

    There are concerns about the impact that global warming will have on our environment, and which will inevitably result in expanding deserts and rising water levels. While a lot of underwater vehicles are utilized, AUVs (Autonomous Underwater Vehicle) were considered and chosen, as the most suitable tool for conduction survey concerning these global environmental problems. AUVs can comprehensive survey because the vehicle does not have to be connected to the support vessel by tether cable. Whe...

  18. Learning Objects and Grasp Affordances through Autonomous Exploration

    DEFF Research Database (Denmark)

    Kraft, Dirk; Detry, Renaud; Pugeault, Nicolas;

    2009-01-01

    We describe a system for autonomous learning of visual object representations and their grasp affordances on a robot-vision system. It segments objects by grasping and moving 3D scene features, and creates probabilistic visual representations for object detection, recognition and pose estimation......, which are then augmented by continuous characterizations of grasp affordances generated through biased, random exploration. Thus, based on a careful balance of generic prior knowledge encoded in (1) the embodiment of the system, (2) a vision system extracting structurally rich information from stereo...... image sequences as well as (3) a number of built-in behavioral modules on the one hand, and autonomous exploration on the other hand, the system is able to generate object and grasping knowledge through interaction with its environment....

  19. Semi autonomous mine detection system

    Energy Technology Data Exchange (ETDEWEB)

    Douglas Few; Roelof Versteeg; Herman Herman

    2010-04-01

    CMMAD is a risk reduction effort for the AMDS program. As part of CMMAD, multiple instances of semi autonomous robotic mine detection systems were created. Each instance consists of a robotic vehicle equipped with sensors required for navigation and marking, a countermine sensors and a number of integrated software packages which provide for real time processing of the countermine sensor data as well as integrated control of the robotic vehicle, the sensor actuator and the sensor. These systems were used to investigate critical interest functions (CIF) related to countermine robotic systems. To address the autonomy CIF, the INL developed RIK was extended to allow for interaction with a mine sensor processing code (MSPC). In limited field testing this system performed well in detecting, marking and avoiding both AT and AP mines. Based on the results of the CMMAD investigation we conclude that autonomous robotic mine detection is feasible. In addition, CMMAD contributed critical technical advances with regard to sensing, data processing and sensor manipulation, which will advance the performance of future fieldable systems. As a result, no substantial technical barriers exist which preclude – from an autonomous robotic perspective – the rapid development and deployment of fieldable systems.

  20. Autonomic neuropathy in diabetes mellitus

    Directory of Open Access Journals (Sweden)

    Alberto eVerrotti

    2014-12-01

    Full Text Available Diabetic autonomic neuropathy (DAN is a serious and common complication of diabetes, often overlooked and misdiagnosed. It is a systemic-wide disorder that may be asymptomatic in the early stages. The most studied and clinically important form of DAN is cardiovascular autonomic neuropathy (CAN defined as the impairment of autonomic control of the cardiovascular system in patients with diabetes after exclusion of other causes. The reported prevalence of DAN varies widely depending on inconsistent definition, different diagnostic method, different patient cohorts studied. The pathogenesis is still unclear and probably multifactorial. Once DAN becomes clinically evident, no form of therapy has been identified which can effectively stop or reverse it. Prevention strategies are based on strict glycemic control with intensive insulin treatment, multifactorial intervention and lifestyle modification including control of hypertension, dyslipidemia, stop smoking, weight loss and adequate physical exercise. The present review summarizes the latest knowledge regarding clinical presentation, epidemiology, pathogenesis and management of DAN, with some mention to childhood and adolescent population.

  1. Evaluating replicability of laboratory experiments in economics.

    Science.gov (United States)

    Camerer, Colin F; Dreber, Anna; Forsell, Eskil; Ho, Teck-Hua; Huber, Jürgen; Johannesson, Magnus; Kirchler, Michael; Almenberg, Johan; Altmejd, Adam; Chan, Taizan; Heikensten, Emma; Holzmeister, Felix; Imai, Taisuke; Isaksson, Siri; Nave, Gideon; Pfeiffer, Thomas; Razen, Michael; Wu, Hang

    2016-03-25

    The replicability of some scientific findings has recently been called into question. To contribute data about replicability in economics, we replicated 18 studies published in the American Economic Review and the Quarterly Journal of Economics between 2011 and 2014. All of these replications followed predefined analysis plans that were made publicly available beforehand, and they all have a statistical power of at least 90% to detect the original effect size at the 5% significance level. We found a significant effect in the same direction as in the original study for 11 replications (61%); on average, the replicated effect size is 66% of the original. The replicability rate varies between 67% and 78% for four additional replicability indicators, including a prediction market measure of peer beliefs. PMID:26940865

  2. Replication of micro and nano surface geometries

    DEFF Research Database (Denmark)

    Hansen, Hans Nørgaard; Hocken, R.J.; Tosello, Guido

    2011-01-01

    The paper describes the state-of-the-art in replication of surface texture and topography at micro and nano scale. The description includes replication of surfaces in polymers, metals and glass. Three different main technological areas enabled by surface replication processes are presented......: manufacture of net-shape micro/nano surfaces, tooling (i.e. master making), and surface quality control (metrology, inspection). Replication processes and methods as well as the metrology of surfaces to determine the degree of replication are presented and classified. Examples from various application areas...... are given including replication for surface texture measurements, surface roughness standards, manufacture of micro and nano structured functional surfaces, replicated surfaces for optical applications (e.g. optical gratings), and process chains based on combinations of repeated surface replication steps....

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

    Energy Technology Data Exchange (ETDEWEB)

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

    1988-05-01

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

  4. Possible applications for replicating HIV 1 vectors

    OpenAIRE

    Das, Atze T.; Jeeninga, Rienk E.; Berkhout, Ben

    2010-01-01

    Since its discovery some 25 years ago, much has been learned about HIV type 1 and the molecular details of its replication cycle. This insight has been used to develop lentiviral vector systems that have advantages over conventional retroviral vector systems. For safety reasons, the lentiviral vector systems are replication incompetent and the risk of generating a replication competent virus has been minimized. Nevertheless, there may be certain applications for replication competent HIV base...

  5. DNA Replication Reaches the Breaking Point

    OpenAIRE

    Petrini, John H.J.

    2009-01-01

    DNA strand breaks that result in stalled or damaged replication forks can be detrimental to the DNA replication process. In this issue, Doksani et al. (2009) examine the impact of a single double-stranded DNA break on replication in the budding yeast, Saccharomyces cerevisiae.

  6. Exploiting replicative stress to treat cancer

    DEFF Research Database (Denmark)

    Dobbelstein, Matthias; Sørensen, Claus Storgaard

    2015-01-01

    DNA replication in cancer cells is accompanied by stalling and collapse of the replication fork and signalling in response to DNA damage and/or premature mitosis; these processes are collectively known as 'replicative stress'. Progress is being made to increase our understanding of the mechanisms...

  7. Chromosome banding and DNA replication patterns in bird karyotypes.

    Science.gov (United States)

    Schmid, M; Enderle, E; Schindler, D; Schempp, W

    1989-01-01

    The karyotypes of the domestic chicken (Gallus domesticus), Japanese quail (Coturnix coturnix), and griffon vulture (Gyps fulvus) were studied with a variety of banding techniques. The DNA replication patterns of bird chromosomes, analyzed by incorporation of 5-bromodeoxyuridine (BrdU) and deoxythymidine (dT), are presented here for the first time. In particular, the time sequence of replication of the ZZ/ZW sex chromosomes throughout the S-phase was meticulously analyzed. BrdU and dT incorporation are very useful methods to identify homoeologies between karyotypes, as well as rearrangements that occurred in the macroautosomes during speciation. The Z chromosomes of the three birds displayed the same replication patterns, indicating a high degree of evolutionary conservation. In the homogametic male, BrdU and dT incorporation revealed no evidence of asynchronous replication between euchromatic bands in the ZZ pair. The same was true of the three Z chromosomes in a triploid-diploid chimeric chicken embryo. Minor replication asynchronies between the homologous ZZ or ZZZ chromosomes were restricted to heterochromatic C-bands. These results confirm that, in the ZZ male/ZW female sex-determining system of birds, dosage compensation for Z-linked genes does not occur by inactivation of one of the two Z chromosomes in the homogametic male. The heterochromatic W chromosomes of the three species showed bright labeling with distamycin A/mithramycin counterstain-enhanced fluorescence and exhibited significantly delayed DNA replication. The nucleolus organizers of birds, frequently located in microchromosomes, were also distinguished by bright distamycin A/mithramycin fluorescence. PMID:2630186

  8. Lipid Membranes in Poxvirus Replication

    Directory of Open Access Journals (Sweden)

    Jason P. Laliberte

    2010-04-01

    Full Text Available Poxviruses replicate in the cytoplasm, where they acquire multiple lipoprotein membranes. Although a proposal that the initial membrane arises de novo has not been substantiated, there is no accepted explanation for its formation from cellular membranes. A subsequent membrane-wrapping step involving modified trans-Golgi or endosomal cisternae results in a particle with three membranes. These wrapped virions traverse the cytoplasm on microtubules; the outermost membrane is lost during exocytosis, the middle one is lost just prior to cell entry, and the remaining membrane fuses with the cell to allow the virus core to enter the cytoplasm and initiate a new infection.

  9. Assessment of the Role of the Central DNA Flap in Human Immunodeficiency Virus Type 1 Replication by Using a Single-Cycle Replication System

    OpenAIRE

    Ao, Zhujun; Yao, Xiaojian; Éric A Cohen

    2004-01-01

    In this study, reverse transcriptase (RT)- and integrase (IN)-defective human immunodeficiency virus type 1 (HIV-1) was transcomplemented with Vpr-RT-IN fusion proteins to delineate pol sequences important for HIV-1 replication. Our results reveal that a 194-bp sequence encompassing the 3′end of the IN gene and containing the central DNA flap is necessary and sufficient for efficient HIV-1 single-cycle replication in dividing and nondividing cells. Furthermore, we show that the central DNA fl...

  10. Autonomic Management for Multi-agent Systems

    OpenAIRE

    Nadir kamal Salih; G. K. Viju; Mohamed, Abdelmotalib A.

    2011-01-01

    Autonomic computing is a computing system that can manage itself by self-configuration, self-healing, self-optimizing and self-protection. Researchers have been emphasizing the strong role that multi agent systems can play progressively towards the design and implementation of complex autonomic systems. The important of autonomic computing is to create computing systems capable of managing themselves to a far greater extent than they do today. With the nature of autonomy, reactivity, socialit...

  11. Gastrointestinal autonomic nerve tumor of the stomach

    OpenAIRE

    Meshikhes, Abdul-Wahed N.; Al-Garni, Ayed A.; Sami A Al-Momen; Al-Nahawi, Mamdouh; Abu Subaih, Jawad

    2014-01-01

    Patient: Female, 32 Final Diagnosis: Gastrintestinal Autonomic Nerve Tumor (GANT) Symptoms: anemia • anorexia • fatigue • fever • hearburn • nausea • weight loss Medication: — Clinical Procedure: — Specialty: Gastroenterology and Hepatology Objective: Rare disease Background: Gastrointestinal autonomic nerve tumors (GANT) are extremely rare tumors that are related to gastrointestinal autonomic nervous plexuses. They are distinguished from stromal tumors by their unique ultrastructural feature...

  12. Autonomic dysfunction in cirrhosis and portal hypertension

    DEFF Research Database (Denmark)

    Dümcke, Christine Winkler; Møller, Søren

    2008-01-01

    Liver cirrhosis and portal hypertension are frequently associated with signs of circulatory dysfunction and peripheral polyneuropathy, which includes defects of the autonomic nervous system. Autonomic dysfunction, which is seen in both alcoholic and non-alcoholic liver cirrhosis and increases wit...... liver disease. A description is given of its aetiology and the typical circulatory dysfunction with characteristic hyperdynamic and hyporeactive circulation and heart failure, and the most important tests of the autonomic nervous system....

  13. Test and Evaluation of Autonomous Ground Vehicles

    OpenAIRE

    Yang Sun; Guangming Xiong; Weilong Song; Jianwei Gong; Huiyan Chen

    2014-01-01

    A preestablished test and evaluation system will benefit the development of autonomous ground vehicles. This paper proposes a design method for a scientific and comprehensive test and evaluation system for autonomous ground vehicles competitions. It can better guide and regulate the development of China’s autonomous ground vehicles. The test and evaluation system includes the test contents, the test environment, the test methods, and the evaluation methods. Using a hierarchical design approac...

  14. Autonomous vehicle control systems for safe crossroads

    OpenAIRE

    Alonso Ruiz, Javier; Milanés Montero, Vicente; Pérez, Joshué; Onieva Caracuel, Enrique; González Fernández-Vallejo, Carlos; Pedro Lucio, María Teresa de

    2011-01-01

    This article presents a cooperative manoeuvre among three dual mode cars – vehicles equipped with sensors and actuators, and that can be driven either manually or autonomously. One vehicle is driven autonomously and the other two are driven manually. The main objective is to test two decision algorithms for priority conflict resolution at intersections so that a vehicle autonomously driven can take their own decision about crossing an intersection mingling with manually driven cars without th...

  15. Self-Adapting Reactive Autonomous Agents

    Science.gov (United States)

    Andrecut, M.; Ali, M. K.

    This paper describes a new self-adapting control algorithm for reactive autonomous agents. The architecture of the autonomous agents integrates the reactive behavior with reinforcement learning. We show how these components perform on-line adaptation of the autonomous agents to various complex navigation situations by constructing an internal model of the environment. Also, a discussion on cooperation and coordination of teams of agents is presented.

  16. Attainability of Carnot efficiency with autonomous engines

    Science.gov (United States)

    Shiraishi, Naoto

    2015-11-01

    The maximum efficiency of autonomous engines with a finite chemical potential difference is investigated. We show that, without a particular type of singularity, autonomous engines cannot attain the Carnot efficiency. This singularity is realized in two ways: single particle transports and the thermodynamic limit. We demonstrate that both of these ways actually lead to the Carnot efficiency in concrete setups. Our results clearly illustrate that the singularity plays a crucial role in the maximum efficiency of autonomous engines.

  17. Attainability of Carnot efficiency with autonomous engines.

    Science.gov (United States)

    Shiraishi, Naoto

    2015-11-01

    The maximum efficiency of autonomous engines with a finite chemical potential difference is investigated. We show that, without a particular type of singularity, autonomous engines cannot attain the Carnot efficiency. This singularity is realized in two ways: single particle transports and the thermodynamic limit. We demonstrate that both of these ways actually lead to the Carnot efficiency in concrete setups. Our results clearly illustrate that the singularity plays a crucial role in the maximum efficiency of autonomous engines.

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

    Directory of Open Access Journals (Sweden)

    Jared M Peace

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

  19. Information for Successful Interaction with Autonomous Systems

    Science.gov (United States)

    Malin, Jane T.; Johnson, Kathy A.

    2003-01-01

    Interaction in heterogeneous mission operations teams is not well matched to classical models of coordination with autonomous systems. We describe methods of loose coordination and information management in mission operations. We describe an information agent and information management tool suite for managing information from many sources, including autonomous agents. We present an integrated model of levels of complexity of agent and human behavior, which shows types of information processing and points of potential error in agent activities. We discuss the types of information needed for diagnosing problems and planning interactions with an autonomous system. We discuss types of coordination for which designs are needed for autonomous system functions.

  20. Design of a Miniature Autonomous Surveillance Robot

    Institute of Scientific and Technical Information of China (English)

    ZHENG Chang-e; HUANG Qiang; HUANG Yuan-can

    2009-01-01

    The small size of miniature robots poses great challenges for the mechanical and deetrieal design and the implementation of autonomous capabilities.In this paper,the mechanical and electrical design for a twowheeled cylindrical miniature autonomous robot ("BMS-1",BIT MicroScout-1) is presented and some autonomous capabilities are implemented by multiple sensors and some arithmetic models.Several experimental results show that BMS-1 is useful for surveillance in confined spaces and suitable for large-scale surveillance due to some autonomous capabilities.

  1. Autonomic dysfunction in primary sleep disorders.

    Science.gov (United States)

    Miglis, Mitchell G

    2016-03-01

    The autonomic nervous system plays an important role in the coordination of many important physiologic functions during sleep. Many patients with untreated sleep disorders will describe symptoms of autonomic impairment, and a majority of patients with autonomic impairment have some form of sleep disorder. This article will explore possible explanations for this connection, as well as review the current literature on autonomic impairment in common primary sleep disorders including obstructive sleep apnea, insomnia, restless legs syndrome, periodic limb movement disorder, narcolepsy, and rapid eye movement sleep behavior disorder. PMID:27198946

  2. A necessary and sufficient condition for transforming autonomous systems into linear autonomous Birkhoffian systems

    International Nuclear Information System (INIS)

    The problem of transforming autonomous systems into Birkhoffian systems is studied. A reasonable form of linear autonomous Birkhoff equations is given. By combining them with the undetermined tensor method, a necessary and sufficient condition for an autonomous system to have a representation in terms of linear autonomous Birkhoff equations is obtained. The methods of constructing Birkhoffian dynamical functions are given. Two examples are given to illustrate the application of the results. (electromagnetism, optics, acoustics, heat transfer, classical mechanics, and fluid dynamics)

  3. Knowledge acquisition for autonomous systems

    Science.gov (United States)

    Lum, Henry; Heer, Ewald

    1988-01-01

    Knowledge-based capabilities for autonomous aerospace systems, such as the NASA Space Station, must encompass conflict-resolution functions comparable to those of human operators, with all elements of the system working toward system goals in a concurrent, asynchronous-but-coordinated fashion. Knowledge extracted from a design database will support robotic systems by furnishing geometric, structural, and causal descriptions required for repair, disassembly, and assembly. The factual knowledge for these databases will be obtained from a master database through a technical management information system, and it will in many cases have to be augmented by domain-specific heuristic knowledge acquired from domain experts.

  4. Autonomous sensor manager agents (ASMA)

    Science.gov (United States)

    Osadciw, Lisa A.

    2004-04-01

    Autonomous sensor manager agents are presented as an algorithm to perform sensor management within a multisensor fusion network. The design of the hybrid ant system/particle swarm agents is described in detail with some insight into their performance. Although the algorithm is designed for the general sensor management problem, a simulation example involving 2 radar systems is presented. Algorithmic parameters are determined by the size of the region covered by the sensor network, the number of sensors, and the number of parameters to be selected. With straight forward modifications, this algorithm can be adapted for most sensor management problems.

  5. Autonomous Dome for Robotic Telescope

    CERN Document Server

    Kumar, Akash; Ganesh, Shashikiran

    2016-01-01

    Physical Research Laboratory operates a 50cm robotic observatory at Mount Abu. This Automated Telescope for Variability Studies (ATVS) makes use of Remote Telescope System 2 (RTS2) for autonomous operations. The observatory uses a 3.5m dome from Sirius Observatories. We have developed electronics using Arduino electronic circuit boards with home grown logic and software to control the dome operations. We are in the process of completing the drivers to link our Arduino based dome controller with RTS2. This document is a short description of the various phases of the development and their integration to achieve the required objective.

  6. Topological entropy of autonomous flows

    Energy Technology Data Exchange (ETDEWEB)

    Badii, R. [Paul Scherrer Inst. (PSI), Villigen (Switzerland)

    1997-06-01

    When studying fluid dynamics, especially in a turbulent regime, it is crucial to estimate the number of active degrees of freedom or of localized structures in the system. The topological entropy quantifies the exponential growth of the number of `distinct` orbits in a dynamical system as a function of their length, in the infinite spatial resolution limit. Here, I illustrate a novel method for its evaluation, which extends beyond maps and is applicable to any system, including autonomous flows: these are characterized by lack of a definite absolute time scale for the orbit lengths. (author) 8 refs.

  7. The Autonomous Pathogen Detection System

    Energy Technology Data Exchange (ETDEWEB)

    Dzenitis, J M; Makarewicz, A J

    2009-01-13

    We developed, tested, and now operate a civilian biological defense capability that continuously monitors the air for biological threat agents. The Autonomous Pathogen Detection System (APDS) collects, prepares, reads, analyzes, and reports results of multiplexed immunoassays and multiplexed PCR assays using Luminex{copyright} xMAP technology and flow cytometer. The mission we conduct is particularly demanding: continuous monitoring, multiple threat agents, high sensitivity, challenging environments, and ultimately extremely low false positive rates. Here, we introduce the mission requirements and metrics, show the system engineering and analysis framework, and describe the progress to date including early development and current status.

  8. Evolution of DNA replication protein complexes in eukaryotes and Archaea.

    Directory of Open Access Journals (Sweden)

    Nicholas Chia

    Full Text Available BACKGROUND: The replication of DNA in Archaea and eukaryotes requires several ancillary complexes, including proliferating cell nuclear antigen (PCNA, replication factor C (RFC, and the minichromosome maintenance (MCM complex. Bacterial DNA replication utilizes comparable proteins, but these are distantly related phylogenetically to their archaeal and eukaryotic counterparts at best. METHODOLOGY/PRINCIPAL FINDINGS: While the structures of each of the complexes do not differ significantly between the archaeal and eukaryotic versions thereof, the evolutionary dynamic in the two cases does. The number of subunits in each complex is constant across all taxa. However, they vary subtly with regard to composition. In some taxa the subunits are all identical in sequence, while in others some are homologous rather than identical. In the case of eukaryotes, there is no phylogenetic variation in the makeup of each complex-all appear to derive from a common eukaryotic ancestor. This is not the case in Archaea, where the relationship between the subunits within each complex varies taxon-to-taxon. We have performed a detailed phylogenetic analysis of these relationships in order to better understand the gene duplications and divergences that gave rise to the homologous subunits in Archaea. CONCLUSION/SIGNIFICANCE: This domain level difference in evolution suggests that different forces have driven the evolution of DNA replication proteins in each of these two domains. In addition, the phylogenies of all three gene families support the distinctiveness of the proposed archaeal phylum Thaumarchaeota.

  9. Structure and Dynamics of Replication-Mutation Systems

    Science.gov (United States)

    Schuster, Peter

    1987-03-01

    The kinetic equations of polynucleotide replication can be brought into fairly simple form provided certain environmental conditions are fulfilled. Two flow reactors, the continuously stirred tank reactor (CSTR) and a special dialysis reactor are particularly suitable for the analysis of replication kinetics. An experimental setup to study the chemical reaction network of RNA synthesis was derived from the bacteriophage Qβ. It consists of a virus specific RNA polymerase, Qβ replicase, the activated ribonucleosides GTP, ATP, CTP and UTP as well as a template suitable for replication. The ordinary differential equations for replication and mutation under the conditions of the flow reactors were analysed by the qualitative methods of bifurcation theory as well as by numerical integration. The various kinetic equations are classified according to their dynamical properties: we distinguish "quasilinear systems" which have uniquely stable point attractors and "nonlinear systems" with inherent nonlinearities which lead to multiple steady states, Hopf bifuractions, Feigenbaum-like sequences and chaotic dynamics for certain parameter ranges. Some examples which are relevant in molecular evolution and population genetics are discussed in detail.

  10. Genome-wide studies highlight indirect links between human replication origins and gene regulation.

    Science.gov (United States)

    Cadoret, Jean-Charles; Meisch, Françoise; Hassan-Zadeh, Vahideh; Luyten, Isabelle; Guillet, Claire; Duret, Laurent; Quesneville, Hadi; Prioleau, Marie-Noëlle

    2008-10-14

    To get insights into the regulation of replication initiation, we systematically mapped replication origins along 1% of the human genome in HeLa cells. We identified 283 origins, 10 times more than previously known. Origin density is strongly correlated with genomic landscapes, with clusters of closely spaced origins in GC-rich regions and no origins in large GC-poor regions. Origin sequences are evolutionarily conserved, and half of them map within or near CpG islands. Most of the origins overlap transcriptional regulatory elements, providing further evidence of a connection with gene regulation. Moreover, we identify c-JUN and c-FOS as important regulators of origin selection. Half of the identified replication initiation sites do not have an open chromatin configuration, showing the absence of a direct link with gene regulation. Replication timing analyses coupled with our origin mapping suggest that a relatively strict origin-timing program regulates the replication of the human genome.

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

    Directory of Open Access Journals (Sweden)

    Amnon Koren

    2010-08-01

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

  12. Automated Search-Based Robustness Testing for Autonomous Vehicle Software

    Directory of Open Access Journals (Sweden)

    Kevin M. Betts

    2016-01-01

    Full Text Available Autonomous systems must successfully operate in complex time-varying spatial environments even when dealing with system faults that may occur during a mission. Consequently, evaluating the robustness, or ability to operate correctly under unexpected conditions, of autonomous vehicle control software is an increasingly important issue in software testing. New methods to automatically generate test cases for robustness testing of autonomous vehicle control software in closed-loop simulation are needed. Search-based testing techniques were used to automatically generate test cases, consisting of initial conditions and fault sequences, intended to challenge the control software more than test cases generated using current methods. Two different search-based testing methods, genetic algorithms and surrogate-based optimization, were used to generate test cases for a simulated unmanned aerial vehicle attempting to fly through an entryway. The effectiveness of the search-based methods in generating challenging test cases was compared to both a truth reference (full combinatorial testing and the method most commonly used today (Monte Carlo testing. The search-based testing techniques demonstrated better performance than Monte Carlo testing for both of the test case generation performance metrics: (1 finding the single most challenging test case and (2 finding the set of fifty test cases with the highest mean degree of challenge.

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

    Directory of Open Access Journals (Sweden)

    Nicolas M Berbenetz

    2010-09-01

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

  14. Tracing the Origin of the Black-spotted Frog, Pelophylax nigromaculatus, in the Xinjiang Uyghur Autonomous Region

    Institute of Scientific and Technical Information of China (English)

    Supen WANG; Conghui LIU; Wei ZHU; Xu GAO; Yiming LI

    2016-01-01

    Identifying the origin of a biological invasion is critical for controlling the invaders. To explore the genetic diversity and identify the source region of introductions of Pelophylax nigromaculatus to the Xinjiang Uyghur Autonomous Region, we sequenced 695 bp of the mitochondrial Cyt b gene in 140 individuals of P. nigromaculatus and identified 42 haplotypes in Heilongjiang, Beijing, Jiangsu, Shaanxi, Zhejiang provinces, Chongqing and the Xinjiang Uyghur Autonomous Region. We detected only four mitochondrial haplotypes in 20 specimens from Yining city in Ili Kazak Autonomous Prefecture. We traced the origin of Yining P. nigromaculatus to the Beijing and Chongqing area. Our results extend the known distribution range of this species in Asia.

  15. Self-replication of DNA rings

    Science.gov (United States)

    Kim, Junghoon; Lee, Junwye; Hamada, Shogo; Murata, Satoshi; Ha Park, Sung

    2015-06-01

    Biology provides numerous examples of self-replicating machines, but artificially engineering such complex systems remains a formidable challenge. In particular, although simple artificial self-replicating systems including wooden blocks, magnetic systems, modular robots and synthetic molecular systems have been devised, such kinematic self-replicators are rare compared with examples of theoretical cellular self-replication. One of the principal reasons for this is the amount of complexity that arises when you try to incorporate self-replication into a physical medium. In this regard, DNA is a prime candidate material for constructing self-replicating systems due to its ability to self-assemble through molecular recognition. Here, we show that DNA T-motifs, which self-assemble into ring structures, can be designed to self-replicate through toehold-mediated strand displacement reactions. The inherent design of these rings allows the population dynamics of the systems to be controlled. We also analyse the replication scheme within a universal framework of self-replication and derive a quantitative metric of the self-replicability of the rings.

  16. Multi-agent autonomous system

    Science.gov (United States)

    Fink, Wolfgang (Inventor); Dohm, James (Inventor); Tarbell, Mark A. (Inventor)

    2010-01-01

    A multi-agent autonomous system for exploration of hazardous or inaccessible locations. The multi-agent autonomous system includes simple surface-based agents or craft controlled by an airborne tracking and command system. The airborne tracking and command system includes an instrument suite used to image an operational area and any craft deployed within the operational area. The image data is used to identify the craft, targets for exploration, and obstacles in the operational area. The tracking and command system determines paths for the surface-based craft using the identified targets and obstacles and commands the craft using simple movement commands to move through the operational area to the targets while avoiding the obstacles. Each craft includes its own instrument suite to collect information about the operational area that is transmitted back to the tracking and command system. The tracking and command system may be further coupled to a satellite system to provide additional image information about the operational area and provide operational and location commands to the tracking and command system.

  17. Plant Watering Autonomous Mobile Robot

    Directory of Open Access Journals (Sweden)

    Hema Nagaraja

    2012-07-01

    Full Text Available Now days, due to busy routine life, people forget to water their plants. In this paper, we present a completely autonomous and a cost-effective system for watering indoor potted plants placed on an even surface. The system comprises of a mobile robot and a temperature-humidity sensing module. The system is fully adaptive to any environment and takes into account the watering needs of the plants using the temperature-humidity sensing module. The paper describes the hardware architecture of the fully automated watering system, which uses wireless communication to communicate between the mobile robot and the sensing module. This gardening robot is completely portable and is equipped with a Radio Frequency Identification (RFID module, a microcontroller, an on-board water reservoir and an attached water pump. It is capable of sensing the watering needs of the plants, locating them and finally watering them autonomously without any human intervention. Mobilization of the robot to the potted plant is achieved by using a predefined path. For identification, an RFID tag is attached to each potted plant. The paper also discusses the detailed implementation of the system supported with complete circuitry. Finally, the paper concludes with system performance including the analysis of the water carrying capacity and time requirements to water a set of plants.

  18. Autonomous Robotic Inspection in Tunnels

    Science.gov (United States)

    Protopapadakis, E.; Stentoumis, C.; Doulamis, N.; Doulamis, A.; Loupos, K.; Makantasis, K.; Kopsiaftis, G.; Amditis, A.

    2016-06-01

    In this paper, an automatic robotic inspector for tunnel assessment is presented. The proposed platform is able to autonomously navigate within the civil infrastructures, grab stereo images and process/analyse them, in order to identify defect types. At first, there is the crack detection via deep learning approaches. Then, a detailed 3D model of the cracked area is created, utilizing photogrammetric methods. Finally, a laser profiling of the tunnel's lining, for a narrow region close to detected crack is performed; allowing for the deduction of potential deformations. The robotic platform consists of an autonomous mobile vehicle; a crane arm, guided by the computer vision-based crack detector, carrying ultrasound sensors, the stereo cameras and the laser scanner. Visual inspection is based on convolutional neural networks, which support the creation of high-level discriminative features for complex non-linear pattern classification. Then, real-time 3D information is accurately calculated and the crack position and orientation is passed to the robotic platform. The entire system has been evaluated in railway and road tunnels, i.e. in Egnatia Highway and London underground infrastructure.

  19. DNA Replication via Entanglement Swapping

    CERN Document Server

    Pusuluk, Onur

    2010-01-01

    Quantum effects are mainly used for the determination of molecular shapes in molecular biology, but quantum information theory may be a more useful tool to understand the physics of life. Molecular biology assumes that function is explained by structure, the complementary geometries of molecules and weak intermolecular hydrogen bonds. However, both this assumption and its converse are possible if organic molecules and quantum circuits/protocols are considered as hardware and software of living systems that are co-optimized during evolution. In this paper, we try to model DNA replication as a multiparticle entanglement swapping with a reliable qubit representation of nucleotides. In the model, molecular recognition of a nucleotide triggers an intrabase entanglement corresponding to a superposition state of different tautomer forms. Then, base pairing occurs by swapping intrabase entanglements with interbase entanglements.

  20. Sequence Classification: 889055 [

    Lifescience Database Archive (English)

    Full Text Available during DNA replication stress, where it forms a replication-pausing complex with Tof1p and is phosphorylated...point protein found at replication forks, required for DNA replication; also required for Rad53p activation

  1. Telomere Replication Stress Induced by POT1 Inactivation Accelerates Tumorigenesis.

    Science.gov (United States)

    Pinzaru, Alexandra M; Hom, Robert A; Beal, Angela; Phillips, Aaron F; Ni, Eric; Cardozo, Timothy; Nair, Nidhi; Choi, Jaehyuk; Wuttke, Deborah S; Sfeir, Agnel; Denchi, Eros Lazzerini

    2016-06-01

    Genome sequencing studies have revealed a number of cancer-associated mutations in the telomere-binding factor POT1. Here, we show that when combined with p53 deficiency, depletion of murine POT1a in common lymphoid progenitor cells fosters genetic instability, accelerates the onset, and increases the severity of T cell lymphomas. In parallel, we examined human and mouse cells carrying POT1 mutations found in cutaneous T cell lymphoma (CTCL) patients. Inhibition of POT1 activates ATR-dependent DNA damage signaling and induces telomere fragility, replication fork stalling, and telomere elongation. Our data suggest that these phenotypes are linked to impaired CST (CTC1-STN1-TEN1) function at telomeres. Lastly, we show that proliferation of cancer cells lacking POT1 is enabled by the attenuation of the ATR kinase pathway. These results uncover a role for defective telomere replication during tumorigenesis.

  2. Telomere Replication Stress Induced by POT1 Inactivation Accelerates Tumorigenesis

    Directory of Open Access Journals (Sweden)

    Alexandra M. Pinzaru

    2016-06-01

    Full Text Available Genome sequencing studies have revealed a number of cancer-associated mutations in the telomere-binding factor POT1. Here, we show that when combined with p53 deficiency, depletion of murine POT1a in common lymphoid progenitor cells fosters genetic instability, accelerates the onset, and increases the severity of T cell lymphomas. In parallel, we examined human and mouse cells carrying POT1 mutations found in cutaneous T cell lymphoma (CTCL patients. Inhibition of POT1 activates ATR-dependent DNA damage signaling and induces telomere fragility, replication fork stalling, and telomere elongation. Our data suggest that these phenotypes are linked to impaired CST (CTC1-STN1-TEN1 function at telomeres. Lastly, we show that proliferation of cancer cells lacking POT1 is enabled by the attenuation of the ATR kinase pathway. These results uncover a role for defective telomere replication during tumorigenesis.

  3. Linking DNA replication to heterochromatin silencing and epigenetic inheritance

    Institute of Scientific and Technical Information of China (English)

    Qing Li; Zhiguo Zhang

    2012-01-01

    Chromatin is organized into distinct functional domains.During mitotic cell division,both genetic information encoded in DNA sequence and epigenetic information embedded in chromatin structure must be faithfully duplicated.The inheritance of epigenetic states is critical in maintaining the genome integrity and gene expression state.In this review,we will discuss recent progress on how proteins known to be involved in DNA replication and DNA replication-coupled nucleosome assembly impact on the inheritance and maintenance of heterochromatin,a tightly compact chromatin structure that silences gene transcription.As heterochromatin is important in regulating gene expression and maintaining genome stability,understanding how heterochromatin states are inherited during S phase of the cell cycle is of fundamental importance.

  4. Intelligent autonomous systems 12. Vol. 2. Proceedings

    Energy Technology Data Exchange (ETDEWEB)

    Lee, Sukhan [Sungkyunkwan Univ., Gyeonggi-Do (Korea, Republic of). College of Information and Communication Engineering; Yoon, Kwang-Joon [Konkuk Univ., Seoul (Korea, Republic of); Cho, Hyungsuck [Daegu Gyeongbuk Institute of Science and Technology, Daegu (Korea, Republic of); Lee, Jangmyung (eds.) [Pusan National Univ. (Korea, Republic of). Dept. of Electronics Engineering

    2013-02-01

    Recent research in Intelligent and Autonomous Systems. Volume 2 of the proceedings of the 12th International Conference IAS-12, held June 26-29, 2012, jeju Island, Korea. Written by leading experts in the field. Intelligent autonomous systems are emerged as a key enabler for the creation of a new paradigm of services to humankind, as seen by the recent advancement of autonomous cars licensed for driving in our streets, of unmanned aerial and underwater vehicles carrying out hazardous tasks on-site, and of space robots engaged in scientific as well as operational missions, to list only a few. This book aims at serving the researchers and practitioners in related fields with a timely dissemination of the recent progress on intelligent autonomous systems, based on a collection of papers presented at the 12th International Conference on Intelligent Autonomous Systems, held in Jeju, Korea, June 26-29, 2012. With the theme of ''Intelligence and Autonomy for the Service to Humankind, the conference has covered such diverse areas as autonomous ground, aerial, and underwater vehicles, intelligent transportation systems, personal/domestic service robots, professional service robots for surgery/rehabilitation, rescue/security and space applications, and intelligent autonomous systems for manufacturing and healthcare. This volume 2 includes contributions devoted to Service Robotics and Human-Robot Interaction and Autonomous Multi-Agent Systems and Life Engineering.

  5. An autonomous weeding robot for organic farming

    NARCIS (Netherlands)

    Bakker, T.; Asselt, van C.J.; Bontsema, J.; Müller, J.; Straten, van G.

    2006-01-01

    The objective of this research is the replacement of hand weeding in organic farming by a device working autonomously at ¯eld level. The autonomous weeding robot was designed using a structured design approach, giving a good overview of the total design. A vehicle was developed with a diesel engine,

  6. Autonomous Control of Space Reactor Systems

    International Nuclear Information System (INIS)

    Autonomous and semi-autonomous control is a key element of space reactor design in order to meet the mission requirements of safety, reliability, survivability, and life expectancy. Interrestrial nuclear power plants, human operators are available to perform intelligent control functions that are necessary for both normal and abnormal operational conditions

  7. Autonomous Control of Space Reactor Systems

    Energy Technology Data Exchange (ETDEWEB)

    Belle R. Upadhyaya; K. Zhao; S.R.P. Perillo; Xiaojia Xu; M.G. Na

    2007-11-30

    Autonomous and semi-autonomous control is a key element of space reactor design in order to meet the mission requirements of safety, reliability, survivability, and life expectancy. Interrestrial nuclear power plants, human operators are avilable to perform intelligent control functions that are necessary for both normal and abnormal operational conditions.

  8. Autonomic Management for Multi-agent Systems

    Directory of Open Access Journals (Sweden)

    Nadir kamal Salih

    2011-09-01

    Full Text Available Autonomic computing is a computing system that can manage itself by self-configuration, self-healing, self-optimizing and self-protection. Researchers have been emphasizing the strong role that multi agent systems can play progressively towards the design and implementation of complex autonomic systems. The important of autonomic computing is to create computing systems capable of managing themselves to a far greater extent than they do today. With the nature of autonomy, reactivity, sociality and pro-activity, software agents are promising to make autonomic computing system a reality. This paper mixed multi-agent system with autonomic feature that completely hides its complexity from users/services. Mentioned Java Application Development Framework (JADE as platform example of this environment, could applied to web services as front end to users. With multi agent support it also provides adaptability, intelligence, collaboration, goal oriented interactions, flexibility, mobility and persistence in software systems.

  9. Cardiovascular autonomic neuropathy in the diabetic patients.

    Directory of Open Access Journals (Sweden)

    Maria Eugenia Niño Mantilla

    2007-11-01

    Full Text Available the dysfunction of the autonomic nervous system is a serious problem in diabetic patients. The cardiovacular autonomic neuropathy is the most important autonomic dysfuntion for it´s implication in the increasesof the mortality rate in diabetis patients. tis ethiopatogenesis is the result of a multifactorial process caused by chronic hyperglycemia, ending up in damage of the autonomic fibers thet innervate the heart and blood vessels, leading to dysfuntional hearth rate control and abnormal vascular dynamics. the associated clinical manifestations include orthotatic hypotension, excecise intolerance, intraoperative cardiovascular liability and silent myocardial ischemia. Being important its recognition, quantitative test to evaluate the cardiovascular funtion, to value its evolution and the effects of the treatment ahould be done, being the most used, the hearth rate response to standing test, and teh valsalva maneuver. the handling of this entity is done improving control of glucose blood levels its the most effective way to prevent the cardiovascular autonomic neuropathy in the diabetic patients.

  10. Federated SPARQL Queries Processing with Replicated Fragments

    OpenAIRE

    Montoya, Gabriela; Skaf-Molli, Hala; Molli, Pascal; Vidal, Maria-Esther

    2015-01-01

    Federated query engines allow to consume linked data from SPARQL endpoints. Replicating data fragments from different sources allows to reorganize data to better fit federated query processing of data consumers. However, existing federated query engines poorly support replication. In this paper, we propose a replication-aware federated query engine that extends state-of-art federated query engine ANAPSID and FedX with Fedra, a source selection strategy that approximates the source selection p...

  11. Replicating organizational knowledge: principles or templates?

    OpenAIRE

    Baden-Fuller, Charles; Winter, Sidney G.

    2005-01-01

    We discuss how firms can replicate practices and knowledge embedded in practices by following principles, with no direct reference to an extant working example (template). Definitions are provided for the key concepts of templates, principles, and background knowledge. We address the challenges of providing operational measures for successful replication, and for comparing the efficacy of principles and templates. By using two longitudinal case studies of replication across the units of two m...

  12. Controlled rereplication at DNA replication origins

    OpenAIRE

    Gómez, María

    2008-01-01

    No-more-than-once per cell cycle initiation of DNA replication is a golden rule to maintain genome stability and guarantee cell survival. In our recent work we discovered that small genome fragments of about 200 bp are repeatedly synthesised at human DNA replication origins at the time of origin firing during S phase in normal cells. Rereplicated DNA fragments coincide physical and temporarily with replication origin activity, implying that their generation is intimately associated with the i...

  13. Replication licensing and the DNA damage checkpoint

    OpenAIRE

    Cook, Jeanette Gowen

    2009-01-01

    Accurate and timely duplication of chromosomal DNA requires that replication be coordinated with processes that ensure genome integrity. Significant advances in determining how the earliest steps in DNA replication are affected by DNA damage have highlighted some of the mechanisms to establish that coordination. Recent insights have expanded the relationship between the ATM and ATR-dependent checkpoint pathways and the proteins that bind and function at replication origins. These findings sug...

  14. Persistent HIV-1 replication during antiretroviral therapy

    OpenAIRE

    Martinez-Picado, Javier; Deeks, Steven G

    2016-01-01

    Purpose of review The present review will highlight some of the recent findings regarding the capacity of HIV-1 to replicate during antiretroviral therapy (ART). Recent findings Although ART is highly effective at inhibiting HIV replication, it is not curative. Several mechanisms contribute to HIV persistence during ART, including HIV latency, immune dysfunction, and perhaps persistent low-level spread of the virus to uninfected cells (replication). The success in curing HIV will depend on ef...

  15. Regulation of chromosomal replication in Caulobacter crescentus.

    Science.gov (United States)

    Collier, Justine

    2012-03-01

    The alpha-proteobacterium Caulobacter crescentus is characterized by its asymmetric cell division, which gives rise to a replicating stalked cell and a non-replicating swarmer cell. Thus, the initiation of chromosomal replication is tightly regulated, temporally and spatially, to ensure that it is coordinated with cell differentiation and cell cycle progression. Waves of DnaA and CtrA activities control when and where the initiation of DNA replication will take place in C. crescentus cells. The conserved DnaA protein initiates chromosomal replication by directly binding to sites within the chromosomal origin (Cori), ensuring that DNA replication starts once and only once per cell cycle. The CtrA response regulator represses the initiation of DNA replication in swarmer cells and in the swarmer compartment of pre-divisional cells, probably by competing with DnaA for binding to Cori. CtrA and DnaA are controlled by multiple redundant regulatory pathways that include DNA methylation-dependent transcriptional regulation, temporally regulated proteolysis and the targeting of regulators to specific locations within the cell. Besides being critical regulators of chromosomal replication, CtrA and DnaA are also master transcriptional regulators that control the expression of many genes, thus connecting DNA replication with other events of the C. crescentus cell cycle.

  16. Cells and prions: a license to replicate.

    Science.gov (United States)

    Nuvolone, Mario; Aguzzi, Adriano; Heikenwalder, Mathias

    2009-08-20

    Prion diseases are neurodegenerative, infectious disorders characterized by the aggregation of a misfolded isoform of the cellular prion protein (PrP(C)). The infectious agent - termed prion - is mainly composed of misfolded PrP(Sc). In addition to the central nervous system prions can colonize secondary lymphoid organs and inflammatory foci. Follicular dendritic cells are important extraneural sites of prion replication. However, recent data point to a broader range of cell types that can replicate prions. Here, we review the state of the art in regards to peripheral prion replication, neuroinvasion and the determinants of prion replication competence. PMID:19527722

  17. Ideas are Not Replicators but Minds Are

    OpenAIRE

    Gabora, Liane M

    2004-01-01

    An idea is not a replicator because it does not consist of coded self-assembly instructions. It may retain structure as it passes from one individual to another, but does not replicate it. The cultural replicator is not an idea but an associatively-structured network of them that together form an internal model of the world, or worldview. A worldview is a primitive, uncoded replicator, like the autocatalytic sets of polymers widely believed to be the earliest form of life. Primitive replicato...

  18. An Autonomous Flight Safety System

    Science.gov (United States)

    Bull, James B.; Lanzi, Raymond J.

    2007-01-01

    The Autonomous Flight Safety System (AFSS) being developed by NASA s Goddard Space Flight Center s Wallops Flight Facility and Kennedy Space Center has completed two successful developmental flights and is preparing for a third. AFSS has been demonstrated to be a viable architecture for implementation of a completely vehicle based system capable of protecting life and property in event of an errant vehicle by terminating the flight or initiating other actions. It is capable of replacing current human-in-the-loop systems or acting in parallel with them. AFSS is configured prior to flight in accordance with a specific rule set agreed upon by the range safety authority and the user to protect the public and assure mission success. This paper discusses the motivation for the project, describes the method of development, and presents an overview of the evolving architecture and the current status.

  19. Testbed for an autonomous system

    Science.gov (United States)

    Dikshit, Piyush; Guimaraes, Katia; Ramamurthy, Maya; Agrawala, Ashok K.; Larsen, Ronald L.

    1989-01-01

    In previous works we have defined a general architectural model for autonomous systems, which can easily be mapped to describe the functions of any automated system (SDAG-86-01), and we illustrated that model by applying it to the thermal management system of a space station (SDAG-87-01). In this note, we will further develop that application and design the detail of the implementation of such a model. First we present the environment of our application by describing the thermal management problem and an abstraction, which was called TESTBED, that includes a specific function for each module in the architecture, and the nature of the interfaces between each pair of blocks.

  20. Design of Autonomous Underwater Vehicle

    Directory of Open Access Journals (Sweden)

    Tadahiro Hyakudome

    2011-03-01

    Full Text Available There are concerns about the impact that global warming will have on our environment, and which will inevitably result in expanding deserts and rising water levels. While a lot of underwater vehicles are utilized, AUVs (Autonomous Underwater Vehicle were considered and chosen, as the most suitable tool for conduction survey concerning these global environmental problems. AUVs can comprehensive survey because the vehicle does not have to be connected to the support vessel by tether cable. When such underwater vehicles are made, it is necessary to consider about the following things. 1 Seawater and Water Pressure Environment, 2 Sink, 3 There are no Gas or Battery Charge Stations, 4 Global Positioning System cannot use, 5 Radio waves cannot use. In the paper, outline of above and how deal about it are explained.

  1. Autonomous navigation system and method

    Science.gov (United States)

    Bruemmer, David J [Idaho Falls, ID; Few, Douglas A [Idaho Falls, ID

    2009-09-08

    A robot platform includes perceptors, locomotors, and a system controller, which executes instructions for autonomously navigating a robot. The instructions repeat, on each iteration through an event timing loop, the acts of defining an event horizon based on the robot's current velocity, detecting a range to obstacles around the robot, testing for an event horizon intrusion by determining if any range to the obstacles is within the event horizon, and adjusting rotational and translational velocity of the robot accordingly. If the event horizon intrusion occurs, rotational velocity is modified by a proportion of the current rotational velocity reduced by a proportion of the range to the nearest obstacle and translational velocity is modified by a proportion of the range to the nearest obstacle. If no event horizon intrusion occurs, translational velocity is set as a ratio of a speed factor relative to a maximum speed.

  2. Autonomous Spacecraft Navigation With Pulsars

    CERN Document Server

    Becker, Werner; Jessner, Axel

    2013-01-01

    An external reference system suitable for deep space navigation can be defined by fast spinning and strongly magnetized neutron stars, called pulsars. Their beamed periodic signals have timing stabilities comparable to atomic clocks and provide characteristic temporal signatures that can be used as natural navigation beacons, quite similar to the use of GPS satellites for navigation on Earth. By comparing pulse arrival times measured on-board a spacecraft with predicted pulse arrivals at a reference location, the spacecraft position can be determined autonomously and with high accuracy everywhere in the solar system and beyond. The unique properties of pulsars make clear already today that such a navigation system will have its application in future astronautics. In this paper we describe the basic principle of spacecraft navigation using pulsars and report on the current development status of this novel technology.

  3. Autonomous navigation system and method

    Energy Technology Data Exchange (ETDEWEB)

    Bruemmer, David J [Idaho Falls, ID; Few, Douglas A [Idaho Falls, ID

    2009-09-08

    A robot platform includes perceptors, locomotors, and a system controller, which executes instructions for autonomously navigating a robot. The instructions repeat, on each iteration through an event timing loop, the acts of defining an event horizon based on the robot's current velocity, detecting a range to obstacles around the robot, testing for an event horizon intrusion by determining if any range to the obstacles is within the event horizon, and adjusting rotational and translational velocity of the robot accordingly. If the event horizon intrusion occurs, rotational velocity is modified by a proportion of the current rotational velocity reduced by a proportion of the range to the nearest obstacle and translational velocity is modified by a proportion of the range to the nearest obstacle. If no event horizon intrusion occurs, translational velocity is set as a ratio of a speed factor relative to a maximum speed.

  4. APDS: Autonomous Pathogen Detection System

    Energy Technology Data Exchange (ETDEWEB)

    Langlois, R G; Brown, S; Burris, L; Colston, B; Jones, L; Makarewicz, T; Mariella, R; Masquelier, D; McBride, M; Milanovich, F; Masarabadi, S; Venkateswaran, K; Marshall, G; Olson, D; Wolcott, D

    2002-02-14

    An early warning system to counter bioterrorism, the Autonomous Pathogen Detection System (APDS) continuously monitors the environment for the presence of biological pathogens (e.g., anthrax) and once detected, it sounds an alarm much like a smoke detector warns of a fire. Long before September 11, 2001, this system was being developed to protect domestic venues and events including performing arts centers, mass transit systems, major sporting and entertainment events, and other high profile situations in which the public is at risk of becoming a target of bioterrorist attacks. Customizing off-the-shelf components and developing new components, a multidisciplinary team developed APDS, a stand-alone system for rapid, continuous monitoring of multiple airborne biological threat agents in the environment. The completely automated APDS samples the air, prepares fluid samples in-line, and performs two orthogonal tests: immunoassay and nucleic acid detection. When compared to competing technologies, APDS is unprecedented in terms of flexibility and system performance.

  5. BLAST Autonomous Daytime Star Cameras

    CERN Document Server

    Rex, M; Devlin, M J; Gundersen, J; Klein, J; Pascale, E; Wiebe, D; Rex, Marie; Chapin, Edward; Devlin, Mark J.; Gundersen, Joshua; Klein, Jeff; Pascale, Enzo; Wiebe, Donald

    2006-01-01

    We have developed two redundant daytime star cameras to provide the fine pointing solution for the balloon-borne submillimeter telescope, BLAST. The cameras are capable of providing a reconstructed pointing solution with an absolute accuracy < 5 arcseconds. They are sensitive to stars down to magnitudes ~ 9 in daytime float conditions. Each camera combines a 1 megapixel CCD with a 200 mm f/2 lens to image a 2 degree x 2.5 degree field of the sky. The instruments are autonomous. An internal computer controls the temperature, adjusts the focus, and determines a real-time pointing solution at 1 Hz. The mechanical details and flight performance of these instruments are presented.

  6. Digital autonomous terminal access communications

    Science.gov (United States)

    Novacki, S.

    1987-01-01

    A significant problem for the Bus Monitor Unit is to identify the source of a given transmission. This problem arises from the fact that the label which identifies the source of the transmission as it is put into the bus is intercepted by the Digital Autonomous Terminal Access Communications (DATAC) terminal and removed from the transmission. Thus, a given subsystem will see only data associated with a label and never the identifying label itself. The Bus Monitor must identify the source of the transmission so as to be able to provide some type of error identification/location in the event that some problem with the data transmission occurs. Steps taken to alleviate this problem by modifications to the DATAC terminal are discussed.

  7. Autonomous Infrastructure for Observatory Operations

    Science.gov (United States)

    Seaman, R.

    This is an era of rapid change from ancient human-mediated modes of astronomical practice to a vision of ever larger time domain surveys, ever bigger "big data", to increasing numbers of robotic telescopes and astronomical automation on every mountaintop. Over the past decades, facets of a new autonomous astronomical toolkit have been prototyped and deployed in support of numerous space missions. Remote and queue observing modes have gained significant market share on the ground. Archives and data-mining are becoming ubiquitous; astroinformatic techniques and virtual observatory standards and protocols are areas of active development. Astronomers and engineers, planetary and solar scientists, and researchers from communities as diverse as particle physics and exobiology are collaborating on a vast range of "multi-messenger" science. What then is missing?

  8. Autonomous caregiver following robotic wheelchair

    Science.gov (United States)

    Ratnam, E. Venkata; Sivaramalingam, Sethurajan; Vignesh, A. Sri; Vasanth, Elanthendral; Joans, S. Mary

    2011-12-01

    In the last decade, a variety of robotic/intelligent wheelchairs have been proposed to meet the need in aging society. Their main research topics are autonomous functions such as moving toward some goals while avoiding obstacles, or user-friendly interfaces. Although it is desirable for wheelchair users to go out alone, caregivers often accompany them. Therefore we have to consider not only autonomous functions and user interfaces but also how to reduce caregivers' load and support their activities in a communication aspect. From this point of view, we have proposed a robotic wheelchair moving with a caregiver side by side based on the MATLAB process. In this project we discussing about robotic wheel chair to follow a caregiver by using a microcontroller, Ultrasonic sensor, keypad, Motor drivers to operate robot. Using camera interfaced with the DM6437 (Davinci Code Processor) image is captured. The captured image are then processed by using image processing technique, the processed image are then converted into voltage levels through MAX 232 level converter and given it to the microcontroller unit serially and ultrasonic sensor to detect the obstacle in front of robot. In this robot we have mode selection switch Automatic and Manual control of robot, we use ultrasonic sensor in automatic mode to find obstacle, in Manual mode to use the keypad to operate wheel chair. In the microcontroller unit, c language coding is predefined, according to this coding the robot which connected to it was controlled. Robot which has several motors is activated by using the motor drivers. Motor drivers are nothing but a switch which ON/OFF the motor according to the control given by the microcontroller unit.

  9. Ground Operations Autonomous Control and Integrated Health Management

    Science.gov (United States)

    Figueroa, Fernando; Walker, Mark; Wilkins, Kim; Johnson, Robert; Sass, Jared; Youney, Justin

    2014-01-01

    An intelligent autonomous control capability has been developed and is currently being validated in ground cryogenic fluid management operations. The capability embodies a physical architecture consistent with typical launch infrastructure and control systems, augmented by a higher level autonomous control (AC) system enabled to make knowledge-based decisions. The AC system is supported by an integrated system health management (ISHM) capability that detects anomalies, diagnoses causes, determines effects, and could predict future anomalies. AC is implemented using the concept of programmed sequences that could be considered to be building blocks of more generic mission plans. A sequence is a series of steps, and each executes actions once conditions for the step are met (e.g. desired temperatures or fluid state are achieved). For autonomous capability, conditions must consider also health management outcomes, as they will determine whether or not an action is executed, or how an action may be executed, or if an alternative action is executed instead. Aside from health, higher level objectives can also drive how a mission is carried out. The capability was developed using the G2 software environment (www.gensym.com) augmented by a NASA Toolkit that significantly shortens time to deployment. G2 is a commercial product to develop intelligent applications. It is fully object oriented. The core of the capability is a Domain Model of the system where all elements of the system are represented as objects (sensors, instruments, components, pipes, etc.). Reasoning and decision making can be done with all elements in the domain model. The toolkit also enables implementation of failure modes and effects analysis (FMEA), which are represented as root cause trees. FMEA's are programmed graphically, they are reusable, as they address generic FMEA referring to classes of subsystems or objects and their functional relationships. User interfaces for integrated awareness by

  10. Current challenges in autonomous vehicle development

    Science.gov (United States)

    Connelly, J.; Hong, W. S.; Mahoney, R. B., Jr.; Sparrow, D. A.

    2006-05-01

    The field of autonomous vehicles is a rapidly growing one, with significant interest from both government and industry sectors. Autonomous vehicles represent the intersection of artificial intelligence (AI) and robotics, combining decision-making with real-time control. Autonomous vehicles are desired for use in search and rescue, urban reconnaissance, mine detonation, supply convoys, and more. The general adage is to use robots for anything dull, dirty, dangerous or dumb. While a great deal of research has been done on autonomous systems, there are only a handful of fielded examples incorporating machine autonomy beyond the level of teleoperation, especially in outdoor/complex environments. In an attempt to assess and understand the current state of the art in autonomous vehicle development, a few areas where unsolved problems remain became clear. This paper outlines those areas and provides suggestions for the focus of science and technology research. The first step in evaluating the current state of autonomous vehicle development was to develop a definition of autonomy. A number of autonomy level classification systems were reviewed. The resulting working definitions and classification schemes used by the authors are summarized in the opening sections of the paper. The remainder of the report discusses current approaches and challenges in decision-making and real-time control for autonomous vehicles. Suggested research focus areas for near-, mid-, and long-term development are also presented.

  11. Depletion of Cellular Pre-Replication Complex Factors Results in Increased Human Cytomegalovirus DNA Replication

    OpenAIRE

    Tamara Evans Braun; Emma Poole; John Sinclair

    2012-01-01

    Although HCMV encodes many genes required for the replication of its DNA genome, no HCMV-encoded orthologue of the origin binding protein, which has been identified in other herpesviruses, has been identified. This has led to speculation that HCMV may use other viral proteins or possibly cellular factors for the initiation of DNA synthesis. It is also unclear whether cellular replication factors are required for efficient replication of viral DNA during or after viral replication origin recog...

  12. Amplified human MYC oncogenes localized to replicating submicroscopic circular DNA molecules

    International Nuclear Information System (INIS)

    Amplification of genes can sometimes be detected by molecular hybridization but not by cytogenetic methods, suggesting that in some cases the units of amplification may be too small to be detected by light microscopy. The experiments reported here investigate whether submicroscopic amplification units are present in early passages of the human tumor cell lines HL-60 and COLO 320. The results show that such cells do contain submicroscopic, extrachromosomal, supercoiled circular molecules harboring MYC genes. The molecules in HL-60 are ∼250 kilobase pairs (kbp), while those in COLO 320 are 120-160 kbp. The extrachromosomal molecules in HL-60 are shown to replicate semiconservatively and approximately once in one cell cycle. The authors propose that these submicroscopic elements are precursors of double-minute chromosomes, the usual extrachromosomal manifestation of gene amplification, since both are structurally similar and replicate autonomously

  13. Replication initiation at the Escherichia coli chromosomal origin

    OpenAIRE

    Kaguni, Jon M.

    2011-01-01

    To initiate DNA replication, DnaA recognizes and binds to specific sequences within the Escherichia coli chromosomal origin (oriC), and then unwinds a region within oriC. Next, DnaA interacts with DnaB helicase in loading the DnaB-DnaC complex on each separated strand. Primer formation by primase (DnaG) induces the dissociation of DnaC from DnaB, which involves the hydrolysis of ATP bound to DnaC. Recent evidence indicates that DnaC acts as a checkpoint in the transition from initiation to th...

  14. Replication and Robustness in Developmental Research

    Science.gov (United States)

    Duncan, Greg J.; Engel, Mimi; Claessens, Amy; Dowsett, Chantelle J.

    2014-01-01

    Replications and robustness checks are key elements of the scientific method and a staple in many disciplines. However, leading journals in developmental psychology rarely include explicit replications of prior research conducted by different investigators, and few require authors to establish in their articles or online appendices that their key…

  15. Recommendations for Replication Research in Special Education: A Framework of Systematic, Conceptual Replications

    Science.gov (United States)

    Coyne, Michael D.; Cook, Bryan G.; Therrien, William J.

    2016-01-01

    Special education researchers conduct studies that can be considered replications. However, they do not often refer to them as replication studies. The purpose of this article is to consider the potential benefits of conceptualizing special education intervention research within a framework of systematic, conceptual replication. Specifically, we…

  16. Autonomous Demand Response for Primary Frequency Regulation

    Energy Technology Data Exchange (ETDEWEB)

    Donnelly, Matt; Trudnowski, Daniel J.; Mattix, S.; Dagle, Jeffery E.

    2012-02-28

    The research documented within this report examines the use of autonomous demand response to provide primary frequency response in an interconnected power grid. The work builds on previous studies in several key areas: it uses a large realistic model (i.e., the interconnection of the western United States and Canada); it establishes a set of metrics that can be used to assess the effectiveness of autonomous demand response; and it independently adjusts various parameters associated with using autonomous demand response to assess effectiveness and to examine possible threats or vulnerabilities associated with the technology.

  17. Autonomic symptoms in idiopathic REM behavior disorder

    DEFF Research Database (Denmark)

    Ferini-Strambi, Luigi; Oertel, Wolfgang; Dauvilliers, Yves;

    2014-01-01

    Patients with idiopathic REM sleep behavior disorder (iRBD) are at very high risk of developing neurodegenerative synucleinopathies, which are disorders with prominent autonomic dysfunction. Several studies have documented autonomic dysfunction in iRBD, but large-scale assessment of autonomic...... symptoms has never been systematically performed. Patients with polysomnography-confirmed iRBD (318 cases) and controls (137 healthy volunteers and 181 sleep center controls with sleep diagnoses other than RBD) were recruited from 13 neurological centers in 10 countries from 2008 to 2011. A validated scale...

  18. Two E2 binding sites alone are sufficient to function as the minimal origin of replication of human papillomavirus type 18 DNA.

    OpenAIRE

    Sverdrup, F; Khan, S. A.

    1995-01-01

    Replication of papillomaviruses requires an origin of replication and two virus-encoded proteins, E1 and E2. Using a transient replication assay for human papillomavirus type 18 (HPV-18) DNA, we have found that two adjacent sequences present within the origin of replication can independently support replication. The first, a 77-bp region, contains one E2 binding site (E2BS) and a 16-bp inverted repeat element that probably corresponds to the E1 binding site (E1BS). The other, an 81-bp region,...

  19. Persistent HIV-1 replication during antiretroviral therapy

    Science.gov (United States)

    Martinez-Picado, Javier; Deeks, Steven G.

    2016-01-01

    Purpose of review The present review will highlight some of the recent findings regarding the capacity of HIV-1 to replicate during antiretroviral therapy (ART). Recent findings Although ART is highly effective at inhibiting HIV replication, it is not curative. Several mechanisms contribute to HIV persistence during ART, including HIV latency, immune dysfunction, and perhaps persistent low-level spread of the virus to uninfected cells (replication). The success in curing HIV will depend on efficiently targeting these three aspects. The degree to which HIV replicates during ART remains controversial. Most studies have failed to find any evidence of HIV evolution in blood, even with samples collected over many years, although a recent very intensive study of three individuals suggested that the virus population does shift, at least during the first few months of therapy. Stronger but still not definitive evidence for replication comes from a series of studies in which standard regimens were intensified with an integration inhibitor, resulting in changes in episomal DNA (blood) and cell-associated RNA (tissue). Limited drug penetration within tissues and the presence of immune sanctuaries have been argued as potential mechanisms allowing HIV to spread during ART. Mathematical models suggest that HIV replication and evolution is possible even without the selection of fully drug-resistant variants. As persistent HIV replication could have clinical consequences and might limit the efficacy of curative interventions, determining if HIV replicates during ART and why, should remain a key focus of the HIV research community. Summary Residual viral replication likely persists in lymphoid tissues, at least in a subset of individuals. Abnormal levels of immune activation might contribute to sustain virus replication. PMID:27078619

  20. Development of an autonomous target tracking system

    Science.gov (United States)

    Gidda, Venkata Ramaiah

    In recent years, surveillance and border patrol have become one of the key research areas in UAV research. Increase in the computational capability of the computers and embedded electronics, coupled with compatibility of various commercial vision algorithms and commercial off the shelf (COTS) embedded electronics, and has further fuelled the research. The basic task in these applications is perception of environment through the available visual sensors like camera. Visual tracking, as the name implies, is tracking of objects using a camera. The process of autonomous target tracking starts with the selection of the target in a sequence of video frames transmitted from the on-board camera. We use an improved fast dynamic template matching algorithm coupled with Kalman Filter to track the selected target in consecutive video frames. The selected target is saved as a reference template. On the ground station computer, the reference template is overlaid on the live streaming video from the on-board system, starting from the upper left corner of the video frame. The template is slid pixel by pixel over the entire source image. A comparison of the pixels is performed between the template and source image. A confidence value R of the match is calculated at each pixel. Based on the method used to perform the template matching, the best match pixel location is found according to the highest or lowest confidence value R. The best match pixel location is communicated to the on-board gimbal controller over the wireless Xbee network. The software on the controller actuates the pan-tilt servos to continuously to hold the selected target at the center of the video frame. The complete system is a portable control system assembled from commercial off the shelf parts. The tracking system is tested on a target having several motion patterns.

  1. Development of a Commercially Viable, Modular Autonomous Robotic Systems for Converting any Vehicle to Autonomous Control

    Science.gov (United States)

    Parish, David W.; Grabbe, Robert D.; Marzwell, Neville I.

    1994-01-01

    A Modular Autonomous Robotic System (MARS), consisting of a modular autonomous vehicle control system that can be retrofit on to any vehicle to convert it to autonomous control and support a modular payload for multiple applications is being developed. The MARS design is scalable, reconfigurable, and cost effective due to the use of modern open system architecture design methodologies, including serial control bus technology to simplify system wiring and enhance scalability. The design is augmented with modular, object oriented (C++) software implementing a hierarchy of five levels of control including teleoperated, continuous guidepath following, periodic guidepath following, absolute position autonomous navigation, and relative position autonomous navigation. The present effort is focused on producing a system that is commercially viable for routine autonomous patrolling of known, semistructured environments, like environmental monitoring of chemical and petroleum refineries, exterior physical security and surveillance, perimeter patrolling, and intrafacility transport applications.

  2. AcMNPV As A Model for Baculovirus DNA Replication

    Institute of Scientific and Technical Information of China (English)

    Eric B. Carstens

    2009-01-01

    Baculoviruses were first identified as insect-specific pathogens, and it was this specificity that lead to their use as safe, target specific biological pesticides. For the past 30 years, AcMNPV has served as the subject of intense basic molecular research into the baculovirus infectious cycle including the interaction of the virus with a continuous insect cell line derived from Spodoptera frugiperda. The studies on baculoviruese have led to an in-depth understanding of the physical organization of the viral genomes including many complete genomic sequences, the time course of gene expression, and the application of this basic research to the use of baculoviruses not only as insecticides, but also as a universal eukaryotic protein expression system, and a potential vector in gene therapy. A great deal has also been discovered about the viral genes required for the replication of the baculovirus genome, while much remains to be learned about the mechanism of viral DNA replication. This report outlines the current knowledge of the factors involved in baculovirus DNA replication, using data on AcMNPV as a model for most members of the Baculoviridae.

  3. Maintaining epigenetic inheritance during DNA replication in plants

    Directory of Open Access Journals (Sweden)

    Francisco eIglesias

    2016-02-01

    Full Text Available Biotic and abiotic stresses alter the pattern of gene expression in plants. Depending on the frequency and duration of stress events, the effects on the transcriptional state of genes are remembered temporally or transmitted to daughter cells and, in some instances, even to offspring (transgenerational epigenetic inheritance. This memory effect, which can be found even in the absence of the original stress, has an epigenetic basis, through molecular mechanisms that take place at the chromatin and DNA level but do not imply changes in the DNA sequence. Many epigenetic mechanisms have been described and involve covalent modifications on the DNA and histones, such as DNA methylation, histone acetylation and methylation, and RNAi dependent silencing mechanisms. Some of these chromatin modifications need to be stable through cell division in order to be truly epigenetic. During DNA replication, histones are recycled during the formation of the new nucleosomes and this process is tightly regulated. Perturbations to the DNA replication process and/or the recycling of histones lead to epigenetic changes. In this mini-review, we discuss recent evidence aimed at linking DNA replication process to epigenetic inheritance in plants.

  4. Registered Replication Report: Hart & Albarracín (2011).

    Science.gov (United States)

    2016-01-01

    Language can be viewed as a complex set of cues that shape people's mental representations of situations. For example, people think of behavior described using imperfective aspect (i.e., what a person was doing) as a dynamic, unfolding sequence of actions, whereas the same behavior described using perfective aspect (i.e., what a person did) is perceived as a completed whole. A recent study found that aspect can also influence how we think about a person's intentions (Hart & Albarracín, 2011). Participants judged actions described in imperfective as being more intentional (d between 0.67 and 0.77) and they imagined these actions in more detail (d = 0.73). The fact that this finding has implications for legal decision making, coupled with the absence of other direct replication attempts, motivated this registered replication report (RRR). Multiple laboratories carried out 12 direct replication studies, including one MTurk study. A meta-analysis of these studies provides a precise estimate of the size of this effect free from publication bias. This RRR did not find that grammatical aspect affects intentionality (d between 0 and -0.24) or imagery (d = -0.08). We discuss possible explanations for the discrepancy between these results and those of the original study. PMID:26817732

  5. Automatic sequences

    CERN Document Server

    Haeseler, Friedrich

    2003-01-01

    Automatic sequences are sequences which are produced by a finite automaton. Although they are not random they may look as being random. They are complicated, in the sense of not being not ultimately periodic, they may look rather complicated, in the sense that it may not be easy to name the rule by which the sequence is generated, however there exists a rule which generates the sequence. The concept automatic sequences has special applications in algebra, number theory, finite automata and formal languages, combinatorics on words. The text deals with different aspects of automatic sequences, in particular:· a general introduction to automatic sequences· the basic (combinatorial) properties of automatic sequences· the algebraic approach to automatic sequences· geometric objects related to automatic sequences.

  6. Inferring Where and When Replication Initiates from Genome-Wide Replication Timing Data

    Science.gov (United States)

    Baker, A.; Audit, B.; Yang, S. C.-H.; Bechhoefer, J.; Arneodo, A.

    2012-06-01

    Based on an analogy between DNA replication and one dimensional nucleation-and-growth processes, various attempts to infer the local initiation rate I(x,t) of DNA replication origins from replication timing data have been developed in the framework of phase transition kinetics theories. These works have all used curve-fit strategies to estimate I(x,t) from genome-wide replication timing data. Here, we show how to invert analytically the Kolmogorov-Johnson-Mehl-Avrami model and extract I(x,t) directly. Tests on both simulated and experimental budding-yeast data confirm the location and firing-time distribution of replication origins.

  7. Data from Investigating Variation in Replicability: A “Many Labs” Replication Project

    Directory of Open Access Journals (Sweden)

    Richard A. Klein

    2014-04-01

    Full Text Available This dataset is from the Many Labs Replication Project in which 13 effects were replicated across 36 samples and over 6,000 participants. Data from the replications are included, along with demographic variables about the participants and contextual information about the environment in which the replication was conducted. Data were collected in-lab and online through a standardized procedure administered via an online link. The dataset is stored on the Open Science Framework website. These data could be used to further investigate the results of the included 13 effects or to study replication and generalizability more broadly.

  8. Autonomic Dysfunction in Patients with Mild to Moderate Alzheimer's Disease

    DEFF Research Database (Denmark)

    Jensen-Dahm, Christina; Waldemar, Gunhild; Staehelin Jensen, Troels;

    2015-01-01

    BACKGROUND: Autonomic function has received little attention in Alzheimer's disease (AD). AD pathology has an impact on brain regions which are important for central autonomic control, but it is unclear if AD is associated with disturbance of autonomic function. OBJECTIVE: To investigate autonomic...

  9. Autonomic testing: common techniques and clinical applications.

    Science.gov (United States)

    Weimer, Louis H

    2010-07-01

    Laboratories able to test autonomic function are increasingly available and rely on batteries of well-accepted, noninvasive tests. Tests of parasympathetic cardiovagal, sympathetic vasoconstriction, and sudomotor (sweating) function are most commonly employed. Common examples include heart rate variability to various challenges, Valsalva maneuver, standing and tilt-table studies, and various sudomotor methods. New techniques and technical refinements continue to be described. Most studies rely on perturbations of complex systems and not direct assessment. Testing has helped to improve disease recognition and prompted advances in classification, pathophysiology, and treatment. Major areas impacted include hereditary and immune-mediated autonomic neuropathy, diabetic autonomic neuropathy, distal symmetric polyneuropathy, Parkinson disease and other autonomic failure syndromes, orthostatic intolerance, and unexplained syncope. PMID:20592565

  10. An introduction to autonomous control systems

    Science.gov (United States)

    Antsaklis, Panos J.; Passino, Kevin M.; Wang, S. J.

    1991-01-01

    The functions, characteristics, and benefits of autonomous control are outlined. An autonomous control functional architecture for future space vehicles that incorporates the concepts and characteristics described is presented. The controller is hierarchical, with an execution level (the lowest level), coordination level (middle level), and management and organization level (highest level). The general characteristics of the overall architecture, including those of the three levels, are explained, and an example to illustrate their functions is given. Mathematical models for autonomous systems, including 'logical' discrete event system models, are discussed. An approach to the quantitative, systematic modeling, analysis, and design of autonomous controllers is also discussed. It is a hybrid approach since it uses conventional analysis techniques based on difference and differential equations and new techniques for the analysis of the systems described with a symbolic formalism such as finite automata. Some recent results from the areas of planning and expert systems, machine learning, artificial neural networks, and the area restructurable controls are briefly outlined.

  11. A Primer on Autonomous Aerial Vehicle Design

    Science.gov (United States)

    Coppejans, Hugo H. G.; Myburgh, Herman C.

    2015-01-01

    There is a large amount of research currently being done on autonomous micro-aerial vehicles (MAV), such as quadrotor helicopters or quadcopters. The ability to create a working autonomous MAV depends mainly on integrating a simultaneous localization and mapping (SLAM) solution with the rest of the system. This paper provides an introduction for creating an autonomous MAV for enclosed environments, aimed at students and professionals alike. The standard autonomous system and MAV automation are discussed, while we focus on the core concepts of SLAM systems and trajectory planning algorithms. The advantages and disadvantages of using remote processing are evaluated, and recommendations are made regarding the viability of on-board processing. Recommendations are made regarding best practices to serve as a guideline for aspirant MAV designers. PMID:26633410

  12. A Primer on Autonomous Aerial Vehicle Design.

    Science.gov (United States)

    Coppejans, Hugo H G; Myburgh, Herman C

    2015-01-01

    There is a large amount of research currently being done on autonomous micro-aerial vehicles (MAV), such as quadrotor helicopters or quadcopters. The ability to create a working autonomous MAV depends mainly on integrating a simultaneous localization and mapping (SLAM) solution with the rest of the system. This paper provides an introduction for creating an autonomous MAV for enclosed environments, aimed at students and professionals alike. The standard autonomous system and MAV automation are discussed, while we focus on the core concepts of SLAM systems and trajectory planning algorithms. The advantages and disadvantages of using remote processing are evaluated, and recommendations are made regarding the viability of on-board processing. Recommendations are made regarding best practices to serve as a guideline for aspirant MAV designers. PMID:26633410

  13. Comparative anatomy of the autonomic nervous system.

    Science.gov (United States)

    Nilsson, Stefan

    2011-11-16

    This short review aims to point out the general anatomical features of the autonomic nervous systems of non-mammalian vertebrates. In addition it attempts to outline the similarities and also the increased complexity of the autonomic nervous patterns from fish to tetrapods. With the possible exception of the cyclostomes, perhaps the most striking feature of the vertebrate autonomic nervous system is the similarity between the vertebrate classes. An evolution of the complexity of the system can be seen, with the segmental ganglia of elasmobranchs incompletely connected longitudinally, while well developed paired sympathetic chains are present in teleosts and the tetrapods. In some groups the sympathetic chains may be reduced (dipnoans and caecilians), and have yet to be properly described in snakes. Cranial autonomic pathways are present in the oculomotor (III) and vagus (X) nerves of gnathostome fish and the tetrapods, and with the evolution of salivary and lachrymal glands in the tetrapods, also in the facial (VII) and glossopharyngeal (IX) nerves.

  14. A Primer on Autonomous Aerial Vehicle Design

    Directory of Open Access Journals (Sweden)

    Hugo H. G. Coppejans

    2015-12-01

    Full Text Available There is a large amount of research currently being done on autonomous micro-aerial vehicles (MAV, such as quadrotor helicopters or quadcopters. The ability to create a working autonomous MAV depends mainly on integrating a simultaneous localization and mapping (SLAM solution with the rest of the system. This paper provides an introduction for creating an autonomous MAV for enclosed environments, aimed at students and professionals alike. The standard autonomous system and MAV automation are discussed, while we focus on the core concepts of SLAM systems and trajectory planning algorithms. The advantages and disadvantages of using remote processing are evaluated, and recommendations are made regarding the viability of on-board processing. Recommendations are made regarding best practices to serve as a guideline for aspirant MAV designers.

  15. Autonomic Closure for Large Eddy Simulation

    Science.gov (United States)

    King, Ryan; Hamlington, Peter; Dahm, Werner J. A.

    2015-11-01

    A new autonomic subgrid-scale closure has been developed for large eddy simulation (LES). The approach poses a supervised learning problem that captures nonlinear, nonlocal, and nonequilibrium turbulence effects without specifying a predefined turbulence model. By solving a regularized optimization problem on test filter scale quantities, the autonomic approach identifies a nonparametric function that represents the best local relation between subgrid stresses and resolved state variables. The optimized function is then applied at the grid scale to determine unknown LES subgrid stresses by invoking scale similarity in the inertial range. A priori tests of the autonomic approach on homogeneous isotropic turbulence show that the new approach is amenable to powerful optimization and machine learning methods and is successful for a wide range of filter scales in the inertial range. In these a priori tests, the autonomic closure substantially improves upon the dynamic Smagorinsky model in capturing the instantaneous, statistical, and energy transfer properties of the subgrid stress field.

  16. LEO AUTONOMOUS NAVIGATION BASED ON IMAGE MOTION

    Institute of Scientific and Technical Information of China (English)

    DUANFang; LIUJian-ye; YUFeng

    2005-01-01

    A method of LEO autonomous navigation is presented based on the nonlinear satellite velocity relative to the earth. The velocity is detected by a high-speed camera, with the attitude information detected by a star sensor. Compared with traditional autonomous navigation by landmark identification, the satellite velocity relarive to the earth is obtained by correlativity analysis of images. It does not need to recognize ground objects or views. Since it is not necessary to pre-store the database of ground marks, lots of memory space can be saved.The state and observation equations are constructed, and the filtering is processed by the Kalman filter. Simulation results show that the system has high autonomous navigation precision in LEO autonomous navigation.

  17. Cranial Autonomic Symptoms in Pediatric Migraine

    Directory of Open Access Journals (Sweden)

    J Gordon Millichap

    2013-09-01

    Full Text Available Investigators at the University of California, San Francisco, examined the frequency of cranial autonomic symptoms in all pediatric and adolescent patients with migraine seen in 4 different clinical settings during July 2010 to June 2012.

  18. Rover: Autonomous concepts for Mars exploration

    Science.gov (United States)

    Baiget, A.; Castets, B.; Chochon, H.; Hayard, M.; Lamarre, H.; Lamothe, A.

    1993-01-01

    The development of a mobile, autonomous vehicle that will be launched towards an unknown planet is considered. The rover significant constraints are: Ariane 5 compatibility, Earth/Mars transfer capability, 1000 km autonomous moving in Mars environment, on board localization, and maximum science capability. Two different types of subsystem were considered: classical subsystems (mechanical and mechanisms, thermal, telecommunications, power, onboard data processing) and robotics subsystem, (perception/navigation, autonomous displacement generation, autonomous localization). The needs of each subsystem were studied in terms of energy and data handling capability, in order to choose an on board architecture which best use the available capability, by means of specialized parts. A compromise must always be done between every subsystem in order to obtain the real need with respect to the goal, for example: between perception/navigation and the motion capability. A compromise must also be found between mechanical assembly and calibration need, which is a real problem.

  19. Autonomic Nervous System Dysfunction in Parkinson's Disease.

    Science.gov (United States)

    Zesiewicz, Theresa A.; Baker, Matthew J.; Wahba, Mervat; Hauser, Robert A.

    2003-03-01

    Autonomic nervous system (ANS) dysfunction is common in Parkinson's disease (PD), affects 70% to 80% of patients, and causes significant morbidity and discomfort. Autonomic nervous system dysfunction symptoms in PD include sexual dysfunction, swallowing and gastrointestinal disorders, bowel and bladder abnormalities, sleep disturbances, and derangements of cardiovascular regulation, particularly, orthostatic hypotension. Autonomic nervous system dysfunction in PD may be caused by an underlying degenerative process that affects the autonomic ganglia, brainstem nuclei, and hypothalamic nuclei. Anti-parkinsonian medications can cause or worsen symptoms of ANS dysfunction. The care of a PD patient with ANS dysfunction relies on its recognition and directed treatment, including coordinated care between the neurologist and appropriate subspecialist. Pharmacotherapy may be useful to treat orthostasis, gastrointestinal, urinary, and sexual dysfunction.

  20. Autonomic html interface generator for web applications

    CERN Document Server

    Bassil, Youssef; 10.5121/ijwest.2012.3104

    2012-01-01

    Recent advances in computing systems have led to a new digital era in which every area of life is nearly interrelated with information technology. However, with the trend towards large-scale IT systems, a new challenge has emerged. The complexity of IT systems is becoming an obstacle that hampers the manageability, operability, and maintainability of modern computing infrastructures. Autonomic computing popped up to provide an answer to these ever-growing pitfalls. Fundamentally, autonomic systems are self-configuring, self-healing, self-optimizing, and self-protecting; hence, they can automate all complex IT processes without human intervention. This paper proposes an autonomic HTML web-interface generator based on XML Schema and Style Sheet specifications for self-configuring graphical user interfaces of web applications. The goal of this autonomic generator is to automate the process of customizing GUI web-interfaces according to the ever-changing business rules, policies, and operating environment with th...

  1. AGATE: Autonomous Go and Touch Exploration Project

    Data.gov (United States)

    National Aeronautics and Space Administration — The innovation (AGATE, for Autonomous Go And Touch Exploration) will enable single-sol "go and touch" instrument placement from distances of up to five meters for...

  2. Autonomic contributions to empathy: evidence from patients with primary autonomic failure.

    Science.gov (United States)

    Chauhan, Bina; Mathias, Christopher J; Critchley, Hugo D

    2008-06-01

    Empathy for the emotions of others may require simulatory engagement of corresponding autonomic arousal states. We tested the hypothesis that disruption of autonomic control impairs the ability to empathize emotionally with others. Fifteen patients with primary autonomic failure showed attenuated scores on the Mehrabian Balanced Emotional Empathy Scale (BEES), compared to both younger and older controls. This effect was not accounted for by age, gender, mood state or functional disability. These early observations provide preliminary evidence for a direct contribution of autonomic responsivity to the 'higher-order' social cognitive process of empathy, and may inform the dynamics of supportive care.

  3. Replication Timing of Human Telomeres is Conserved during Immortalization and Influenced by Respective Subtelomeres.

    Science.gov (United States)

    Piqueret-Stephan, Laure; Ricoul, Michelle; Hempel, William M; Sabatier, Laure

    2016-01-01

    Telomeres are specific structures that protect chromosome ends and act as a biological clock, preventing normal cells from replicating indefinitely. Mammalian telomeres are replicated throughout S-phase in a predetermined order. However, the mechanism of this regulation is still unknown. We wished to investigate this phenomenon under physiological conditions in a changing environment, such as the immortalization process to better understand the mechanism for its control. We thus examined the timing of human telomere replication in normal and SV40 immortalized cells, which are cytogenetically very similar to cancer cells. We found that the timing of telomere replication was globally conserved under different conditions during the immortalization process. The timing of telomere replication was conserved despite changes in telomere length due to endogenous telomerase reactivation, in duplicated homologous chromosomes, and in rearranged chromosomes. Importantly, translocated telomeres, possessing their initial subtelomere, retained the replication timing of their homolog, independently of the proportion of the translocated arm, even when the remaining flanking DNA is restricted to its subtelomere, the closest chromosome-specific sequences (inferior to 500 kb). Our observations support the notion that subtelomere regions strongly influence the replication timing of the associated telomere. PMID:27587191

  4. Anti-HCV RNA Aptamers Targeting the Genomic cis-Acting Replication Element

    Directory of Open Access Journals (Sweden)

    Alfredo Berzal-Herranz

    2011-12-01

    Full Text Available Hepatitis C virus (HCV replication is dependent on the existence of several highly conserved functional genomic RNA domains. The cis-acting replication element (CRE, located within the 3' end of the NS5B coding region of the HCV genome, has been shown essential for efficient viral replication. Its sequence and structural features determine its involvement in functional interactions with viral RNA-dependent RNA polymerase and distant RNA domains of the viral genome. This work reports the use of an in vitro selection strategy to select aptamer RNA molecules against the complete HCV-CRE. After six selection cycles, five potential target sites were identified within this domain. Inhibition assays using a sample of representative aptamers showed that the selected RNAs significantly inhibit the replication (>80% of a subgenomic HCV replicon in Huh-7 cell cultures. These results highlight the potential of aptamer RNA molecules as therapeutic antiviral agents.

  5. Semi-Autonomous Vehicle Project

    Science.gov (United States)

    Stewart, Christopher

    2016-01-01

    The primary objective this summer is "evaluating standards for wireless architecture for the internet of things". The Internet of Things is the network of physical objects or "things" embedded with electronics, software, sensors and network connectivity which enables these objects to collect and exchange data and make decisions based on said data. This was accomplished by creating a semi-autonomous vehicle that takes advantage of multiple sensors, cameras, and onboard computers and combined them with a mesh network which enabled communication across large distances with little to no interruption. The mesh network took advantage of what is known as DTN - Disruption Tolerant Networking which according to NASA is the new communications protocol that is "the first step towards interplanetary internet." The use of DTN comes from the fact that it will store information if an interruption in communications is detected and even forward that information via other relays within range so that the data is not lost. This translates well into the project because as the car moves further away from whatever is sending it commands (in this case a joystick), the information can still be forwarded to the car with little to no loss of information thanks to the mesh nodes around the driving area.

  6. Autonomic dysregulation in headache patients.

    Science.gov (United States)

    Gass, Jason J; Glaros, Alan G

    2013-12-01

    To analyze autonomic nervous system activity in headache subjects, measurements of heart rate variability (HRV), skin temperature, skin conductance, and respiration were compared to a matched control group. HRV data were recorded in time and frequency domains. Subjects also completed self-report questionnaires assessing psychological distress, fatigue, and sleep dysfunction. Twenty-one headache and nineteen control subjects participated. In the time domain, the number of consecutive R-to-R intervals that varied by more than 50 ms and the standard deviation of the normalized R-to-R intervals, both indices of parasympathetic nervous system activity, were significantly lower in the headache group than the control group. Groups did not differ statistically on HRV measures in the frequency domain. Self-report measures showed significantly increased somatization, hostility, anxiety, symptom distress, fatigue, and sleep problems in the headache group. The results suggest headache subjects have increased sympathetic nervous system activity and decreased parasympathetic activity compared to non-headache control subjects. Headaches subjects also showed greater emotional distress, fatigue, and sleep problems. The results indicate an association between headaches and cardiovascular functioning suggestive of sympathetic nervous system activation in this sample of mixed migraine and tension-type headache sufferers. PMID:23912525

  7. Autonomous Systems Developments and Trends

    CERN Document Server

    Kyamaky, Kyandoghere; Kacprzyk, Janusz

    2012-01-01

    The Workshops on Autonomous Systems emanated from a gathering with the doctoral students of just three chairs at Fernuniversität in Hagen, which we organise twice per year for a number of years now. Their purpose is to discuss on-going research and to create a community spirit. Furthermore, they serve as a means of structuring the students' research processes. The workshop has grown and matured in several respects. The doctoral students presenting their work do not come from a single university anymore, but from three. Besides them and their supervisors, also other scientists became interested in the event and contribute to its programme. Following the model of Advanced Study Institutes, they are available on the premises for relaxed, informal discussions outside the formal sessions. Finally, with the co-sponsorship of Gesellschaft für Informatik, the German Computer Society, and this surprisingly comprehensive volume of contributions published by Springer-Verlag the workshop turned into a visible scientifi...

  8. Autonomous intelligent cruise control system

    Science.gov (United States)

    Baret, Marc; Bomer, Thierry T.; Calesse, C.; Dudych, L.; L'Hoist, P.

    1995-01-01

    Autonomous intelligent cruise control (AICC) systems are not only controlling vehicles' speed but acting on the throttle and eventually on the brakes they could automatically maintain the relative speed and distance between two vehicles in the same lane. And more than just for comfort it appears that these new systems should improve the safety on highways. By applying a technique issued from the space research carried out by MATRA, a sensor based on a charge coupled device (CCD) was designed to acquire the reflected light on standard-mounted car reflectors of pulsed laser diodes emission. The CCD is working in a unique mode called flash during transfer (FDT) which allows identification of target patterns in severe optical environments. It provides high accuracy for distance and angular position of targets. The absence of moving mechanical parts ensures high reliability for this sensor. The large field of view and the high measurement rate give a global situation assessment and a short reaction time. Then, tracking and filtering algorithms have been developed in order to select the target, on which the equipped vehicle determines its safety distance and speed, taking into account its maneuvering and the behaviors of other vehicles.

  9. Mechanical Autonomous Stochastic Heat Engine

    Science.gov (United States)

    Serra-Garcia, Marc; Foehr, André; Molerón, Miguel; Lydon, Joseph; Chong, Christopher; Daraio, Chiara

    2016-07-01

    Stochastic heat engines are devices that generate work from random thermal motion using a small number of highly fluctuating degrees of freedom. Proposals for such devices have existed for more than a century and include the Maxwell demon and the Feynman ratchet. Only recently have they been demonstrated experimentally, using, e.g., thermal cycles implemented in optical traps. However, recent experimental demonstrations of classical stochastic heat engines are nonautonomous, since they require an external control system that prescribes a heating and cooling cycle and consume more energy than they produce. We present a heat engine consisting of three coupled mechanical resonators (two ribbons and a cantilever) subject to a stochastic drive. The engine uses geometric nonlinearities in the resonating ribbons to autonomously convert a random excitation into a low-entropy, nonpassive oscillation of the cantilever. The engine presents the anomalous heat transport property of negative thermal conductivity, consisting in the ability to passively transfer energy from a cold reservoir to a hot reservoir.

  10. Environmental data collection using autonomous Wave Gliders

    OpenAIRE

    Hermsdorfer, Kathryn M.

    2014-01-01

    Approved for public release; distribution is unlimited The Sensor Hosting Autonomous Remote Craft (SHARC), also known as Wave Glider, is an autonomous ocean vehicle powered by wave motion. This slow-moving platform makes long-term deployments and environmental data collection feasible, especially in data sparse regions or hazardous environments. The standard SHARC hosts a meteorological station (Airmar PB200) that samples air pressure, temperature, wind speed and wind direction at 1.12 m. ...

  11. A middleware architecture for autonomic software deployment

    OpenAIRE

    Matougui, Mohamed El Amine; LERICHE, Sébastien

    2012-01-01

    International audience Autonomic software deployment in open networked environments such as mobile and ad hoc networks is an open issue. Some solutions to software deployment exist; but, they are usable only within static topologies of devices. We propose a middleware architecture providing a constraint-based language guiding the deployment process at a high level and an autonomous agent-based system for establishing and maintaining a software deployment according to a deployment plan. Con...

  12. Decentralized Coordination of Autonomous Vehicles at intersections

    OpenAIRE

    Makarem, Laleh; Gillet, Denis

    2011-01-01

    In this paper, the decentralized coordination of point-mass autonomous vehicles at intersections using navigation functions is considered. As main contribution, the inertia of the vehicles is taken into account to enable on-board energy optimization for crossing. In such a way, heavier vehicles that need more energy and time for acceleration or breaking are given an indirect priority at intersections. The proposed decentralized coordination scheme of autonomous vehicles at intersection is com...

  13. Omnidirectional Stereo Vision for Autonomous Vehicles

    OpenAIRE

    Schönbein, Miriam

    2014-01-01

    Environment perception with cameras is an important requirement for many applications for autonomous vehicles and robots. This work presents a stereoscopic omnidirectional camera system for autonomous vehicles which resolves the problem of a limited field of view and provides a 360° panoramic view of the environment. We present a new projection model for these cameras and show that the camera setup overcomes major drawbacks of traditional perspective cameras in many applications.

  14. TRIDENT: A Framework for Autonomous Underwater Intervention

    OpenAIRE

    Sanz Valero, Pedro José; Ridao, Pere; Oliver, Gabriel; Melchiorri, Claudio; Casalino, Giuseppe; Silvestre, Carlos; Petillot, Yvan; Turetta, Alessio

    2011-01-01

    TRIDENT is a STREP project recently approved by the European Commission whose proposal was submitted to the ICT call 4 of the 7th Framework Program. The project proposes a new methodology for multipurpose underwater intervention tasks. To that end, a cooperative team formed with an Autonomous Surface Craft and an Intervention Autonomous Underwater Vehicle will be used. The proposed methodology splits the mission in two stages mainly devoted to survey and intervention tasks, res...

  15. Visual navigation for an autonomous mobile vehicle

    OpenAIRE

    Peterson, Kevin Robert

    1992-01-01

    Approved for public release; distribution is unlimited Image understanding for a mobile robotic vehicle is an important and complex task for ensuring safe navigation and extended autonomous operations. The goal of this work is to implement a working vision-based navigation control mechanism within a known environment onboard the autonomous mobile vehicle Yamabico-II. Although installing a working hardware system was not accomplished, the image processing, model description, pattern match...

  16. Automated cartography by an autonomous mobile robot

    OpenAIRE

    Merrell, Mark L.

    1999-01-01

    The major goal of this thesis was to create a map of a room by an autonomous mobile robot using the robot's internal odometry measurements and ultrasonic sensors. Yamabico, an autonomous mobile robot, will be controlled by Model-based Mobile robot Language (MML). The research for this thesis included the development of an algorithm to use information from the line-fitting capability of MML. It also included research about the inherent errors that are incurred using sonar for precise measureme...

  17. Control of the MARES Autonomous Underwater Vehicle

    OpenAIRE

    Bruno Ferreira; Miguel Pinto; Anibal Matos; Nuno Cruz

    2009-01-01

    This paper focuses the control problem of a nonholonomic autonomous underwater vehicle, moving in the tridimensional space. The dynamic of a body in submarine environments is strongly nonlinear. This implies that classical linear controllers are often inadequate whereby Lyapunov theory is here considered. Methods based in this theory are promising tools to design controllers and are applied to the case of MARES, a small-sized autonomous underwater vehicle. Several controllers based only on Ly...

  18. Autonomous vehicle development for vertical submarine observation

    OpenAIRE

    Gomáriz Castro, Spartacus; Prat Tasias, Jordi; Arbós, Alejandro; Viñolo Monzoncillo, Carlos; Pallares, Oriol

    2009-01-01

    This work proposes the development of an ocean observation vehicle. This vehicle, a hybrid between Autonomous Underwater Vehicles (AUV) and Autonomous Surface Vehicles (ASV) moves on the surface of the sea and makes vertical immersions to obtain the profiles of a water column according to a pre-established plan. Its design provides lower production cost and higher efficiency. GPS navigation allows the platform to move along the surface of the water while a radio-modem provid...

  19. Operations on Rigid Formations of Autonomous Agents

    OpenAIRE

    Eren, Tolga; Anderson, Brian D. O.; Morse, A. Stephen; Whiteley, Walter; Belhumeur, Peter N.

    2003-01-01

    This paper is concerned with the maintenance of rigid formations of mobile autonomous agents. A key element in all future multi-agent systems will be the role of sensor and communication networks as an integral part of coordination. Network topologies are critically important for autonomous systems involving mobile underwater, ground and air vehicles and for sensor networks. This paper focuses on developing techniques and strategies for the analysis and design of sensor a...

  20. Targeting DNA Replication Stress for Cancer Therapy

    Directory of Open Access Journals (Sweden)

    Jun Zhang

    2016-08-01

    Full Text Available The human cellular genome is under constant stress from extrinsic and intrinsic factors, which can lead to DNA damage and defective replication. In normal cells, DNA damage response (DDR mediated by various checkpoints will either activate the DNA repair system or induce cellular apoptosis/senescence, therefore maintaining overall genomic integrity. Cancer cells, however, due to constitutive growth signaling and defective DDR, may exhibit “replication stress” —a phenomenon unique to cancer cells that is described as the perturbation of error-free DNA replication and slow-down of DNA synthesis. Although replication stress has been proven to induce genomic instability and tumorigenesis, recent studies have counterintuitively shown that enhancing replicative stress through further loosening of the remaining checkpoints in cancer cells to induce their catastrophic failure of proliferation may provide an alternative therapeutic approach. In this review, we discuss the rationale to enhance replicative stress in cancer cells, past approaches using traditional radiation and chemotherapy, and emerging approaches targeting the signaling cascades induced by DNA damage. We also summarize current clinical trials exploring these strategies and propose future research directions including the use of combination therapies, and the identification of potential new targets and biomarkers to track and predict treatment responses to targeting DNA replication stress.

  1. Targeting DNA Replication Stress for Cancer Therapy

    Science.gov (United States)

    Zhang, Jun; Dai, Qun; Park, Dongkyoo; Deng, Xingming

    2016-01-01

    The human cellular genome is under constant stress from extrinsic and intrinsic factors, which can lead to DNA damage and defective replication. In normal cells, DNA damage response (DDR) mediated by various checkpoints will either activate the DNA repair system or induce cellular apoptosis/senescence, therefore maintaining overall genomic integrity. Cancer cells, however, due to constitutive growth signaling and defective DDR, may exhibit “replication stress” —a phenomenon unique to cancer cells that is described as the perturbation of error-free DNA replication and slow-down of DNA synthesis. Although replication stress has been proven to induce genomic instability and tumorigenesis, recent studies have counterintuitively shown that enhancing replicative stress through further loosening of the remaining checkpoints in cancer cells to induce their catastrophic failure of proliferation may provide an alternative therapeutic approach. In this review, we discuss the rationale to enhance replicative stress in cancer cells, past approaches using traditional radiation and chemotherapy, and emerging approaches targeting the signaling cascades induced by DNA damage. We also summarize current clinical trials exploring these strategies and propose future research directions including the use of combination therapies, and the identification of potential new targets and biomarkers to track and predict treatment responses to targeting DNA replication stress. PMID:27548226

  2. Three-dimensional morphology, ultrastructure, and replication of Mycoplasma felis.

    Science.gov (United States)

    Boatman, E S; Kenny, G E

    1970-01-01

    The morphology and replication of Mycoplasma felis in relation to growth phase in culture were studied by electron microscopy. The organisms showed 1.0 to 1.45-hr doubling times with typical bacterial-type growth curves when grown in dialysate broth supplemented with horse serum. Organisms were fixed for electron microscopy by using Veronal acetate-buffered 0.8% OsO(4) (pH 6.1) in 20% sucrose. The morphology of exponential-phase organisms differed markedly from that of stationary or death-phase organisms, which were essentially large round forms with either dispersed or abnormally aggregated cytoplasm. Plasticine models prepared from serial sections of organisms in exponential phase showed the organisms to be either disc-shaped, triangular, horseshoe-shaped, or multilobular. A central "hole" was frequently present in these structures and could be visualized in the lobular forms as an interconnecting circular membrane. The inner surface of this membrane often showed contact with a small membranous body about 0.12 mum in diameter. The significance of this body is unknown. The morphology of the various shapes was confirmed by using the phosphotungstic acid and critical point methods. When the ratios of the various forms in exponential-phase cultures were determined, it was found that a replication sequence could be proposed which accounted for not only the volume increase required to accommodate deoxyribonucleic acid (DNA) replication but also the distribution of that DNA. Although it is likely that DNA replication in M. felis is a binary process, it appears that the mechanism for production of new cells need not be a binary process. PMID:5411752

  3. Autonomous control systems - Architecture and fundamental issues

    Science.gov (United States)

    Antsaklis, P. J.; Passino, K. M.; Wang, S. J.

    1988-01-01

    A hierarchical functional autonomous controller architecture is introduced. In particular, the architecture for the control of future space vehicles is described in detail; it is designed to ensure the autonomous operation of the control system and it allows interaction with the pilot and crew/ground station, and the systems on board the autonomous vehicle. The fundamental issues in autonomous control system modeling and analysis are discussed. It is proposed to utilize a hybrid approach to modeling and analysis of autonomous systems. This will incorporate conventional control methods based on differential equations and techniques for the analysis of systems described with a symbolic formalism. In this way, the theory of conventional control can be fully utilized. It is stressed that autonomy is the design requirement and intelligent control methods appear at present, to offer some of the necessary tools to achieve autonomy. A conventional approach may evolve and replace some or all of the `intelligent' functions. It is shown that in addition to conventional controllers, the autonomous control system incorporates planning, learning, and FDI (fault detection and identification).

  4. Advancing Autonomous Operations for Deep Space Vehicles

    Science.gov (United States)

    Haddock, Angie T.; Stetson, Howard K.

    2014-01-01

    Starting in Jan 2012, the Advanced Exploration Systems (AES) Autonomous Mission Operations (AMO) Project began to investigate the ability to create and execute "single button" crew initiated autonomous activities [1]. NASA Marshall Space Flight Center (MSFC) designed and built a fluid transfer hardware test-bed to use as a sub-system target for the investigations of intelligent procedures that would command and control a fluid transfer test-bed, would perform self-monitoring during fluid transfers, detect anomalies and faults, isolate the fault and recover the procedures function that was being executed, all without operator intervention. In addition to the development of intelligent procedures, the team is also exploring various methods for autonomous activity execution where a planned timeline of activities are executed autonomously and also the initial analysis of crew procedure development. This paper will detail the development of intelligent procedures for the NASA MSFC Autonomous Fluid Transfer System (AFTS) as well as the autonomous plan execution capabilities being investigated. Manned deep space missions, with extreme communication delays with Earth based assets, presents significant challenges for what the on-board procedure content will encompass as well as the planned execution of the procedures.

  5. Study on the micro-replication of shark skin

    Institute of Scientific and Technical Information of China (English)

    2008-01-01

    Direct replication of creatural scarfskins to form biomimetic surfaces with relatively vivid morphology is a new attempt of the bio-replicated forming technology at animal body. Taking shark skins as the replication templates, and the micro-embossing and micro-molding as the material forming methods, the micro-replicating technology of the outward morphology on shark skins was demonstrated. The preliminary analysis on replication precision indicates that the bio-replicated forming technology can replicate the outward morphology of the shark scales with good precision, which validates the application of the bio-replicated forming technology in the direct morphology replication of the firm creatural scarfskins.

  6. Replicated Data Management for Mobile Computing

    CERN Document Server

    Douglas, Terry

    2008-01-01

    Managing data in a mobile computing environment invariably involves caching or replication. In many cases, a mobile device has access only to data that is stored locally, and much of that data arrives via replication from other devices, PCs, and services. Given portable devices with limited resources, weak or intermittent connectivity, and security vulnerabilities, data replication serves to increase availability, reduce communication costs, foster sharing, and enhance survivability of critical information. Mobile systems have employed a variety of distributed architectures from client-server

  7. Replication and Analysis of Ebbinghaus' Forgetting Curve.

    Directory of Open Access Journals (Sweden)

    Jaap M J Murre

    Full Text Available We present a successful replication of Ebbinghaus' classic forgetting curve from 1880 based on the method of savings. One subject spent 70 hours learning lists and relearning them after 20 min, 1 hour, 9 hours, 1 day, 2 days, or 31 days. The results are similar to Ebbinghaus' original data. We analyze the effects of serial position on forgetting and investigate what mathematical equations present a good fit to the Ebbinghaus forgetting curve and its replications. We conclude that the Ebbinghaus forgetting curve has indeed been replicated and that it is not completely smooth but most probably shows a jump upwards starting at the 24 hour data point.

  8. [Autonomic dysfunction syndrome and diabetic cardiac autonomic neuropathy in children with diabetes mellitus type I. The correction method].

    Science.gov (United States)

    Manukian, V Iu; Bolotova, N V; Aver'ianov, A P; Filina, N Iu; Raĭgorodskiĭ, Iu M

    2011-01-01

    We assessed the state of the autonomic nervous system in 90 children with diabetes mellitus type I. The autonomic dysfunction syndrome was found in 58,9% and diabetic cardiac autonomic neuropathy in 28,9% of patients. We revealed the high risk of the development of diabetic cardiac autonomic neuropathy in children with diabetes mellitus type I in the presence of the autonomic dysfunction syndrome. It has been shown that the early treatment of functional disturbances of the autonomic nervous system using transcranial magnetic stimulation is necessary to prevent the manifestation of diabetic cardiac autonomic neuropathy.

  9. CRISPR-Cas9 Can Inhibit HIV-1 Replication but NHEJ Repair Facilitates Virus Escape

    OpenAIRE

    Wang, Gang; Zhao, Na; Berkhout, Ben; Das, Atze T.

    2016-01-01

    Several recent studies demonstrated that the clustered regularly interspaced short palindromic repeats (CRISPR)-associated endonuclease Cas9 can be used for guide RNA (gRNA)-directed, sequence-specific cleavage of HIV proviral DNA in infected cells. We here demonstrate profound inhibition of HIV-1 replication by harnessing T cells with Cas9 and antiviral gRNAs. However, the virus rapidly and consistently escaped from this inhibition. Sequencing of the HIV-1 escape variants revealed nucleotide...

  10. Regulation of Human Adenovirus Replication by RNA Interference.

    Science.gov (United States)

    Nikitenko, N A; Speiseder, T; Lam, E; Rubtsov, P M; Tonaeva, Kh D; Borzenok, S A; Dobner, T; Prassolov, V S

    2015-01-01

    Adenoviruses cause a wide variety of human infectious diseases. Adenoviral conjunctivitis and epidemic keratoconjunctivitis are commonly associated with human species D adenoviruses. Currently, there is no sufficient or appropriate treatment to counteract these adenovirus infections. Thus, there is an urgent need for new etiology-directed therapies with selective activity against human adenoviruses. To address this problem, the adenoviral early genes E1A and E2B (viral DNA polymerase) seem to be promising targets. Here, we propose an effective approach to downregulate the replication of human species D adenoviruses by means of RNA interference. We generated E1A expressing model cell lines enabling fast evaluation of the RNA interference potential. Small interfering RNAs complementary to the E1A mRNA sequences of human species D adenoviruses mediate significant suppression of the E1A expression in model cells. Furthermore, we observed a strong downregulation of replication of human adenoviruses type D8 and D37 by small hairpin RNAs complementary to the E1A or E2B mRNA sequences in primary human limbal cells. We believe that our results will contribute to the development of efficient anti-adenoviral therapy.

  11. What Should Researchers Expect When They Replicate Studies? A Statistical View of Replicability in Psychological Science.

    Science.gov (United States)

    Patil, Prasad; Peng, Roger D; Leek, Jeffrey T

    2016-07-01

    A recent study of the replicability of key psychological findings is a major contribution toward understanding the human side of the scientific process. Despite the careful and nuanced analysis reported, the simple narrative disseminated by the mass, social, and scientific media was that in only 36% of the studies were the original results replicated. In the current study, however, we showed that 77% of the replication effect sizes reported were within a 95% prediction interval calculated using the original effect size. Our analysis suggests two critical issues in understanding replication of psychological studies. First, researchers' intuitive expectations for what a replication should show do not always match with statistical estimates of replication. Second, when the results of original studies are very imprecise, they create wide prediction intervals-and a broad range of replication effects that are consistent with the original estimates. This may lead to effects that replicate successfully, in that replication results are consistent with statistical expectations, but do not provide much information about the size (or existence) of the true effect. In this light, the results of the Reproducibility Project: Psychology can be viewed as statistically consistent with what one might expect when performing a large-scale replication experiment. PMID:27474140

  12. Priming DNA Replication from Triple Helix Oligonucleotides: Possible Threestranded DNA in DNA Polymerases

    Directory of Open Access Journals (Sweden)

    Patrick P. Lestienne

    2011-01-01

    Full Text Available Triplex associate with a duplex DNA presenting the same polypurine or polypyrimidine-rich sequence in an antiparallel orientation. So far, triplex forming oligonucleotides (TFOs are known to inhibit transcription, replication, and to induce mutations. A new property of TFO is reviewed here upon analysis of DNA breakpoint yielding DNA rearrangements; the synthesized sequence of the first direct repeat displays a skewed polypurine- rich sequence. This synthesized sequence can bind the second homologous duplex sequence through the formation of a triple helix, which is able to prime further DNA replication. In these case, the d(G-rich Triple Helix Primers (THP bind the homologous strand in a parallel manner, possibly via a RecA-like mechanism. This novel property is shared by all tested DNA polymerases: phage, retrovirus, bacteria, and human. These features may account for illegitimate initiation of replication upon single-strand breakage and annealing to a homologous sequence where priming may occur. Our experiments suggest that DNA polymerases can bind three instead of two polynucleotide strands in their catalytic centre.

  13. Priming DNA replication from triple helix oligonucleotides: possible threestranded DNA in DNA polymerases.

    Science.gov (United States)

    Lestienne, Patrick P

    2011-01-01

    Triplex associate with a duplex DNA presenting the same polypurine or polypyrimidine-rich sequence in an antiparallel orientation. So far, triplex forming oligonucleotides (TFOs) are known to inhibit transcription, replication, and to induce mutations. A new property of TFO is reviewed here upon analysis of DNA breakpoint yielding DNA rearrangements; the synthesized sequence of the first direct repeat displays a skewed polypurine- rich sequence. This synthesized sequence can bind the second homologous duplex sequence through the formation of a triple helix, which is able to prime further DNA replication. In these case, the d(G)-rich Triple Helix Primers (THP) bind the homologous strand in a parallel manner, possibly via a RecA-like mechanism. This novel property is shared by all tested DNA polymerases: phage, retrovirus, bacteria, and human. These features may account for illegitimate initiation of replication upon single-strand breakage and annealing to a homologous sequence where priming may occur. Our experiments suggest that DNA polymerases can bind three instead of two polynucleotide strands in their catalytic centre. PMID:22229092

  14. LHCb Data Replication During SC3

    CERN Multimedia

    Smith, A

    2006-01-01

    LHCb's participation in LCG's Service Challenge 3 involves testing the bulk data transfer infrastructure developed to allow high bandwidth distribution of data across the grid in accordance with the computing model. To enable reliable bulk replication of data, LHCb's DIRAC system has been integrated with gLite's File Transfer Service middleware component to make use of dedicated network links between LHCb computing centres. DIRAC's Data Management tools previously allowed the replication, registration and deletion of files on the grid. For SC3 supplementary functionality has been added to allow bulk replication of data (using FTS) and efficient mass registration to the LFC replica catalog.Provisional performance results have shown that the system developed can meet the expected data replication rate required by the computing model in 2007. This paper details the experience and results of integration and utilisation of DIRAC with the SC3 transfer machinery.

  15. Molecular Mechanisms of DNA Replication Checkpoint Activation

    Directory of Open Access Journals (Sweden)

    Bénédicte Recolin

    2014-03-01

    Full Text Available The major challenge of the cell cycle is to deliver an intact, and fully duplicated, genetic material to the daughter cells. To this end, progression of DNA synthesis is monitored by a feedback mechanism known as replication checkpoint that is untimely linked to DNA replication. This signaling pathway ensures coordination of DNA synthesis with cell cycle progression. Failure to activate this checkpoint in response to perturbation of DNA synthesis (replication stress results in forced cell division leading to chromosome fragmentation, aneuploidy, and genomic instability. In this review, we will describe current knowledge of the molecular determinants of the DNA replication checkpoint in eukaryotic cells and discuss a model of activation of this signaling pathway crucial for maintenance of genomic stability.

  16. Compact Autonomous Hemispheric Vision System

    Science.gov (United States)

    Pingree, Paula J.; Cunningham, Thomas J.; Werne, Thomas A.; Eastwood, Michael L.; Walch, Marc J.; Staehle, Robert L.

    2012-01-01

    Solar System Exploration camera implementations to date have involved either single cameras with wide field-of-view (FOV) and consequently coarser spatial resolution, cameras on a movable mast, or single cameras necessitating rotation of the host vehicle to afford visibility outside a relatively narrow FOV. These cameras require detailed commanding from the ground or separate onboard computers to operate properly, and are incapable of making decisions based on image content that control pointing and downlink strategy. For color, a filter wheel having selectable positions was often added, which added moving parts, size, mass, power, and reduced reliability. A system was developed based on a general-purpose miniature visible-light camera using advanced CMOS (complementary metal oxide semiconductor) imager technology. The baseline camera has a 92 FOV and six cameras are arranged in an angled-up carousel fashion, with FOV overlaps such that the system has a 360 FOV (azimuth). A seventh camera, also with a FOV of 92 , is installed normal to the plane of the other 6 cameras giving the system a > 90 FOV in elevation and completing the hemispheric vision system. A central unit houses the common electronics box (CEB) controlling the system (power conversion, data processing, memory, and control software). Stereo is achieved by adding a second system on a baseline, and color is achieved by stacking two more systems (for a total of three, each system equipped with its own filter.) Two connectors on the bottom of the CEB provide a connection to a carrier (rover, spacecraft, balloon, etc.) for telemetry, commands, and power. This system has no moving parts. The system's onboard software (SW) supports autonomous operations such as pattern recognition and tracking.

  17. Improved autonomous star identification algorithm

    Science.gov (United States)

    Luo, Li-Yan; Xu, Lu-Ping; Zhang, Hua; Sun, Jing-Rong

    2015-06-01

    The log-polar transform (LPT) is introduced into the star identification because of its rotation invariance. An improved autonomous star identification algorithm is proposed in this paper to avoid the circular shift of the feature vector and to reduce the time consumed in the star identification algorithm using LPT. In the proposed algorithm, the star pattern of the same navigation star remains unchanged when the stellar image is rotated, which makes it able to reduce the star identification time. The logarithmic values of the plane distances between the navigation and its neighbor stars are adopted to structure the feature vector of the navigation star, which enhances the robustness of star identification. In addition, some efforts are made to make it able to find the identification result with fewer comparisons, instead of searching the whole feature database. The simulation results demonstrate that the proposed algorithm can effectively accelerate the star identification. Moreover, the recognition rate and robustness by the proposed algorithm are better than those by the LPT algorithm and the modified grid algorithm. Project supported by the National Natural Science Foundation of China (Grant Nos. 61172138 and 61401340), the Open Research Fund of the Academy of Satellite Application, China (Grant No. 2014_CXJJ-DH_12), the Fundamental Research Funds for the Central Universities, China (Grant Nos. JB141303 and 201413B), the Natural Science Basic Research Plan in Shaanxi Province, China (Grant No. 2013JQ8040), the Research Fund for the Doctoral Program of Higher Education of China (Grant No. 20130203120004), and the Xi’an Science and Technology Plan, China (Grant. No CXY1350(4)).

  18. Surface Micro Topography Replication in Injection Moulding

    DEFF Research Database (Denmark)

    Arlø, Uffe Rolf; Hansen, Hans Nørgaard; Kjær, Erik Michael

    2005-01-01

    The surface micro topography of injection moulded plastic parts can be important for aesthetical and technical reasons. The quality of replication of mould surface topography onto the plastic surface depends among other factors on the process conditions. A study of this relationship has been...... carried out with rough EDM (electrical discharge machining) mould surfaces, a PS grade, and by applying established three-dimensional topography parameters. Significant quantitative relationships between process parameters and topography parameters were established. It further appeared that replication...

  19. The Anisotropy of Replicated Aluminum Foams

    OpenAIRE

    Furman, Eugeny L.; Arcady B. Finkelstein; Maxim L. Cherny

    2014-01-01

    The replication casting process gives the open-cell aluminum foams that can be used in many industrial applications as well as in filtering technology. The essential requirement for filters is the uniformity of filtering degree which is defined by the minimal pore size. However the structure of replication castings is often inhomogeneous and the minimal pore radius is decreasing in the direction of melt infiltration. The objective of this investigation is to study the dynamics of melt impregn...

  20. Database Replication Using Generalized Snapshot Isolation

    OpenAIRE

    Elnikety, Sameh; Pedone, Fernando; Zwaenepoel, Willy

    2005-01-01

    Generalized snapshot isolation extends snapshot isolation as used in Oracle and other databases in a manner suitable for replicated databases. While (conventional) snapshot isolation requires that transactions observe the “latest” snapshot of the database, generalized snapshot isolation allows the use of “older” snapshots, facilitating a replicated implementation. We show that many of the desirable properties of snapshot isolation remain. In particular, read-only transactions never block or a...

  1. Autogenesis: the evolution of replicative systems.

    Science.gov (United States)

    Csányi, V; Kampis, G

    1985-05-21

    Questions concerning the nature and origin of living systems and the hierarchy of their evolutionary processes are considered, and several problems which arise in connection with formerly developed theories--the autopoiesis of Maturana & Varela, the POL theory of Haukioja and the earlier developed evolutionary theory of Csányi--are discussed. The organization of living systems, the use of informational terms and the question how reproduction can enter into their characterization, problems of autonomy and identity are included in the list. It is suggested that replication--a copying process achieved by a special network of interrelatedness of components and component-producing processes that produces the same network as that which produced them--characterizes the living organization. The information "used" in this copying process, whether it is stored by special means or distributed in the whole system, is called replicative information. A theoretical model is introduced for the spontaneous emergence of replicative organization, called autogenesis. Autogenesis commences in a system by an organized "small" subsystem, referred to as AutoGenetic System Precursor (AGSP), which conveys replicative information to the system. During autogenesis, replicative information increases in system and compartment(s) form. A compartment is the co-replicating totality of components. The end state of autogenesis is an invariantly self-replicating organization which is unable to undergo further intrinsic organizational changes. It is suggested that replicative unities--such as living organisms--evolve via autogenesis. Levels of evolution emerge as a consequence of the relative autonomy of the autogenetic unities. On the next level they can be considered as components endowed with functions and a new autogenetic process can commence. Thus evolution proceeds towards its end state through the parallel autogenesis of the various levels. In terms of applications, ontogenesis is dealt with

  2. Autonomous and autonomic systems with applications to NASA intelligent spacecraft operations and exploration systems

    CERN Document Server

    Truszkowski, Walt; Rouff, Christopher; Karlin, Jay; Rash, James; Hinchey, Michael; Sterritt, Roy

    2009-01-01

    This book provides an in-depth discussion of autonomous and autonomic systems, their interdependencies, differences and similarities. Current and pending issues in these evermore increasingly important subjects are highlighted and discussed. Concepts, ideas and experiences are explored in relation to real-life NASA systems in spacecraft control and in the exploration domain.

  3. Supervised autonomous robotic soft tissue surgery.

    Science.gov (United States)

    Shademan, Azad; Decker, Ryan S; Opfermann, Justin D; Leonard, Simon; Krieger, Axel; Kim, Peter C W

    2016-05-01

    The current paradigm of robot-assisted surgeries (RASs) depends entirely on an individual surgeon's manual capability. Autonomous robotic surgery-removing the surgeon's hands-promises enhanced efficacy, safety, and improved access to optimized surgical techniques. Surgeries involving soft tissue have not been performed autonomously because of technological limitations, including lack of vision systems that can distinguish and track the target tissues in dynamic surgical environments and lack of intelligent algorithms that can execute complex surgical tasks. We demonstrate in vivo supervised autonomous soft tissue surgery in an open surgical setting, enabled by a plenoptic three-dimensional and near-infrared fluorescent (NIRF) imaging system and an autonomous suturing algorithm. Inspired by the best human surgical practices, a computer program generates a plan to complete complex surgical tasks on deformable soft tissue, such as suturing and intestinal anastomosis. We compared metrics of anastomosis-including the consistency of suturing informed by the average suture spacing, the pressure at which the anastomosis leaked, the number of mistakes that required removing the needle from the tissue, completion time, and lumen reduction in intestinal anastomoses-between our supervised autonomous system, manual laparoscopic surgery, and clinically used RAS approaches. Despite dynamic scene changes and tissue movement during surgery, we demonstrate that the outcome of supervised autonomous procedures is superior to surgery performed by expert surgeons and RAS techniques in ex vivo porcine tissues and in living pigs. These results demonstrate the potential for autonomous robots to improve the efficacy, consistency, functional outcome, and accessibility of surgical techniques. PMID:27147588

  4. Conditionally replicating HIV and SIV variants.

    Science.gov (United States)

    Das, Atze T; Berkhout, Ben

    2016-05-01

    Conditionally replicating human immunodeficiency virus (HIV) and simian immunodeficiency virus (SIV) variants that can be switched on and off at will are attractive tools for HIV and SIV research. We constructed HIV and SIV variants in which the natural transcription control mechanism was replaced by the doxycycline (dox)-inducible Tet-On gene expression mechanism. These HIV-rtTA and SIV-rtTA variants are fully replication-competent, but replication is critically dependent on dox administration. We here describe how the dox-dependent virus variants may improve the safety of live-attenuated virus vaccines and how they can be used to study the immune responses that correlate with vaccine-induced protection. Furthermore, we review how these variants were initially designed and subsequently optimized by spontaneous viral evolution. These efforts yielded efficiently replicating and tightly dox-controlled HIV-rtTA and SIV-rtTA variants that replicate in a variety of cell and tissue culture systems, and in human immune system (HIS) mice and macaques, respectively. These viruses can be used as a tool in HIV and SIV biology studies and in vaccine research. We review how HIV-rtTA and SIV-rtTA were used to study the role of the viral TAR and Tat elements in virus replication. PMID:25982510

  5. Commercial Building Partnerships Replication and Diffusion

    Energy Technology Data Exchange (ETDEWEB)

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

    2013-09-16

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

  6. Dynamics of Escherichia coli Chromosome Segregation during Multifork Replication

    DEFF Research Database (Denmark)

    Nielsen, Henrik Jørck; Youngren, Brenda; Hansen, Flemming G.;

    2007-01-01

    Slowly growing Escherichia coli cells have a simple cell cycle, with replication and progressive segregation of the chromosome completed before cell division. In rapidly growing cells, initiation of replication occurs before the previous replication rounds are complete. At cell division...

  7. Genome instability induced by structured DNA and replication fork restart

    OpenAIRE

    Schalbetter, Stephanie

    2012-01-01

    DNA replication is a central mechanism to all forms of life. Errors occurring during DNA replication can result in mutagenesis and genome rearrangements, which can cause various diseases. In this work I have investigated the stability of direct tandem repeats (TRs) in the context of replication and replication-associated repair mechanisms. During DNA replication the replication fork encounters many obstacles, such as DNA-protein barriers, secondary DNA structures and DNA lesions. How and if r...

  8. Polymorphism and divergence in the beta-globin replication origin initiation region.

    Science.gov (United States)

    Fullerton, S M; Bond, J; Schneider, J A; Hamilton, B; Harding, R M; Boyce, A J; Clegg, J B

    2000-01-01

    DNA sequence polymorphism and divergence was examined in the vicinity of the human beta-globin gene cluster origin of replication initiation region (IR), a 1.3-kb genomic region located immediately 5' of the adult-expressed beta-globin gene. DNA sequence variation in the replication origin IR and 5 kb of flanking DNA was surveyed in samples drawn from two populations, one African (from the Gambia, West Africa) and the other European (from Oxford, England). In these samples, levels of nucleotide and length polymorphism in the IR were found to be more than two times as high as adjacent non-IR-associated regions (estimates of per-nucleotide heterozygosity were 0.30% and 0.12%, respectively). Most polymorphic positions identified in the origin IR fall within or just adjacent to a 52-bp alternating purine-pyrimidine ((RY)n) sequence repeat. Within- and between-populations divergence is highest in this portion of the IR, and interspecific divergence in the same region, determined by comparison with an orthologous sequence from the chimpanzee, is also pronounced. Higher levels of diversity in this subregion are not, however, primarily attributable to slippage-mediated repeat unit changes, as nucleotide substitution contributes disproportionately to allelic heterogeneity. An estimate of helical stability in the sequenced region suggests that the hypervariable (RY)n constitutes the major DNA unwinding element (DUE) of the replication origin IR, the location at which the DNA duplex first unwinds and new strand synthesis begins. These findings suggest that the beta-globin IR experiences a higher underlying rate of neutral mutation than do adjacent genomic regions and that enzyme fidelity associated with the initiation of DNA replication at this origin may be compromised. The significance of these findings for our understanding of eukaryotic replication origin biology is discussed. PMID:10666717

  9. Replication protein A: directing traffic at the intersection of replication and repair

    OpenAIRE

    Oakley, Greg G.; Patrick, Steve M.

    2010-01-01

    Since the initial discovery of replication protein A (RPA) as a DNA replication factor, much progress has been made on elucidating critical roles for RPA in other DNA metabolic pathways. RPA has been shown to be required for DNA replication, DNA repair, DNA recombination, and the DNA damage response pathway with roles in checkpoint activation. This review summarizes the current understanding of RPA structure, phosphorylation and protein-protein interactions in mediating these DNA metabolic pr...

  10. Cutaneous autonomic denervation in Parkinson's disease.

    Science.gov (United States)

    Navarro-Otano, Judith; Casanova-Mollà, Jordi; Morales, Merche; Valls-Solé, Josep; Tolosa, Eduard

    2015-08-01

    Numerous studies have detailed involvement of the peripheral autonomic nervous system (PANS) in Parkinson's disease (PD). We assessed autonomic innervation of dermal annexes through quantitative fluorescence measurement from skin obtained via punch biopsies at distal leg region in PD and control subjects. We defined a ratio between the area corresponding to protein gen product (PGP) immunoreactivity and the area corresponding to blood vessel or sweat gland as a quantitative measure of autonomic innervation. Presence of alpha-synuclein (AS) deposits in dermis and hypodermis was also assessed by immunohistochemistry. Skin biopsies form six PD patients and six healthy controls were studied. Autonomic innervation scores were lower in PD than in controls in both blood vessels and sweat glands. No AS or phosphorylated AS (pAS) immunoreactivity was detected in dermis or hypodermis in any of the studied subjects. The results of this investigation suggest that autonomic innervation of dermal annexes in living patients with PD is reduced compared to controls. AS or pAS deposits were not found in dermis or hypodermis suggesting that distal leg skin study is not useful for in vivo detection of AS in PD.

  11. Cardiovascular autonomic dysfunction in Parkinson's disease.

    Science.gov (United States)

    Ziemssen, Tjalf; Reichmann, Heinz

    2010-02-15

    Symptoms of cardiovascular dysautonomia are a common occurrence in Parkinson's disease (PD). In addition to this dysautonomia as part of PD itself, dysfunction of the autonomic nervous system (ANS) can be triggered as a side-effect of drug treatment interacting with the ANS or - if prominent and early - an indication of a different disease such as multiple system atrophy (MSA). Various diagnostic tests are available to demonstrate autonomic failure. While autonomic function tests can differentiate parasympathetic from sympathetic dysfunction, cardiac imaging can define the pathophysiologically involved site of a lesion. Standard tests such as 24-h ambulatory blood pressure measurements can identify significant autonomic failure which needs treatment. The most frequent and disturbing symptom of cardiovascular autonomic dysfunction is orthostatic hypotension. Symptoms include generalized weakness, light-headiness, mental "clouding" up to syncope. Factors like heat, food, alcohol, exercise, activities which increase intrathoraric pressure (e.g. defecation, coughing) and certain drugs (e.g. vasodilators) can worsen a probably asymptomatic orthostatic hypotension. Non-medical and medical therapies can help the patient to cope with a disabling symptomatic orthostatic hypotension. Supine hypertension is often associated with orthostatic hypotension. The prognostic role of cardiovagal and baroreflex dysfunction is still not yet known.

  12. Autonomous Learning and Improving Communicative Competence

    Institute of Scientific and Technical Information of China (English)

    李宝红; 孙晓黎

    2013-01-01

    Nowadays, English as a world language becomes more and more important. Consequently, English learning becomes more and more popular. As we know, an important object for English learners is to improve their communicative competence. So autonomous learning is a good way to improve communicative competence. In this paper, two terms, autonomous learning and communicative competence, and their relationship will be introduced from the perspective of English learning. Autonomous learning is self-managed learning, which is contrary to passive learning and mechanical learning, according to intrinsic property of language learning. Communicative competence is a concept introduced by Dell Hymes and is discussed and refined by many oth⁃er linguists. According to Hymes, communicative competence is the ability not only to apply the grammatical rules of language in order to form grammatically correct sentences but also to know when and where to use these sentences and to whom. Communi⁃cative competence includes 4 aspects: Possibility, feasibility, appropriateness and performance. Improving communicative compe⁃tence is the result of autonomous learning, autonomous learning is the motivation of improving communicative competence. English, of course, is a bridge connecting China to the world, and fostering students’communicative competence through auton⁃omous learning is the vital element of improving English learning in China.

  13. Road network modeling in open source GIS to manage the navigation of autonomous robots

    Science.gov (United States)

    Mangiameli, Michele; Muscato, Giovanni; Mussumeci, Giuseppe

    2013-10-01

    The autonomous navigation of a robot can be accomplished through the assignment of a sequence of waypoints previously identified in the territory to be explored. In general, the starting point is a vector graph of the network consisting of possible paths. The vector graph can be directly available in the case of actual road networks, or it can be modeled, i.e. on the basis of cartographic supports or, even better, of a digital terrain model (DTM). In this paper we present software procedures developed in Grass-GIS, PostGIS and QGIS environments to identify, model, and visualize a road graph and to extract and normalize sequence of waypoints which can be transferred to a robot for its autonomous navigation.

  14. Characterization of the replication, transfer, and plasmid/lytic phage cycle of the Streptomyces plasmid-phage pZL12.

    Science.gov (United States)

    Zhong, Li; Cheng, Qiuxiang; Tian, Xinli; Zhao, Liqian; Qin, Zhongjun

    2010-07-01

    We report here the isolation and recombinational cloning of a large plasmid, pZL12, from endophytic Streptomyces sp. 9R-2. pZL12 comprises 90,435 bp, encoding 112 genes, 30 of which are organized in a large operon resembling bacteriophage genes. A replication locus (repA) and a conjugal transfer locus (traA-traC) were identified in pZL12. Surprisingly, the supernatant of a 9R-2 liquid culture containing partially purified phage particles infected 9R-2 cured of pZL12 (9R-2X) to form plaques, and a phage particle (phiZL12) was observed by transmission electron microscopy. Major structural proteins (capsid, portal, and tail) of phiZL12 virions were encoded by pZL12 genes. Like bacteriophage P1, linear phiZL12 DNA contained ends from a largely random pZL12 sequence. There was also a hot end sequence in linear phiZL12. phiZL12 virions efficiently infected only one host, 9R-2X, but failed to infect and form plaques in 18 other Streptomyces strains. Some 9R-2X spores rescued from lysis by infection of phiZL12 virions contained a circular pZL12 plasmid, completing a cycle comprising autonomous plasmid pZL12 and lytic phage phiZL12. These results confirm pZL12 as the first example of a plasmid-phage in Streptomyces.

  15. Phosphoproteomics Identified an NS5A Phosphorylation Site Involved in Hepatitis C Virus Replication.

    Science.gov (United States)

    Chong, Weng Man; Hsu, Shih-Chin; Kao, Wei-Ting; Lo, Chieh-Wen; Lee, Kuan-Ying; Shao, Jheng-Syuan; Chen, Yi-Hung; Chang, Justin; Chen, Steve S-L; Yu, Ming-Jiun

    2016-02-19

    The non-structural protein 5A (NS5A) is a hepatitis C virus (HCV) protein indispensable for the viral life cycle. Many prior papers have pinpointed several serine residues in the low complexity sequence I region of NS5A responsible for NS5A phosphorylation; however, the functions of specific phosphorylation sites remained obscure. Using phosphoproteomics, we identified three phosphorylation sites (serines 222, 235, and 238) in the NS5A low complexity sequence I region. Reporter virus and replicon assays using phosphorylation-ablated alanine mutants of these sites showed that Ser-235 dominated over Ser-222 and Ser-238 in HCV replication. Immunoblotting using an Ser-235 phosphorylation-specific antibody showed a time-dependent increase in Ser-235 phosphorylation that correlated with the viral replication activity. Ser-235 phosphorylated NS5A co-localized with double-stranded RNA, consistent with its role in HCV replication. Mechanistically, Ser-235 phosphorylation probably promotes the replication complex formation via increasing NS5A interaction with the human homologue of the 33-kDa vesicle-associated membrane protein-associated protein. Casein kinase Iα (CKIα) directly phosphorylated Ser-235 in vitro. Inhibition of CKIα reduced Ser-235 phosphorylation and the HCV RNA levels in the infected cells. We concluded that NS5A Ser-235 phosphorylated by CKIα probably promotes HCV replication via increasing NS5A interaction with the 33-kDa vesicle-associated membrane protein-associated protein. PMID:26702051

  16. The barley EST DNA Replication and Repair Database (bEST-DRRD as a tool for the identification of the genes involved in DNA replication and repair

    Directory of Open Access Journals (Sweden)

    Gruszka Damian

    2012-06-01

    Full Text Available Abstract Background The high level of conservation of genes that regulate DNA replication and repair indicates that they may serve as a source of information on the origin and evolution of the species and makes them a reliable system for the identification of cross-species homologs. Studies that had been conducted to date shed light on the processes of DNA replication and repair in bacteria, yeast and mammals. However, there is still much to be learned about the process of DNA damage repair in plants. Description These studies, which were conducted mainly using bioinformatics tools, enabled the list of genes that participate in various pathways of DNA repair in Arabidopsis thaliana (L. Heynh to be outlined; however, information regarding these mechanisms in crop plants is still very limited. A similar, functional approach is particularly difficult for a species whose complete genomic sequences are still unavailable. One of the solutions is to apply ESTs (Expressed Sequence Tags as the basis for gene identification. For the construction of the barley EST DNA Replication and Repair Database (bEST-DRRD, presented here, the Arabidopsis nucleotide and protein sequences involved in DNA replication and repair were used to browse for and retrieve the deposited sequences, derived from four barley (Hordeum vulgare L. sequence databases, including the “Barley Genome version 0.05” database (encompassing ca. 90% of barley coding sequences and from two databases covering the complete genomes of two monocot models: Oryza sativa L. and Brachypodium distachyon L. in order to identify homologous genes. Sequences of the categorised Arabidopsis queries are used for browsing the repositories, which are located on the ViroBLAST platform. The bEST-DRRD is currently used in our project during the identification and validation of the barley genes involved in DNA repair. Conclusions The presented database provides information about the Arabidopsis genes involved in

  17. High-Resolution Profiling of Drosophila Replication Start Sites Reveals a DNA Shape and Chromatin Signature of Metazoan Origins

    Directory of Open Access Journals (Sweden)

    Federico Comoglio

    2015-05-01

    Full Text Available At every cell cycle, faithful inheritance of metazoan genomes requires the concerted activation of thousands of DNA replication origins. However, the genetic and chromatin features defining metazoan replication start sites remain largely unknown. Here, we delineate the origin repertoire of the Drosophila genome at high resolution. We address the role of origin-proximal G-quadruplexes and suggest that they transiently stall replication forks in vivo. We dissect the chromatin configuration of replication origins and identify a rich spatial organization of chromatin features at initiation sites. DNA shape and chromatin configurations, not strict sequence motifs, mark and predict origins in higher eukaryotes. We further examine the link between transcription and origin firing and reveal that modulation of origin activity across cell types is intimately linked to cell-type-specific transcriptional programs. Our study unravels conserved origin features and provides unique insights into the relationship among DNA topology, chromatin, transcription, and replication initiation across metazoa.

  18. Identification of replication factor C from Saccharomyces cerevisiae: a component of the leading-strand DNA replication complex.

    OpenAIRE

    Fien, K; Stillman, B

    1992-01-01

    A number of proteins have been isolated from human cells on the basis of their ability to support DNA replication in vitro of the simian virus 40 (SV40) origin of DNA replication. One such protein, replication factor C (RFC), functions with the proliferating cell nuclear antigen (PCNA), replication protein A (RPA), and DNA polymerase delta to synthesize the leading strand at a replication fork. To determine whether these proteins perform similar roles during replication of DNA from origins in...

  19. Surrounding Moving Obstacle Detection for Autonomous Driving Using Stereo Vision

    Directory of Open Access Journals (Sweden)

    Hao Sun

    2013-06-01

    Full Text Available Detection and tracking surrounding moving obstacles such as vehicles and pedestrians are crucial for the safety of mobile robotics and autonomous vehicles. This is especially the case in urban driving scenarios. This paper presents a novel framework for surrounding moving obstacles detection using binocular stereo vision. The contributions of our work are threefold. Firstly, a multiview feature matching scheme is presented for simultaneous stereo correspondence and motion correspondence searching. Secondly, the multiview geometry constraint derived from the relative camera positions in pairs of consecutive stereo views is exploited for surrounding moving obstacles detection. Thirdly, an adaptive particle filter is proposed for tracking of multiple moving obstacles in surrounding areas. Experimental results from real‐world driving sequences demonstrate the effectiveness and robustness of the proposed framework.

  20. Insights into the Determination of the Templating Nucleotide at the Initiation of φ29 DNA Replication.

    Science.gov (United States)

    del Prado, Alicia; Lázaro, José M; Longás, Elisa; Villar, Laurentino; de Vega, Miguel; Salas, Margarita

    2015-11-01

    Bacteriophage φ29 from Bacillus subtilis starts replication of its terminal protein (TP)-DNA by a protein-priming mechanism. To start replication, the DNA polymerase forms a heterodimer with a free TP that recognizes the replication origins, placed at both 5' ends of the linear chromosome, and initiates replication using as primer the OH-group of Ser-232 of the TP. The initiation of φ29 TP-DNA replication mainly occurs opposite the second nucleotide at the 3' end of the template. Earlier analyses of the template position that directs the initiation reaction were performed using single-stranded and double-stranded oligonucleotides containing the replication origin sequence without the parental TP. Here, we show that the parental TP has no influence in the determination of the nucleotide used as template in the initiation reaction. Previous studies showed that the priming domain of the primer TP determines the template position used for initiation. The results obtained here using mutant TPs at the priming loop where Ser-232 is located indicate that the aromatic residue Phe-230 is one of the determinants that allows the positioning of the penultimate nucleotide at the polymerization active site to direct insertion of the initiator dAMP during the initiation reaction. The role of Phe-230 in limiting the internalization of the template strand in the polymerization active site is discussed. PMID:26400085

  1. Separation of the transcriptional activation and replication functions of the bovine papillomavirus-1 E2 protein.

    Science.gov (United States)

    Winokur, P L; McBride, A A

    1992-11-01

    Replication of bovine papillomavirus-1 (BPV-1) DNA requires two viral gene products, the E1 protein and the full-length E2 protein. The 48 kDa E2 protein is a site-specific DNA-binding protein that binds to several sites which lie adjacent to the BPV-1 origin of replication. The 85 amino acid C-terminal domain contains the specific DNA binding and dimerization properties of the protein. The approximately 200 amino acid N-terminal domain is crucial for transcriptional activation. Both of these domains are highly conserved among different papillomaviruses. An internal hinge region separates the two functional domains. The region varies in amino acid sequence and length among the E2 proteins of different papillomaviruses. A series of mutations were constructed within the E2 open reading frame which delete various regions of the conserved DNA binding and transactivation domains as well as the internal hinge region. Two mutated E2 proteins that lack portions of the conserved DNA-binding domain but which support DNA replication were identified using transient replication assays. These mutated E2 proteins were unable to function as transcriptional activators. Conversely, two E2 proteins containing large deletions of the hinge region were able to activate transcription, but were defective for replication. Thus, the replication and transactivation functions of the E2 protein are separable. PMID:1327758

  2. DNA moves sequentially towards the nuclear matrix during DNA replication in vivo

    Directory of Open Access Journals (Sweden)

    Aranda-Anzaldo Armando

    2011-01-01

    Full Text Available Abstract Background In the interphase nucleus of metazoan cells DNA is organized in supercoiled loops anchored to a nuclear matrix (NM. There is varied evidence indicating that DNA replication occurs in replication factories organized upon the NM and that DNA loops may correspond to the actual replicons in vivo. In normal rat liver the hepatocytes are arrested in G0 but they synchronously re-enter the cell cycle after partial-hepatectomy leading to liver regeneration in vivo. We have previously determined in quiescent rat hepatocytes that a 162 kbp genomic region containing members of the albumin gene family is organized into five structural DNA loops. Results In the present work we tracked down the movement relative to the NM of DNA sequences located at different points within such five structural DNA loops during the S phase and after the return to cellular quiescence during liver regeneration. Our results indicate that looped DNA moves sequentially towards the NM during replication and then returns to its original position in newly quiescent cells, once the liver regeneration has been achieved. Conclusions Looped DNA moves in a sequential fashion, as if reeled in, towards the NM during DNA replication in vivo thus supporting the notion that the DNA template is pulled progressively towards the replication factories on the NM so as to be replicated. These results provide further evidence that the structural DNA loops correspond to the actual replicons in vivo.

  3. Elements of Autonomous Self-Reconfigurable Robots

    DEFF Research Database (Denmark)

    Christensen, David Johan

    In this thesis, we study several central elements of autonomous self-reconfigurable modular robots. Unlike conventional robots such robots are: i) Modular, since robots are assembled from numerous robotic modules. ii) Reconfigurable, since the modules can be combined in a variety of ways. iii) Self......-reconfigurable, since the modules themselves are able to change how they are combined. iv) Autonomous, since robots control themselves without human guidance. Such robots are attractive to study since they in theory have several desirable characteristics, such as versatility, reliability and cheapness. In practice...... however, it is challenging to realize such characteristics since state-of-the-art systems and solutions suffer from several inherent technical and theoretical problems and limitations. In this thesis, we address these challenges by exploring four central elements of autonomous self-reconfigurable modular...

  4. A Collaborative Knowledge Plane for Autonomic Networks

    Science.gov (United States)

    Mbaye, Maïssa; Krief, Francine

    Autonomic networking aims to give network components self-managing capabilities. Several autonomic architectures have been proposed. Each of these architectures includes sort of a knowledge plane which is very important to mimic an autonomic behavior. Knowledge plane has a central role for self-functions by providing suitable knowledge to equipment and needs to learn new strategies for more accuracy.However, defining knowledge plane's architecture is still a challenge for researchers. Specially, defining the way cognitive supports interact each other in knowledge plane and implementing them. Decision making process depends on these interactions between reasoning and learning parts of knowledge plane. In this paper we propose a knowledge plane's architecture based on machine learning (inductive logic programming) paradigm and situated view to deal with distributed environment. This architecture is focused on two self-functions that include all other self-functions: self-adaptation and self-organization. Study cases are given and implemented.

  5. An Autonomous Reference Frame for Relativistic GNSS

    CERN Document Server

    Kostić, Uroš; Carloni, Sante; Delva, Pacôme; Gomboc, Andreja

    2014-01-01

    Current GNSS systems rely on global reference frames which are fixed to the Earth (via the ground stations) so their precision and stability in time are limited by our knowledge of the Earth dynamics. These drawbacks could be avoided by giving to the constellation of satellites the possibility of constituting by itself a primary and autonomous positioning system, without any a priori realization of a terrestrial reference frame. Our work shows that it is possible to construct such a system, an Autonomous Basis of Coordinates, via emission coordinates. Here we present the idea of the Autonomous Basis of Coordinates and its implementation in the perturbed space-time of Earth, where the motion of satellites, light propagation, and gravitational perturbations are treated in the formalism of general relativity.

  6. Autonomic dysfunction in chronic liver disease

    Directory of Open Access Journals (Sweden)

    Frith J

    2011-08-01

    Full Text Available James Frith, Julia L NewtonNIHR Biomedical Research Centre in Ageing, Institute for Ageing and Health, Newcastle University, Newcastle, UKAbstract: It is becoming increasingly clear that quality of life (QOL is impaired in those with chronic liver disease (CLD. One of the most important contributors to impaired QOL is the symptomatic burden which can range from slight to debilitating. Autonomic dysfunction accounts for a significant proportion of these symptoms, which can be common, non-specific and challenging to treat. Investigating the autonomic nervous system can be straight forward and can assist the clinician to diagnose and treat specific symptoms. Evidence-based treatment options for autonomic symptoms, specifically in CLD, can be lacking and must be extrapolated from other studies and expert opinion. For those with severely impaired quality of life, liver transplantation may offer an improvement; however, more research is needed to confirm this.Keywords: quality of life, treatment, fatigue, angiotensin II

  7. Enhanced mission performance from autonomous instrument guidance

    DEFF Research Database (Denmark)

    Jørgensen, John Leif; Jørgensen, Peter Siegbjørn; Betto, Maurizio;

    2006-01-01

    During the last decade improvements in electronics, on-board processing power and software design has lead to significant advances in the development of autonomous instrumentation for spacecraft use. The Advanced Stellar Compass (ASC) and the newly developed micro-ASC (mu ASC) are excellent...... and power consumption makes the mu ASC an ideal instrument for small, high yielding satellite missions. The ASC has hitherto been used by the satellite AOCS and the high accuracy scientific instrument for attitude recovery (among others onboard ORSTED, CHAMP, and GRACE), and satellite high accuracy target...... acquisition and pointing (PROBA). Here three applications of the mu ASC as an autonomous onboard precision guide for precision vector instrumentation are presented. These are autonomous onboard antenna guidance, telescope guidance and tracking and high accuracy and wide range laser rangers....

  8. Autonomous driving technical, legal and social aspects

    CERN Document Server

    Gerdes, J; Lenz, Barbara; Winner, Hermann

    2016-01-01

    This book takes a look at fully automated, autonomous vehicles and discusses many open questions: How can autonomous vehicles be integrated into the current transportation system with diverse users and human drivers? Where do automated vehicles fall under current legal frameworks? What risks are associated with automation and how will society respond to these risks? How will the marketplace react to automated vehicles and what changes may be necessary for companies? Experts from Germany and the United States define key societal, engineering, and mobility issues related to the automation of vehicles. They discuss the decisions programmers of automated vehicles must make to enable vehicles to perceive their environment, interact with other road users, and choose actions that may have ethical consequences. The authors further identify expectations and concerns that will form the basis for individual and societal acceptance of autonomous driving. While the safety benefits of such vehicles are tremendous, the auth...

  9. Autonomous forward inference via DNA computing

    Institute of Scientific and Technical Information of China (English)

    Fu Yan; Li Gen; Li Yin; Meng Dazhi

    2007-01-01

    Recent studies direct the researchers into building DNA computing machines with intelligence, which is measured by three main points: autonomous, programmable and able to learn and adapt. Logical inference plays an important role in programmable information processing or computing. Here we present a new method to perform autonomous molecular forward inference for expert system.A novel repetitive recognition site (RRS) technique is invented to design rule-molecules in knowledge base. The inference engine runs autonomously by digesting the rule-molecule, using a Class ⅡB restriction enzyme PpiⅠ. Concentration model has been built to show the feasibility of the inference process under ideal chemical reaction conditions. Moreover, we extend to implement a triggering communication between molecular automata, as a further application of the RRS technique in our model.

  10. Technology readiness level six and autonomous mobility

    Science.gov (United States)

    Bodt, Barry A.; Camden, Rick S.

    2004-09-01

    During FY03, the U.S. Army Research Laboratory undertook a series of experiments designed to assess the maturity of autonomous mobility technology for the Future Combat Systems Armed Robotic Vehicle concept. The experiments assessed the technology against a level 6 standard in the technology readiness level (TRL) maturation schedule identified by a 1999 Government Accounting Office report. During the course of experimentation, 646 missions were conducted over a total distance of ~560 km and time of ~100 hr. Autonomous operation represented 96% and 88% of total distance and time, respectively. To satisfy the TRL 6 "relevant environment" standard, several experimental factors were varied over the three-site test as part of a formal, statistical, experimental design. This paper reports the specific findings pertaining to relevant-environment questions that were posed for the study and lends additional support to the Lead System Integrator decision that TRL 6 has been attained for the autonomous navigation system.

  11. Blood pressure regulation in diabetic autonomic neuropathy

    DEFF Research Database (Denmark)

    Hilsted, J

    1985-01-01

    Defective blood pressure responses to standing, exercise and epinephrine infusions have been demonstrated in diabetic patients with autonomic neuropathy. The circulatory mechanisms underlying blood pressure responses to exercise and standing up in these patients are well characterized: In both...... experimental situations insufficient contraction of resistance vessels has been demonstrated. The vasoconstrictor defects demonstrated are of a magnitude sufficient to account for the prevailing hypotension. Furthermore, during exercise cardiac output is low in patients with autonomic neuropathy, a finding...... which may contribute to exercise hypotension in these patients. During hypoglycemia, blood pressure regulation seems intact in patients with autonomic neuropathy. This is probably due to release of substantial amounts of catecholamines during these experiments. During epinephrine infusions a substantial...

  12. Allele-specific analysis of DNA replication origins in mammalian cells.

    Science.gov (United States)

    Bartholdy, Boris; Mukhopadhyay, Rituparna; Lajugie, Julien; Aladjem, Mirit I; Bouhassira, Eric E

    2015-01-01

    The mechanisms that control the location and timing of firing of replication origins are poorly understood. Using a novel functional genomic approach based on the analysis of SNPs and indels in phased human genomes, we observe that replication asynchrony is associated with small cumulative variations in the initiation efficiency of multiple origins between the chromosome homologues, rather than with the activation of dormant origins. Allele-specific measurements demonstrate that the presence of G-quadruplex-forming sequences does not correlate with the efficiency of initiation. Sequence analysis reveals that the origins are highly enriched in sequences with profoundly asymmetric G/C and A/T nucleotide distributions and are almost completely depleted of antiparallel triplex-forming sequences. We therefore propose that although G4-forming sequences are abundant in replication origins, an asymmetry in nucleotide distribution, which increases the propensity of origins to unwind and adopt non-B DNA structure, rather than the ability to form G4, is directly associated with origin activity. PMID:25987481

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

    Science.gov (United States)

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

    2007-12-01

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

  14. Spacetime replication of continuous variable quantum information

    Science.gov (United States)

    Hayden, Patrick; Nezami, Sepehr; Salton, Grant; Sanders, Barry C.

    2016-08-01

    The theory of relativity requires that no information travel faster than light, whereas the unitarity of quantum mechanics ensures that quantum information cannot be cloned. These conditions provide the basic constraints that appear in information replication tasks, which formalize aspects of the behavior of information in relativistic quantum mechanics. In this article, we provide continuous variable (CV) strategies for spacetime quantum information replication that are directly amenable to optical or mechanical implementation. We use a new class of homologically constructed CV quantum error correcting codes to provide efficient solutions for the general case of information replication. As compared to schemes encoding qubits, our CV solution requires half as many shares per encoded system. We also provide an optimized five-mode strategy for replicating quantum information in a particular configuration of four spacetime regions designed not to be reducible to previously performed experiments. For this optimized strategy, we provide detailed encoding and decoding procedures using standard optical apparatus and calculate the recovery fidelity when finite squeezing is used. As such we provide a scheme for experimentally realizing quantum information replication using quantum optics.

  15. COPI is required for enterovirus 71 replication.

    Directory of Open Access Journals (Sweden)

    Jianmin Wang

    Full Text Available Enterovirus 71 (EV71, a member of the Picornaviridae family, is found in Asian countries where it causes a wide range of human diseases. No effective therapy is available for the treatment of these infections. Picornaviruses undergo RNA replication in association with membranes of infected cells. COPI and COPII have been shown to be involved in the formation of picornavirus-induced vesicles. Replication of several picornaviruses, including poliovirus and Echovirus 11 (EV11, is dependent on COPI or COPII. Here, we report that COPI, but not COPII, is required for EV71 replication. Replication of EV71 was inhibited by brefeldin A and golgicide A, inhibitors of COPI activity. Furthermore, we found EV71 2C protein interacted with COPI subunits by co-immunoprecipitation and GST pull-down assay, indicating that COPI coatomer might be directed to the viral replication complex through viral 2C protein. Additionally, because the pathway is conserved among different species of enteroviruses, it may represent a novel target for antiviral therapies.

  16. Extremal dynamics in random replicator ecosystems

    Energy Technology Data Exchange (ETDEWEB)

    Kärenlampi, Petri P., E-mail: petri.karenlampi@uef.fi

    2015-10-02

    The seminal numerical experiment by Bak and Sneppen (BS) is repeated, along with computations with replicator models, including a greater amount of features. Both types of models do self-organize, and do obey power-law scaling for the size distribution of activity cycles. However species extinction within the replicator models interferes with the BS self-organized critical (SOC) activity. Speciation–extinction dynamics ruins any stationary state which might contain a steady size distribution of activity cycles. The BS-type activity appears as a dissimilar phenomenon in comparison to speciation–extinction dynamics in the replicator system. No criticality is found from the speciation–extinction dynamics. Neither are speciations and extinctions in real biological macroevolution known to contain any diverging distributions, or self-organization towards any critical state. Consequently, biological macroevolution probably is not a self-organized critical phenomenon. - Highlights: • Extremal Dynamics organizes random replicator ecosystems to two phases in fitness space. • Replicator systems show power-law scaling of activity. • Species extinction interferes with Bak–Sneppen type mutation activity. • Speciation–extinction dynamics does not show any critical phase transition. • Biological macroevolution probably is not a self-organized critical phenomenon.

  17. TSH RECEPTOR GENETIC ALTERATIONS IN THE AUTONOMOUSLY FUNCTIONING THYROID ADENOMAS

    Institute of Scientific and Technical Information of China (English)

    施秉银; 李雪萍; 李社莉; 薛明战; 王毅; 徐莉

    2004-01-01

    Objective To determine the relationship between TSH receptor gene mutations and autonomously functioning thyroid adenomas (AFTAs). Methods The thyroid samples from 14 cases of diagnosed AFTAs were analyzed, with normal thyroid specimens adjacent to the tumors as controls. The 155 base pairs DNA fragments which encompassed the third cytoplasmic loop and the sixth transmembrane segments in the TSH receptor gene exon 10 were amplified by Polymerase chain reaction (PCR) and analyzed by the single-strand conformation polymorphism (SSCP). Direct sequencing of the PCR products was performed with Prism Dye Terminator Cycle Sequencing Core Kit. Results 6 of 14 AFTA specimens displayed abnormal migration in SSCP analysis. In sequence analysis of 3 abnormally migrated samples, one base substitution at nucleotide 1957 (A to C) and two same insertion mutations of one adenosine nucleotide between nucleotide 1972 and 1973 were identified. No mutations were found in controls. Conclusion This study confirmed the presence of TSH receptor gene mutations in AFTAs; both one-point substitution mutation and one-base insertion mutation were found to be responsible for the pathogenesis of AFTAs.

  18. Connecting orbits of autonomous Lagrangian systems

    International Nuclear Information System (INIS)

    In contrast to the time-dependent case, the time-t-section of Mañé set of autonomous Lagrangian systems is independent of time, thus, it is nowhere disconnected. This causes some difference in the study of dynamics, for instance, Mather's c-equivalence cannot exist among different cohomology classes if they are not in a flat of the α-function (cf (Bernard 2002 Ann. Inst. Fourier 52 1533–68.)). In this paper, we show how to construct connecting orbits in autonomous systems, and propose a modified notion of c-equivalence. We also apply the result to construct diffusion orbits in an energy surface

  19. Dynamic biomaterials: toward engineering autonomous feedback.

    Science.gov (United States)

    Morris, Eliza; Chavez, Michael; Tan, Cheemeng

    2016-06-01

    Dynamic biomaterials are biocompatible engineered systems capable of sensing and actively responding to their surrounding environment. They are of growing interest, both as models in basic research to understand complex cellular systems and in medical applications. Here, we review recent advances in nano-scale and micro-scale biomaterials, specifically artificial cells consisting of compartmentalized biochemical reactions and biologically compatible hydrogels. These dynamic biomaterials respond to stimuli through triggered reactions, reaction cascades, logic gates, and autonomous feedback loops. We outline the advances and remaining challenges in implementing such 'smart' biomaterials capable of autonomously responding to environmental stimuli. PMID:26974245

  20. Autonomous operations through onboard artificial intelligence

    Science.gov (United States)

    Sherwood, R. L.; Chien, S.; Castano, R.; Rabideau, G.

    2002-01-01

    The Autonomous Sciencecraft Experiment (ASE) will fly onboard the Air Force TechSat 21 constellation of three spacecraft scheduled for launch in 2006. ASE uses onboard continuous planning, robust task and goal-based execution, model-based mode identification and reconfiguration, and onboard machine learning and pattern recognition to radically increase science return by enabling intelligent downlink selection and autonomous retargeting. Demonstration of these capabilities in a flight environment will open up tremendous new opportunities in planetary science, space physics, and earth science that would be unreachable without this technology.

  1. Advanced control architecture for autonomous vehicles

    Science.gov (United States)

    Maurer, Markus; Dickmanns, Ernst D.

    1997-06-01

    An advanced control architecture for autonomous vehicles is presented. The hierarchical architecture consists of four levels: a vehicle level, a control level, a rule-based level and a knowledge-based level. A special focus is on forms of internal representation, which have to be chosen adequately for each level. The control scheme is applied to VaMP, a Mercedes passenger car which autonomously performs missions on German freeways. VaMP perceives the environment with its sense of vision and conventional sensors. It controls its actuators for locomotion and attention focusing. Modules for perception, cognition and action are discussed.

  2. Autonomous control of distributed storages in microgrids

    DEFF Research Database (Denmark)

    Loh, Poh Chiang; Blaabjerg, Frede

    2011-01-01

    Operation of distributed generators in microgrids has widely been discussed, but would not be fully autonomous, if distributed storages are not considered. Storages in general are important, since they provide energy buffering to load changes, energy leveling to source variations and ride......-through enhancement to the overall microgrids. Recognizing their importance, this paper presents a scheme for sharing power among multiple distributed storages, in coordination with the distributed sources and loads. The scheme prompts the storages to autonomously sense for system conditions, requesting for maximum...

  3. Towards Autonomous Control of HVAC Systems

    DEFF Research Database (Denmark)

    Brath, P.

    This thesis considered development of an autonomous control system for heating ventilation and air conditioning applications. By including auto-tuning, adaptation, diagnosis and supervision functions in the control system used in the HVAC industry will move the control of HVAC systems towards...... autonomous control. Together with better tuned controllers and more dedicated control it would be possible to decrease the energy consumption, save money and increase the indoor air climate. A flexible HVAC test system was designed and implemented. Standard components and sensors were used in the design...... experiments on the HVAC test system and by using simulations....

  4. Evolutionary strategy for achieving autonomous navigation

    Science.gov (United States)

    Gage, Douglas W.

    1999-01-01

    An approach is presented for the evolutionary development of supervised autonomous navigation capabilities for small 'backpackable' ground robots, in the context of a DARPA- sponsored program to provide robotic support to small units of dismounted warfighters. This development approach relies on the implementation of a baseline visual serving navigation capability, including tools to support operator oversight and override, which is then enhanced with semantically referenced commands and a mission scripting structure. As current and future machine perception techniques are able to automatically designate visual serving goal points, this approach should provide a natural evolutionary pathway to higher levels of autonomous operation and reduced requirements for operator intervention.

  5. Blunted autonomic response in cluster headache patients

    DEFF Research Database (Denmark)

    Barloese, Mads; Brinth, Louise; Mehlsen, Jesper;

    2015-01-01

    BACKGROUND: Cluster headache (CH) is a disabling headache disorder with chronobiological features. The posterior hypothalamus is involved in CH pathophysiology and is a hub for autonomic control. We studied autonomic response to the head-up tilt table test (HUT) including heart rate variability...... (HRV) in CH patients and compared results to healthy controls. METHODS AND MATERIALS: Twenty-seven episodic and chronic CH patients and an equal number of age-, sex- and BMI-matched controls were included. We analyzed responses to HUT in the time and frequency domain and by non-linear analysis. RESULTS...

  6. Emerging Technologies for Autonomous Language Learning

    Directory of Open Access Journals (Sweden)

    Mark Warschauer

    2011-09-01

    Full Text Available Drawing on a lengthier review completed for the US National Institute for Literacy, this paper examines emerging technologies that are applicable to self-access and autonomous learning in the areas of listening and speaking, collaborative writing, reading and language structure, and online interaction. Digital media reviewed include podcasts, blogs, wikis, online writing sites, text-scaffolding software, concordancers, multiuser virtual environments, multiplayer games, and chatbots. For each of these technologies, we summarize recent research and discuss possible uses for autonomous language learning.

  7. Autonomous control of multi-fingered hand

    Institute of Scientific and Technical Information of China (English)

    JIANG Li; LIU Hong

    2006-01-01

    This paper describes a novel autonomous control strategy of multi-fingered hand based on a modular control system of dexterous manipulation. A simple proportional-integral-derivative(PID) position control with friction compensation, which requires few friction parameters, is used to realize accurate and smooth trajectory tracking in pregrasp phase. In grasp and manipulation phases, an event-driven switcher is adopted to determine the switching between unconstrained position control and constrained torque control, and an improved explicit integral force control strategy is implemented to realize simultaneously stable contact transition and accurate force tracking. Experimental results have verified the effectiveness of the proposed autonomous control strategy of multi-fingered hand.

  8. The V Protein of Canine Distemper Virus Is Required for Virus Replication in Human Epithelial Cells

    OpenAIRE

    Noriyuki Otsuki; Yuichiro Nakatsu; Toru Kubota; Tsuyoshi Sekizuka; Fumio Seki; Kouji Sakai; Makoto Kuroda; Ryoji Yamaguchi; Makoto Takeda

    2013-01-01

    Canine distemper virus (CDV) becomes able to use human receptors through a single amino acid substitution in the H protein. In addition, CDV strains possessing an intact C protein replicate well in human epithelial H358 cells. The present study showed that CDV strain 007Lm, which was isolated from lymph node tissue of a dog with distemper, failed to replicate in H358 cells, although it possessed an intact C protein. Sequence analyses suggested that a cysteine-to-tyrosine substitution at posit...

  9. Monitoring the determinants of efficient viral replication using Classical Swine Fever Virus-reporter replicons

    DEFF Research Database (Denmark)

    Risager, Peter Christian; Everett, Helen; Crooke, Helen;

    2012-01-01

    proteins considered non-essential for RNA replication were constructed and these deletions were replaced with an in-frame insertion of the Renilla luciferase (Rluc) sequence. RNA transcripts from these replicons should be translated as a single functional open reading frame. Full-genome cDNAs (~10-12,3 kb......) were amplified from the BACs using a stable long-PCR method and in vitro transcripts were assayed in permissive cells. The CSFV-Rluc replicons were evaluated for their ability to replicate using immunofluorescence staining (-NS3 and -E2), and the Renilla luciferase assay. We conclude that Rluc...

  10. Initiating chromosome replication in E. coli: it makes sense to recycle

    OpenAIRE

    Leonard, Alan C.; Grimwade, Julia E.

    2009-01-01

    Initiating new rounds of Escherichia coli chromosome replication requires DnaA-ATP to unwind the replication origin, oriC, and load DNA helicase. In this issue of Genes & Development, Fujimitsu and colleagues (pp. 1221–1233) demonstrate that two chromosomal sites, termed DARS (DnaA-reactivating sequences), recycle inactive DnaA-ADP into DnaA-ATP. Fujimitsu and colleagues propose these sites are necessary to attain the DnaA-ATP threshold during normal growth and are important regulators of ini...

  11. Less can be more: RNA-adapters may enhance coding capacity of replicators.

    Directory of Open Access Journals (Sweden)

    Folkert K de Boer

    Full Text Available It is still not clear how prebiotic replicators evolved towards the complexity found in present day organisms. Within the most realistic scenario for prebiotic evolution, known as the RNA world hypothesis, such complexity has arisen from replicators consisting solely of RNA. Within contemporary life, remarkably many RNAs are involved in modifying other RNAs. In hindsight, such RNA-RNA modification might have helped in alleviating the limits of complexity posed by the information threshold for RNA-only replicators. Here we study the possible role of such self-modification in early evolution, by modeling the evolution of protocells as evolving replicators, which have the opportunity to incorporate these mechanisms as a molecular tool. Evolution is studied towards a set of 25 arbitrary 'functional' structures, while avoiding all other (misfolded structures, which are considered to be toxic and increase the death-rate of a protocell. The modeled protocells contain a genotype of different RNA-sequences while their phenotype is the ensemble of secondary structures they can potentially produce from these RNA-sequences. One of the secondary structures explicitly codes for a simple sequence-modification tool. This 'RNA-adapter' can block certain positions on other RNA-sequences through antisense base-pairing. The altered sequence can produce an alternative secondary structure, which may or may not be functional. We show that the modifying potential of interacting RNA-sequences enables these protocells to evolve high fitness under high mutation rates. Moreover, our model shows that because of toxicity of misfolded molecules, redundant coding impedes the evolution of self-modification machinery, in effect restraining the evolvability of coding structures. Hence, high mutation rates can actually promote the evolution of complex coding structures by reducing redundant coding. Protocells can successfully use RNA-adapters to modify their genotype

  12. PTEN Controls the DNA Replication Process through MCM2 in Response to Replicative Stress

    Directory of Open Access Journals (Sweden)

    Jiawen Feng

    2015-11-01

    Full Text Available PTEN is a tumor suppressor frequently mutated in human cancers. PTEN inhibits the phosphatidylinositol 3-kinase (PI3K-AKT cascade, and nuclear PTEN guards the genome by multiple mechanisms. Here, we report that PTEN physically associates with the minichromosome maintenance complex component 2 (MCM2, which is essential for DNA replication. Specifically, PTEN dephosphorylates MCM2 at serine 41 (S41 and restricts replication fork progression under replicative stress. PTEN disruption results in unrestrained fork progression upon replication stalling, which is similar to the phenotype of cells expressing the phosphomimic MCM2 mutant S41D. Moreover, PTEN is necessary for prevention of chromosomal aberrations under replication stress. This study demonstrates that PTEN regulates DNA replication through MCM2 and loss of PTEN function leads to replication defects and genomic instability. We propose that PTEN plays a critical role in maintaining genetic stability through a replication-specific mechanism, and this is a crucial facet of PTEN tumor suppressor activity.

  13. 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...

  14. A Priori User Acceptance and the Perceived Driving Pleasure in Semi-autonomous and Autonomous Vehicles

    DEFF Research Database (Denmark)

    Bjørner, Thomas

    The aim of this minor pilot study is, from a sociological user perspective, to explore a priori user acceptance and the perceived driving pleasure in semi- autonomous and autonomous vehicles. The methods used were 13 in-depth interviews while having participants watch video examples within four...... different scenarios. After each scenario, two different numerical rating scales were used. There was a tendency toward positive attitudes regarding semi- autonomous driving systems, especially the use of a parking assistant and while driving in city traffic congestion. However, there were also major...

  15. Evolution of Database Replication Technologies for WLCG

    Science.gov (United States)

    Baranowski, Zbigniew; Lobato Pardavila, Lorena; Blaszczyk, Marcin; Dimitrov, Gancho; Canali, Luca

    2015-12-01

    In this article we summarize several years of experience on database replication technologies used at WLCG and we provide a short review of the available Oracle technologies and their key characteristics. One of the notable changes and improvement in this area in recent past has been the introduction of Oracle GoldenGate as a replacement of Oracle Streams. We report in this article on the preparation and later upgrades for remote replication done in collaboration with ATLAS and Tier 1 database administrators, including the experience from running Oracle GoldenGate in production. Moreover, we report on another key technology in this area: Oracle Active Data Guard which has been adopted in several of the mission critical use cases for database replication between online and offline databases for the LHC experiments.

  16. Extremal dynamics in random replicator ecosystems

    Science.gov (United States)

    Kärenlampi, Petri P.

    2015-10-01

    The seminal numerical experiment by Bak and Sneppen (BS) is repeated, along with computations with replicator models, including a greater amount of features. Both types of models do self-organize, and do obey power-law scaling for the size distribution of activity cycles. However species extinction within the replicator models interferes with the BS self-organized critical (SOC) activity. Speciation-extinction dynamics ruins any stationary state which might contain a steady size distribution of activity cycles. The BS-type activity appears as a dissimilar phenomenon in comparison to speciation-extinction dynamics in the replicator system. No criticality is found from the speciation-extinction dynamics. Neither are speciations and extinctions in real biological macroevolution known to contain any diverging distributions, or self-organization towards any critical state. Consequently, biological macroevolution probably is not a self-organized critical phenomenon.

  17. Replicating Cardiovascular Condition-Birth Month Associations

    Science.gov (United States)

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

    2016-01-01

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

  18. Evolution of Database Replication Technologies for WLCG

    CERN Document Server

    Baranowski, Zbigniew; Blaszczyk, Marcin; Dimitrov, Gancho; Canali, Luca

    2015-01-01

    In this article we summarize several years of experience on database replication technologies used at WLCG and we provide a short review of the available Oracle technologies and their key characteristics. One of the notable changes and improvement in this area in recent past has been the introduction of Oracle GoldenGate as a replacement of Oracle Streams. We report in this article on the preparation and later upgrades for remote replication done in collaboration with ATLAS and Tier 1 database administrators, including the experience from running Oracle GoldenGate in production. Moreover, we report on another key technology in this area: Oracle Active Data Guard which has been adopted in several of the mission critical use cases for database replication between online and offline databases for the LHC experiments.

  19. New stopping criteria for segmenting DNA sequences

    CERN Document Server

    Li, W

    2001-01-01

    We propose a solution on the stopping criterion in segmenting inhomogeneous DNA sequences with complex statistical patterns. This new stopping criterion is based on Bayesian Information Criterion (BIC) in the model selection framework. When this stopping criterion is applied to a left telomere sequence of yeast Saccharomyces cerevisiae and the complete genome sequence of bacterium Escherichia coli, borders of biologically meaningful units were identified (e.g. subtelomeric units, replication origin, and replication terminus), and a more reasonable number of domains was obtained. We also introduce a measure called segmentation strength which can be used to control the delineation of large domains. The relationship between the average domain size and the threshold of segmentation strength is determined for several genome sequences.

  20. ADDING A NEW SITE IN AN EXISTING ORACLE MULTIMASTER REPLICATION WITHOUT QUIESCING THE REPLICATION

    Directory of Open Access Journals (Sweden)

    Hakik Paci

    2011-09-01

    Full Text Available This paper presents a new solution, which adds a new database server on an existing Oracle MultimasterData replication system with Online Instantiation method. During this time the system is down, because wecannot execute DML statements on replication objects but we can only make queries. The time for addingthe new database server depends on the number of objects, on the replication group and on the networkconditions. We propose to add a new layer between replication objects and the database sessions, whichcontain DML statements. The layer eliminates the system down time exploiting our developed packages.The packages will be active only during the addition of a new site process and will modify all DMLstatements and queries based on replication objects.

  1. Advances in autonomous systems for space exploration missions

    Science.gov (United States)

    Smith, B. D.; Gross, A. R.; Clancy, D. J.; Cannon, H. N.; Barrett, A.; Mjolssness, E.; Muscettola, N.; Chien, S.; Johnson, A.

    2001-01-01

    This paper focuses on new and innovative software for remote, autonomous, space systems flight operation, including distributed autonomous systems, flight test results, and implications and directions for future systems.

  2. A Rare Association of Trigeminal Autonomic Cephalgia: Pontine Capillary Telangiectasia

    OpenAIRE

    Gocmen, Rahsan; Kurt, Erdal; Arslan, Sabina; Unal-Cevik, Isin; Karli Oguz, Kader; Tezer, F Irsel

    2015-01-01

    This report describes a case of pontine capillary telangiectasia in a 43-year-old woman with a clinical diagnosis of trigeminal autonomic cephalgia. The possible association with pontine capillary telangiectasia and trigeminal autonomic cephalgia is discussed.

  3. The replication of expansive production knowledge

    DEFF Research Database (Denmark)

    Wæhrens, Brian Vejrum; Yang, Cheng; Madsen, Erik Skov

    2012-01-01

    ; and (2) rather than being viewed as alternative approaches, templates and principles should be seen as complementary once the transfer motive moves beyond pure replication. Research limitations – The concepts introduced in this paper were derived from two Danish cases. While acceptable for theory...... exploration, the small sample size is an obvious limitation for generalisation. Practical implications – A roadmap for knowledge transfer within the replication of a production line is suggested, which, together with four managerial suggestions, provides strong support and clear directions to managers...

  4. Research on Distributed Dynamic Replication Management Policy

    Institute of Scientific and Technical Information of China (English)

    ZHOU Xu; LU Xian-liang; HOU Meng-shu; WU Jin

    2005-01-01

    This paper introduces replication management policies in distributed file system, and presents a novel decentralized dynamic replication management mechanism based on accessing frequency detecting named FDRM. In FDRM, in order to provide better system performance and reduce network traffic, system nodes scan their local replicas to monitor replicas' access pattern, and makes decision independently to add, delete or migrate replicas. In addition, the scanning interval of a replica is variable according to the accessing frequency to that replica, which makes FDRM more sensitive to the change of system behaviors, so that one can get better performance with less system overhead. Experiments show the efficiency and performance improvement of FSRM.

  5. Surface Microstructure Replication in Injection Moulding

    DEFF Research Database (Denmark)

    Hansen, Hans Nørgaard; Arlø, Uffe Rolf

    2005-01-01

    In recent years polymer components with surface microstructures have been in rising demand for applications such as lab-on-a-chip and optical components. Injection moulding has proven to be a feasible and efficient way to manufacture such components. In injection moulding the mould surface...... moulding of surface microstructures. Emphasis is put on the ability to replicate surface microstructures under normal injection moulding conditions, notably with low cost materials at low mould temperatures. The replication of surface microstructures in injection moulding has been explored...

  6. Replication technology for photonic band gap applications

    Science.gov (United States)

    Grigaliunas, V.; Kopustinskas, V.; Meskinis, S.; Margelevicius, M.; Mikulskas, I.; Tomasiunas, R.

    2001-06-01

    Replication technology was applied for photonic structure fabrication in silicon substrate. It was revealed, that thin thermoplastic polymer layers on silicon substrates may be patterned by hot embossing technique for dry etching masking. Ni mold used for plain hot embossing into polymer layers was fabricated by Ni electrochemical deposition on the reference silicon surface structure, which was obtained by direct electron beam (EB) writing and SF 6/N 2 reactive ion etching (RIE) technique. It is shown that the shape of replicated photonic structures is determined by RIE parameters.

  7. Replication, recombination, and repair: going for the gold.

    Science.gov (United States)

    Klein, Hannah L; Kreuzer, Kenneth N

    2002-03-01

    DNA recombination is now appreciated to be integral to DNA replication and cell survival. Recombination allows replication to successfully maneuver through the roadblocks of damaged or collapsed replication forks. The signals and controls that permit cells to transition between replication and recombination modes are now being identified.

  8. Origin of replication of the DNA of a herpesvirus (pseudorabies).

    OpenAIRE

    Ben-Porat, T; Veach, R A

    1980-01-01

    During the first round of the replication of pseudorabies virus DNA, replicating DNA is mainly in the form of circles. The main origin of replication is located inthe region of the molecule bearing the inverted repeat. Replication proceeds unidirectionally from the origin.

  9. The spatiotemporal program of DNA replication is associated with specific combinations of chromatin marks in human cells.

    Directory of Open Access Journals (Sweden)

    Franck Picard

    2014-05-01

    Full Text Available The duplication of mammalian genomes is under the control of a spatiotemporal program that orchestrates the positioning and the timing of firing of replication origins. The molecular mechanisms coordinating the activation of about [Formula: see text] predicted origins remain poorly understood, partly due to the intrinsic rarity of replication bubbles, making it difficult to purify short nascent strands (SNS. The precise identification of origins based on the high-throughput sequencing of SNS constitutes a new methodological challenge. We propose a new statistical method with a controlled resolution, adapted to the detection of replication origins from SNS data. We detected an average of 80,000 replication origins in different cell lines. To evaluate the consistency between different protocols, we compared SNS detections with bubble trapping detections. This comparison demonstrated a good agreement between genome-wide methods, with 65% of SNS-detected origins validated by bubble trapping, and 44% of bubble trapping origins validated by SNS origins, when compared at the same resolution. We investigated the interplay between the spatial and the temporal programs of replication at fine scales. We show that most of the origins detected in regions replicated in early S phase are shared by all the cell lines investigated whereas cell-type-specific origins tend to be replicated in late S phase. We shed a new light on the key role of CpG islands, by showing that 80% of the origins associated with CGIs are constitutive. Our results further show that at least 76% of CGIs are origins of replication. The analysis of associations with chromatin marks at different timing of cell division revealed new potential epigenetic regulators driving the spatiotemporal activity of replication origins. We highlight the potential role of H4K20me1 and H3K27me3, the coupling of which is correlated with increased efficiency of replication origins, clearly identifying those

  10. College English Students’ Autonomous Learning Motivation and Cultivation Model Research

    Institute of Scientific and Technical Information of China (English)

    王艳荣; 李娥

    2015-01-01

    Studying the autonomous learning motivation and excitation model can stimulate intrinsic motivation of foreign language learners,develop students self-management strategy evaluation are very necessary.The purpose of this paper is to give students the skills of listening and speaking for their autonomous learning.Then study the cultivation and motivation of college English students autonomous learning,hoping to make students to learn autonomous learning and stimulate their motivation fully.

  11. Geometric integration of non-autonomous Hamiltonian problems

    OpenAIRE

    Marthinsen, Håkon; Owren, Brynjulf

    2014-01-01

    Symplectic integration of autonomous Hamiltonian systems is a well-known field of study in geometric numerical integration, but for non-autonomous systems the situation is less clear, since symplectic structure requires an even number of dimensions. We show that one possible extension of symplectic methods in the autonomous setting to the non-autonomous setting is obtained by using canonical transformations. Many existing methods fit into this framework. We also perform experiments which indi...

  12. Engineering an Ontology for Autonomous Systems - The OASys Ontology

    OpenAIRE

    Bermejo Alonso, Julita; Sanz Bravo, Ricardo; Rodríguez, Manuel; Hernández Corbato, Carlos

    2011-01-01

    This paper describes the development of an ontology for autonomous systems, as the initial stage of a research programe on autonomous systems’ engineering within a model-based control approach. The ontology aims at providing a unified conceptual framework for the autonomous systems’ stakeholders, from developers to software engineers. The modular ontology contains both generic and domain-specific concepts for autonomous systems description and engineering. The ontology serves as the basis in a ...

  13. A programming model and execution environment for autonomous systems

    OpenAIRE

    Razafimahefa, Chrislain

    2004-01-01

    This thesis presents the design and implementation of a programming model for autonomous systems. Autonomous systems are distributed systems based on wireless networks, mobile devices and the Internet. They are characterized by the high dynamics with which their configuration evolves. Ad hoc networks, a member of autonomous systems, illustrate this point since in these networks participants can join and leave at any time. Similarly in Peer-to-Peer networks, another member of autonomous system...

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

    Science.gov (United States)

    Natsume, Toyoaki; Tanaka, Tomoyuki U

    2010-01-01

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

  15. Regulation of eukaryotic DNA replication and nuclear structure

    Institute of Scientific and Technical Information of China (English)

    WUJIARUI

    1999-01-01

    In eukaryote,nuclear structure is a key component for the functions of eukaryotic cells.More and more evidences show that the nuclear structure plays important role in regulating DNA replication.The nuclear structure provides a physical barrier for the replication licensing,participates in the decision where DNA replication initiates,and organizes replication proteins as replication factory for DNA replication.Through these works,new concepts on the regulation of DNA replication have emerged,which will be discussed in this minireview.

  16. Sequence assembly

    DEFF Research Database (Denmark)

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

    2009-01-01

    and plays an important role in processing the information generated by these methods. Here, we provide a comprehensive overview of the current publicly available sequence assembly programs. We describe the basic principles of computational assembly along with the main concerns, such as repetitive sequences...

  17. Spatial abstraction for autonomous robot navigation.

    Science.gov (United States)

    Epstein, Susan L; Aroor, Anoop; Evanusa, Matthew; Sklar, Elizabeth I; Parsons, Simon

    2015-09-01

    Optimal navigation for a simulated robot relies on a detailed map and explicit path planning, an approach problematic for real-world robots that are subject to noise and error. This paper reports on autonomous robots that rely on local spatial perception, learning, and commonsense rationales instead. Despite realistic actuator error, learned spatial abstractions form a model that supports effective travel. PMID:26227680

  18. The CASCADAS Framework for Autonomic Communications

    Science.gov (United States)

    Baresi, Luciano; Ferdinando, Antonio Di; Manzalini, Antonio; Zambonelli, Franco

    An interesting approach to the design and development of the future Internet foresees a networked service eco-system capable of seamlessly offering services for human-to-human, human-to-machine and machine-to-machine interactions. This chapter builds in this direction by describing a distributed component-ware framework for autonomic and situation-aware communication developed within the CASCADAS project. The core of this framework is the Autonomic Communication Element (ACE), an innovative software abstraction capable of providing dynamically adaptable services that can be built, composed, and let evolve according to autonomic principles. Services are capable of adapting their logic to the dynamically changing context they operate in without human intervention. As a result, whenever the need arises, ACEs can be federated autonomously and produce new services on a situation-aware basis. Systems and, in particular, eco-systems can thus be conceived as collections of ACEs. The chapter introduces the concept of ACE and its different facets. It also presents the architecture of a prototype ACE-based platform and exemplifies the different concepts through a future Pervasive Behavioral Advertisement scenario.

  19. Control algorithms for autonomous robot navigation

    International Nuclear Information System (INIS)

    This paper examines control algorithm requirements for autonomous robot navigation outside laboratory environments. Three aspects of navigation are considered: navigation control in explored terrain, environment interactions with robot sensors, and navigation control in unanticipated situations. Major navigation methods are presented and relevance of traditional human learning theory is discussed. A new navigation technique linking graph theory and incidental learning is introduced

  20. Distributed formation control for autonomous robots

    NARCIS (Netherlands)

    Garcia de Marina Peinado, Hector Jesús

    2016-01-01

    This thesis addresses several theoretical and practical problems related to formation-control of autonomous robots. Formation-control aims to simultaneously accomplish the tasks of forming a desired shape by the robots and controlling their coordinated collective motion. This kind of robot performan

  1. Autonomous Robot Navigation In Public Nature Park

    DEFF Research Database (Denmark)

    Andersen, Jens Christian; Andersen, Nils Axel; Ravn, Ole;

    2005-01-01

    This extended abstract describes a project to make a robot travel autonomously across a public nature park. The challenge is to detect and follow the right path across junctions and open squares avoiding people and obstacles. The robot is equipped with a laser scanner, a (low accuracy) GPS, wheel...

  2. Simple autonomic seizures and ictal enuresis

    DEFF Research Database (Denmark)

    Rosenzweig, Ivana; Varga, Edina T; Akeson, Per;

    2011-01-01

    manifestation of the de novo post-traumatic simple autonomic seizures. Source analysis of the ictal epileptiform discharges showed activation of the cortical areas surrounding the right inferior frontal sulcus, adjacent to the lesional zone. The case depicted here further endorses recent neuroimaging studies...

  3. Autonomous biomorphic robots as platforms for sensors

    Energy Technology Data Exchange (ETDEWEB)

    Tilden, M.; Hasslacher, B.; Mainieri, R.; Moses, J.

    1996-10-01

    The idea of building autonomous robots that can carry out complex and nonrepetitive tasks is an old one, so far unrealized in any meaningful hardware. Tilden has shown recently that there are simple, processor-free solutions to building autonomous mobile machines that continuously adapt to unknown and hostile environments, are designed primarily to survive, and are extremely resistant to damage. These devices use smart mechanics and simple (low component count) electronic neuron control structures having the functionality of biological organisms from simple invertebrates to sophisticated members of the insect and crab family. These devices are paradigms for the development of autonomous machines that can carry out directed goals. The machine then becomes a robust survivalist platform that can carry sensors or instruments. These autonomous roving machines, now in an early stage of development (several proof-of-concept prototype walkers have been built), can be developed so that they are inexpensive, robust, and versatile carriers for a variety of instrument packages. Applications are immediate and many, in areas as diverse as prosthetics, medicine, space, construction, nanoscience, defense, remote sensing, environmental cleanup, and biotechnology.

  4. Autonomous biomorphic robots as platforms for sensors

    International Nuclear Information System (INIS)

    The idea of building autonomous robots that can carry out complex and nonrepetitive tasks is an old one, so far unrealized in any meaningful hardware. Tilden has shown recently that there are simple, processor-free solutions to building autonomous mobile machines that continuously adapt to unknown and hostile environments, are designed primarily to survive, and are extremely resistant to damage. These devices use smart mechanics and simple (low component count) electronic neuron control structures having the functionality of biological organisms from simple invertebrates to sophisticated members of the insect and crab family. These devices are paradigms for the development of autonomous machines that can carry out directed goals. The machine then becomes a robust survivalist platform that can carry sensors or instruments. These autonomous roving machines, now in an early stage of development (several proof-of-concept prototype walkers have been built), can be developed so that they are inexpensive, robust, and versatile carriers for a variety of instrument packages. Applications are immediate and many, in areas as diverse as prosthetics, medicine, space, construction, nanoscience, defense, remote sensing, environmental cleanup, and biotechnology

  5. Autonomous behavior of hematopoietic stem cells

    NARCIS (Netherlands)

    Kamminga, LM; Akkerman, [No Value; Weersing, E; Ausema, A; Dontje, B; Van Zant, G; de Haan, G

    2000-01-01

    Objective. Mechanisms that affect the function of primitive hematopoietic stem cells with long-term proliferative potential remain largely unknown. Here we assessed whether properties of stem cells are cell-extrinsically or cell-autonomously regulated. Materials and Methods. We developed a model in

  6. [Emotion, amygdala, and autonomic nervous system].

    Science.gov (United States)

    Ueyama, Takashi

    2012-10-01

    Emotion refers to the dynamic changes of feeling accompanied by the alteration of physical and visceral activities. Autonomic nervous system (sympathetic and parasympathetic) regulates the visceral activities. Therefore, monitoring and analyzing autonomic nervous activity help understand the emotional changes. To this end, the survey of the expression of immediate early genes (IEGs), such as c-Fos in the brain and target organs, and the viral transneuronal labeling method using the pseudorabies virus (PRV) have enabled the visualization of the neurocircuitry of emotion. By comparing c-Fos expression and data from PRV or other neuroanatomical labeling techniques, the central sites that regulate emotional stress-induced autonomic activation can be deduced. Such regions have been identified in the limbic system (e. g., the extended amygdaloid complex; lateral septum; and infralimbic, insular, and ventromedial temporal cortical regions), as well as in several hypothalamic and brainstem nuclei. The amygdala is structurally diverse and comprises several subnuclei, which play a role in emotional process via projections from the cortex and a variety of subcortical structures. All amygdaloid subnuclei receive psychological information from other limbic systems, while the lateral and central subnuclei receive peripheral and sensory information. Output to the hypothalamus and peripheral sympathetic system mainly originates from the medial amygdala. As estrogen receptor α, estrogen receptor β, and androgen receptor are expressed in the medial amygdala, sex steroids may modulate the autonomic nervous activities.

  7. Information Engineering in Autonomous Robot Software

    NARCIS (Netherlands)

    Ziafati, P.

    2015-01-01

    In order to engage and help in our daily life, autonomous robots are to operate in dynamic and unstructured environments and interact with people. As the robot's environment and its behaviour are getting more complex, so are the robot's software and the knowledge that the robot needs to carry out it

  8. Autonomous Learning from a Social Cognitive Perspective

    Science.gov (United States)

    Ponton, Michael K.; Rhea, Nancy E.

    2006-01-01

    The current perspective of autonomous learning defines it as the agentive exhibition of resourcefulness, initiative, and persistence in self-directed learning. As a form of human agency, it has been argued in the literature that this perspective should be consistent with Bandura's (1986) Social Cognitive Theory (SCT). The purpose of this article…

  9. Control algorithms for autonomous robot navigation

    Energy Technology Data Exchange (ETDEWEB)

    Jorgensen, C.C.

    1985-09-20

    This paper examines control algorithm requirements for autonomous robot navigation outside laboratory environments. Three aspects of navigation are considered: navigation control in explored terrain, environment interactions with robot sensors, and navigation control in unanticipated situations. Major navigation methods are presented and relevance of traditional human learning theory is discussed. A new navigation technique linking graph theory and incidental learning is introduced.

  10. Autonomous operation of distributed storages in microgrids

    DEFF Research Database (Denmark)

    Loh, Poh Chiang; Chai, Yi Kai; Li, Ding;

    2014-01-01

    Operation of distributed generators in microgrids has been widely discussed, but would not be fully autonomous if distributed energy storages are not considered. Storages are important since they provide energy buffering to load changes, energy levelling to source variations and ride-through enha......Operation of distributed generators in microgrids has been widely discussed, but would not be fully autonomous if distributed energy storages are not considered. Storages are important since they provide energy buffering to load changes, energy levelling to source variations and ride......-through enhancement to the microgrids. Recognising their importance, this study presents a scheme for sharing power among multiple distributed storages in coordination with the distributed sources and loads. The scheme prompts the storages to autonomously sense for local operating conditions, requesting for maximum...... to help with meeting the extra load demand. The described process takes place autonomously with energy eventually shared among the storages in proportion to their ratings. To test the concepts discussed, experiments have been performed with favourable results obtained for performance verification....

  11. A Multifunctional Coating for Autonomous Corrosion Control

    Science.gov (United States)

    Calle, Luz M.; Li, Wenyan; Buhrow, Jerry W.; Jolley, Scott t.

    2011-01-01

    Nearly all metals and their alloys are subject to corrosion that causes them to lose their structural integrity or other critical functionality. Protective coatings are the most commonly used method of corrosion control. However, progressively stricter environmental regulations have resulted in the ban of many commercially available corrosion protective coatings due to the harmful effects of their solvents or corrosion inhibitors. This work concerns the development of a multifunctional smart coating for the autonomous control of corrosion. This coating is being developed to have the inherent ability to detect the chemical changes associated with the onset of corrosion and respond autonomously to indicate it and control it. The multi-functionality of the coating is based on microencapsulation technology specifically designed for corrosion control applications. This design has, in addition to all the advantages of existing microcapsulation designs, the corrosion controlled release function that triggers the delivery of corrosion indicators and inhibitors on demand, only when and where needed. Microencapsulation of self-healing agents for autonomous repair of mechanical damage to the coating is also being pursued. Corrosion indicators, corrosion inhibitors, as well as self-healing agents, have been encapsulated and dispersed into several paint systems to test the corrosion detection, inhibition, and self-healing properties of the coating. Key words: Corrosion, coating, autonomous corrosion control, corrosion indication, corrosion inhibition, self-healing coating, smart coating, multifunctional coating, microencapsulation.

  12. Integrating the autonomous subsystems management process

    Science.gov (United States)

    Ashworth, Barry R.

    1992-01-01

    Ways in which the ranking of the Space Station Module Power Management and Distribution testbed may be achieved and an individual subsystem's internal priorities may be managed within the complete system are examined. The application of these results in the integration and performance leveling of the autonomously managed system is discussed.

  13. Spatial abstraction for autonomous robot navigation.

    Science.gov (United States)

    Epstein, Susan L; Aroor, Anoop; Evanusa, Matthew; Sklar, Elizabeth I; Parsons, Simon

    2015-09-01

    Optimal navigation for a simulated robot relies on a detailed map and explicit path planning, an approach problematic for real-world robots that are subject to noise and error. This paper reports on autonomous robots that rely on local spatial perception, learning, and commonsense rationales instead. Despite realistic actuator error, learned spatial abstractions form a model that supports effective travel.

  14. Autonomic Modification of Intestinal Smooth Muscle Contractility

    Science.gov (United States)

    Montgomery, Laura E. A.; Tansey, Etain A.; Johnson, Chris D.; Roe, Sean M.; Quinn, Joe G.

    2016-01-01

    Intestinal smooth muscle contracts rhythmically in the absence of nerve and hormonal stimulation because of the activity of pacemaker cells between and within the muscle layers. This means that the autonomic nervous system modifies rather than initiates intestinal contractions. The practical described here gives students an opportunity to observe…

  15. My Understanding on Cultivation of Autonomous Learning

    Institute of Scientific and Technical Information of China (English)

    张金玉

    2007-01-01

    Autonomous learning has been popular in western education system for some time, this article aims to analyze the connotation and the necessity of cultivating learner autonomy, and then offer some strategies about the cultivation of learner autonomy from a chinese perspective.

  16. Applying energy autonomous robots for dike inspection

    NARCIS (Netherlands)

    Dresscher, Douwe; Vries, de Theo J.A.; Stramigioli, Stefano

    2015-01-01

    This article presents an exploratory study of an energy-autonomous robot that can be deployed on the Dutch dykes. Based on theory in energy harvesting from sun and wind and the energy-cost of locomotion an analytic expression to determine the feasible daily operational time of such a vehicle is comp

  17. Autonomic dysfunction in a Jack Russell terrier

    OpenAIRE

    Caines, Deanne; Pinard, Chantale L.; Kruth, Stephen; Orr, Jeremy; James, Fiona

    2011-01-01

    A 4-year-old Jack Russell terrier was presented with an array of clinical signs suggestive of autonomic dysfunction. Many of the clinical signs were consistent with a diagnosis of dysautonomia; however, both chronicity and resolution of signs contradicted a diagnosis of this disease.

  18. Non-autonomous second order Hamiltonian systems

    OpenAIRE

    Pipan, J; Schechter, M

    2014-01-01

    We study the existence of periodic solutions for a second order non-autonomous dynamical system containing variable kinetic energy terms. Our assumptions balance the interaction between the kinetic energy and the potential energy with neither one dominating the other. We study sublinear problems and the existence of non-constant solutions. © 2014 Elsevier Inc.

  19. Advanced manipulation for autonomous mobile robots

    Energy Technology Data Exchange (ETDEWEB)

    Babcock, S.M.; Hamel, W.R.; Killough, S.M.

    1986-01-01

    This paper describes the development, mechanical configuration, and control system architecture of a lightweight, high performance, seven-degree-of-freedom manipulator at the Center for Engineering Systems Advanced Research (CESAR). Current activities focusing on modeling and parameter identification will provide a well-characterized manipulator for analytical and experimental research in manipulator dynamics and controls, coordinated manipulation, and autonomous mobile robotics.

  20. Chromosome catastrophes involve replication mechanisms generating complex genomic rearrangements.

    Science.gov (United States)

    Liu, Pengfei; Erez, Ayelet; Nagamani, Sandesh C Sreenath; Dhar, Shweta U; Kołodziejska, Katarzyna E; Dharmadhikari, Avinash V; Cooper, M Lance; Wiszniewska, Joanna; Zhang, Feng; Withers, Marjorie A; Bacino, Carlos A; Campos-Acevedo, Luis Daniel; Delgado, Mauricio R; Freedenberg, Debra; Garnica, Adolfo; Grebe, Theresa A; Hernández-Almaguer, Dolores; Immken, LaDonna; Lalani, Seema R; McLean, Scott D; Northrup, Hope; Scaglia, Fernando; Strathearn, Lane; Trapane, Pamela; Kang, Sung-Hae L; Patel, Ankita; Cheung, Sau Wai; Hastings, P J; Stankiewicz, Paweł; Lupski, James R; Bi, Weimin

    2011-09-16

    Complex genomic rearrangements (CGRs) consisting of two or more breakpoint junctions have been observed in genomic disorders. Recently, a chromosome catastrophe phenomenon termed chromothripsis, in which numerous genomic rearrangements are apparently acquired in one single catastrophic event, was described in multiple cancers. Here, we show that constitutionally acquired CGRs share similarities with cancer chromothripsis. In the 17 CGR cases investigated, we observed localization and multiple copy number changes including deletions, duplications, and/or triplications, as well as extensive translocations and inversions. Genomic rearrangements involved varied in size and complexities; in one case, array comparative genomic hybridization revealed 18 copy number changes. Breakpoint sequencing identified characteristic features, including small templated insertions at breakpoints and microhomology at breakpoint junctions, which have been attributed to replicative processes. The resemblance between CGR and chromothripsis suggests similar mechanistic underpinnings. Such chromosome catastrophic events appear to reflect basic DNA metabolism operative throughout an organism's life cycle.