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Sample records for conditions direct sequencing

  1. Direct, rapid RNA sequence analysis

    International Nuclear Information System (INIS)

    Peattie, D.A.

    1987-01-01

    The original methods of RNA sequence analysis were based on enzymatic production and chromatographic separation of overlapping oligonucleotide fragments from within an RNA molecule followed by identification of the mononucleotides comprising the oligomer. Over the past decade the field of nucleic acid sequencing has changed dramatically, however, and RNA molecules now can be sequenced in a variety of more streamlined fashions. Most of the more recent advances in RNA sequencing have involved one-dimensional electrophoretic separation of 32 P-end-labeled oligoribonucleotides on polyacrylamide gels. In this chapter the author discusses two of these methods for determining the nucleotide sequences of RNA molecules rapidly: the chemical method and the enzymatic method. Both methods are direct and degradative, i.e., they rely on fragmatic and chemical approaches should be utilized. The single-strand-specific ribonucleases (A, T 1 , T 2 , and S 1 ) provide an efficient means to locate double-helical regions rapidly, and the chemical reactions provide a means to determine the RNA sequence within these regions. In addition, the chemical reactions allow one to assign interactions to specific atoms and to distinguish secondary interactions from tertiary ones. If the RNA molecule is small enough to be sequenced directly by the enzymatic or chemical method, the probing reactions can be done easily at the same time as sequencing reactions

  2. Interference management using direct sequence spread spectrum ...

    African Journals Online (AJOL)

    Interference management using direct sequence spread spectrum (DSSS) technique ... Journal of Fundamental and Applied Sciences ... Keywords: DSSS, LTE network; Wi-Fi network; SINR; interference management and interference power.

  3. Analysis of Pteridium ribosomal RNA sequences by rapid direct sequencing.

    Science.gov (United States)

    Tan, M K

    1991-08-01

    A total of 864 bases from 5 regions interspersed in the 18S and 26S rRNA molecules from various clones of Pteridium covering the general geographical distribution of the genus was analysed using a rapid rRNA sequencing technique. No base difference has been detected amongst the three major lineages, two of which apparently separated before the breakup of the ancient supercontinent, Pangaea. These regions of the rRNA sequences have thus been conserved for at least 160 million years and are here compared with other eukaryotic, especially plant rRNAs.

  4. Ancestral sequence alignment under optimal conditions

    Directory of Open Access Journals (Sweden)

    Brown Daniel G

    2005-11-01

    Full Text Available Abstract Background Multiple genome alignment is an important problem in bioinformatics. An important subproblem used by many multiple alignment approaches is that of aligning two multiple alignments. Many popular alignment algorithms for DNA use the sum-of-pairs heuristic, where the score of a multiple alignment is the sum of its induced pairwise alignment scores. However, the biological meaning of the sum-of-pairs of pairs heuristic is not obvious. Additionally, many algorithms based on the sum-of-pairs heuristic are complicated and slow, compared to pairwise alignment algorithms. An alternative approach to aligning alignments is to first infer ancestral sequences for each alignment, and then align the two ancestral sequences. In addition to being fast, this method has a clear biological basis that takes into account the evolution implied by an underlying phylogenetic tree. In this study we explore the accuracy of aligning alignments by ancestral sequence alignment. We examine the use of both maximum likelihood and parsimony to infer ancestral sequences. Additionally, we investigate the effect on accuracy of allowing ambiguity in our ancestral sequences. Results We use synthetic sequence data that we generate by simulating evolution on a phylogenetic tree. We use two different types of phylogenetic trees: trees with a period of rapid growth followed by a period of slow growth, and trees with a period of slow growth followed by a period of rapid growth. We examine the alignment accuracy of four ancestral sequence reconstruction and alignment methods: parsimony, maximum likelihood, ambiguous parsimony, and ambiguous maximum likelihood. Additionally, we compare against the alignment accuracy of two sum-of-pairs algorithms: ClustalW and the heuristic of Ma, Zhang, and Wang. Conclusion We find that allowing ambiguity in ancestral sequences does not lead to better multiple alignments. Regardless of whether we use parsimony or maximum likelihood, the

  5. Direct chloroplast sequencing: comparison of sequencing platforms and analysis tools for whole chloroplast barcoding.

    Directory of Open Access Journals (Sweden)

    Marta Brozynska

    Full Text Available Direct sequencing of total plant DNA using next generation sequencing technologies generates a whole chloroplast genome sequence that has the potential to provide a barcode for use in plant and food identification. Advances in DNA sequencing platforms may make this an attractive approach for routine plant identification. The HiSeq (Illumina and Ion Torrent (Life Technology sequencing platforms were used to sequence total DNA from rice to identify polymorphisms in the whole chloroplast genome sequence of a wild rice plant relative to cultivated rice (cv. Nipponbare. Consensus chloroplast sequences were produced by mapping sequence reads to the reference rice chloroplast genome or by de novo assembly and mapping of the resulting contigs to the reference sequence. A total of 122 polymorphisms (SNPs and indels between the wild and cultivated rice chloroplasts were predicted by these different sequencing and analysis methods. Of these, a total of 102 polymorphisms including 90 SNPs were predicted by both platforms. Indels were more variable with different sequencing methods, with almost all discrepancies found in homopolymers. The Ion Torrent platform gave no apparent false SNP but was less reliable for indels. The methods should be suitable for routine barcoding using appropriate combinations of sequencing platform and data analysis.

  6. Methods of conditioning direct methanol fuel cells

    Science.gov (United States)

    Rice, Cynthia; Ren, Xiaoming; Gottesfeld, Shimshon

    2005-11-08

    Methods for conditioning the membrane electrode assembly of a direct methanol fuel cell ("DMFC") are disclosed. In a first method, an electrical current of polarity opposite to that used in a functioning direct methanol fuel cell is passed through the anode surface of the membrane electrode assembly. In a second method, methanol is supplied to an anode surface of the membrane electrode assembly, allowed to cross over the polymer electrolyte membrane of the membrane electrode assembly to a cathode surface of the membrane electrode assembly, and an electrical current of polarity opposite to that in a functioning direct methanol fuel cell is drawn through the membrane electrode assembly, wherein methanol is oxidized at the cathode surface of the membrane electrode assembly while the catalyst on the anode surface is reduced. Surface oxides on the direct methanol fuel cell anode catalyst of the membrane electrode assembly are thereby reduced.

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

    Directory of Open Access Journals (Sweden)

    Preissler Steffen

    2011-09-01

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

  8. Direct chromosome-length haplotyping by single-cell sequencing

    NARCIS (Netherlands)

    Porubský, David; Sanders, Ashley D; van Wietmarschen, Niek; Falconer, Ester; Hills, Mark; Spierings, Diana C J; Bevova, Marianna R; Guryev, Victor; Lansdorp, Peter Michael

    Haplotypes are fundamental to fully characterize the diploid genome of an individual, yet methods to directly chart the unique genetic makeup of each parental chromosome are lacking. Here we introduce single-cell DNA template strand sequencing (Strand-seq) as a novel approach to phasing diploid

  9. Constructing and sampling directed graphs with given degree sequences

    International Nuclear Information System (INIS)

    Kim, H; Del Genio, C I; Bassler, K E; Toroczkai, Z

    2012-01-01

    The interactions between the components of complex networks are often directed. Proper modeling of such systems frequently requires the construction of ensembles of digraphs with a given sequence of in- and out-degrees. As the number of simple labeled graphs with a given degree sequence is typically very large even for short sequences, sampling methods are needed for statistical studies. Currently, there are two main classes of methods that generate samples. One of the existing methods first generates a restricted class of graphs and then uses a Markov chain Monte-Carlo algorithm based on edge swaps to generate other realizations. As the mixing time of this process is still unknown, the independence of the samples is not well controlled. The other class of methods is based on the configuration model that may lead to unacceptably many sample rejections due to self-loops and multiple edges. Here we present an algorithm that can directly construct all possible realizations of a given bi-degree sequence by simple digraphs. Our method is rejection-free, guarantees the independence of the constructed samples and provides their weight. The weights can then be used to compute statistical averages of network observables as if they were obtained from uniformly distributed sampling or from any other chosen distribution. (paper)

  10. Ultra-fast evaluation of protein energies directly from sequence.

    Directory of Open Access Journals (Sweden)

    Gevorg Grigoryan

    2006-06-01

    Full Text Available The structure, function, stability, and many other properties of a protein in a fixed environment are fully specified by its sequence, but in a manner that is difficult to discern. We present a general approach for rapidly mapping sequences directly to their energies on a pre-specified rigid backbone, an important sub-problem in computational protein design and in some methods for protein structure prediction. The cluster expansion (CE method that we employ can, in principle, be extended to model any computable or measurable protein property directly as a function of sequence. Here we show how CE can be applied to the problem of computational protein design, and use it to derive excellent approximations of physical potentials. The approach provides several attractive advantages. First, following a one-time derivation of a CE expansion, the amount of time necessary to evaluate the energy of a sequence adopting a specified backbone conformation is reduced by a factor of 10(7 compared to standard full-atom methods for the same task. Second, the agreement between two full-atom methods that we tested and their CE sequence-based expressions is very high (root mean square deviation 1.1-4.7 kcal/mol, R2 = 0.7-1.0. Third, the functional form of the CE energy expression is such that individual terms of the expansion have clear physical interpretations. We derived expressions for the energies of three classic protein design targets-a coiled coil, a zinc finger, and a WW domain-as functions of sequence, and examined the most significant terms. Single-residue and residue-pair interactions are sufficient to accurately capture the energetics of the dimeric coiled coil, whereas higher-order contributions are important for the two more globular folds. For the task of designing novel zinc-finger sequences, a CE-derived energy function provides significantly better solutions than a standard design protocol, in comparable computation time. Given these advantages

  11. Directional Convexity and Finite Optimality Conditions.

    Science.gov (United States)

    1984-03-01

    system, Necessary Conditions for optimality. Work Unit Number 5 (Optimization and Large Scale Systems) *Istituto di Matematica Applicata, Universita...that R(T) is convex would then imply x(u,T) e int R(T). Cletituto di Matematica Applicata, Universita di Padova, 35100 ITALY. Sponsored by the United

  12. Human genome sequencing with direct x-ray holographic imaging

    International Nuclear Information System (INIS)

    Rhodes, C.K.

    1993-01-01

    Direct holographic imaging of biological materials is widely applicable to the study of the structure, properties and action of genetic material. This particular application involves the sequencing of the human genome where prospective genomic imaging technology is composed of three subtechnologies, name an x-ray holographic camera, suitable chemistry and enzymology for the preparation of tagged DNA samples, and the illuminator in the form of an x-ray laser. We report appropriate x-ray camera, embodied by the instrument developed by MCR, is available and that suitable chemical and enzymatic procedures exist for the preparation of the necessary tagged DNA strands. Concerning the future development of the x-ray illuminator. We find that a practical small scale x-ray light source is indeed feasible. This outcome requires the use of unconventional physical processes in order to achieve the necessary power-compression in the amplifying medium. The understanding of these new physical mechanisms is developing rapidly. Importantly, although the x-ray source does not currently exist, the understanding of these new physical mechanisms is developing rapidly and the research has established the basic scaling laws that will determine the properties of the x-ray illuminator. When this x-ray source becomes available, an extremely rapid and cost effective instrument for 3-D imaging of biological materials can be applied to a wide range of biological structural assays, including the base-pair sequencing of the human genome and many questions regarding its higher levels of organization

  13. Maximum likelihood sequence estimation for optical complex direct modulation.

    Science.gov (United States)

    Che, Di; Yuan, Feng; Shieh, William

    2017-04-17

    Semiconductor lasers are versatile optical transmitters in nature. Through the direct modulation (DM), the intensity modulation is realized by the linear mapping between the injection current and the light power, while various angle modulations are enabled by the frequency chirp. Limited by the direct detection, DM lasers used to be exploited only as 1-D (intensity or angle) transmitters by suppressing or simply ignoring the other modulation. Nevertheless, through the digital coherent detection, simultaneous intensity and angle modulations (namely, 2-D complex DM, CDM) can be realized by a single laser diode. The crucial technique of CDM is the joint demodulation of intensity and differential phase with the maximum likelihood sequence estimation (MLSE), supported by a closed-form discrete signal approximation of frequency chirp to characterize the MLSE transition probability. This paper proposes a statistical method for the transition probability to significantly enhance the accuracy of the chirp model. Using the statistical estimation, we demonstrate the first single-channel 100-Gb/s PAM-4 transmission over 1600-km fiber with only 10G-class DM lasers.

  14. PMS2 gene mutational analysis: direct cDNA sequencing to circumvent pseudogene interference.

    Science.gov (United States)

    Wimmer, Katharina; Wernstedt, Annekatrin

    2014-01-01

    The presence of highly homologous pseudocopies can compromise the mutation analysis of a gene of interest. In particular, when using PCR-based strategies, pseudogene co-amplification has to be effectively prevented. This is often achieved by using primers designed to be parental gene specific according to the reference sequence and by applying stringent PCR conditions. However, there are cases in which this approach is of limited utility. For example, it has been shown that the PMS2 gene exchanges sequences with one of its pseudogenes, named PMS2CL. This results in functional PMS2 alleles containing pseudogene-derived sequences at their 3'-end and in nonfunctional PMS2CL pseudogene alleles that contain gene-derived sequences. Hence, the paralogues cannot be distinguished according to the reference sequence. This shortcoming can be effectively circumvented by using direct cDNA sequencing. This approach is based on the selective amplification of PMS2 transcripts in two overlapping 1.6-kb RT-PCR products. In addition to avoiding pseudogene co-amplification and allele dropout, this method has also the advantage that it allows to effectively identify deletions, splice mutations, and de novo retrotransposon insertions that escape the detection of most DNA-based mutation analysis protocols.

  15. Detection of nucleic acid sequences by invader-directed cleavage

    Science.gov (United States)

    Brow, Mary Ann D.; Hall, Jeff Steven Grotelueschen; Lyamichev, Victor; Olive, David Michael; Prudent, James Robert

    1999-01-01

    The present invention relates to means for the detection and characterization of nucleic acid sequences, as well as variations in nucleic acid sequences. The present invention also relates to methods for forming a nucleic acid cleavage structure on a target sequence and cleaving the nucleic acid cleavage structure in a site-specific manner. The 5' nuclease activity of a variety of enzymes is used to cleave the target-dependent cleavage structure, thereby indicating the presence of specific nucleic acid sequences or specific variations thereof. The present invention further relates to methods and devices for the separation of nucleic acid molecules based by charge.

  16. PNA Directed Sequence Addressed Self-Assembly of DNA Nanostructures

    DEFF Research Database (Denmark)

    Nielsen, Peter E.

    2008-01-01

    sequence specifically recognize another PNA oligomer. We describe how such three domain PNAs have utility for assembling dsDNA grid and clover leaf structures, and in combination with SNAP-tag technol. of protein dsDNA structures. (c) 2008 American Institute of Physics. [on SciFinder (R)] Udgivelsesdato...

  17. Exploiting sequence and stability information for directing nanobody stability engineering.

    Science.gov (United States)

    Kunz, Patrick; Flock, Tilman; Soler, Nicolas; Zaiss, Moritz; Vincke, Cécile; Sterckx, Yann; Kastelic, Damjana; Muyldermans, Serge; Hoheisel, Jörg D

    2017-09-01

    Variable domains of camelid heavy-chain antibodies, commonly named nanobodies, have high biotechnological potential. In view of their broad range of applications in research, diagnostics and therapy, engineering their stability is of particular interest. One important aspect is the improvement of thermostability, because it can have immediate effects on conformational stability, protease resistance and aggregation propensity of the protein. We analyzed the sequences and thermostabilities of 78 purified nanobody binders. From this data, potentially stabilizing amino acid variations were identified and studied experimentally. Some mutations improved the stability of nanobodies by up to 6.1°C, with an average of 2.3°C across eight modified nanobodies. The stabilizing mechanism involves an improvement of both conformational stability and aggregation behavior, explaining the variable degree of stabilization in individual molecules. In some instances, variations predicted to be stabilizing actually led to thermal destabilization of the proteins. The reasons for this contradiction between prediction and experiment were investigated. The results reveal a mutational strategy to improve the biophysical behavior of nanobody binders and indicate a species-specificity of nanobody architecture. This study illustrates the potential and limitations of engineering nanobody thermostability by merging sequence information with stability data, an aspect that is becoming increasingly important with the recent development of high-throughput biophysical methods. Copyright © 2017 The Authors. Published by Elsevier B.V. All rights reserved.

  18. On the nonparametric prediction of conditionally stationary sequences

    NARCIS (Netherlands)

    S. Caires; J.A. Ferreira

    2003-01-01

    textabstractWe prove the strong consistency of estimators of the conditional distribution function and conditional expectation of a future observation of a discrete time stochastic process given a fixed number of past observations. The results apply to conditionally stationary processes (a class of

  19. On conditioned and directed freedom of contrats between business entity

    Directory of Open Access Journals (Sweden)

    Đurđević Marko

    2016-01-01

    Full Text Available The term conditioned freedom of contracts appeared in our legal theory before the adoption of the Obligations Relations Act, whereas the term directed freedom of contracts occurred after the Act's entry into force. Both terms were used to signify transformation of freedom of con tracts within the legal system based on ideology of socialism, social ownership of the means of production and government ruled economy and, afterwards, 'coordinated economy'. Conditioned freedom of contracts originated from the right to use the means of production in social ownership. This right, which belonged to social (state-owned companies, consisted of two components. The first, public-law component conditioned the second, private law component, by means of norms in individual administrative acts and administrative regulations. As these norms were an expression of state power, they make the contract subordinate: individual administrative act is a condition for the conclusion of contract, and administrative regulations for its validity. Directed freedom of contracts is freedom of making contracts directed by economic order established by the Constitution, systemic laws, and partially by the norms of the basic principles of the Obligations Relations Act which are related to social companies. As regards freedom of contracts it can be said that even today it is directed by legal principles and norms of economic-legal public policy through which the state interferes in business enterprises.

  20. Collective properties of injection-induced earthquake sequences: 1. Model description and directivity bias

    Science.gov (United States)

    Dempsey, David; Suckale, Jenny

    2016-05-01

    Induced seismicity is of increasing concern for oil and gas, geothermal, and carbon sequestration operations, with several M > 5 events triggered in recent years. Modeling plays an important role in understanding the causes of this seismicity and in constraining seismic hazard. Here we study the collective properties of induced earthquake sequences and the physics underpinning them. In this first paper of a two-part series, we focus on the directivity ratio, which quantifies whether fault rupture is dominated by one (unilateral) or two (bilateral) propagating fronts. In a second paper, we focus on the spatiotemporal and magnitude-frequency distributions of induced seismicity. We develop a model that couples a fracture mechanics description of 1-D fault rupture with fractal stress heterogeneity and the evolving pore pressure distribution around an injection well that triggers earthquakes. The extent of fault rupture is calculated from the equations of motion for two tips of an expanding crack centered at the earthquake hypocenter. Under tectonic loading conditions, our model exhibits a preference for unilateral rupture and a normal distribution of hypocenter locations, two features that are consistent with seismological observations. On the other hand, catalogs of induced events when injection occurs directly onto a fault exhibit a bias toward ruptures that propagate toward the injection well. This bias is due to relatively favorable conditions for rupture that exist within the high-pressure plume. The strength of the directivity bias depends on a number of factors including the style of pressure buildup, the proximity of the fault to failure and event magnitude. For injection off a fault that triggers earthquakes, the modeled directivity bias is small and may be too weak for practical detection. For two hypothetical injection scenarios, we estimate the number of earthquake observations required to detect directivity bias.

  1. An Extended Multilocus Sequence Typing (MLST) Scheme for Rapid Direct Typing of Leptospira from Clinical Samples

    OpenAIRE

    Weiss, Sabrina; Menezes, Angela; Woods, Kate; Chanthongthip, Anisone; Dittrich, Sabine; Opoku-Boateng, Agatha; Kimuli, Maimuna; Chalker, Victoria

    2016-01-01

    Background Rapid typing of Leptospira is currently impaired by requiring time consuming culture of leptospires. The objective of this study was to develop an assay that provides multilocus sequence typing (MLST) data direct from patient specimens while minimising costs for subsequent sequencing. Methodology and Findings An existing PCR based MLST scheme was modified by designing nested primers including anchors for facilitated subsequent sequencing. The assay was applied to various specimen t...

  2. Performance analysis of a SOFC under direct internal reforming conditions

    Energy Technology Data Exchange (ETDEWEB)

    Janardhanan, Vinod M.; Deutschmann, Olaf [Institute for Chemical Technology and Polymer Chemistry, Engesserstr 20, D-76131 Karlsruhe, University of Karlsruhe (Germany); Heuveline, Vincent [Institute for Applied and Numerical Mathematics, Kaiserstr. 12, D-76128 Karlsruhe (Germany)

    2007-10-11

    This paper presents the performance analysis of a planar solid-oxide fuel cell (SOFC) under direct internal reforming conditions. A detailed solid-oxide fuel cell model is used to study the influences of various operating parameters on cell performance. Significant differences in efficiency and power density are observed for isothermal and adiabatic operational regimes. The influence of air number, specific catalyst area, anode thickness, steam to carbon (s/c) ratio of the inlet fuel, and extend of pre-reforming on cell performance is analyzed. In all cases except for the case of pre-reformed fuel, adiabatic operation results in lower performance compared to isothermal operation. It is further discussed that, though direct internal reforming may lead to cost reduction and increased efficiency by effective utilization of waste heat, the efficiency of the fuel cell itself is higher for pre-reformed fuel compared to non-reformed fuel. Furthermore, criteria for the choice of optimal operating conditions for cell stacks operating under direct internal reforming conditions are discussed. (author)

  3. Performance analysis of a SOFC under direct internal reforming conditions

    Science.gov (United States)

    Janardhanan, Vinod M.; Heuveline, Vincent; Deutschmann, Olaf

    This paper presents the performance analysis of a planar solid-oxide fuel cell (SOFC) under direct internal reforming conditions. A detailed solid-oxide fuel cell model is used to study the influences of various operating parameters on cell performance. Significant differences in efficiency and power density are observed for isothermal and adiabatic operational regimes. The influence of air number, specific catalyst area, anode thickness, steam to carbon (s/c) ratio of the inlet fuel, and extend of pre-reforming on cell performance is analyzed. In all cases except for the case of pre-reformed fuel, adiabatic operation results in lower performance compared to isothermal operation. It is further discussed that, though direct internal reforming may lead to cost reduction and increased efficiency by effective utilization of waste heat, the efficiency of the fuel cell itself is higher for pre-reformed fuel compared to non-reformed fuel. Furthermore, criteria for the choice of optimal operating conditions for cell stacks operating under direct internal reforming conditions are discussed.

  4. Direct typing of Canine parvovirus (CPV) from infected dog faeces by rapid mini sequencing technique.

    Science.gov (United States)

    V, Pavana Jyothi; S, Akila; Selvan, Malini K; Naidu, Hariprasad; Raghunathan, Shwethaa; Kota, Sathish; Sundaram, R C Raja; Rana, Samir Kumar; Raj, G Dhinakar; Srinivasan, V A; Mohana Subramanian, B

    2016-12-01

    Canine parvovirus (CPV) is a non-enveloped single stranded DNA virus with an icosahedral capsid. Mini-sequencing based CPV typing was developed earlier to detect and differentiate all the CPV types and FPV in a single reaction. This technique was further evaluated in the present study by performing the mini-sequencing directly from fecal samples which avoided tedious virus isolation steps by cell culture system. Fecal swab samples were collected from 84 dogs with enteritis symptoms, suggestive of parvoviral infection from different locations across India. Seventy six of these samples were positive by PCR; the subsequent mini-sequencing reaction typed 74 of them as type 2a virus, and 2 samples as type 2b. Additionally, 25 of the positive samples were typed by cycle sequencing of PCR products. Direct CPV typing from fecal samples using mini-sequencing showed 100% correlation with CPV typing by cycle sequencing. Moreover, CPV typing was achieved by mini-sequencing even with faintly positive PCR amplicons which was not possible by cycle sequencing. Therefore, the mini-sequencing technique is recommended for regular epidemiological follow up of CPV types, since the technique is rapid, highly sensitive and high capacity method for CPV typing. Copyright © 2016. Published by Elsevier B.V.

  5. Identification of rat genes by TWINSCAN gene prediction, RT-PCR, and direct sequencing

    DEFF Research Database (Denmark)

    Wu, Jia Qian; Shteynberg, David; Arumugam, Manimozhiyan

    2004-01-01

    an alternative approach: reverse transcription-polymerase chain reaction (RT-PCR) and direct sequencing based on dual-genome de novo predictions from TWINSCAN. We tested 444 TWINSCAN-predicted rat genes that showed significant homology to known human genes implicated in disease but that were partially...... in the single-intron experiment. Spliced sequences were amplified in 46 cases (34%). We conclude that this procedure for elucidating gene structures with native cDNA sequences is cost-effective and will become even more so as it is further optimized.......The publication of a draft sequence of a third mammalian genome--that of the rat--suggests a need to rethink genome annotation. New mammalian sequences will not receive the kind of labor-intensive annotation efforts that are currently being devoted to human. In this paper, we demonstrate...

  6. DeepProbe: Information Directed Sequence Understanding and Chatbot Design via Recurrent Neural Networks

    OpenAIRE

    Yin, Zi; Chang, Keng-hao; Zhang, Ruofei

    2017-01-01

    Information extraction and user intention identification are central topics in modern query understanding and recommendation systems. In this paper, we propose DeepProbe, a generic information-directed interaction framework which is built around an attention-based sequence to sequence (seq2seq) recurrent neural network. DeepProbe can rephrase, evaluate, and even actively ask questions, leveraging the generative ability and likelihood estimation made possible by seq2seq models. DeepProbe makes...

  7. Direct sequencing of FAH gene in Pakistani tyrosinemia type 1 families reveals a novel mutation.

    Science.gov (United States)

    Ijaz, Sadaqat; Zahoor, Muhammad Yasir; Imran, Muhammad; Afzal, Sibtain; Bhinder, Munir A; Ullah, Ihsan; Cheema, Huma Arshad; Ramzan, Khushnooda; Shehzad, Wasim

    2016-03-01

    Hereditary tyrosinemia type 1 (HT1) is a rare inborn error of tyrosine catabolism with a worldwide prevalence of one out of 100,000 live births. HT1 is clinically characterized by hepatic and renal dysfunction resulting from the deficiency of fumarylacetoacetate hydrolase (FAH) enzyme, caused by recessive mutations in the FAH gene. We present here the first report on identification of FAH mutations in HT1 patients from Pakistan with a novel one. Three Pakistani families, each having one child affected with HT1, were enrolled over a period of 1.5 years. Two of the affected children had died as they were presented late with acute form. All regions of the FAH gene spanning exons and splicing sites were amplified by polymerase chain reaction (PCR) and mutation analysis was carried out by direct sequencing. Results of sequencing were confirmed by restriction fragment length polymorphism (PCR-RFLP) analysis. Three different FAH mutations, one in each family, were found to co-segregate with the disease phenotype. Two of these FAH mutations have been known (c.192G>T and c.1062+5G>A [IVS12+5G>A]), while c.67T>C (p.Ser23Pro) was a novel mutation. The novel variant was not detected in any of 120 chromosomes from normal ethnically matched individuals. Most of the HT1 patients die before they present to hospitals in Pakistan, as is indicated by enrollment of only three families in 1.5 years. Most of those with late clinical presentation do not survive due to delayed diagnosis followed by untimely treatment. This tragic condition advocates the establishment of expanded newborn screening program for HT1 within Pakistan.

  8. Chiron: translating nanopore raw signal directly into nucleotide sequence using deep learning

    KAUST Repository

    Teng, Haotian; Cao, Minh Duc; Hall, Michael B; Duarte, Tania; Wang, Sheng; Coin, Lachlan J M

    2018-01-01

    Sequencing by translocating DNA fragments through an array of nanopores is a rapidly maturing technology that offers faster and cheaper sequencing than other approaches. However, accurately deciphering the DNA sequence from the noisy and complex electrical signal is challenging. Here, we report Chiron, the first deep learning model to achieve end-to-end basecalling and directly translate the raw signal to DNA sequence without the error-prone segmentation step. Trained with only a small set of 4,000 reads, we show that our model provides state-of-the-art basecalling accuracy, even on previously unseen species. Chiron achieves basecalling speeds of more than 2,000 bases per second using desktop computer graphics processing units.

  9. Chiron: translating nanopore raw signal directly into nucleotide sequence using deep learning

    KAUST Repository

    Teng, Haotian

    2018-04-10

    Sequencing by translocating DNA fragments through an array of nanopores is a rapidly maturing technology that offers faster and cheaper sequencing than other approaches. However, accurately deciphering the DNA sequence from the noisy and complex electrical signal is challenging. Here, we report Chiron, the first deep learning model to achieve end-to-end basecalling and directly translate the raw signal to DNA sequence without the error-prone segmentation step. Trained with only a small set of 4,000 reads, we show that our model provides state-of-the-art basecalling accuracy, even on previously unseen species. Chiron achieves basecalling speeds of more than 2,000 bases per second using desktop computer graphics processing units.

  10. Direct whole-genome sequencing of Plasmodium falciparum specimens from dried erythrocyte spots

    DEFF Research Database (Denmark)

    Nag, Sidsel; Kofoed, Poul Erik; Ursing, Johan

    2018-01-01

    -infected individuals living in rural areas, away from main infrastructure and the electrical grid. The aim of this study was to describe a low-tech procedure to sample P. falciparum specimens for direct whole genome sequencing (WGS), without use of electricity and cold-chain. Methods: Venous blood samples were...

  11. Direct amplification, sequencing and profiling of Chlamydia trachomatis strains in single and mixed infection clinical samples.

    Directory of Open Access Journals (Sweden)

    Sandeep J Joseph

    Full Text Available Sequencing bacterial genomes from DNA isolated directly from clinical samples offers the promise of rapid and precise acquisition of informative genetic information. In the case of Chlamydia trachomatis, direct sequencing is particularly desirable because it obviates the requirement for culture in mammalian cells, saving time, cost and the possibility of missing low abundance strains. In this proof of concept study, we developed methodology that would allow genome-scale direct sequencing, using a multiplexed microdroplet PCR enrichment technology to amplify a 100 kb region of the C. trachomatis genome with 500 1.1-1.3 kb overlapping amplicons (5-fold amplicon redundancy. We integrated comparative genomic data into a pipeline to preferentially select conserved sites for amplicon design. The 100 kb target region could be amplified from clinical samples, including remnants from diagnostics tests, originating from the cervix, urethra and urine, For rapid analysis of these data, we developed a framework for whole-genome based genotyping called binstrain. We used binstrain to estimate the proportion of SNPs originating from 14 C. trachomatis reference serotype genomes in each sample. Direct DNA sequencing methods such as the one described here may have an important role in understanding the biology of C. trachomatis mixed infections and the natural genetic variation of the species within clinically relevant ecological niches.

  12. Rapid whole genome sequencing for the detection and characterization of microorganisms directly from clinical samples

    DEFF Research Database (Denmark)

    Hasman, Henrik; Saputra, Dhany; Sicheritz-Pontén, Thomas

    2014-01-01

    Whole genome sequencing (WGS) is becoming available as a routine tool for clinical microbiology. If applied directly on clinical samples this could further reduce diagnostic time and thereby improve control and treatment. A major bottle-neck is the availability of fast and reliable bioinformatics...

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

    Science.gov (United States)

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

    2007-02-01

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

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

    Science.gov (United States)

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

    2007-02-01

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

  15. Modeling the Process of Event Sequence Data Generated for Working Condition Diagnosis

    Directory of Open Access Journals (Sweden)

    Jianwei Ding

    2015-01-01

    Full Text Available Condition monitoring systems are widely used to monitor the working condition of equipment, generating a vast amount and variety of telemetry data in the process. The main task of surveillance focuses on analyzing these routinely collected telemetry data to help analyze the working condition in the equipment. However, with the rapid increase in the volume of telemetry data, it is a nontrivial task to analyze all the telemetry data to understand the working condition of the equipment without any a priori knowledge. In this paper, we proposed a probabilistic generative model called working condition model (WCM, which is capable of simulating the process of event sequence data generated and depicting the working condition of equipment at runtime. With the help of WCM, we are able to analyze how the event sequence data behave in different working modes and meanwhile to detect the working mode of an event sequence (working condition diagnosis. Furthermore, we have applied WCM to illustrative applications like automated detection of an anomalous event sequence for the runtime of equipment. Our experimental results on the real data sets demonstrate the effectiveness of the model.

  16. A direct-gradient multivariate index of biotic condition

    Science.gov (United States)

    Miranda, Leandro E.; Aycock, J.N.; Killgore, K. J.

    2012-01-01

    Multimetric indexes constructed by summing metric scores have been criticized despite many of their merits. A leading criticism is the potential for investigator bias involved in metric selection and scoring. Often there is a large number of competing metrics equally well correlated with environmental stressors, requiring a judgment call by the investigator to select the most suitable metrics to include in the index and how to score them. Data-driven procedures for multimetric index formulation published during the last decade have reduced this limitation, yet apprehension remains. Multivariate approaches that select metrics with statistical algorithms may reduce the level of investigator bias and alleviate a weakness of multimetric indexes. We investigated the suitability of a direct-gradient multivariate procedure to derive an index of biotic condition for fish assemblages in oxbow lakes in the Lower Mississippi Alluvial Valley. Although this multivariate procedure also requires that the investigator identify a set of suitable metrics potentially associated with a set of environmental stressors, it is different from multimetric procedures because it limits investigator judgment in selecting a subset of biotic metrics to include in the index and because it produces metric weights suitable for computation of index scores. The procedure, applied to a sample of 35 competing biotic metrics measured at 50 oxbow lakes distributed over a wide geographical region in the Lower Mississippi Alluvial Valley, selected 11 metrics that adequately indexed the biotic condition of five test lakes. Because the multivariate index includes only metrics that explain the maximum variability in the stressor variables rather than a balanced set of metrics chosen to reflect various fish assemblage attributes, it is fundamentally different from multimetric indexes of biotic integrity with advantages and disadvantages. As such, it provides an alternative to multimetric procedures.

  17. Infants learn better from left to right: a directional bias in infants' sequence learning.

    Science.gov (United States)

    Bulf, Hermann; de Hevia, Maria Dolores; Gariboldi, Valeria; Macchi Cassia, Viola

    2017-05-26

    A wealth of studies show that human adults map ordered information onto a directional spatial continuum. We asked whether mapping ordinal information into a directional space constitutes an early predisposition, already functional prior to the acquisition of symbolic knowledge and language. While it is known that preverbal infants represent numerical order along a left-to-right spatial continuum, no studies have investigated yet whether infants, like adults, organize any kind of ordinal information onto a directional space. We investigated whether 7-month-olds' ability to learn high-order rule-like patterns from visual sequences of geometric shapes was affected by the spatial orientation of the sequences (left-to-right vs. right-to-left). Results showed that infants readily learn rule-like patterns when visual sequences were presented from left to right, but not when presented from right to left. This result provides evidence that spatial orientation critically determines preverbal infants' ability to perceive and learn ordered information in visual sequences, opening to the idea that a left-to-right spatially organized mental representation of ordered dimensions might be rooted in biologically-determined constraints on human brain development.

  18. Evaluating next-generation sequencing for direct clinical diagnostics in diarrhoeal disease

    DEFF Research Database (Denmark)

    Joensen, Katrine Grimstrup; Engsbro, A L Ø; Lukjancenko, Oksana

    2017-01-01

    The accurate microbiological diagnosis of diarrhoea involves numerous laboratory tests and, often, the pathogen is not identified in time to guide clinical management. With next-generation sequencing (NGS) becoming cheaper, it has huge potential in routine diagnostics. The aim of this study...... was to evaluate the potential of NGS-based diagnostics through direct sequencing of faecal samples. Fifty-eight clinical faecal samples were obtained from patients with diarrhoea as part of the routine diagnostics at Hvidovre University Hospital, Denmark. Ten samples from healthy individuals were also included...

  19. Directional analysis of extreme winds under mixed climate conditions

    CSIR Research Space (South Africa)

    Kruger, A

    2013-07-01

    Full Text Available Directional statistics provide design engineers with the opportunity to realise considerable cost savings, but these are not yet provided for in the South African standard for wind loading. The development of the directional statistics of extreme...

  20. Engineering of a DNA Polymerase for Direct m6 A Sequencing.

    Science.gov (United States)

    Aschenbrenner, Joos; Werner, Stephan; Marchand, Virginie; Adam, Martina; Motorin, Yuri; Helm, Mark; Marx, Andreas

    2018-01-08

    Methods for the detection of RNA modifications are of fundamental importance for advancing epitranscriptomics. N 6 -methyladenosine (m 6 A) is the most abundant RNA modification in mammalian mRNA and is involved in the regulation of gene expression. Current detection techniques are laborious and rely on antibody-based enrichment of m 6 A-containing RNA prior to sequencing, since m 6 A modifications are generally "erased" during reverse transcription (RT). To overcome the drawbacks associated with indirect detection, we aimed to generate novel DNA polymerase variants for direct m 6 A sequencing. Therefore, we developed a screen to evolve an RT-active KlenTaq DNA polymerase variant that sets a mark for N 6 -methylation. We identified a mutant that exhibits increased misincorporation opposite m 6 A compared to unmodified A. Application of the generated DNA polymerase in next-generation sequencing allowed the identification of m 6 A sites directly from the sequencing data of untreated RNA samples. © 2017 The Authors. Published by Wiley-VCH Verlag GmbH & Co. KGaA.

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

    Science.gov (United States)

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

    2017-12-01

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

  2. Multiple aspects of ATP-dependent nucleosome translocation by RSC and Mi-2 are directed by the underlying DNA sequence.

    Directory of Open Access Journals (Sweden)

    Joke J F A van Vugt

    Full Text Available BACKGROUND: Chromosome structure, DNA metabolic processes and cell type identity can all be affected by changing the positions of nucleosomes along chromosomal DNA, a reaction that is catalysed by SNF2-type ATP-driven chromatin remodelers. Recently it was suggested that in vivo, more than 50% of the nucleosome positions can be predicted simply by DNA sequence, especially within promoter regions. This seemingly contrasts with remodeler induced nucleosome mobility. The ability of remodeling enzymes to mobilise nucleosomes over short DNA distances is well documented. However, the nucleosome translocation processivity along DNA remains elusive. Furthermore, it is unknown what determines the initial direction of movement and how new nucleosome positions are adopted. METHODOLOGY/PRINCIPAL FINDINGS: We have used AFM imaging and high resolution PAGE of mononucleosomes on 600 and 2500 bp DNA molecules to analyze ATP-dependent nucleosome repositioning by native and recombinant SNF2-type enzymes. We report that the underlying DNA sequence can control the initial direction of translocation, translocation distance, as well as the new positions adopted by nucleosomes upon enzymatic mobilization. Within a strong nucleosomal positioning sequence both recombinant Drosophila Mi-2 (CHD-type and native RSC from yeast (SWI/SNF-type repositioned the nucleosome at 10 bp intervals, which are intrinsic to the positioning sequence. Furthermore, RSC-catalyzed nucleosome translocation was noticeably more efficient when beyond the influence of this sequence. Interestingly, under limiting ATP conditions RSC preferred to position the nucleosome with 20 bp intervals within the positioning sequence, suggesting that native RSC preferentially translocates nucleosomes with 15 to 25 bp DNA steps. CONCLUSIONS/SIGNIFICANCE: Nucleosome repositioning thus appears to be influenced by both remodeler intrinsic and DNA sequence specific properties that interplay to define ATPase

  3. Gradient-recalled echo sequences in direct shoulder MR arthrography for evaluating the labrum

    International Nuclear Information System (INIS)

    Lee, Marc J.; Motamedi, Kambiz; Chow, Kira; Seeger, Leanne L.

    2008-01-01

    The purpose of this study was to determine the utility of fat-suppressed gradient-recalled echo (GRE) compared with conventional spin echo T1-weighted (T1W) sequences in direct shoulder MR arthrography for evaluating labral tears. Three musculoskeletal radiologists retrospectively reviewed MR arthrograms performed over a 12-month period for which surgical correlation was available. Of 180 serial arthrograms, 31 patients had surgery with a mean of 48 days following imaging. Paired coronal oblique and axial T1W or GRE sequences were analyzed by consensus for labral tear (coronal oblique two-dimensional multi-echo data image combination, 2D MEDIC; and axial three-dimensional double-echo steady-state, 3D DESS; Siemens MAGNETOM Sonata 1.5-T MR system). Interpretations were correlated with operative reports. Of 31 shoulders, 25 had labral tears at surgery. The GRE sequences depicted labral tears in 22, while T1W images depicted tears in 16 (sensitivity 88% versus 64%; p 0.7). Specificities were somewhat lower for GRE. Thin section GRE sequences are more sensitive than T1W for the detection of anterior and posterior labral tears. As the specificity of GRE was lower, it should be considered as an adjunctive imaging sequence that may improve depiction of labral tears, particularly smaller tears, in routine MR arthrography protocols. (orig.)

  4. Paleoenvironmental conditions at the loess paleosol sequence Bodrogkeresztúr in NE Hungary

    Science.gov (United States)

    Bösken, Janina; Obreht, Igor; Zeeden, Christian; Klasen, Nicole; Hambach, Ulrich; Sümegi, Pál; Lehmkuhl, Frank

    2017-04-01

    Loess paleosol sequences (LPS) have the ability to preserve past environmental and climatic conditions. Therefore, they are a widely used terrestrial archive for the reconstruction of paleoclimatic dynamics. In this study, we use several proxies (grain size distributions, geochemical analysis, rock magnetism, and color measurements) to study past environmental changes in a LPS covering the MIS 2/MIS 3 transition. Geochronological control is given by post infrared infrared stimulated luminescence dating of polymineral fine grains. The research aim lies in the reconstruction of the paleoenvironmental conditions at the loess-paleosol sequence Bodrogkeresztúr in northeastern Hungary using a multi-proxy approach. The sequence is located at the foot of the Kopasz hill, the southernmost part of the Tokaj Mountains, which belong to the Carpathian mountain range. The area is famous for the Bodrogkeresztúr-Henye Gravettian site (Lengyel, 2015). The profile contains eolian loess deposits intercalated by two paleosols. The lower paleosol overlays possibly fluvial clay (fine overbank deposits) forming the base of the profile. The luminescence samples have been tested thoroughly and have been measured with the pIR50IR290 protocol (Thiel et al., 2011). The final age assessment between 28.0±2.1 ka and 33.5±2.5 ka fits well to the established geochronologies of the Kopasz hill (Sümegi and Hertelendi, 1998) and the Tokaj section (Schatz et al., 2012). Paleoenvironmental conditions are investigated through the multi-proxy approach. The measurement of the anisotropy of magnetic susceptibility is interpreted in regard of paleowind directions. The magnetic susceptibility is enhanced in paleosols, especially in the lower one, indicating strong pedogenesis. Grain size parameters also show high clay contribution in the lower paleosol, but also indicate two distinct features of stronger wind dynamics in the loess layer in the middle of the profile (double sigmoidal fluctuations in all

  5. Formative Research on the Simplifying Conditions Method (SCM) for Task Analysis and Sequencing.

    Science.gov (United States)

    Kim, YoungHwan; Reigluth, Charles M.

    The Simplifying Conditions Method (SCM) is a set of guidelines for task analysis and sequencing of instructional content under the Elaboration Theory (ET). This article introduces the fundamentals of SCM and presents the findings from a formative research study on SCM. It was conducted in two distinct phases: design and instruction. In the first…

  6. Synthetic biology for the directed evolution of protein biocatalysts: navigating sequence space intelligently

    Science.gov (United States)

    Currin, Andrew; Swainston, Neil; Day, Philip J.

    2015-01-01

    The amino acid sequence of a protein affects both its structure and its function. Thus, the ability to modify the sequence, and hence the structure and activity, of individual proteins in a systematic way, opens up many opportunities, both scientifically and (as we focus on here) for exploitation in biocatalysis. Modern methods of synthetic biology, whereby increasingly large sequences of DNA can be synthesised de novo, allow an unprecedented ability to engineer proteins with novel functions. However, the number of possible proteins is far too large to test individually, so we need means for navigating the ‘search space’ of possible protein sequences efficiently and reliably in order to find desirable activities and other properties. Enzymologists distinguish binding (K d) and catalytic (k cat) steps. In a similar way, judicious strategies have blended design (for binding, specificity and active site modelling) with the more empirical methods of classical directed evolution (DE) for improving k cat (where natural evolution rarely seeks the highest values), especially with regard to residues distant from the active site and where the functional linkages underpinning enzyme dynamics are both unknown and hard to predict. Epistasis (where the ‘best’ amino acid at one site depends on that or those at others) is a notable feature of directed evolution. The aim of this review is to highlight some of the approaches that are being developed to allow us to use directed evolution to improve enzyme properties, often dramatically. We note that directed evolution differs in a number of ways from natural evolution, including in particular the available mechanisms and the likely selection pressures. Thus, we stress the opportunities afforded by techniques that enable one to map sequence to (structure and) activity in silico, as an effective means of modelling and exploring protein landscapes. Because known landscapes may be assessed and reasoned about as a whole

  7. A simple condition monitoring model for a direct monitoring process

    NARCIS (Netherlands)

    Christer, A.H.; Wang, Wenbin

    1995-01-01

    This paper addresses the problem of condition monitoring of a component which has available a measure of condition called wear. Wear accumulates over time and monitoring inspections are performed at chosen times to monitor and measure the cumulative wear. If past measurements of wear are available

  8. A Chaos-Based Secure Direct-Sequence/Spread-Spectrum Communication System

    Directory of Open Access Journals (Sweden)

    Nguyen Xuan Quyen

    2013-01-01

    Full Text Available This paper proposes a chaos-based secure direct-sequence/spread-spectrum (DS/SS communication system which is based on a novel combination of the conventional DS/SS and chaos techniques. In the proposed system, bit duration is varied according to a chaotic behavior but is always equal to a multiple of the fixed chip duration in the communication process. Data bits with variable duration are spectrum-spread by multiplying directly with a pseudonoise (PN sequence and then modulated onto a sinusoidal carrier by means of binary phase-shift keying (BPSK. To recover exactly the data bits, the receiver needs an identical regeneration of not only the PN sequence but also the chaotic behavior, and hence data security is improved significantly. Structure and operation of the proposed system are analyzed in detail. Theoretical evaluation of bit-error rate (BER performance in presence of additive white Gaussian noise (AWGN is provided. Parameter choice for different cases of simulation is also considered. Simulation and theoretical results are shown to verify the reliability and feasibility of the proposed system. Security of the proposed system is also discussed.

  9. Inferring the Directionality of Coupling with Conditional Mutual Information

    Czech Academy of Sciences Publication Activity Database

    Vejmelka, Martin; Paluš, Milan

    2008-01-01

    Roč. 77, - (2008), Art.no.-026214 ISSN 1539-3755 EU Projects: European Commission(XE) 517133 - BRACCIA Institutional research plan: CEZ:AV0Z10300504 Keywords : directionality * chaotic oscillators * time series analysis * information theory * phase dynamics Subject RIV: BB - Applied Statistics, Operational Research Impact factor: 2.508, year: 2008

  10. Gradient-recalled echo sequences in direct shoulder MR arthrography for evaluating the labrum

    Energy Technology Data Exchange (ETDEWEB)

    Lee, Marc J.; Motamedi, Kambiz; Chow, Kira; Seeger, Leanne L. [David Geffen School of Medicine at UCLA, Department of Radiology, 200 UCLA Medical Plaza, Suite 165-59, Box 956952, Los Angeles, CA (United States)

    2008-01-15

    The purpose of this study was to determine the utility of fat-suppressed gradient-recalled echo (GRE) compared with conventional spin echo T1-weighted (T1W) sequences in direct shoulder MR arthrography for evaluating labral tears. Three musculoskeletal radiologists retrospectively reviewed MR arthrograms performed over a 12-month period for which surgical correlation was available. Of 180 serial arthrograms, 31 patients had surgery with a mean of 48 days following imaging. Paired coronal oblique and axial T1W or GRE sequences were analyzed by consensus for labral tear (coronal oblique two-dimensional multi-echo data image combination, 2D MEDIC; and axial three-dimensional double-echo steady-state, 3D DESS; Siemens MAGNETOM Sonata 1.5-T MR system). Interpretations were correlated with operative reports. Of 31 shoulders, 25 had labral tears at surgery. The GRE sequences depicted labral tears in 22, while T1W images depicted tears in 16 (sensitivity 88% versus 64%; p < 0.05). Subdividing the labrum, GRE was significantly more sensitive for the posterior labrum (75% versus 25%; p < 0.05) with a trend toward greater sensitivity at the anterior labrum (78% versus 56%; p = 0.157) but not significantly different for the superior labrum (50% versus 57%; p > 0.7). Specificities were somewhat lower for GRE. Thin section GRE sequences are more sensitive than T1W for the detection of anterior and posterior labral tears. As the specificity of GRE was lower, it should be considered as an adjunctive imaging sequence that may improve depiction of labral tears, particularly smaller tears, in routine MR arthrography protocols. (orig.)

  11. An adaptive digital suppression filter for direct-sequence spread-spectrum communications

    Science.gov (United States)

    Saulnier, G. J.; Das, P. K.; Milstein, L. B.

    1985-09-01

    This paper describes the structure of a digital implementation of the Widrow-Hoff LMS algorithm which uses a burst processing technique to obtain some hardware simplification. This adaptive system is used to suppress narrow-band interference in a direct-sequence spread-spectrum communication system. Several different narrow-band interferers are considered, and probability of error results are presented for all cases. While, in general, the results show significant improvement in performance when the LMS algorithm is used, certain disadvantages are also present and are discussed in this paper.

  12. Lateralized implicit sequence learning in uni- and bi-manual conditions.

    Science.gov (United States)

    Schmitz, Rémy; Pasquali, Antoine; Cleeremans, Axel; Peigneux, Philippe

    2013-02-01

    It has been proposed that the right hemisphere (RH) is better suited to acquire novel material whereas the left hemisphere (LH) is more able to process well-routinized information. Here, we ask whether this potential dissociation also manifests itself in an implicit learning task. Using a lateralized version of the serial reaction time task (SRT), we tested whether participants trained in a divided visual field condition primarily stimulating the RH would learn the implicit regularities embedded in sequential material faster than participants in a condition favoring LH processing. In the first study, half of participants were presented sequences in the left (vs. right) visual field, and had to respond using their ipsilateral hand (unimanual condition), hence making visuo-motor processing possible within the same hemisphere. Results showed successful implicit sequence learning, as indicated by increased reaction time for a transfer sequence in both hemispheric conditions and lack of conscious knowledge in a generation task. There was, however, no evidence of interhemispheric differences. In the second study, we hypothesized that a bimanual response version of the lateralized SRT, which requires interhemispheric communication and increases computational and cognitive processing loads, would favor RH-dependent visuospatial/attentional processes. In this bimanual condition, our results revealed a much higher transfer effect in the RH than in the LH condition, suggesting higher RH sensitivity to the processing of novel sequential material. This LH/RH difference was interpreted within the framework of the Novelty-Routinization model [Goldberg, E., & Costa, L. D. (1981). Hemisphere differences in the acquisition and use of descriptive systems. Brain and Language, 14(1), 144-173] and interhemispheric interactions in attentional processing [Banich, M. T. (1998). The missing link: the role of interhemispheric interaction in attentional processing. Brain and Cognition, 36

  13. Underground localization using dual magnetic field sequence measurement and pose graph SLAM for directional drilling

    International Nuclear Information System (INIS)

    Park, Byeolteo; Myung, Hyun

    2014-01-01

    With the development of unconventional gas, the technology of directional drilling has become more advanced. Underground localization is the key technique of directional drilling for real-time path following and system control. However, there are problems such as vibration, disconnection with external infrastructure, and magnetic field distortion. Conventional methods cannot solve these problems in real time or in various environments. In this paper, a novel underground localization algorithm using a re-measurement of the sequence of the magnetic field and pose graph SLAM (simultaneous localization and mapping) is introduced. The proposed algorithm exploits the property of the drilling system that the body passes through the previous pass. By comparing the recorded measurement from one magnetic sensor and the current re-measurement from another magnetic sensor, the proposed algorithm predicts the pose of the drilling system. The performance of the algorithm is validated through simulations and experiments. (paper)

  14. Underground localization using dual magnetic field sequence measurement and pose graph SLAM for directional drilling

    Science.gov (United States)

    Park, Byeolteo; Myung, Hyun

    2014-12-01

    With the development of unconventional gas, the technology of directional drilling has become more advanced. Underground localization is the key technique of directional drilling for real-time path following and system control. However, there are problems such as vibration, disconnection with external infrastructure, and magnetic field distortion. Conventional methods cannot solve these problems in real time or in various environments. In this paper, a novel underground localization algorithm using a re-measurement of the sequence of the magnetic field and pose graph SLAM (simultaneous localization and mapping) is introduced. The proposed algorithm exploits the property of the drilling system that the body passes through the previous pass. By comparing the recorded measurement from one magnetic sensor and the current re-measurement from another magnetic sensor, the proposed algorithm predicts the pose of the drilling system. The performance of the algorithm is validated through simulations and experiments.

  15. Direct liquefaction of low-rank coals under mild conditions

    Energy Technology Data Exchange (ETDEWEB)

    Braun, N.; Rinaldi, R. [Max-Planck-Institut fuer Kohlenforschung, Muelheim an der Ruhr (Germany)

    2013-11-01

    Due to decreasing of petroleum reserves, direct coal liquefaction is attracting renewed interest as an alternative process to produce liquid fuels. The combination of hydrogen peroxide and coal is not a new one. In the early 1980, Vasilakos and Clinton described a procedure for desulfurization by leaching coal with solutions of sulphuric acid/H{sub 2}O{sub 2}. But so far, H{sub 2}O{sub 2} has never been ascribed a major role in coal liquefaction. Herein, we describe a novel approach for liquefying low-rank coals using a solution of H{sub 2}O{sub 2} in presence of a soluble non-transition metal catalyst. (orig.)

  16. An Extended Multilocus Sequence Typing (MLST Scheme for Rapid Direct Typing of Leptospira from Clinical Samples.

    Directory of Open Access Journals (Sweden)

    Sabrina Weiss

    2016-09-01

    Full Text Available Rapid typing of Leptospira is currently impaired by requiring time consuming culture of leptospires. The objective of this study was to develop an assay that provides multilocus sequence typing (MLST data direct from patient specimens while minimising costs for subsequent sequencing.An existing PCR based MLST scheme was modified by designing nested primers including anchors for facilitated subsequent sequencing. The assay was applied to various specimen types from patients diagnosed with leptospirosis between 2014 and 2015 in the United Kingdom (UK and the Lao Peoples Democratic Republic (Lao PDR. Of 44 clinical samples (23 serum, 6 whole blood, 3 buffy coat, 12 urine PCR positive for pathogenic Leptospira spp. at least one allele was amplified in 22 samples (50% and used for phylogenetic inference. Full allelic profiles were obtained from ten specimens, representing all sample types (23%. No nonspecific amplicons were observed in any of the samples. Of twelve PCR positive urine specimens three gave full allelic profiles (25% and two a partial profile. Phylogenetic analysis allowed for species assignment. The predominant species detected was L. interrogans (10/14 and 7/8 from UK and Lao PDR, respectively. All other species were detected in samples from only one country (Lao PDR: L. borgpetersenii [1/8]; UK: L. kirschneri [1/14], L. santarosai [1/14], L. weilii [2/14].Typing information of pathogenic Leptospira spp. was obtained directly from a variety of clinical samples using a modified MLST assay. This assay negates the need for time-consuming culture of Leptospira prior to typing and will be of use both in surveillance, as single alleles enable species determination, and outbreaks for the rapid identification of clusters.

  17. Magnetic resonance visualization of conductive structures by sequence-triggered direct currents and spin-echo phase imaging

    Energy Technology Data Exchange (ETDEWEB)

    Eibofner, Frank; Wojtczyk, Hanne; Graf, Hansjörg, E-mail: hansjoerg.graf@med.uni-tuebingen.de, E-mail: drGraf@t-online.de [Section on Experimental Radiology, University Hospital Tübingen, Tübingen D-72076 (Germany); Clasen, Stephan [Department of Diagnostic and Interventional Radiology, University Hospital Tübingen, Tübingen D-72076 (Germany)

    2014-06-15

    Purpose: Instrument visualization in interventional magnetic resonance imaging (MRI) is commonly performed via susceptibility artifacts. Unfortunately, this approach suffers from limited conspicuity in inhomogeneous tissue and disturbed spatial encoding. Also, susceptibility artifacts are controllable only by sequence parameters. This work presents the basics of a new visualization method overcoming such problems by applying sequence-triggered direct current (DC) pulses in spin-echo (SE) imaging. SE phase images allow for background free current path localization. Methods: Application of a sequence-triggered DC pulse in SE imaging, e.g., during a time period between radiofrequency excitation and refocusing, results in transient field inhomogeneities. Dependent on the additional z-magnetic field from the DC, a phase offset results despite the refocusing pulse. False spatial encoding is avoided by DC application during periods when read-out or slice-encoding gradients are inactive. A water phantom containing a brass conductor (water equivalent susceptibility) and a titanium needle (serving as susceptibility source) was used to demonstrate the feasibility. Artifact dependence on current strength and orientation was examined. Results: Without DC, the brass conductor was only visible due to its water displacement. The titanium needle showed typical susceptibility artifacts. Applying triggered DC pulses, the phase offset of spins near the conductor appeared. Because SE phase images are homogenous also in regions of persistent field inhomogeneities, the position of the conductor could be determined with high reliability. Artifact characteristic could be easily controlled by amperage leaving sequence parameters unchanged. For an angle of 30° between current and static field visualization was still possible. Conclusions: SE phase images display the position of a conductor carrying pulsed DC free from artifacts caused by persistent field inhomogeneities. Magnitude and phase

  18. Numerical simulation of controlled directional solidification under microgravity conditions

    Science.gov (United States)

    Holl, S.; Roos, D.; Wein, J.

    The computer-assisted simulation of solidification processes influenced by gravity has gained increased importance during the previous years regarding ground-based as well as microgravity research. Depending on the specific needs of the investigator, the simulation model ideally covers a broad spectrum of applications. These primarily include the optimization of furnace design in interaction with selected process parameters to meet the desired crystallization conditions. Different approaches concerning the complexity of the simulation models as well as their dedicated applications will be discussed in this paper. Special emphasis will be put on the potential of software tools to increase the scientific quality and cost-efficiency of microgravity experimentation. The results gained so far in the context of TEXUS, FSLP, D-1 and D-2 (preparatory program) experiments, highlighting their simulation-supported preparation and evaluation will be discussed. An outlook will then be given on the possibilities to enhance the efficiency of pre-industrial research in the Columbus era through the incorporation of suitable simulation methods and tools.

  19. Development of a Single Locus Sequence Typing (SLST) Scheme for Typing Bacterial Species Directly from Complex Communities.

    Science.gov (United States)

    Scholz, Christian F P; Jensen, Anders

    2017-01-01

    The protocol describes a computational method to develop a Single Locus Sequence Typing (SLST) scheme for typing bacterial species. The resulting scheme can be used to type bacterial isolates as well as bacterial species directly from complex communities using next-generation sequencing technologies.

  20. Complete Genome Sequence of the Goatpox Virus Strain Gorgan Obtained Directly from a Commercial Live Attenuated Vaccine

    Science.gov (United States)

    Mathijs, Elisabeth; Vandenbussche, Frank; Haegeman, Andy; Al-Majali, Ahmad; De Clercq, Kris

    2016-01-01

    This is a report of the complete genome sequence of the goatpox virus strain Gorgan, which was obtained directly from a commercial live attenuated vaccine (Caprivac, Jordan Bio-Industries Centre). PMID:27738031

  1. The myoglobin of Emperor penguin (Aptenodytes forsteri): amino acid sequence and functional adaptation to extreme conditions.

    Science.gov (United States)

    Tamburrini, M; Romano, M; Giardina, B; di Prisco, G

    1999-02-01

    In the framework of a study on molecular adaptations of the oxygen-transport and storage systems to extreme conditions in Antarctic marine organisms, we have investigated the structure/function relationship in Emperor penguin (Aptenodytes forsteri) myoglobin, in search of correlation with the bird life style. In contrast with previous reports, the revised amino acid sequence contains one additional residue and 15 differences. The oxygen-binding parameters seem well adapted to the diving behaviour of the penguin and to the environmental conditions of the Antarctic habitat. Addition of lactate has no major effect on myoglobin oxygenation over a large temperature range. Therefore, metabolic acidosis does not impair myoglobin function under conditions of prolonged physical effort, such as diving.

  2. Effect of redox conditions on pharmaceutical loss during biological wastewater treatment using sequencing batch reactors

    Energy Technology Data Exchange (ETDEWEB)

    Stadler, Lauren B., E-mail: lstadler@umich.edu [Department of Civil and Environmental Engineering, University of Michigan, 1351 Beal Avenue, EWRE, Ann Arbor, MI 48109 (United States); Su, Lijuan, E-mail: lijuansu@buffalo.edu [Department of Chemistry, University at Buffalo, State University of New York, Buffalo, NY 14260 (United States); Moline, Christopher J., E-mail: christopher.moline@hdrinc.com [Department of Civil and Environmental Engineering, University of Michigan, 1351 Beal Avenue, EWRE, Ann Arbor, MI 48109 (United States); Ernstoff, Alexi S., E-mail: alexer@dtu.dk [Department of Civil and Environmental Engineering, University of Michigan, 1351 Beal Avenue, EWRE, Ann Arbor, MI 48109 (United States); Aga, Diana S., E-mail: dianaaga@buffalo.edu [Department of Chemistry, University at Buffalo, State University of New York, Buffalo, NY 14260 (United States); Love, Nancy G., E-mail: nglove@umich.edu [Department of Civil and Environmental Engineering, University of Michigan, 1351 Beal Avenue, EWRE, Ann Arbor, MI 48109 (United States)

    2015-01-23

    Highlights: • Pharmaceutical fate was studied in SBRs operated at different redox conditions. • Stable carbon oxidation and nitrification occurred under microaerobic conditions. • Losses of atenolol and trimethoprim were highest under fully aerobic conditions. • Loss of sulfamethoxazole was highest under microaerobic conditions. • Deconjugation occurred during treatment to form sulfamethoxazole and desvenlafaxine. - Abstract: We lack a clear understanding of how wastewater treatment plant (WWTP) process parameters, such as redox environment, impact pharmaceutical fate. WWTPs increasingly install more advanced aeration control systems to save energy and achieve better nutrient removal performance. The impact of redox condition, and specifically the use of microaerobic (low dissolved oxygen) treatment, is poorly understood. In this study, the fate of a mixture of pharmaceuticals and several of their transformation products present in the primary effluent of a local WWTP was assessed in sequencing batch reactors operated under different redox conditions: fully aerobic, anoxic/aerobic, and microaerobic (DO concentration ≈0.3 mg/L). Among the pharmaceuticals that were tracked during this study (atenolol, trimethoprim, sulfamethoxazole, desvenlafaxine, venlafaxine, and phenytoin), overall loss varied between them and between redox environments. Losses of atenolol and trimethoprim were highest in the aerobic reactor; sulfamethoxazole loss was highest in the microaerobic reactors; and phenytoin was recalcitrant in all reactors. Transformation products of sulfamethoxazole and desvenlafaxine resulted in the reformation of their parent compounds during treatment. The results suggest that transformation products must be accounted for when assessing removal efficiencies and that redox environment influences the degree of pharmaceutical loss.

  3. Effect of redox conditions on pharmaceutical loss during biological wastewater treatment using sequencing batch reactors

    International Nuclear Information System (INIS)

    Stadler, Lauren B.; Su, Lijuan; Moline, Christopher J.; Ernstoff, Alexi S.; Aga, Diana S.; Love, Nancy G.

    2015-01-01

    Highlights: • Pharmaceutical fate was studied in SBRs operated at different redox conditions. • Stable carbon oxidation and nitrification occurred under microaerobic conditions. • Losses of atenolol and trimethoprim were highest under fully aerobic conditions. • Loss of sulfamethoxazole was highest under microaerobic conditions. • Deconjugation occurred during treatment to form sulfamethoxazole and desvenlafaxine. - Abstract: We lack a clear understanding of how wastewater treatment plant (WWTP) process parameters, such as redox environment, impact pharmaceutical fate. WWTPs increasingly install more advanced aeration control systems to save energy and achieve better nutrient removal performance. The impact of redox condition, and specifically the use of microaerobic (low dissolved oxygen) treatment, is poorly understood. In this study, the fate of a mixture of pharmaceuticals and several of their transformation products present in the primary effluent of a local WWTP was assessed in sequencing batch reactors operated under different redox conditions: fully aerobic, anoxic/aerobic, and microaerobic (DO concentration ≈0.3 mg/L). Among the pharmaceuticals that were tracked during this study (atenolol, trimethoprim, sulfamethoxazole, desvenlafaxine, venlafaxine, and phenytoin), overall loss varied between them and between redox environments. Losses of atenolol and trimethoprim were highest in the aerobic reactor; sulfamethoxazole loss was highest in the microaerobic reactors; and phenytoin was recalcitrant in all reactors. Transformation products of sulfamethoxazole and desvenlafaxine resulted in the reformation of their parent compounds during treatment. The results suggest that transformation products must be accounted for when assessing removal efficiencies and that redox environment influences the degree of pharmaceutical loss

  4. Direct sequencing of mitochondrial DNA detects highly divergent haplotypes in blue marlin (Makaira nigricans).

    Science.gov (United States)

    Finnerty, J R; Block, B A

    1992-06-01

    We were able to differentiate between species of billfish (Istiophoridae family) and to detect considerable intraspecific variation in the blue marlin (Makaira nigricans) by directly sequencing a polymerase chain reaction (PCR)-amplified, 612-bp fragment of the mitochondrial cytochrome b gene. Thirteen variable nucleotide sites separated blue marlin (n = 26) into 7 genotypes. On average, these genotypes differed by 5.7 base substitutions. A smaller sample of swordfish from an equally broad geographic distribution displayed relatively little intraspecific variation, with an average of 1.3 substitutions separating different genotypes. A cladistic analysis of blue marlin cytochrome b variants indicates two major divergent evolutionary lines within the species. The frequencies of these two major evolutionary lines differ significantly between Atlantic and Pacific ocean basins. This finding is important given that the Atlantic stocks of blue marlin are considered endangered. Migration from the Pacific can help replenish the numbers of blue marlin in the Atlantic, but the loss of certain mitochondrial DNA haplotypes in the Atlantic due to overfishing probably could not be remedied by an influx of Pacific fish because of their absence in the Pacific population. Fishery management strategies should attempt to preserve the genetic diversity within the species. The detection of DNA sequence polymorphism indicates the utility of PCR technology in pelagic fishery genetics.

  5. A Remote Direct Sequence Spread Spectrum Communications Lab Utilising the Emona DATEx

    Directory of Open Access Journals (Sweden)

    Cosmas Mwikirize

    2012-12-01

    Full Text Available Remote labs have become popular learning aids due to their versatility and considerable ease of utilisation as compared to their physical counterparts. At Makerere University, the remote labs are based on the standard Massachusetts Institute of Technology (MIT iLabs Shared Architecture (ISA - a scalable and generic platform. Presented in this paper is such a lab, addressing the key practical aspects of Direct Sequence Spread Spectrum (DSSS communication. The lab is built on the National Instruments Educational Laboratory Virtual Instrumentation Suite (NI ELVIS with the Emona Digital and Analog Telecommunications Experimenter (DATEx add-on board. It also incorporates switching hardware. The lab facilitates real-time control of the equipment, with users able to set, manipulate and observe signal parameters in both the frequency and the time domains. Simulation and data Acquisition modes of the experiment are supported to provide a richer learning experience.

  6. Electrochemical direct immobilization of DNA sequences for label-free herpes virus detection

    Science.gov (United States)

    Tam, Phuong Dinh; Trung, Tran; Tuan, Mai Anh; Chien, Nguyen Duc

    2009-09-01

    DNA sequences/bio-macromolecules of herpes virus (5'-AT CAC CGA CCC GGA GAG GGA C-3') were directly immobilized into polypyrrole matrix by using the cyclic voltammetry method, and grafted onto arrays of interdigitated platinum microelectrodes. The morphology surface of the obtained PPy/DNA of herpes virus composite films was investigated by a FESEM Hitachi-S 4800. Fourier transform infrared spectroscopy (FTIR) was used to characterize the PPy/DNA film and to study the specific interactions that may exist between DNA biomacromolecules and PPy chains. Attempts are made to use these PPy/DNA composite films for label-free herpes virus detection revealed a response time of 60 s in solutions containing as low as 2 nM DNA concentration, and self life of six months when immerged in double distilled water and kept refrigerated.

  7. Chromatic dispersion compensation and Coherent Direct-Sequence OCDMA operation on a single super structured FBG.

    Science.gov (United States)

    Baños, Rocío; Pastor, Daniel; Amaya, Waldimar; Garcia-Munoz, Victor

    2012-06-18

    We have proposed, fabricated and demonstrated experimentally a set of Coherent Direct Sequence-OCDMA en/decoders based on Super Structured Fiber Bragg Gratings (SSFBGs) which are able to compensate the fiber chromatic dispersion at the same time that they perform the en/decoding task. The proposed devices avoid the use of additional dispersion compensation stages reducing system complexity and losses. This performance was evaluated for 5.4, 11.4 and 16.8 km of SSMF. The twofold performance was verified in Low Reflectivity regime employing only one GVD compensating device at decoder or sharing out the function between encoder and decoder devices. Shared functionality requires shorter SSFBGs designs and also provides added flexibility to the optical network design. Moreover, dispersion compensated en/decoders were also designed into the High Reflectivity regime employing synthesis methods achieving more than 9 dB reduction of insertion loss for each device.

  8. Electrochemical direct immobilization of DNA sequences for label-free herpes virus detection

    International Nuclear Information System (INIS)

    Phuong Dinh Tam; Mai Anh Tuan; Tran Trung; Nguyen Duc Chien

    2009-01-01

    DNA sequences/bio-macromolecules of herpes virus (5'-AT CAC CGA CCC GGA GAG GGA C-3') were directly immobilized into polypyrrole matrix by using the cyclic voltammetry method, and grafted onto arrays of interdigitated platinum microelectrodes. The morphology surface of the obtained PPy/DNA of herpes virus composite films was investigated by a FESEM Hitachi-S 4800. Fourier transform infrared spectroscopy (FTIR) was used to characterize the PPy/DNA film and to study the specific interactions that may exist between DNA biomacromolecules and PPy chains. Attempts are made to use these PPy/DNA composite films for label-free herpes virus detection revealed a response time of 60 s in solutions containing as low as 2 nM DNA concentration, and self life of six months when emerged in double distilled water and kept refrigerated.

  9. Electrochemical direct immobilization of DNA sequences for label-free herpes virus detection

    Energy Technology Data Exchange (ETDEWEB)

    Phuong Dinh Tam; Mai Anh Tuan [International Training Institute for Materials Science (Viet Nam); Tran Trung [Department of Electrochemistry, Hung-Yen University of Technology and Education (Viet Nam); Nguyen Duc Chien [Institute of Engineering Physics, Hanoi University of Technology, 1 Dai Co Viet Road, Hanoi (Viet Nam)], E-mail: tr_trunghut@yahoo.com

    2009-09-01

    DNA sequences/bio-macromolecules of herpes virus (5'-AT CAC CGA CCC GGA GAG GGA C-3') were directly immobilized into polypyrrole matrix by using the cyclic voltammetry method, and grafted onto arrays of interdigitated platinum microelectrodes. The morphology surface of the obtained PPy/DNA of herpes virus composite films was investigated by a FESEM Hitachi-S 4800. Fourier transform infrared spectroscopy (FTIR) was used to characterize the PPy/DNA film and to study the specific interactions that may exist between DNA biomacromolecules and PPy chains. Attempts are made to use these PPy/DNA composite films for label-free herpes virus detection revealed a response time of 60 s in solutions containing as low as 2 nM DNA concentration, and self life of six months when emerged in double distilled water and kept refrigerated.

  10. A single session of prefrontal cortex transcranial direct current stimulation does not modulate implicit task sequence learning and consolidation.

    Science.gov (United States)

    Savic, Branislav; Müri, René; Meier, Beat

    Transcranial direct current stimulation (tDCS) is assumed to affect cortical excitability and dependent on the specific stimulation conditions either to increase or decrease learning. The purpose of this study was to modulate implicit task sequence learning with tDCS. As cortico-striatal loops are critically involved in implicit task sequence learning, tDCS was applied above the dorsolateral prefrontal cortex (DLPFC). In Experiment 1, anodal, cathodal, or sham tDCS was applied before the start of the sequence learning task. In Experiment 2, stimulation was applied during the sequence learning task. Consolidation of learning was assessed after 24 h. The results of both experiments showed that implicit task sequence learning occurred consistently but it was not modulated by different tDCS conditions. Similarly, consolidation measured after a 24 h-interval including sleep was also not affected by stimulation. These results indicate that a single session of DLPFC tDCS is not sufficient to modulate implicit task sequence learning. This study adds to the accumulating evidence that tDCS may not be as effective as originally thought. Copyright © 2017 Elsevier Inc. All rights reserved.

  11. Subjective quality of video sequences rendered on LCD with local backlight dimming at different lighting conditions

    Science.gov (United States)

    Mantel, Claire; Korhonen, Jari; Pedersen, Jesper M.; Bech, Søren; Andersen, Jakob Dahl; Forchhammer, Søren

    2015-01-01

    This paper focuses on the influence of ambient light on the perceived quality of videos displayed on Liquid Crystal Display (LCD) with local backlight dimming. A subjective test assessing the quality of videos with two backlight dimming methods and three lighting conditions, i.e. no light, low light level (5 lux) and higher light level (60 lux) was organized to collect subjective data. Results show that participants prefer the method exploiting local dimming possibilities to the conventional full backlight but that this preference varies depending on the ambient light level. The clear preference for one method at the low light conditions decreases at the high ambient light, confirming that the ambient light significantly attenuates the perception of the leakage defect (light leaking through dark pixels). Results are also highly dependent on the content of the sequence, which can modulate the effect of the ambient light from having an important influence on the quality grades to no influence at all.

  12. Subjective quality of video sequences rendered on LCD with local backlight dimming at different lighting conditions

    DEFF Research Database (Denmark)

    Mantel, Claire; Korhonen, Jari; Pedersen, Jesper Mørkhøj

    2015-01-01

    This paper focuses on the influence of ambient light on the perceived quality of videos displayed on Liquid Crystal Display (LCD) with local backlight dimming. A subjective test assessing the quality of videos with two backlight dimming methods and three lighting conditions, i.e. no light, low...... light level (5 lux) and higher light level (60 lux) was organized to collect subjective data. Results show that participants prefer the method exploiting local dimming possibilities to the conventional full backlight but that this preference varies depending on the ambient light level. The clear...... preference for one method at the low light conditions decreases at the high ambient light, confirming that the ambient light significantly attenuates the perception of the leakage defect (light leaking through dark pixels). Results are also highly dependent on the content of the sequence, which can modulate...

  13. Genetic Barrier to Direct Acting Antivirals in HCV Sequences Deposited in the European Databank.

    Directory of Open Access Journals (Sweden)

    Dimas Alexandre Kliemann

    /N/R positions required only one transition for up to 98.8% of the sequences analyzed. A single variant in position 448 in genotype 1a is less likely to become the resistance variant 448H because it requires two transversions. Also, in the position 559D a transversion and a transition were necessary to generate the resistance mutant D559H.Results revealed that in 14 out of 16 positions, conversion to a drug-resistant variant of HCV required only one single nucleotide substitutions threatening direct acting antivirals from all three classes.

  14. Structured Semantic Knowledge Can Emerge Automatically from Predicting Word Sequences in Child-Directed Speech

    Directory of Open Access Journals (Sweden)

    Philip A. Huebner

    2018-02-01

    Full Text Available Previous research has suggested that distributional learning mechanisms may contribute to the acquisition of semantic knowledge. However, distributional learning mechanisms, statistical learning, and contemporary “deep learning” approaches have been criticized for being incapable of learning the kind of abstract and structured knowledge that many think is required for acquisition of semantic knowledge. In this paper, we show that recurrent neural networks, trained on noisy naturalistic speech to children, do in fact learn what appears to be abstract and structured knowledge. We trained two types of recurrent neural networks (Simple Recurrent Network, and Long Short-Term Memory to predict word sequences in a 5-million-word corpus of speech directed to children ages 0–3 years old, and assessed what semantic knowledge they acquired. We found that learned internal representations are encoding various abstract grammatical and semantic features that are useful for predicting word sequences. Assessing the organization of semantic knowledge in terms of the similarity structure, we found evidence of emergent categorical and hierarchical structure in both models. We found that the Long Short-term Memory (LSTM and SRN are both learning very similar kinds of representations, but the LSTM achieved higher levels of performance on a quantitative evaluation. We also trained a non-recurrent neural network, Skip-gram, on the same input to compare our results to the state-of-the-art in machine learning. We found that Skip-gram achieves relatively similar performance to the LSTM, but is representing words more in terms of thematic compared to taxonomic relations, and we provide reasons why this might be the case. Our findings show that a learning system that derives abstract, distributed representations for the purpose of predicting sequential dependencies in naturalistic language may provide insight into emergence of many properties of the developing

  15. Structured Semantic Knowledge Can Emerge Automatically from Predicting Word Sequences in Child-Directed Speech

    Science.gov (United States)

    Huebner, Philip A.; Willits, Jon A.

    2018-01-01

    Previous research has suggested that distributional learning mechanisms may contribute to the acquisition of semantic knowledge. However, distributional learning mechanisms, statistical learning, and contemporary “deep learning” approaches have been criticized for being incapable of learning the kind of abstract and structured knowledge that many think is required for acquisition of semantic knowledge. In this paper, we show that recurrent neural networks, trained on noisy naturalistic speech to children, do in fact learn what appears to be abstract and structured knowledge. We trained two types of recurrent neural networks (Simple Recurrent Network, and Long Short-Term Memory) to predict word sequences in a 5-million-word corpus of speech directed to children ages 0–3 years old, and assessed what semantic knowledge they acquired. We found that learned internal representations are encoding various abstract grammatical and semantic features that are useful for predicting word sequences. Assessing the organization of semantic knowledge in terms of the similarity structure, we found evidence of emergent categorical and hierarchical structure in both models. We found that the Long Short-term Memory (LSTM) and SRN are both learning very similar kinds of representations, but the LSTM achieved higher levels of performance on a quantitative evaluation. We also trained a non-recurrent neural network, Skip-gram, on the same input to compare our results to the state-of-the-art in machine learning. We found that Skip-gram achieves relatively similar performance to the LSTM, but is representing words more in terms of thematic compared to taxonomic relations, and we provide reasons why this might be the case. Our findings show that a learning system that derives abstract, distributed representations for the purpose of predicting sequential dependencies in naturalistic language may provide insight into emergence of many properties of the developing semantic system. PMID

  16. A comparison of EGFR mutation testing methods in lung carcinoma: direct sequencing, real-time PCR and immunohistochemistry.

    Directory of Open Access Journals (Sweden)

    Bárbara Angulo

    Full Text Available The objective of this study is to compare two EGFR testing methodologies (a commercial real-time PCR kit and a specific EGFR mutant immunohistochemistry, with direct sequencing and to investigate the limit of detection (LOD of both PCR-based methods. We identified EGFR mutations in 21 (16% of the 136 tumours analyzed by direct sequencing. Interestingly, the Therascreen EGFR Mutation Test kit was able to characterize as wild-type one tumour that could not be analyzed by direct sequencing of the PCR product. We then compared the LOD of the kit and that of direct sequencing using the available mutant tumours. The kit was able to detect the presence of a mutation in a 1% dilution of the total DNA in nine of the 18 tumours (50%, which tested positive with the real-time quantitative PCR method. In all cases, EGFR mutation was identified at a dilution of 5%. Where the mutant DNA represented 30% of the total DNA, sequencing was able to detect mutations in 12 out of 19 cases (63%. Additional experiments with genetically defined standards (EGFR ΔE746-A750/+ and EGFR L858R/+ yielded similar results. Immunohistochemistry (IHC staining with exon 19-specific antibody was seen in eight out of nine cases with E746-A750del detected by direct sequencing. Neither of the two tumours with complex deletions were positive. Of the five L858R-mutated tumours detected by the PCR methods, only two were positive for the exon 21-specific antibody. The specificity was 100% for both antibodies. The LOD of the real-time PCR method was lower than that of direct sequencing. The mutation specific IHC produced excellent specificity.

  17. Direct evidence for sequence-dependent attraction between double-stranded DNA controlled by methylation.

    Science.gov (United States)

    Yoo, Jejoong; Kim, Hajin; Aksimentiev, Aleksei; Ha, Taekjip

    2016-03-22

    Although proteins mediate highly ordered DNA organization in vivo, theoretical studies suggest that homologous DNA duplexes can preferentially associate with one another even in the absence of proteins. Here we combine molecular dynamics simulations with single-molecule fluorescence resonance energy transfer experiments to examine the interactions between duplex DNA in the presence of spermine, a biological polycation. We find that AT-rich DNA duplexes associate more strongly than GC-rich duplexes, regardless of the sequence homology. Methyl groups of thymine acts as a steric block, relocating spermine from major grooves to interhelical regions, thereby increasing DNA-DNA attraction. Indeed, methylation of cytosines makes attraction between GC-rich DNA as strong as that between AT-rich DNA. Recent genome-wide chromosome organization studies showed that remote contact frequencies are higher for AT-rich and methylated DNA, suggesting that direct DNA-DNA interactions that we report here may play a role in the chromosome organization and gene regulation.

  18. Variations of the ISM conditions accross the Main Sequence of star forming galaxies: observations and simulations.

    Science.gov (United States)

    Martinez Galarza, Juan R.; Smith, Howard Alan; Lanz, Lauranne; Hayward, Christopher C.; Zezas, Andreas; Hung, Chao-Ling; Rosenthal, Lee; Weiner, Aaron

    2015-01-01

    A significant amount of evidence has been gathered that leads to the existence of a main sequence (MS) of star formation in galaxies. This MS is expressed in terms of a correlation between the SFR and the stellar mass of the form SFR ∝ M* and spans a few orders of magnitude in both quantities. Several ideas have been suggested to explain fundamental properties of the MS, such as its slope, its dispersion, and its evolution with redshift, but no consensus has been reached regarding its true nature, and whether the membership or not of particular galaxies to this MS underlies the existence of two different modes of star formation. In order to advance in the understanding of the MS, here we use a statistically robust Bayesian SED analysis method (CHIBURST) to consistently analyze the star-forming properties of a set of hydro-dynamical simulations of mergers, as well as observations of real mergers, both local and at intermediate redshift. We find a remarkable, very tight correlation between the specific star formation rate (sSFR) of galaxies, and the typical ISM conditions near their inernal star-forming regions, parametrized via a novel quantity: the compactness parameter (C). The evolution of mergers along this correlation explains the spread of the MS, and implies that the physical conditions of the ISM smoothly evolve between on-MS (secular) conditions and off-MS (coalescence/starburst) conditions. Furthermore, we show that the slope of the correlation can be interpreted in terms of the efficiency in the conversion of gas into stars, and that this efficiency remains unchanged along and across the MS. Finally, we discuss differences in the normalization of the correlation as a function of merger mass and redshift, and conclude that these differences imply the existence of two different modes of star formation, unrelated to the smooth evolution across the MS: a disk-like, low pressure mode and a compact nuclear-starburst mode.

  19. Radiation-induced germ-line mutations detected by a direct comparison of parents and children DNA sequences containing SNPs

    International Nuclear Information System (INIS)

    Morimyo, M.; Hongo, E.; Higashi, T.; Wu, J.; Matsumoto, I.; Okamoto, M.; Kawano, A.; Tsuji, S.

    2003-01-01

    Full text: Germ-line mutation is detected in mice but not in humans. To estimate genetic risk of humans, a new approach to extrapolate from animal data to humans or to directly detect radiation-induced mutations in man is expected. We have developed a new method to detect germ-line mutations by directly comparing DNA sequences of parents and children. The nucleotide sequences among mouse strains are almost identical except SNP markers that are detected at 1/1000 frequency. When gamma-irradiated male mice are mated with female mice, heterogeneous nucleotide sequences induced in children DNA are a candidate of mutation, whose assignment can be done by SNP analysis. This system can easily detect all types of mutations such as transition, transversion, frameshift and deletion induced by radiation and can be applied to humans having genetically heterogeneous nucleotide sequences and many SNP markers. C3H male mice of 8 weeks of gestation were irradiated with gamma rays of 3 and 1 Gy and after 3 weeks, they were mated with the same aged C57BL female mice. After 3 weeks breeding, DNA was extracted from parents and children mice. The nucleotide sequences of 150 STS markers containing 300-900 bp and SNPs of parents and children DNA were determined by a direct sequencing; amplification of STS markers by Taq DNA polymerase, purification of PCR products, and DNA sequencing with a dye-terminator method. At each radiation dose, a total amount of 5 Mb DNA sequences were examined to detect radiation-induced mutations. We could find 6 deletions in 3 Gy irradiated mice but not in 1 Gy and control mice. The mutation frequency was about 4.0 x 10 -7 /bp/ Gy or 1.6 x 10 -4 /locus/Gy, and suggested the non-linear increase of mutation rate with dose

  20. Shared investment projects and forecasting errors: setting framework conditions for coordination and sequencing data quality activities.

    Science.gov (United States)

    Leitner, Stephan; Brauneis, Alexander; Rausch, Alexandra

    2015-01-01

    In this paper, we investigate the impact of inaccurate forecasting on the coordination of distributed investment decisions. In particular, by setting up a computational multi-agent model of a stylized firm, we investigate the case of investment opportunities that are mutually carried out by organizational departments. The forecasts of concern pertain to the initial amount of money necessary to launch and operate an investment opportunity, to the expected intertemporal distribution of cash flows, and the departments' efficiency in operating the investment opportunity at hand. We propose a budget allocation mechanism for coordinating such distributed decisions The paper provides guidance on how to set framework conditions, in terms of the number of investment opportunities considered in one round of funding and the number of departments operating one investment opportunity, so that the coordination mechanism is highly robust to forecasting errors. Furthermore, we show that-in some setups-a certain extent of misforecasting is desirable from the firm's point of view as it supports the achievement of the corporate objective of value maximization. We then address the question of how to improve forecasting quality in the best possible way, and provide policy advice on how to sequence activities for improving forecasting quality so that the robustness of the coordination mechanism to errors increases in the best possible way. At the same time, we show that wrong decisions regarding the sequencing can lead to a decrease in robustness. Finally, we conduct a comprehensive sensitivity analysis and prove that-in particular for relatively good forecasters-most of our results are robust to changes in setting the parameters of our multi-agent simulation model.

  1. Shared Investment Projects and Forecasting Errors: Setting Framework Conditions for Coordination and Sequencing Data Quality Activities

    Science.gov (United States)

    Leitner, Stephan; Brauneis, Alexander; Rausch, Alexandra

    2015-01-01

    In this paper, we investigate the impact of inaccurate forecasting on the coordination of distributed investment decisions. In particular, by setting up a computational multi-agent model of a stylized firm, we investigate the case of investment opportunities that are mutually carried out by organizational departments. The forecasts of concern pertain to the initial amount of money necessary to launch and operate an investment opportunity, to the expected intertemporal distribution of cash flows, and the departments’ efficiency in operating the investment opportunity at hand. We propose a budget allocation mechanism for coordinating such distributed decisions The paper provides guidance on how to set framework conditions, in terms of the number of investment opportunities considered in one round of funding and the number of departments operating one investment opportunity, so that the coordination mechanism is highly robust to forecasting errors. Furthermore, we show that—in some setups—a certain extent of misforecasting is desirable from the firm’s point of view as it supports the achievement of the corporate objective of value maximization. We then address the question of how to improve forecasting quality in the best possible way, and provide policy advice on how to sequence activities for improving forecasting quality so that the robustness of the coordination mechanism to errors increases in the best possible way. At the same time, we show that wrong decisions regarding the sequencing can lead to a decrease in robustness. Finally, we conduct a comprehensive sensitivity analysis and prove that—in particular for relatively good forecasters—most of our results are robust to changes in setting the parameters of our multi-agent simulation model. PMID:25803736

  2. Shared investment projects and forecasting errors: setting framework conditions for coordination and sequencing data quality activities.

    Directory of Open Access Journals (Sweden)

    Stephan Leitner

    Full Text Available In this paper, we investigate the impact of inaccurate forecasting on the coordination of distributed investment decisions. In particular, by setting up a computational multi-agent model of a stylized firm, we investigate the case of investment opportunities that are mutually carried out by organizational departments. The forecasts of concern pertain to the initial amount of money necessary to launch and operate an investment opportunity, to the expected intertemporal distribution of cash flows, and the departments' efficiency in operating the investment opportunity at hand. We propose a budget allocation mechanism for coordinating such distributed decisions The paper provides guidance on how to set framework conditions, in terms of the number of investment opportunities considered in one round of funding and the number of departments operating one investment opportunity, so that the coordination mechanism is highly robust to forecasting errors. Furthermore, we show that-in some setups-a certain extent of misforecasting is desirable from the firm's point of view as it supports the achievement of the corporate objective of value maximization. We then address the question of how to improve forecasting quality in the best possible way, and provide policy advice on how to sequence activities for improving forecasting quality so that the robustness of the coordination mechanism to errors increases in the best possible way. At the same time, we show that wrong decisions regarding the sequencing can lead to a decrease in robustness. Finally, we conduct a comprehensive sensitivity analysis and prove that-in particular for relatively good forecasters-most of our results are robust to changes in setting the parameters of our multi-agent simulation model.

  3. Conditional Probabilities of Large Earthquake Sequences in California from the Physics-based Rupture Simulator RSQSim

    Science.gov (United States)

    Gilchrist, J. J.; Jordan, T. H.; Shaw, B. E.; Milner, K. R.; Richards-Dinger, K. B.; Dieterich, J. H.

    2017-12-01

    Within the SCEC Collaboratory for Interseismic Simulation and Modeling (CISM), we are developing physics-based forecasting models for earthquake ruptures in California. We employ the 3D boundary element code RSQSim (Rate-State Earthquake Simulator of Dieterich & Richards-Dinger, 2010) to generate synthetic catalogs with tens of millions of events that span up to a million years each. This code models rupture nucleation by rate- and state-dependent friction and Coulomb stress transfer in complex, fully interacting fault systems. The Uniform California Earthquake Rupture Forecast Version 3 (UCERF3) fault and deformation models are used to specify the fault geometry and long-term slip rates. We have employed the Blue Waters supercomputer to generate long catalogs of simulated California seismicity from which we calculate the forecasting statistics for large events. We have performed probabilistic seismic hazard analysis with RSQSim catalogs that were calibrated with system-wide parameters and found a remarkably good agreement with UCERF3 (Milner et al., this meeting). We build on this analysis, comparing the conditional probabilities of sequences of large events from RSQSim and UCERF3. In making these comparisons, we consider the epistemic uncertainties associated with the RSQSim parameters (e.g., rate- and state-frictional parameters), as well as the effects of model-tuning (e.g., adjusting the RSQSim parameters to match UCERF3 recurrence rates). The comparisons illustrate how physics-based rupture simulators might assist forecasters in understanding the short-term hazards of large aftershocks and multi-event sequences associated with complex, multi-fault ruptures.

  4. A 135-kilodalton surface antigen of Mycoplasma hominis PG21 contains multiple directly repeated sequences

    DEFF Research Database (Denmark)

    Ladefoged, Søren; Birkelund, Svend; Hauge, S

    1995-01-01

    gene was sequenced, and its gene product was characterized with the goal of elucidating the structure and function of Lmp1. A total of 7,196 bp in the lmp1 region was sequenced. An open reading frame of 4,032 bp, encoding a protein of 1,344 amino acids with a calculated molecular weight of 147...

  5. The impact of cerebellar transcranial direct current stimulation (tDCS) on learning fine-motor sequences.

    Science.gov (United States)

    Shimizu, Renee E; Wu, Allan D; Samra, Jasmine K; Knowlton, Barbara J

    2017-01-05

    The cerebellum has been shown to be important for skill learning, including the learning of motor sequences. We investigated whether cerebellar transcranial direct current stimulation (tDCS) would enhance learning of fine motor sequences. Because the ability to generalize or transfer to novel task variations or circumstances is a crucial goal of real world training, we also examined the effect of tDCS on performance of novel sequences after training. In Study 1, participants received either anodal, cathodal or sham stimulation while simultaneously practising three eight-element key press sequences in a non-repeating, interleaved order. Immediately after sequence practice with concurrent tDCS, a transfer session was given in which participants practised three interleaved novel sequences. No stimulation was given during transfer. An inhibitory effect of cathodal tDCS was found during practice, such that the rate of learning was slowed in comparison to the anodal and sham groups. In Study 2, participants received anodal or sham stimulation and a 24 h delay was added between the practice and transfer sessions to reduce mental fatigue. Although this consolidation period benefitted subsequent transfer for both tDCS groups, anodal tDCS enhanced transfer performance. Together, these studies demonstrate polarity-specific effects on fine motor sequence learning and generalization.This article is part of the themed issue 'New frontiers for statistical learning in the cognitive sciences'. © 2016 The Author(s).

  6. Effects of a Self-Directed Nutrition Intervention among Adults with Chronic Health Conditions

    Science.gov (United States)

    Baruth, Meghan; Wilcox, Sara; Jake-Schoffman, Danielle E.; Schlaff, Rebecca A.; Goldufsky, Tatum M.

    2018-01-01

    Chronic diseases are common among adults. A healthy diet may be beneficial for managing the consequences of such conditions. The purpose of this study was to evaluate the effects of a self-directed nutrition program on dietary behaviors among adults with chronic health conditions. As part of a larger trial examining the effects of a self-directed…

  7. Assessment of importance of elements for systems that condition depends on the sequence of elements failures

    International Nuclear Information System (INIS)

    Povyakalo, A.A.

    1996-01-01

    This paper proposes new general formulas for calculation of indices of elements importance for systems whose condition depends on sequence of elements failures. These systems have been called as systems with memory of failures (M-systems). Techniques existing for assessment of importance of elements are based on the Bool's models of system reliability, for which it is significant to suggest, that in every period of time system state depends only on a combination of states of elements at that very moment of time. These systems have been called as combinational systems (C-systems). Reliability of M-systems at any moment of operating time is a functional having distributions of elements time before failure as its arguments. Bool's models and methods of assessment of element importance, based on these models, are not appropriate for these systems. Pereguda and Povyakalo proposed the new techniques for assessment of elements importance for PO-SS systems that includes Protection Object (PO) and Safety System (PO). PO-SS system is an example of M-system. That technique is used at this paper as a basis for more general consideration. It has been shown that technique proposed for assessment of elements importance for M-systems has well-known Birnbaum's method as its particular case. Also the system with double protection is considered as an example

  8. Synchronized moving aperture radiation therapy (SMART): superimposing tumor motion on IMRT MLC leaf sequences under realistic delivery conditions

    International Nuclear Information System (INIS)

    Xu Jun; Papanikolaou, Nikos; Shi Chengyu; Jiang, Steve B

    2009-01-01

    Synchronized moving aperture radiation therapy (SMART) has been proposed to account for tumor motions during radiotherapy in prior work. The basic idea of SMART is to synchronize the moving radiation beam aperture formed by a dynamic multileaf collimator (DMLC) with the tumor motion induced by respiration. In this paper, a two-dimensional (2D) superimposing leaf sequencing method is presented for SMART. A leaf sequence optimization strategy was generated to assure the SMART delivery under realistic delivery conditions. The study of delivery performance using the Varian LINAC and the Millennium DMLC showed that clinical factors such as collimator angle, dose rate, initial phase and machine tolerance affect the delivery accuracy and efficiency. An in-house leaf sequencing software was developed to implement the 2D superimposing leaf sequencing method and optimize the motion-corrected leaf sequence under realistic clinical conditions. The analysis of dynamic log (Dynalog) files showed that optimization of the leaf sequence for various clinical factors can avoid beam hold-offs which break the synchronization of SMART and fail the SMART dose delivery. Through comparison between the simulated delivered fluence map and the planed fluence map, it was shown that the motion-corrected leaf sequence can greatly reduce the dose error.

  9. Direct comparisons of Illumina vs. Roche 454 sequencing technologies on the same microbial community DNA sample.

    Directory of Open Access Journals (Sweden)

    Chengwei Luo

    Full Text Available Next-generation sequencing (NGS is commonly used in metagenomic studies of complex microbial communities but whether or not different NGS platforms recover the same diversity from a sample and their assembled sequences are of comparable quality remain unclear. We compared the two most frequently used platforms, the Roche 454 FLX Titanium and the Illumina Genome Analyzer (GA II, on the same DNA sample obtained from a complex freshwater planktonic community. Despite the substantial differences in read length and sequencing protocols, the platforms provided a comparable view of the community sampled. For instance, derived assemblies overlapped in ~90% of their total sequences and in situ abundances of genes and genotypes (estimated based on sequence coverage correlated highly between the two platforms (R(2>0.9. Evaluation of base-call error, frameshift frequency, and contig length suggested that Illumina offered equivalent, if not better, assemblies than Roche 454. The results from metagenomic samples were further validated against DNA samples of eighteen isolate genomes, which showed a range of genome sizes and G+C% content. We also provide quantitative estimates of the errors in gene and contig sequences assembled from datasets characterized by different levels of complexity and G+C% content. For instance, we noted that homopolymer-associated, single-base errors affected ~1% of the protein sequences recovered in Illumina contigs of 10× coverage and 50% G+C; this frequency increased to ~3% when non-homopolymer errors were also considered. Collectively, our results should serve as a useful practical guide for choosing proper sampling strategies and data possessing protocols for future metagenomic studies.

  10. Direct comparisons of Illumina vs. Roche 454 sequencing technologies on the same microbial community DNA sample.

    Science.gov (United States)

    Luo, Chengwei; Tsementzi, Despina; Kyrpides, Nikos; Read, Timothy; Konstantinidis, Konstantinos T

    2012-01-01

    Next-generation sequencing (NGS) is commonly used in metagenomic studies of complex microbial communities but whether or not different NGS platforms recover the same diversity from a sample and their assembled sequences are of comparable quality remain unclear. We compared the two most frequently used platforms, the Roche 454 FLX Titanium and the Illumina Genome Analyzer (GA) II, on the same DNA sample obtained from a complex freshwater planktonic community. Despite the substantial differences in read length and sequencing protocols, the platforms provided a comparable view of the community sampled. For instance, derived assemblies overlapped in ~90% of their total sequences and in situ abundances of genes and genotypes (estimated based on sequence coverage) correlated highly between the two platforms (R(2)>0.9). Evaluation of base-call error, frameshift frequency, and contig length suggested that Illumina offered equivalent, if not better, assemblies than Roche 454. The results from metagenomic samples were further validated against DNA samples of eighteen isolate genomes, which showed a range of genome sizes and G+C% content. We also provide quantitative estimates of the errors in gene and contig sequences assembled from datasets characterized by different levels of complexity and G+C% content. For instance, we noted that homopolymer-associated, single-base errors affected ~1% of the protein sequences recovered in Illumina contigs of 10× coverage and 50% G+C; this frequency increased to ~3% when non-homopolymer errors were also considered. Collectively, our results should serve as a useful practical guide for choosing proper sampling strategies and data possessing protocols for future metagenomic studies.

  11. Reproductive effort of some annual and perennial plant species: impact of successional sequence, habitat conditions and plant size

    International Nuclear Information System (INIS)

    Shaukat, S.; Khan, M.A.; Zaidi, S.; Siddiqui, M.F.; Khan, N.; Zafar, H.

    2013-01-01

    The reproductive effort of some annual and perennial plant species was investigated with respect to successional sequence, habitat conditions and plant size. in the psammosere succession (dune succession), the reproductive effort (RE) of Cressa cretica and A triplex griffithii was significantly greater in the early stage compared to that in late succession. Likewise, in relation to lithosere succession, Sporobolus arabicus. Pluchea lanceolata and Vernonia cenerescens all showed high reproductive effort in early part of succession compared to that of late succession. The annuals (S. arabicus and P lance/ala) exhibited greater reproductive effort compared to the perennial species Vernonia cinerescens. Examination of the Impact of site differences on reproductive effort showed that four grasses including Selaria intermedia, Chioris harbata, Cenchrus hiflorus, and Eragroslis pilosa were found to have significantly (P<0.05) greater reproductive effort in site 1 (near cultivated field), compared to site 2 (a vacant lot), which had low nutrient level compared to site 1. The reproductive effort of Sonclius asper (a composite) did not exhibit significant difference between sites. The investigation of relationships between plant size (volume) and reproductive effort of Solanuin forskalii, Senna holosericea and Heliolropium ophioglossum showed positive correlations between plant size and reproductive effort. Solanum forskalii and Senna holosericca, in particular, exhibited a close association in this respect. It is concluded that: 1) RE is greater in early compared to late succession, 2) RE changes with the habitat and 3) there seems to be a direct relationship between RE and plant size. (author)

  12. A direct method for computing extreme value (Gumbel) parameters for gapped biological sequence alignments.

    Science.gov (United States)

    Quinn, Terrance; Sinkala, Zachariah

    2014-01-01

    We develop a general method for computing extreme value distribution (Gumbel, 1958) parameters for gapped alignments. Our approach uses mixture distribution theory to obtain associated BLOSUM matrices for gapped alignments, which in turn are used for determining significance of gapped alignment scores for pairs of biological sequences. We compare our results with parameters already obtained in the literature.

  13. Intubation conditions after rocuronium or succinylcholine for rapid sequence induction with alfentanil and propofol in the emergency patient

    DEFF Research Database (Denmark)

    Larsen, P B; Hansen, E G; Jacobsen, L S

    2005-01-01

    Background and objective: Previous studies mainly conducted on elective patients recommend doses of 0.9-1.2 mg kg[-1] rocuronium to obtain comparable intubation conditions with succinylcholine 1.0 mg kg[-1] after 60 s during a rapid-sequence induction. We decided to compare the overall intubating...... conditions of standard doses of rocuronium 0.6 mg kg[-1] and succinylcholine 1.0 mg kg[-1] during a strict rapid-sequence induction regimen including propofol and alfentanil. Methods: Male and female patients (ASA I-III) older than 17 yr scheduled for emergency abdominal or gynaecological surgery...... and with increased risk of pulmonary aspiration of gastric content were randomized to a rapid-sequence induction with succinylcholine 1.0 mg kg[-1] or rocuronium 0.6 mg kg[-1]. Patients with a predicted difficult airway were excluded. A senior anaesthesiologist 'blinded' for the randomization performed...

  14. DNA-directed alkylating ligands as potential antitumor agents: sequence specificity of alkylation by intercalating aniline mustards.

    Science.gov (United States)

    Prakash, A S; Denny, W A; Gourdie, T A; Valu, K K; Woodgate, P D; Wakelin, L P

    1990-10-23

    The sequence preferences for alkylation of a series of novel parasubstituted aniline mustards linked to the DNA-intercalating chromophore 9-aminoacridine by an alkyl chain of variable length were studied by using procedures analogous to Maxam-Gilbert reactions. The compounds alkylate DNA at both guanine and adenine sites. For mustards linked to the acridine by a short alkyl chain through a para O- or S-link group, 5'-GT sequences are the most preferred sites at which N7-guanine alkylation occurs. For analogues with longer chain lengths, the preference of 5'-GT sequences diminishes in favor of N7-adenine alkylation at the complementary 5'-AC sequence. Magnesium ions are shown to selectively inhibit alkylation at the N7 of adenine (in the major groove) by these compounds but not the alkylation at the N3 of adenine (in the minor groove) by the antitumor antibiotic CC-1065. Effects of chromophore variation were also studied by using aniline mustards linked to quinazoline and sterically hindered tert-butyl-9-aminoacridine chromophores. The results demonstrate that in this series of DNA-directed mustards the noncovalent interactions of the carrier chromophores with DNA significantly modify the sequence selectivity of alkylation by the mustard. Relationships between the DNA alkylation patterns of these compounds and their biological activities are discussed.

  15. Characterization of Human Cytomegalovirus Genome Diversity in Immunocompromised Hosts by Whole-Genome Sequencing Directly From Clinical Specimens.

    Science.gov (United States)

    Hage, Elias; Wilkie, Gavin S; Linnenweber-Held, Silvia; Dhingra, Akshay; Suárez, Nicolás M; Schmidt, Julius J; Kay-Fedorov, Penelope C; Mischak-Weissinger, Eva; Heim, Albert; Schwarz, Anke; Schulz, Thomas F; Davison, Andrew J; Ganzenmueller, Tina

    2017-06-01

    Advances in next-generation sequencing (NGS) technologies allow comprehensive studies of genetic diversity over the entire genome of human cytomegalovirus (HCMV), a significant pathogen for immunocompromised individuals. Next-generation sequencing was performed on target enriched sequence libraries prepared directly from a variety of clinical specimens (blood, urine, breast milk, respiratory samples, biopsies, and vitreous humor) obtained longitudinally or from different anatomical compartments from 20 HCMV-infected patients (renal transplant recipients, stem cell transplant recipients, and congenitally infected children). De novo-assembled HCMV genome sequences were obtained for 57 of 68 sequenced samples. Analysis of longitudinal or compartmental HCMV diversity revealed various patterns: no major differences were detected among longitudinal, intraindividual blood samples from 9 of 15 patients and in most of the patients with compartmental samples, whereas a switch of the major HCMV population was observed in 6 individuals with sequential blood samples and upon compartmental analysis of 1 patient with HCMV retinitis. Variant analysis revealed additional aspects of minor virus population dynamics and antiviral-resistance mutations. In immunosuppressed patients, HCMV can remain relatively stable or undergo drastic genomic changes that are suggestive of the emergence of minor resident strains or de novo infection. © The Author 2017. Published by Oxford University Press for the Infectious Diseases Society of America. All rights reserved. For permissions, e-mail journals.permissions@oup.com.

  16. OPTIMAL practice conditions enhance the benefits of gradually increasing error opportunities on retention of a stepping sequence task.

    Science.gov (United States)

    Levac, Danielle; Driscoll, Kate; Galvez, Jessica; Mercado, Kathleen; O'Neil, Lindsey

    2017-12-01

    Physical therapists should implement practice conditions that promote motor skill learning after neurological injury. Errorful and errorless practice conditions are effective for different populations and tasks. Errorful learning provides opportunities for learners to make task-relevant choices. Enhancing learner autonomy through choice opportunities is a key component of the Optimizing Performance through Intrinsic Motivation and Attention for Learning (OPTIMAL) theory of motor learning. The objective of this study was to evaluate the interaction between error opportunity frequency and OPTIMAL (autonomy-supportive) practice conditions during stepping sequence acquisition in a virtual environment. Forty healthy young adults were randomized to autonomy-supportive or autonomy-controlling practice conditions, which differed in instructional language, focus of attention (external vs internal) and positive versus negative nature of verbal and visual feedback. All participants practiced 40 trials of 4, six-step stepping sequences in a random order. Each of the 4 sequences offered different amounts of choice opportunities about the next step via visual cue presentation (4 choices; 1 choice; gradually increasing [1-2-3-4] choices, and gradually decreasing [4-3-2-1] choices). Motivation and engagement were measured by the Intrinsic Motivation Inventory (IMI) and the User Engagement Scale (UES). Participants returned 1-3 days later for retention tests, where learning was measured by time to complete each sequence. No choice cues were offered on retention. Participants in the autonomy-supportive group outperformed the autonomy-controlling group at retention on all sequences (mean difference 2.88s, p errorful (4 choice) sequence (p error opportunities over time, suggest that participants relied on implicit learning strategies for this full body task and that feedback about successes minimized errors and reduced their potential information-processing benefits. Subsequent

  17. The active sequence in the acth molecule responsible for inhibition of the extinction of conditioned avoidance behaviour in rats

    NARCIS (Netherlands)

    Greven, H.M.; Wied, D. de

    1967-01-01

    The effect of structural analogues of the N-terminal decapeptide of ACTH on inhibition of extinction of a conditioned avoidance response in rats has been studied. Studies involving the relation between chain length and behavioural activity revealed that the sequence 4–10 is the shortest peptide

  18. Sequence Directionality Dramatically Affects LCST Behavior of Elastin-Like Polypeptides.

    Science.gov (United States)

    Li, Nan K; Roberts, Stefan; Quiroz, Felipe Garcia; Chilkoti, Ashutosh; Yingling, Yaroslava G

    2018-04-30

    Elastin-like polypeptides (ELP) exhibit an inverse temperature transition or lower critical solution temperature (LCST) transition phase behavior in aqueous solutions. In this paper, the thermal responsive properties of the canonical ELP, poly(VPGVG), and its reverse sequence poly(VGPVG) were investigated by turbidity measurements of the cloud point behavior, circular dichroism (CD) measurements, and all-atom molecular dynamics (MD) simulations to gain a molecular understanding of mechanism that controls hysteretic phase behavior. It was shown experimentally that both poly(VPGVG) and poly(VGPVG) undergo a transition from soluble to insoluble in aqueous solution upon heating above the transition temperature ( T t ). However, poly(VPGVG) resolubilizes upon cooling below its T t , whereas the reverse sequence, poly(VGPVG), remains aggregated despite significant undercooling below the T t . The results from MD simulations indicated that a change in sequence order results in significant differences in the dynamics of the specific residues, especially valines, which lead to extensive changes in the conformations of VPGVG and VGPVG pentamers and, consequently, dissimilar propensities for secondary structure formation and overall structure of polypeptides. These changes affected the relative hydrophilicities of polypeptides above T t , where poly(VGPVG) is more hydrophilic than poly(VPGVG) with more extended conformation and larger surface area, which led to formation of strong interchain hydrogen bonds responsible for stabilization of the aggregated phase and the observed thermal hysteresis for poly(VGPVG).

  19. Air conditioning system and component therefore distributing air flow from opposite directions

    Science.gov (United States)

    Obler, H. D.; Bauer, H. B. (Inventor)

    1974-01-01

    The air conditioning system comprises a plurality of separate air conditioning units coupled to a common supply duct such that air may be introduced into the supply duct in two opposite flow directions. A plurality of outlets such as registers or auxiliary or branch ducts communicate with the supply duct and valve means are disposed in the supply duct at at least some of the outlets for automatically channelling a controllable amount of air from the supply duct to the associated outlet regardless of the direction of air flow within the supply duct. The valve means comprises an automatic air volume control apparatus for distribution within the air supply duct into which air may be introduced from two opposite directions. The apparatus incorporates a freely swinging movable vane in the supply duct to automatically channel into the associated outlet only the deflected air flow which has the higher relative pressure.

  20. Towards clinical molecular diagnosis of inherited cardiac conditions: a comparison of bench-top genome DNA sequencers.

    Directory of Open Access Journals (Sweden)

    Xinzhong Li

    Full Text Available Molecular genetic testing is recommended for diagnosis of inherited cardiac disease, to guide prognosis and treatment, but access is often limited by cost and availability. Recently introduced high-throughput bench-top DNA sequencing platforms have the potential to overcome these limitations.We evaluated two next-generation sequencing (NGS platforms for molecular diagnostics. The protein-coding regions of six genes associated with inherited arrhythmia syndromes were amplified from 15 human samples using parallelised multiplex PCR (Access Array, Fluidigm, and sequenced on the MiSeq (Illumina and Ion Torrent PGM (Life Technologies. Overall, 97.9% of the target was sequenced adequately for variant calling on the MiSeq, and 96.8% on the Ion Torrent PGM. Regions missed tended to be of high GC-content, and most were problematic for both platforms. Variant calling was assessed using 107 variants detected using Sanger sequencing: within adequately sequenced regions, variant calling on both platforms was highly accurate (Sensitivity: MiSeq 100%, PGM 99.1%. Positive predictive value: MiSeq 95.9%, PGM 95.5%. At the time of the study the Ion Torrent PGM had a lower capital cost and individual runs were cheaper and faster. The MiSeq had a higher capacity (requiring fewer runs, with reduced hands-on time and simpler laboratory workflows. Both provide significant cost and time savings over conventional methods, even allowing for adjunct Sanger sequencing to validate findings and sequence exons missed by NGS.MiSeq and Ion Torrent PGM both provide accurate variant detection as part of a PCR-based molecular diagnostic workflow, and provide alternative platforms for molecular diagnosis of inherited cardiac conditions. Though there were performance differences at this throughput, platforms differed primarily in terms of cost, scalability, protocol stability and ease of use. Compared with current molecular genetic diagnostic tests for inherited cardiac arrhythmias

  1. Infants learn better from left to right: a directional bias in infants? sequence learning

    OpenAIRE

    Bulf, Hermann; de Hevia, Maria Dolores; Gariboldi, Valeria; Macchi Cassia, Viola

    2017-01-01

    A wealth of studies show that human adults map ordered information onto a directional spatial continuum. We asked whether mapping ordinal information into a directional space constitutes an early predisposition, already functional prior to the acquisition of symbolic knowledge and language. While it is known that preverbal infants represent numerical order along a left-to-right spatial continuum, no studies have investigated yet whether infants, like adults, organize any kind of ordinal infor...

  2. Next-generation DNA sequencing of HEXA: a step in the right direction for carrier screening

    OpenAIRE

    Hoffman, Jodi D; Greger, Valerie; Strovel, Erin T; Blitzer, Miriam G; Umbarger, Mark A; Kennedy, Caleb; Bishop, Brian; Saunders, Patrick; Porreca, Gregory J; Schienda, Jaclyn; Davie, Jocelyn; Hallam, Stephanie; Towne, Charles

    2013-01-01

    Tay-Sachs disease (TSD) is the prototype for ethnic-based carrier screening, with a carrier rate of ∼1/27 in Ashkenazi Jews and French Canadians. HexA enzyme analysis is the current gold standard for TSD carrier screening (detection rate ∼98%), but has technical limitations. We compared DNA analysis by next-generation DNA sequencing (NGS) plus an assay for the 7.6 kb deletion to enzyme analysis for TSD carrier screening using 74 samples collected from participants at a TSD family conference. ...

  3. Analyses of conditions in a large, dry PWR containment during an TMLB' accident sequence

    International Nuclear Information System (INIS)

    Sweet, D.W.; Roberts, G.J.

    1994-01-01

    The aim of the paper is to give an assessment of the conditions which would develop in the large, dry containment of a modern Westinghouse-type PWR during a severe accident where all safety systems are unavailable. The analysis is based principally on the results of calculations using the CONTAIN code, with a 4 cell model of the containment, for a station blackout (TMLB') scenario in which the vessel is assumed to fail at high pressure. In particular, the following are noted: (i) If much of the debris is in contact with water, so that decay heat can boil water directly, then the pressure rises steadily to reach the assumed containment failure point after 11/2 to 2 days. If most of the debris becomes isolated from water, for example, because of water is held up on the containment floors and in sumps and drains, the pressure rises too slowly to threaten the containment on this timescale. (ii) If a core-concrete interaction occurs, most of the associated fission product release takes place soon after relocation of molten fuel to the containment. The aerosols which transport these (and other non-gaseous fission products released earlier in the accident) in the containment agglomerate and settle. As a result, 0.1% or less of the aerosols remain airborne a day after the start of the accident. (iii) Hydrogen and carbon monoxide, which would accumulate in the containment are not expected to burn because the atmosphere would be inerted by steam. If, however, enough of the steam is condensed, for example, by recovering the containment sprays, a burn could occur but the resulting pressure spike is unlikely to threaten the containment unless a transition to detonation occurs. 6 refs., 6 tabs., 12 figs

  4. Application of Massively Parallel Sequencing in the Clinical Diagnostic Testing of Inherited Cardiac Conditions

    Directory of Open Access Journals (Sweden)

    Ivone U. S. Leong

    2014-06-01

    Full Text Available Sudden cardiac death in people between the ages of 1–40 years is a devastating event and is frequently caused by several heritable cardiac disorders. These disorders include cardiac ion channelopathies, such as long QT syndrome, catecholaminergic polymorphic ventricular tachycardia and Brugada syndrome and cardiomyopathies, such as hypertrophic cardiomyopathy and arrhythmogenic right ventricular cardiomyopathy. Through careful molecular genetic evaluation of DNA from sudden death victims, the causative gene mutation can be uncovered, and the rest of the family can be screened and preventative measures implemented in at-risk individuals. The current screening approach in most diagnostic laboratories uses Sanger-based sequencing; however, this method is time consuming and labour intensive. The development of massively parallel sequencing has made it possible to produce millions of sequence reads simultaneously and is potentially an ideal approach to screen for mutations in genes that are associated with sudden cardiac death. This approach offers mutation screening at reduced cost and turnaround time. Here, we will review the current commercially available enrichment kits, massively parallel sequencing (MPS platforms, downstream data analysis and its application to sudden cardiac death in a diagnostic environment.

  5. Aerosol retention during SGTR meltdown sequences under different conditions of tubes vibration

    International Nuclear Information System (INIS)

    Delgado Tardaguila, R.; Herranz, L. E.

    2014-01-01

    The containment bypass of the fission products during SGTR meltdown sequences makes this scenario be a significant risk contributor in PWRs. The EU-SGTR, ARTIST 1 and 2 and the on-going ARTIST-extension programs have investigated the potential attenuation of the source term reaching the secondary side of a failed SG even in the absence of water. (Author)

  6. Directed evolution of a β-mannanase from Rhizomucor miehei to improve catalytic activity in acidic and thermophilic conditions.

    Science.gov (United States)

    Li, Yan-Xiao; Yi, Ping; Yan, Qiao-Juan; Qin, Zhen; Liu, Xue-Qiang; Jiang, Zheng-Qiang

    2017-01-01

    β-Mannanase randomly cleaves the β-1,4-linked mannan backbone of hemicellulose, which plays the most important role in the enzymatic degradation of mannan. Although the industrial applications of β-mannanase have tremendously expanded in recent years, the wild-type β-mannanases are still defective for some industries. The glycoside hydrolase (GH) family 5 β-mannanase ( Rm Man5A) from Rhizomucor miehei shows many outstanding properties, such as high specific activity and hydrolysis property. However, owing to the low catalytic activity in acidic and thermophilic conditions, the application of Rm Man5A to the biorefinery of mannan biomasses is severely limited. To overcome the limitation, Rm Man5A was successfully engineered by directed evolution. Through two rounds of screening, a mutated β-mannanase (m Rm Man5A) with high catalytic activity in acidic and thermophilic conditions was obtained, and then characterized. The mutant displayed maximal activity at pH 4.5 and 65 °C, corresponding to acidic shift of 2.5 units in optimal pH and increase by 10 °C in optimal temperature. The catalytic efficiencies ( k cat / K m ) of m Rm Man5A towards many mannan substrates were enhanced more than threefold in acidic and thermophilic conditions. Meanwhile, the high specific activity and excellent hydrolysis property of Rm Man5A were inherited by the mutant m Rm Man5A after directed evolution. According to the result of sequence analysis, three amino acid residues were substituted in m Rm Man5A, namely Tyr233His, Lys264Met, and Asn343Ser. To identify the function of each substitution, four site-directed mutations (Tyr233His, Lys264Met, Asn343Ser, and Tyr233His/Lys264Met) were subsequently generated, and the substitutions at Tyr233 and Lys264 were found to be the main reason for the changes of m Rm Man5A. Through directed evolution of Rm Man5A, two key amino acid residues that controlled its catalytic efficiency under acidic and thermophilic conditions were identified

  7. Direct sequencing for rapid detection of multidrug resistant Mycobacterium tuberculosis strains in Morocco.

    Science.gov (United States)

    Zakham, Fathiah; Chaoui, Imane; Echchaoui, Amina Hadbae; Chetioui, Fouad; Elmessaoudi, My Driss; Ennaji, My Mustapha; Abid, Mohammed; Mzibri, Mohammed El

    2013-01-01

    Tuberculosis (TB) is a major public health problem with high mortality and morbidity rates, especially in low-income countries. Disturbingly, the emergence of multidrug resistant (MDR) and extensively drug resistant (XDR) TB cases has worsened the situation, raising concerns of a future epidemic of virtually untreatable TB. Indeed, the rapid diagnosis of MDR TB is a critical issue for TB management. This study is an attempt to establish a rapid diagnosis of MDR TB by sequencing the target fragments of the rpoB gene which linked to resistance against rifampicin and the katG gene and inhA promoter region, which are associated with resistance to isoniazid. For this purpose, 133 sputum samples of TB patients from Morocco were enrolled in this study. One hundred samples were collected from new cases, and the remaining 33 were from previously treated patients (drug relapse or failure, chronic cases) and did not respond to anti-TB drugs after a sufficient duration of treatment. All samples were subjected to rpoB, katG and pinhA mutation analysis by polymerase chain reaction and DNA sequencing. Molecular analysis showed that seven strains were isoniazid-monoresistant and 17 were rifampicin-monoresistant. MDR TB strains were identified in nine cases (6.8%). Among them, eight were traditionally diagnosed as critical cases, comprising four chronic and four drug-relapse cases. The last strain was isolated from a new case. The most recorded mutation in the rpoB gene was the substitution TCG > TTG at codon 531 (Ser531 Leu), accounting for 46.15%. Significantly, the only mutation found in the katG gene was at codon 315 (AGC to ACC) with a Ser315Thr amino acid change. Only one sample harbored mutation in the inhA promoter region and was a point mutation at the -15p position (C > T). The polymerase chain reaction sequencing approach is an accurate and rapid method for detection of drug-resistant TB in clinical specimens, and could be of great interest in the management of TB in

  8. Defining a conformational consensus motif in cotransin-sensitive signal sequences: a proteomic and site-directed mutagenesis study.

    Directory of Open Access Journals (Sweden)

    Wolfgang Klein

    Full Text Available The cyclodepsipeptide cotransin was described to inhibit the biosynthesis of a small subset of proteins by a signal sequence-discriminatory mechanism at the Sec61 protein-conducting channel. However, it was not clear how selective cotransin is, i.e. how many proteins are sensitive. Moreover, a consensus motif in signal sequences mediating cotransin sensitivity has yet not been described. To address these questions, we performed a proteomic study using cotransin-treated human hepatocellular carcinoma cells and the stable isotope labelling by amino acids in cell culture technique in combination with quantitative mass spectrometry. We used a saturating concentration of cotransin (30 micromolar to identify also less-sensitive proteins and to discriminate the latter from completely resistant proteins. We found that the biosynthesis of almost all secreted proteins was cotransin-sensitive under these conditions. In contrast, biosynthesis of the majority of the integral membrane proteins was cotransin-resistant. Cotransin sensitivity of signal sequences was neither related to their length nor to their hydrophobicity. Instead, in the case of signal anchor sequences, we identified for the first time a conformational consensus motif mediating cotransin sensitivity.

  9. Defining a Conformational Consensus Motif in Cotransin-Sensitive Signal Sequences: A Proteomic and Site-Directed Mutagenesis Study

    Science.gov (United States)

    Klein, Wolfgang; Westendorf, Carolin; Schmidt, Antje; Conill-Cortés, Mercè; Rutz, Claudia; Blohs, Marcus; Beyermann, Michael; Protze, Jonas; Krause, Gerd; Krause, Eberhard; Schülein, Ralf

    2015-01-01

    The cyclodepsipeptide cotransin was described to inhibit the biosynthesis of a small subset of proteins by a signal sequence-discriminatory mechanism at the Sec61 protein-conducting channel. However, it was not clear how selective cotransin is, i.e. how many proteins are sensitive. Moreover, a consensus motif in signal sequences mediating cotransin sensitivity has yet not been described. To address these questions, we performed a proteomic study using cotransin-treated human hepatocellular carcinoma cells and the stable isotope labelling by amino acids in cell culture technique in combination with quantitative mass spectrometry. We used a saturating concentration of cotransin (30 micromolar) to identify also less-sensitive proteins and to discriminate the latter from completely resistant proteins. We found that the biosynthesis of almost all secreted proteins was cotransin-sensitive under these conditions. In contrast, biosynthesis of the majority of the integral membrane proteins was cotransin-resistant. Cotransin sensitivity of signal sequences was neither related to their length nor to their hydrophobicity. Instead, in the case of signal anchor sequences, we identified for the first time a conformational consensus motif mediating cotransin sensitivity. PMID:25806945

  10. A rapid screening with direct sequencing from blood samples for the diagnosis of Leigh syndrome

    Directory of Open Access Journals (Sweden)

    Hiroko Shimbo

    2014-01-01

    Full Text Available Large numbers of genes are responsible for Leigh syndrome (LS, making genetic confirmation of LS difficult. We screened our patients with LS using a limited set of 21 primers encompassing the frequently reported gene for the respiratory chain complexes I (ND1–ND6, and ND4L, IV(SURF1, and V(ATP6 and the pyruvate dehydrogenase E1α-subunit. Of 18 LS patients, we identified mutations in 11 patients, including 7 in mDNA (two with ATP6, 4 in nuclear (three with SURF1. Overall, we identified mutations in 61% of LS patients (11/18 individuals in this cohort. Sanger sequencing with our limited set of primers allowed us a rapid genetic confirmation of more than half of the LS patients and it appears to be efficient as a primary genetic screening in this cohort.

  11. DNA sequence-directed shape change of photopatterned hydrogels via high-degree swelling

    Science.gov (United States)

    Cangialosi, Angelo; Yoon, ChangKyu; Liu, Jiayu; Huang, Qi; Guo, Jingkai; Nguyen, Thao D.; Gracias, David H.; Schulman, Rebecca

    2017-09-01

    Shape-changing hydrogels that can bend, twist, or actuate in response to external stimuli are critical to soft robots, programmable matter, and smart medicine. Shape change in hydrogels has been induced by global cues, including temperature, light, or pH. Here we demonstrate that specific DNA molecules can induce 100-fold volumetric hydrogel expansion by successive extension of cross-links. We photopattern up to centimeter-sized gels containing multiple domains that undergo different shape changes in response to different DNA sequences. Experiments and simulations suggest a simple design rule for controlled shape change. Because DNA molecules can be coupled to molecular sensors, amplifiers, and logic circuits, this strategy introduces the possibility of building soft devices that respond to diverse biochemical inputs and autonomously implement chemical control programs.

  12. A digital computer simulation and study of a direct-energy-transfer power-conditioning system

    Science.gov (United States)

    Burns, W. W., III; Owen, H. A., Jr.; Wilson, T. G.; Rodriguez, G. E.; Paulkovich, J.

    1975-01-01

    An investigation of the behavior of the power-conditioning system as a whole is a necessity to ensure the integrity of the aggregate system in the case of space applications. An approach for conducting such an investigation is considered. A description is given of the application of a general digital analog simulator program to the study of an aggregate power-conditioning system which is being developed for use on the International Ultraviolet Explorer spacecraft. The function of the direct energy transfer system studied involves a coupling of a solar array through a main distribution bus to the spacecraft electrical loads.

  13. Structure Based Sequence Dependent Stiffness Scale for Trinucleotides: A Direct Method

    OpenAIRE

    Gromiha, M. Michael

    2000-01-01

    A new set of stiffness parameters for all the 32trinucleotide units has been set up directly from thethree dimensional structures of DNA molecules. It wasobserved that GAC/GTC is the stiffest trinucleotideand ACC/GGT is the most flexible one. The averagestiffness values computed for a set of operatorsequences using the new parameters correlate very wellwith the protein-DNA binding specificity and bindingfree energy change of 434 repressor and Cro repressor,respectively. The new structure base...

  14. Direct gaze elicits atypical activation of the theory-of-mind network in autism spectrum conditions.

    Science.gov (United States)

    von dem Hagen, Elisabeth A H; Stoyanova, Raliza S; Rowe, James B; Baron-Cohen, Simon; Calder, Andrew J

    2014-06-01

    Eye contact plays a key role in social interaction and is frequently reported to be atypical in individuals with autism spectrum conditions (ASCs). Despite the importance of direct gaze, previous functional magnetic resonance imaging in ASC has generally focused on paradigms using averted gaze. The current study sought to determine the neural processing of faces displaying direct and averted gaze in 18 males with ASC and 23 matched controls. Controls showed an increased response to direct gaze in brain areas implicated in theory-of-mind and gaze perception, including medial prefrontal cortex, temporoparietal junction, posterior superior temporal sulcus region, and amygdala. In contrast, the same regions showed an increased response to averted gaze in individuals with an ASC. This difference was confirmed by a significant gaze direction × group interaction. Relative to controls, participants with ASC also showed reduced functional connectivity between these regions. We suggest that, in the typical brain, perceiving another person gazing directly at you triggers spontaneous attributions of mental states (e.g. he is "interested" in me), and that such mental state attributions to direct gaze may be reduced or absent in the autistic brain.

  15. Direct sequencing for rapid detection of multidrug resistant Mycobacterium tuberculosis strains in Morocco

    Directory of Open Access Journals (Sweden)

    Zakham F

    2013-11-01

    Full Text Available Fathiah Zakham,1,4 Imane Chaoui,1 Amina Hadbae Echchaoui,2 Fouad Chetioui,3 My Driss Elmessaoudi,3 My Mustapha Ennaji,4 Mohammed Abid,2 Mohammed El Mzibri11Unité de Biologie et Recherché Médicale, Centre National de l'Energie, des Sciences et des Techniques Nucléaires (CNESTEN, Rabat, 2Laboratoire de Génétique Mycobacterienne, Institut Pasteur, Tangier, 3Laboratoire de Tuberculose Institut Pasteur, Casablanca, 4Laboratoire de Microbiologie, Hygiène et Virologie, Faculté des Sciences et Techniques, Mohammedia, MoroccoBackground: Tuberculosis (TB is a major public health problem with high mortality and morbidity rates, especially in low-income countries. Disturbingly, the emergence of multidrug resistant (MDR and extensively drug resistant (XDR TB cases has worsened the situation, raising concerns of a future epidemic of virtually untreatable TB. Indeed, the rapid diagnosis of MDR TB is a critical issue for TB management. This study is an attempt to establish a rapid diagnosis of MDR TB by sequencing the target fragments of the rpoB gene which linked to resistance against rifampicin and the katG gene and inhA promoter region, which are associated with resistance to isoniazid.Methods: For this purpose, 133 sputum samples of TB patients from Morocco were enrolled in this study. One hundred samples were collected from new cases, and the remaining 33 were from previously treated patients (drug relapse or failure, chronic cases and did not respond to anti-TB drugs after a sufficient duration of treatment. All samples were subjected to rpoB, katG and pinhA mutation analysis by polymerase chain reaction and DNA sequencing.Results: Molecular analysis showed that seven strains were isoniazid-monoresistant and 17 were rifampicin-monoresistant. MDR TB strains were identified in nine cases (6.8%. Among them, eight were traditionally diagnosed as critical cases, comprising four chronic and four drug-relapse cases. The last strain was isolated from a

  16. Modeling Macrosegregation in Directionally Solidified Aluminum Alloys under Gravitational and Microgravitational Conditions.

    Energy Technology Data Exchange (ETDEWEB)

    Lauer, Mark A.; Poirier, David R.; Erdmann, Robert G.; Tewari, Surendra N.; Madison, Jonathan D

    2014-09-01

    This report covers the modeling of seven directionally solidified samples, five under normal gravitational conditions and two in microgravity. A model is presented to predict macrosegregation during the melting phases of samples solidified under microgravitational conditions. The results of this model are compared against two samples processed in microgravity and good agreement is found. A second model is presented that captures thermosolutal convection during directional solidification. Results for this model are compared across several experiments and quantitative comparisons are made between the model and the experimentally obtained radial macrosegregation profiles with good agreement being found. Changes in cross section were present in some samples and micrographs of these are qualitatively compared with the results of the simulations. It is found that macrosegregation patterns can be affected by changing the mold material.

  17. A thaumatin-like genomic sequence identification in Vitis vinifera l., stormy wines and musts based on direct pcr

    Directory of Open Access Journals (Sweden)

    Jana Žiarovská

    2018-03-01

    Full Text Available Normal 0 21 false false false MicrosoftInternetExplorer4 Direct polymerase chain reaction method was use to amplify a thaumatin-like sequence of Vitis vinifera L. in grapes as well as in stormy wines and musts. Thaumatin-like proteins (TLPs of Vitis vinifera possess beside its function in abiotic and biotic stress response another one - they are able to cause protein haze in wine unless removed prior to bottling. Direct PCR is an approach where omission of DNA extraction is typical prior the amplification of the target site of plant genome. Crude extract or small pieces of plant tissues are used in the analysis directly without steps of extraction and purification of gDNA. The biological material that was used in analysis was collected during August - October 2017 in local stores and winery Sabo and comprises from cultivars Iršai, Muškát, Savignon Blanc, Svätovavrinecké, Dornfelder and Pálava. Direct PCR was performed by a cutted piece of grape tissue and a dilution buffer was use in 1:2 for stormy wine or must, respectively. Direct amplification of thaumatin-like protein sequence of Vitis vinifera was performed along with the control reactions with the primers for conserved region of plant chloroplast. Possitive amplification of thaumatin-like allergen sequence resulted in 570 bp amplicon. The most abundant amplicons were amplified in stormy wines, followed by musts and the amplicons from grapes were weaker when comparing them to others. The amplicon specificity checking of obtained PCR product of thaumatin-like allergen was performed by restriction cleavage by Psi I and resulted in restriction amplicons of the 80 bp, 81 bp, 94 bp and 315 bp in length. Confirmation of the amplicon specificity by restriction cleavage support the potential of direct PCR to become a reproducible method that will be fully applicable in routine analysis of not only plant genomes in the future, but it was demonstrated, that it works in liquids, too.  

  18. Using Information Systems as Directions of the State Support for the Conditionally Depressive Regions

    OpenAIRE

    Morhachov Ilya V.

    2017-01-01

    The article is aimed at substantiating the perspectivity of information systems and technologies as a direction of the State support for the conditionally depressive regions. The article clarifies the assumption that an increase in the number of freelancers in region (even evaders from taxation), causes the growth of both the regional enterprises’ revenues and the tax revenues to budgets. Such freelancers become customers of works, services and goods, and, accordingly, employers for other per...

  19. Next-generation DNA sequencing of HEXA: a step in the right direction for carrier screening

    Science.gov (United States)

    Hoffman, Jodi D; Greger, Valerie; Strovel, Erin T; Blitzer, Miriam G; Umbarger, Mark A; Kennedy, Caleb; Bishop, Brian; Saunders, Patrick; Porreca, Gregory J; Schienda, Jaclyn; Davie, Jocelyn; Hallam, Stephanie; Towne, Charles

    2013-01-01

    Tay-Sachs disease (TSD) is the prototype for ethnic-based carrier screening, with a carrier rate of ∼1/27 in Ashkenazi Jews and French Canadians. HexA enzyme analysis is the current gold standard for TSD carrier screening (detection rate ∼98%), but has technical limitations. We compared DNA analysis by next-generation DNA sequencing (NGS) plus an assay for the 7.6 kb deletion to enzyme analysis for TSD carrier screening using 74 samples collected from participants at a TSD family conference. Fifty-one of 74 participants had positive enzyme results (46 carriers, five late-onset Tay-Sachs [LOTS]), 16 had negative, and seven had inconclusive results. NGS + 7.6 kb del screening of HEXA found a pathogenic mutation, pseudoallele, or variant of unknown significance (VUS) in 100% of the enzyme-positive or obligate carrier/enzyme-inconclusive samples. NGS detected the B1 allele in two enzyme-negative obligate carriers. Our data indicate that NGS can be used as a TSD clinical carrier screening tool. We demonstrate that NGS can be superior in detecting TSD carriers compared to traditional enzyme and genotyping methodologies, which are limited by false-positive and false-negative results and ethnically focused, limited mutation panels, respectively, but is not ready for sole use due to lack of information regarding some VUS. PMID:24498621

  20. Update Direct-Strike Lightning Environment for Stockpile-to-Target Sequence

    International Nuclear Information System (INIS)

    Uman, M.A.; Rakov, V.A.; Elisme, J.O.; Jordan, D.M.; Biagi, C.J.; Hill, J.D.

    2008-01-01

    The University of Florida has surveyed all relevant publications reporting lightning characteristics and presents here an up-to-date version of the direct-strike lightning environment specifications for nuclear weapons published in 1989 by R. J. Fisher and M. A. Uman. Further, we present functional expressions for current vs. time, current derivative vs. time, second current derivative vs. time, charge transfer vs. time, and action integral (specific energy) vs. time for first return strokes, for subsequent return strokes, and for continuing currents; and we give sets of constants for these expressions so that they yield approximately the median and extreme negative lightning parameters presented in this report. Expressions for the median negative lightning waveforms are plotted. Finally, we provide information on direct-strike lightning damage to metals such as stainless steel, which could be used as components of storage containers for nuclear waste materials; and we describe UF's new experimental research program to add to the sparse data base on the properties of positive lightning. Our literature survey, referred to above, is included in four Appendices. The following four sections (II, III, IV, and V) of this final report deal with related aspects of the research: Section II. Recommended Direct-Strike Median and Extreme Parameters; Section III. Time-Domain Waveforms for First Strokes, Subsequent Strokes, and Continuing Currents; Section IV. Damage to Metal Surfaces by Lightning Currents; and Section V. Measurement of the Characteristics of Positive Lightning. Results of the literature search used to derive the material in Section II and Section IV are found in the Appendices: Appendix 1. Return Stroke Current, Appendix 2. Continuing Current, Appendix 3. Positive Lightning, and Appendix 4. Lightning Damage to Metal Surfaces

  1. Characterization of the genomic organization of the region bordering the centromere of chromosome V of Podospora anserina by direct sequencing.

    Science.gov (United States)

    Silar, Philippe; Barreau, Christian; Debuchy, Robert; Kicka, Sébastien; Turcq, Béatrice; Sainsard-Chanet, Annie; Sellem, Carole H; Billault, Alain; Cattolico, Laurence; Duprat, Simone; Weissenbach, Jean

    2003-08-01

    A Podospora anserina BAC library of 4800 clones has been constructed in the vector pBHYG allowing direct selection in fungi. Screening of the BAC collection for centromeric sequences of chromosome V allowed the recovery of clones localized on either sides of the centromere, but no BAC clone was found to contain the centromere. Seven BAC clones containing 322,195 and 156,244bp from either sides of the centromeric region were sequenced and annotated. One 5S rRNA gene, 5 tRNA genes, and 163 putative coding sequences (CDS) were identified. Among these, only six CDS seem specific to P. anserina. The gene density in the centromeric region is approximately one gene every 2.8kb. Extrapolation of this gene density to the whole genome of P. anserina suggests that the genome contains about 11,000 genes. Synteny analyses between P. anserina and Neurospora crassa show that co-linearity extends at the most to a few genes, suggesting rapid genome rearrangements between these two species.

  2. Floodplain Condition and Water Framework Directive River Classification in England: Evidence of a Disconnect.

    Science.gov (United States)

    Bentley, S.

    2017-12-01

    The European Union Water Framework Directive came into force in October 2000 committing European Union member states to achieve Good Ecological Status for all water bodies. By 2015 29% of rivers across England had achieved this level suggesting that these watercourse units are now functioning well. This study utilises recently published land cover data for England clipped to the floodplain boundary as defined by the 100 year return period discharge to examine the state of valley bottom vegetation and function for these Good Status rivers. Agricultural use of floodplain areas is high with cereal and horticulture covering an average of 24% and pasture accounting for some 37% of the area. Maximum values increase to 77% and 92% respectively. In all cases wetland accounts for less than 2% of the floodplain and rough grassland averages 7%. Such significant and widespread alteration to floodplain vegetation character suggests that the ecological functioning of this component of the fluvial system has been severely negatively impacted calling into question the Water Framework Directive status level. This is a fault of the Water Framework Directive process which only explicitly evaluates the hydromorphological component of the fluvial system for high status rivers preferring to infer functioning from biological indicators that are focused on in-channel assessments. The fundamental omission of floodplain condition in the Water Framework Directive process will result in only partial achievement of the original goals of the Directive with the majority of Europe's floodplains remaining in a highly degraded, non-functional state.

  3. Importance of the Sequence-Directed DNA Shape for Specific Binding Site Recognition by the Estrogen-Related Receptor

    Directory of Open Access Journals (Sweden)

    Kareem Mohideen-Abdul

    2017-06-01

    Full Text Available Most nuclear receptors (NRs bind DNA as dimers, either as hetero- or as homodimers on DNA sequences organized as two half-sites with specific orientation and spacing. The dimerization of NRs on their cognate response elements (REs involves specific protein–DNA and protein–protein interactions. The estrogen-related receptor (ERR belongs to the steroid hormone nuclear receptor (SHR family and shares strong similarity in its DNA-binding domain (DBD with that of the estrogen receptor (ER. In vitro, ERR binds with high affinity inverted repeat REs with a 3-bps spacing (IR3, but in vivo, it preferentially binds to single half-site REs extended at the 5′-end by 3 bp [estrogen-related response element (ERREs], thus explaining why ERR was often inferred as a purely monomeric receptor. Since its C-terminal ligand-binding domain is known to homodimerize with a strong dimer interface, we investigated the binding behavior of the isolated DBDs to different REs using electrophoretic migration, multi-angle static laser light scattering (MALLS, non-denaturing mass spectrometry, and nuclear magnetic resonance. In contrast to ER DBD, ERR DBD binds as a monomer to EREs (IR3, such as the tff1 ERE-IR3, but we identified a DNA sequence composed of an extended half-site embedded within an IR3 element (embedded ERRE/IR3, where stable dimer binding is observed. Using a series of chimera and mutant DNA sequences of ERREs and IR3 REs, we have found the key determinants for the binding of ERR DBD as a dimer. Our results suggest that the sequence-directed DNA shape is more important than the exact nucleotide sequence for the binding of ERR DBD to DNA as a dimer. Our work underlines the importance of the shape-driven DNA readout mechanisms based on minor groove recognition and electrostatic potential. These conclusions may apply not only to ERR but also to other members of the SHR family, such as androgen or glucocorticoid, for which a strong well-conserved half

  4. Direct metagenomic detection of viral pathogens in nasal and fecal specimens using an unbiased high-throughput sequencing approach.

    Directory of Open Access Journals (Sweden)

    Shota Nakamura

    Full Text Available With the severe acute respiratory syndrome epidemic of 2003 and renewed attention on avian influenza viral pandemics, new surveillance systems are needed for the earlier detection of emerging infectious diseases. We applied a "next-generation" parallel sequencing platform for viral detection in nasopharyngeal and fecal samples collected during seasonal influenza virus (Flu infections and norovirus outbreaks from 2005 to 2007 in Osaka, Japan. Random RT-PCR was performed to amplify RNA extracted from 0.1-0.25 ml of nasopharyngeal aspirates (N = 3 and fecal specimens (N = 5, and more than 10 microg of cDNA was synthesized. Unbiased high-throughput sequencing of these 8 samples yielded 15,298-32,335 (average 24,738 reads in a single 7.5 h run. In nasopharyngeal samples, although whole genome analysis was not available because the majority (>90% of reads were host genome-derived, 20-460 Flu-reads were detected, which was sufficient for subtype identification. In fecal samples, bacteria and host cells were removed by centrifugation, resulting in gain of 484-15,260 reads of norovirus sequence (78-98% of the whole genome was covered, except for one specimen that was under-detectable by RT-PCR. These results suggest that our unbiased high-throughput sequencing approach is useful for directly detecting pathogenic viruses without advance genetic information. Although its cost and technological availability make it unlikely that this system will very soon be the diagnostic standard worldwide, this system could be useful for the earlier discovery of novel emerging viruses and bioterrorism, which are difficult to detect with conventional procedures.

  5. Using Information Systems as Directions of the State Support for the Conditionally Depressive Regions

    Directory of Open Access Journals (Sweden)

    Morhachov Ilya V.

    2017-12-01

    Full Text Available The article is aimed at substantiating the perspectivity of information systems and technologies as a direction of the State support for the conditionally depressive regions. The article clarifies the assumption that an increase in the number of freelancers in region (even evaders from taxation, causes the growth of both the regional enterprises’ revenues and the tax revenues to budgets. Such freelancers become customers of works, services and goods, and, accordingly, employers for other persons who work officially. The State support for the concentration of such persons in the region contributes to reducing the «brain drain» abroad. The article substantiates prospective directions of the State support for the conditionally depressive regions by means of information systems, the basic elements of which are IT-specialists; as well as economic expediency of priority of the State support for the regions with presence of high level of unemployment of working population. The ways of solution of contradictions between the State and the freelancer in the part of payment of taxes and accrual of the insurance period for the future pension have been suggested. The ultimate goal of the State support for the conditionally depressive regions with use of information systems has been defined, which is to achieve the stage of the multiplied effect of growth of income of economic entities and tax revenues to the budget due to the implementation of innovation projects as result of the concentration of IT specialists in region.

  6. Forecasting the Rupture Directivity of Large Earthquakes: Centroid Bias of the Conditional Hypocenter Distribution

    Science.gov (United States)

    Donovan, J.; Jordan, T. H.

    2012-12-01

    Forecasting the rupture directivity of large earthquakes is an important problem in probabilistic seismic hazard analysis (PSHA), because directivity is known to strongly influence ground motions. We describe how rupture directivity can be forecast in terms of the "conditional hypocenter distribution" or CHD, defined to be the probability distribution of a hypocenter given the spatial distribution of moment release (fault slip). The simplest CHD is a uniform distribution, in which the hypocenter probability density equals the moment-release probability density. For rupture models in which the rupture velocity and rise time depend only on the local slip, the CHD completely specifies the distribution of the directivity parameter D, defined in terms of the degree-two polynomial moments of the source space-time function. This parameter, which is zero for a bilateral rupture and unity for a unilateral rupture, can be estimated from finite-source models or by the direct inversion of seismograms (McGuire et al., 2002). We compile D-values from published studies of 65 large earthquakes and show that these data are statistically inconsistent with the uniform CHD advocated by McGuire et al. (2002). Instead, the data indicate a "centroid biased" CHD, in which the expected distance between the hypocenter and the hypocentroid is less than that of a uniform CHD. In other words, the observed directivities appear to be closer to bilateral than predicted by this simple model. We discuss the implications of these results for rupture dynamics and fault-zone heterogeneities. We also explore their PSHA implications by modifying the CyberShake simulation-based hazard model for the Los Angeles region, which assumed a uniform CHD (Graves et al., 2011).

  7. Operant conditioning of rat navigation using electrical stimulation for directional cues and rewards.

    Science.gov (United States)

    Lee, Maan-Gee; Jun, Gayoung; Choi, Hyo-Soon; Jang, Hwan Soo; Bae, Yong Chul; Suk, Kyoungho; Jang, Il-Sung; Choi, Byung-Ju

    2010-07-01

    Operant conditioning is often used to train a desired behavior in an animal. The contingency between a specific behavior and a reward is required for successful training. Here, we compared the effectiveness of two different mazes for training turning behaviors in response to directional cues in Sprague-Dawley rats. Forty-three rats were implanted with electrodes into the medial forebrain bundle and the left and right somatosensory cortices for reward and cues. Among them, thirteen rats discriminated between the left and right somatosensory stimulations to obtain rewards. They were trained to learn ipsilateral turning response to the stimulation of the left or right somatosensory cortex in either the T-maze (Group T) or the E| maze (Group W). Performance was measured by the navigation speed in the mazes. Performances of rats in Group T were enhanced faster than those in Group W. A significant correlation between performances during training and performance in final testing was observed in Group T starting with the fifth training session while such a correlation was not observed in Group W until the tenth training session. The training mazes did not however affect the performances in the final test. These results suggest that a simple maze is better than a complicated maze for training animals to learn directions and direct cortical stimulation can be used as a cue for direction training. Copyright (c) 2010 Elsevier B.V. All rights reserved.

  8. Effect of Boundary Condition on the Shear Behaviour of Rock Joints in the Direct Shear Test

    Science.gov (United States)

    Bahaaddini, M.

    2017-05-01

    The common method for determination of the mechanical properties of the rock joints is the direct shear test. This paper aims to study the effect of boundary condition on the results of direct shear tests. Experimental studies undertaken in this research showed that the peak shear strength is mostly overestimated. This problem is more pronounced for steep asperities and under high normal stresses. Investigation of the failure mode of these samples showed that tensile cracks are generated at the boundary of sample close to the specimen holders and propagated inside the intact materials. In order to discover the reason of observed failure mechanism in experiments, the direct shear test was simulated using PFC2D. Results of numerical models showed that the gap zone size between the upper and lower specimen holders has a significant effect on the shear mechanism. For the high gap size, stresses concentrate at the vicinity of the tips of specimen holders and result in generation and propagation of tensile cracks inside the intact material. However, by reducing the gap size, stresses are concentrated on asperities, and damage of specimen at its boundary is not observed. Results of this paper show that understanding the shear mechanism of rock joints is an essential step prior to interpreting the results of direct shear tests.

  9. Compact high order schemes with gradient-direction derivatives for absorbing boundary conditions

    Science.gov (United States)

    Gordon, Dan; Gordon, Rachel; Turkel, Eli

    2015-09-01

    We consider several compact high order absorbing boundary conditions (ABCs) for the Helmholtz equation in three dimensions. A technique called "the gradient method" (GM) for ABCs is also introduced and combined with the high order ABCs. GM is based on the principle of using directional derivatives in the direction of the wavefront propagation. The new ABCs are used together with the recently introduced compact sixth order finite difference scheme for variable wave numbers. Experiments on problems with known analytic solutions produced very accurate results, demonstrating the efficacy of the high order schemes, particularly when combined with GM. The new ABCs are then applied to the SEG/EAGE Salt model, showing the advantages of the new schemes.

  10. ON TESTING OF CRYPTOGRAPHYC GENERATORS OUTPUT SEQUENCES USING MARKOV CHAINS OF CONDITIONAL ORDER

    Directory of Open Access Journals (Sweden)

    M. V. Maltsev

    2013-01-01

    Full Text Available The paper deals with the Markov chain of conditional order, which is used for statisticaltesting of cryptographic generators. Statistical estimations of model parameters are given. Consistency of the order estimator is proved. Results of computer experiments are presented.

  11. Historical Review of Uncommanded Lateral-Directional Motions at Transonic Conditions

    Science.gov (United States)

    Chambers, Joseph R.; Hall, Robert M.

    2003-01-01

    This paper presents the results of a survey of past experiences with uncommanded lateral-directional motions at transonic speeds during specific military aircraft programs. The effort was undertaken to provide qualitative and quantitative information on past airplane programs that might be of use to the participants in the joint NASA/Navy/Air Force Abrupt Wing Stall (AWS) Program. The AWS Program was initiated because of the experiences of the F/A-l8E/F development program, during which unexpected, severe wing-drop motions were encountered by preproduction aircraft at transonic conditions. These motions were judged to be significantly degrading to the primary mission requirements of the aircraft. Although the problem was subsequently solved for the production version of the F/A-l8E/F, a high-level review panel emphasized the poor understanding of such phenomena and issued a strong recommendation to: "Initiate a national research effort to thoroughly and systematically study the wing drop phenomena." A comprehensive, cooperative NASA/Navy/Air Force AWS Program was designed to respond to provide the required technology requirements. As part of the AWS Program, a work element was directed at a historical review of wing-drop experiences in past aircraft development programs at high subsonic and transonic speeds. In particular, information was requested regarding: specific aircraft configurations that exhibited uncommanded motions and the nature of the motions; geometric characteristics of the air- planes; flight conditions involved in occurrences; relevant data, including wind-tunnel, computational, and flight sources; figures of merit used for analyses; and approaches used to alleviate the problem. An attempt was also made to summarize some of the more important lessons learned from past experiences, and to recommend specific research efforts. In addition to providing technical information to assist the AWS research objectives, the study produced fundamental

  12. Historical Review of Uncommanded Lateral-Directional Motions At Transonic Conditions (Invited)

    Science.gov (United States)

    Chambers, Joseph R.; Hall, Robert M.

    2003-01-01

    This paper presents the results of a survey of past experiences with uncommanded lateral-directional motions at transonic speeds during specific military aircraft programs. The effort was undertaken to provide qualitative and quantitative information on past airplane programs that might be of use to the participants in the joint NASA/Navy/Air Force Abrupt Wing Stall (AWS) Program. The AWS Program was initiated because of the experiences of the F/A-18E/F development program, during which unexpected, severe wing-drop motions were encountered by preproduction aircraft at transonic conditions. These motions were judged to be significantly degrading to the primary mission requirements of the aircraft. Although the problem was subsequently solved for the production version of the F/A-l8E/F, a high-level review panel emphasized the poor understanding of such phenomena and issued a strong recommendation to: Initiate a national research effort to thoroughly and systematically study the wing drop phenomena. A comprehensive, cooperative NASA/Navy/Air Force AWS Program was designed to respond to provide the required technology requirements. As part of the AWS Program, a work element was directed at a historical review of wing-drop experiences in past aircraft development programs at high subsonic and transonic speeds. In particular, information was requested regarding: specific aircraft configurations that exhibited uncommanded motions and the nature of the motions; geometric characteristics of the air- planes; flight conditions involved in occurrences; relevant data, including wind-tunnel, computational, and flight sources; figures of merit used for analyses; and approaches used to alleviate the problem. An attempt was also made to summarize some of the more important lessons learned from past experiences, and to recommend specific research efforts. In addition to providing technical information to assist the AWS research objectives, the study produced fundamental information

  13. Energy and cusp-conditions study for the He isoelectronic sequence

    Energy Technology Data Exchange (ETDEWEB)

    Otranto, S. E-mail: sotranto@uns.edu.ar; Gasaneo, G. E-mail: ggasaneo@criba.edu.ar; Garibotti, C.R

    2004-03-01

    We present variational wave functions for He-like atoms with nuclear charge Z=1,...,10. We propose modifications of some usual simple correlated wave functions to account for the integration factor required in the evaluation of atomic ionization and excitation amplitudes with distorted wave methods. We determine the parameters of the trial functions and the resulting energies. We introduce new procedures to test the cusp conditions at the singularities of the Coulomb field.

  14. Economic evaluation of therapeutic sequences in the treatment of patients with chronic lymphocytic leukemia and coexisting conditions

    Directory of Open Access Journals (Sweden)

    Antonio Cuneo

    2017-10-01

    Full Text Available Economic evaluation of therapeutic sequences in the treatment of patients with chronic lymphocytic leukemia and coexisting conditionsIntroductionChronic lymphocytic leukemia (CLL is a chronic lymphoproliferative syndrome and it is the most common hematological malignancy in Western countries. It has a tendency to develop subsequent relapses, so affected patients are likely to undergo more than one line of treatment.MethodsRather than evaluating the cost-effectiveness of individual therapeutic agents, it becomes therefore recommendable for decision-makers to identify an optimal sequencing of such agents. A four-year cost-consequence analysis was conducted, comparing three alternative strategies for the first-line treatment of patients with previously untreated CLL and coexisting conditions: i obinutuzumab with chlorambucil (Obi-Clb, ii rituximab with chlorambucil (Rtx-Clb, and iii ofatumumab with chlorambucil (Ofa-Clb. Only drug costs were considered in the analysis.ResultsIn two trials, median time to next treatment (TTNT was longer in Obi-Clb (51.1 months as compared to Rtx-Clb (38.2 months or to Ofa-Clb (39.8 months. Therefore, during a 48-month time horizon, patients treated with Obi-Clb would maintain on average the first line treatment; on the contrary, patients treated with Rtx-Clb or with Ofa-Clb would receive on average a second line treatment consisting in the majority of cases of ibrutinib monotherapy, or rituximab with idelalisib or rituximab with bendamustine. The sequence using Obi-Clb regimen in first line showed the lower mean cost of treatment: €22,958 over the 48-month time horizon. Sensitivity analyses on a couple of scenarios provided similar conclusions in terms of overall costs.ConclusionObi-Clb as first-line treatment appears a recommendable strategy in terms of drug costs in the treatment of patients with previously untreated CLL and coexisting conditions.

  15. Specific nuclear localizing sequence directs two myosin isoforms to the cell nucleus in calmodulin-sensitive manner.

    Science.gov (United States)

    Dzijak, Rastislav; Yildirim, Sukriye; Kahle, Michal; Novák, Petr; Hnilicová, Jarmila; Venit, Tomáš; Hozák, Pavel

    2012-01-01

    Nuclear myosin I (NM1) was the first molecular motor identified in the cell nucleus. Together with nuclear actin, they participate in crucial nuclear events such as transcription, chromatin movements, and chromatin remodeling. NM1 is an isoform of myosin 1c (Myo1c) that was identified earlier and is known to act in the cytoplasm. NM1 differs from the "cytoplasmic" myosin 1c only by additional 16 amino acids at the N-terminus of the molecule. This amino acid stretch was therefore suggested to direct NM1 into the nucleus. We investigated the mechanism of nuclear import of NM1 in detail. Using over-expressed GFP chimeras encoding for truncated NM1 mutants, we identified a specific sequence that is necessary for its import to the nucleus. This novel nuclear localization sequence is placed within calmodulin-binding motif of NM1, thus it is present also in the Myo1c. We confirmed the presence of both isoforms in the nucleus by transfection of tagged NM1 and Myo1c constructs into cultured cells, and also by showing the presence of the endogenous Myo1c in purified nuclei of cells derived from knock-out mice lacking NM1. Using pull-down and co-immunoprecipitation assays we identified importin beta, importin 5 and importin 7 as nuclear transport receptors that bind NM1. Since the NLS sequence of NM1 lies within the region that also binds calmodulin we tested the influence of calmodulin on the localization of NM1. The presence of elevated levels of calmodulin interfered with nuclear localization of tagged NM1. We have shown that the novel specific NLS brings to the cell nucleus not only the "nuclear" isoform of myosin I (NM1 protein) but also its "cytoplasmic" isoform (Myo1c protein). This opens a new field for exploring functions of this molecular motor in nuclear processes, and for exploring the signals between cytoplasm and the nucleus.

  16. Unbiased Strain-Typing of Arbovirus Directly from Mosquitoes Using Nanopore Sequencing: A Field-forward Biosurveillance Protocol.

    Science.gov (United States)

    Russell, Joseph A; Campos, Brittany; Stone, Jennifer; Blosser, Erik M; Burkett-Cadena, Nathan; Jacobs, Jonathan L

    2018-04-03

    The future of infectious disease surveillance and outbreak response is trending towards smaller hand-held solutions for point-of-need pathogen detection. Here, samples of Culex cedecei mosquitoes collected in Southern Florida, USA were tested for Venezuelan Equine Encephalitis Virus (VEEV), a previously-weaponized arthropod-borne RNA-virus capable of causing acute and fatal encephalitis in animal and human hosts. A single 20-mosquito pool tested positive for VEEV by quantitative reverse transcription polymerase chain reaction (RT-qPCR) on the Biomeme two3. The virus-positive sample was subjected to unbiased metatranscriptome sequencing on the Oxford Nanopore MinION and shown to contain Everglades Virus (EVEV), an alphavirus in the VEEV serocomplex. Our results demonstrate, for the first time, the use of unbiased sequence-based detection and subtyping of a high-consequence biothreat pathogen directly from an environmental sample using field-forward protocols. The development and validation of methods designed for field-based diagnostic metagenomics and pathogen discovery, such as those suitable for use in mobile "pocket laboratories", will address a growing demand for public health teams to carry out their mission where it is most urgent: at the point-of-need.

  17. Accurate and simple wavefunctions for the helium isoelectronic sequence with correct cusp conditions

    Energy Technology Data Exchange (ETDEWEB)

    Rodriguez, K V [Departamento de Fisica, Universidad Nacional del Sur and Consejo Nacional de Investigaciones CientIficas y Tecnicas, 8000 BahIa Blanca, Buenos Aires (Argentina); Gasaneo, G [Departamento de Fisica, Universidad Nacional del Sur and Consejo Nacional de Investigaciones CientIficas y Tecnicas, 8000 BahIa Blanca, Buenos Aires (Argentina); Mitnik, D M [Instituto de AstronomIa y Fisica del Espacio, and Departamento de Fisica, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, C C 67, Suc. 28 (C1428EGA) Buenos Aires (Argentina)

    2007-10-14

    Simple and accurate wavefunctions for the He atom and He-like isoelectronic ions are presented. These functions-the product of hydrogenic one-electron solutions and a fully correlated part-satisfy all the coalescence cusp conditions at the Coulomb singularities. Functions with different numbers of parameters and different degrees of accuracy are discussed. Simple analytic expressions for the wavefunction and the energy, valid for a wide range of nuclear charges, are presented. The wavefunctions are tested, in the case of helium, through the calculations of various cross sections which probe different regions of the configuration space, mostly those close to the two-particle coalescence points.

  18. Effect of redox conditions on pharmaceutical loss during biological wastewater treatment using sequencing batch reactors

    DEFF Research Database (Denmark)

    Stadler, Lauren B.; Su, Lijuan; Moline, Christopher J.

    2015-01-01

    We lack a clear understanding of how wastewater treatment plant (WWTP) process parameters, such as redox environment, impact pharmaceutical fate. WWTPs increasingly install more advanced aeration control systems to save energy and achieve better nutrient removal performance. The impact of redox...... under different redox conditions: fully aerobic, anoxic/aerobic, and microaerobic (DO concentration ≈0.3 mg/L). Among the pharmaceuticals that were tracked during this study (atenolol, trimethoprim, sulfamethoxazole, desvenlafaxine, venlafaxine, and phenytoin), overall loss varied between them...... and between redox environments. Losses of atenolol and trimethoprim were highest in the aerobic reactor; sulfamethoxazole loss was highest in the microaerobic reactors; and phenytoin was recalcitrant in all reactors. Transformation products of sulfamethoxazole and desvenlafaxine resulted in the reformation...

  19. Characterization of juvenile maritime pine (Pinus pinaster Ait.) ectomycorrhizal fungal community using morphotyping, direct sequencing and fruitbodies sampling.

    Science.gov (United States)

    Pestaña Nieto, Montserrat; Santolamazza Carbone, Serena

    2009-02-01

    Using ectomycorrhizal root tip morphotyping (anatomical and morphological identification), molecular analysis (internal transcribed spacer region amplification and sequencing), and fruitbody sampling, we assessed diversity and composition of the ectomycorrhizal fungal community colonizing juvenile Pinus pinaster Ait. under natural conditions in NW Spain. Overall, we found 15 Basidiomycetes and two Ascomycetes. Members of the family Thelephoraceae represented up to 59.4% of the samples. The most frequent species was Tomentella sublilacina followed by Thelephora terrestris, Russula drimeia, Suillus bovinus, and Paxillus involutus, while the less frequent were Pseudotomentella tristis, Lactarius subdulcis, Russula ochroleuca, and Entoloma conferendum. From October 2007 to June 2008, we sampled 208 sporocarps belonging to seven genera and nine species: Thelephora terrestris, Paxillus involutus, Suillus bovinus, Xerocomus badius, Scleroderma verrucosum, Amanita gemmata, A. rubescens, Amanita sp., and Russula sp. The species belonging to the genus Amanita, X. badius and S. verrucosum were not found on root samples. By comparing our results with a bibliographic review of papers published from 1922 to 2006, we found five genera and six species which have not been previously reported in symbiosis with P. pinaster. This is the first time that the diversity of the ectomycorrhizal fungal community associated with P. pinaster was investigated using molecular techniques. Considering that only 38% of the genera found by sequencing were found as fruitbodies, we conclude that integrating morphotyping and sporocarps surveys with molecular analysis of ectomycorrhizas is important to documenting the ectomycorrhizal fungus community.

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

    Directory of Open Access Journals (Sweden)

    Zeng An-Ping

    2004-08-01

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

  1. Direct and Indirect Effects of Pesticides on the Insidious Flower Bug (Hemiptera: Anthocoridae) Under Laboratory Conditions.

    Science.gov (United States)

    Herrick, Nathan J; Cloyd, Raymond A

    2017-06-01

    Greenhouse producers are interested in integrating natural enemies along with pesticides to suppress western flower thrips, Frankliniella occidentalis (Pergande), populations. The insidious flower bug, Orius insidiosus (Say), is a commercially available natural enemy of western flower thrips. We conducted a series of laboratory experiments to determine the direct and indirect effects of 28 pesticides (insecticides, miticides, and fungicides), 4 pesticide mixtures, and 4 surfactants (36 total treatments plus a water control) on the adult O. insidiosus survival and predation on western flower thrips adults under laboratory conditions. The number of live and dead O. insidiosus adults was recorded after 24, 48, 72, and 96 h. The results of the study indicate that the fungicides (aluminum tris, azoxystrobin, fenhexamid, and kresoxim-methyl), insect growth regulators (azadirachtin, buprofezin, kinoprene, and pyriproxyfen), botanicals (Capsicum oleoresin extract, garlic oil, soybean oil; and rosemary, rosemary oil, peppermint oil, and cottonseed oil), and entomopathogenic fungi (Beauveria bassiana and Metarhizium anisopliae) were minimally directly harmful to adult O. insidiosus, with 80% to 100% adult survival. However, abamectin, spinosad, pyridalyl, chlorfenapyr, tau-fluvalinate, imidacloprid, dinotefuran, acetamiprid, and thiamethoxam directly affected O. insidiosus survival after 96 h (0-60% adult survival). The pesticide mixtures of abamectin + spinosad and chlorfenapyr + dinotefuran reduced adult survival (20% and 0%, respectively, after 48 h). Furthermore, the surfactants were not directly harmful to O. insidiosus adults. All western flower thrips adults were killed by the surviving adult O. insidiosus after 48 h, indicating no indirect effects of the pesticides on predation. © The Authors 2017. Published by Oxford University Press on behalf of Entomological Society of America. All rights reserved. For Permissions, please email: journals.permissions@oup.com.

  2. Direct numerical simulation of turbulent flows over superhydrophobic surfaces with gas pockets using linearized boundary conditions

    Science.gov (United States)

    Seo, Jongmin; Bose, Sanjeeb; Garcia-Mayoral, Ricardo; Mani, Ali

    2012-11-01

    Superhydrophobic surfaces are shown to be effective for surface drag reduction under laminar regime by both experiments and simulations (see for example, Ou and Rothstein, Phys. Fluids 17:103606, 2005). However, such drag reduction for fully developed turbulent flow maintaining the Cassie-Baxter state remains an open problem due to high shear rates and flow unsteadiness of turbulent boundary layer. Our work aims to develop an understanding of mechanisms leading to interface breaking and loss of gas pockets due to interactions with turbulent boundary layers. We take advantage of direct numerical simulation of turbulence with slip and no-slip patterned boundary conditions mimicking the superhydrophobic surface. In addition, we capture the dynamics of gas-water interface, by deriving a proper linearized boundary condition taking into account the surface tension of the interface and kinematic matching of interface deformation and normal velocity conditions on the wall. We will show results from our simulations predicting the dynamical behavior of gas pocket interfaces over a wide range of dimensionless surface tensions. Supported by the Office of Naval Research and the Kwanjeong Educational Scholarship Foundation.

  3. Direct conversion of wet algae to crude biodiesel under supercritical ethanol conditions

    Energy Technology Data Exchange (ETDEWEB)

    Reddy, Harvind K. [New Mexico State Univ., Las Cruces, NM (United States). Chemical Engineering Dept.; Muppaneni, Tapaswy [New Mexico State Univ., Las Cruces, NM (United States). Chemical Engineering Dept.; Patil, Prafulla D. [American Refining Group, Inc., Bradford, PA (United States); Ponnusamy, Sundaravadivelnathan [New Mexico State Univ., Las Cruces, NM (United States). Chemical Engineering Dept.; Cooke, Peter [New Mexico State Univ., Las Cruces, NM (United States). Core University Research Resource Lab.; Schaub, Tanner [New Mexico State Univ., Las Cruces, NM (United States). Bio Security and Food Safety Center; Deng, Shuguang [New Mexico State Univ., Las Cruces, NM (United States). Chemical Engineering Dept.

    2013-08-06

    This paper presents a single-step, environmentally friendly approach for the direct conversion of wet algae to crude biodiesel under supercritical ethanol conditions. Ethanol was used for the simultaneous extraction and transesterification of lipids in algae to produce fatty acid ethyl esters at supercritical conditions. In this work the effects of process parameters dry algae to ethanol (wt./vol.) ratio (1:6-1:15), reaction temperature (245-270 C), and reaction time (2-30 min.) on the yield of fatty acid ethyl esters (FAEE) were studied. 67% conversion was achieved at 265 C and 20 min of reaction time. The calorific value of a purified biodiesel sample produced at optimum conditions was measured to be 43 MJ/kg, which is higher than that of fatty acid methyl esters produced from the same biomass. The purified fatty acid ethyl esters were analyzed using GC-MS and FTIR. TGA analysis of algal biomass and purified FAEE was presented along with TEM images of the biomass captured before and after supercritical ethanol transesterification. This green conversion process has the potential to provide an energy-efficient and economical route for the production of renewable biodiesel production.

  4. System and method of providing quick thermal comfort with reduced energy by using directed spot conditioning

    Science.gov (United States)

    Wang, Mingyu; Kadle, Prasad S.; Ghosh, Debashis; Zima, Mark J.; Wolfe, IV, Edward; Craig, Timothy D

    2016-10-04

    A heating, ventilation, and air conditioning (HVAC) system and a method of controlling a HVAC system that is configured to provide a perceived comfortable ambient environment to an occupant seated in a vehicle cabin. The system includes a nozzle configured to direct an air stream from the HVAC system to the location of a thermally sensitive portion of the body of the occupant. The system also includes a controller configured to determine an air stream temperature and an air stream flow rate necessary to establish the desired heat supply rate for the sensitive portion and provide a comfortable thermal environment by thermally isolating the occupant from the ambient vehicle cabin temperature. The system may include a sensor to determine the location of the sensitive portion. The nozzle may include a thermoelectric device to heat or cool the air stream.

  5. Directional Wigner-Ville distribution and its application for rotating-machinery condition monitoring

    International Nuclear Information System (INIS)

    Kim, Dong Wan; Ha, Jae HOng; Shin, Hae Gon; Lee, Yoon Hee; Kim, Young Baik

    1996-01-01

    Vibration analysis is one of the most powerful tools available for the detection and isolation of incipient faults in mechanical systems. The methods of vibration analysis in use today and under continuous study are broad band vibration monitoring, time domain analysis, and frequency domain analysis. In recent years, great interest has been generated concerning the use of time-frequency representation and its application for a machinery diagnostics and condition monitoring system. The objective of the research described in this paper was to develop a new diagnostic tool for the rotating machinery. This paper introduces a new time-frequency representation, Directional Wigner-Ville Distribution, which analyses the time-frequency structure of the rotating machinery vibration

  6. Task partitioning in a robot swarm: object retrieval as a sequence of subtasks with direct object transfer.

    Science.gov (United States)

    Pini, Giovanni; Brutschy, Arne; Scheidler, Alexander; Dorigo, Marco; Birattari, Mauro

    2014-01-01

    We study task partitioning in the context of swarm robotics. Task partitioning is the decomposition of a task into subtasks that can be tackled by different workers. We focus on the case in which a task is partitioned into a sequence of subtasks that must be executed in a certain order. This implies that the subtasks must interface with each other, and that the output of a subtask is used as input for the subtask that follows. A distinction can be made between task partitioning with direct transfer and with indirect transfer. We focus our study on the first case: The output of a subtask is directly transferred from an individual working on that subtask to an individual working on the subtask that follows. As a test bed for our study, we use a swarm of robots performing foraging. The robots have to harvest objects from a source, situated in an unknown location, and transport them to a home location. When a robot finds the source, it memorizes its position and uses dead reckoning to return there. Dead reckoning is appealing in robotics, since it is a cheap localization method and it does not require any additional external infrastructure. However, dead reckoning leads to errors that grow in time if not corrected periodically. We compare a foraging strategy that does not make use of task partitioning with one that does. We show that cooperation through task partitioning can be used to limit the effect of dead reckoning errors. This results in improved capability of locating the object source and in increased performance of the swarm. We use the implemented system as a test bed to study benefits and costs of task partitioning with direct transfer. We implement the system with real robots, demonstrating the feasibility of our approach in a foraging scenario.

  7. Intracellular directed evolution of proteins from combinatorial libraries based on conditional phage replication.

    Science.gov (United States)

    Brödel, Andreas K; Jaramillo, Alfonso; Isalan, Mark

    2017-09-01

    Directed evolution is a powerful tool to improve the characteristics of biomolecules. Here we present a protocol for the intracellular evolution of proteins with distinct differences and advantages in comparison with established techniques. These include the ability to select for a particular function from a library of protein variants inside cells, minimizing undesired coevolution and propagation of nonfunctional library members, as well as allowing positive and negative selection logics using basally active promoters. A typical evolution experiment comprises the following stages: (i) preparation of a combinatorial M13 phagemid (PM) library expressing variants of the gene of interest (GOI) and preparation of the Escherichia coli host cells; (ii) multiple rounds of an intracellular selection process toward a desired activity; and (iii) the characterization of the evolved target proteins. The system has been developed for the selection of new orthogonal transcription factors (TFs) but is capable of evolving any gene-or gene circuit function-that can be linked to conditional M13 phage replication. Here we demonstrate our approach using as an example the directed evolution of the bacteriophage λ cI TF against two synthetic bidirectional promoters. The evolved TF variants enable simultaneous activation and repression against their engineered promoters and do not cross-react with the wild-type promoter, thus ensuring orthogonality. This protocol requires no special equipment, allowing synthetic biologists and general users to evolve improved biomolecules within ∼7 weeks.

  8. Direct measurement of thermal conductivity in solid iron at planetary core conditions.

    Science.gov (United States)

    Konôpková, Zuzana; McWilliams, R Stewart; Gómez-Pérez, Natalia; Goncharov, Alexander F

    2016-06-02

    The conduction of heat through minerals and melts at extreme pressures and temperatures is of central importance to the evolution and dynamics of planets. In the cooling Earth's core, the thermal conductivity of iron alloys defines the adiabatic heat flux and therefore the thermal and compositional energy available to support the production of Earth's magnetic field via dynamo action. Attempts to describe thermal transport in Earth's core have been problematic, with predictions of high thermal conductivity at odds with traditional geophysical models and direct evidence for a primordial magnetic field in the rock record. Measurements of core heat transport are needed to resolve this difference. Here we present direct measurements of the thermal conductivity of solid iron at pressure and temperature conditions relevant to the cores of Mercury-sized to Earth-sized planets, using a dynamically laser-heated diamond-anvil cell. Our measurements place the thermal conductivity of Earth's core near the low end of previous estimates, at 18-44 watts per metre per kelvin. The result is in agreement with palaeomagnetic measurements indicating that Earth's geodynamo has persisted since the beginning of Earth's history, and allows for a solid inner core as old as the dynamo.

  9. Enhancement the conditioning of waste activated sludge through a sequence of freeze/thaw-electro-Fenton process

    Directory of Open Access Journals (Sweden)

    Shahheidar Narjes

    2018-03-01

    Full Text Available Sludge conditioning is an important stage in sludge management. In the present study, a sequence of freeze/thaw-electro-Fenton process was designed and specific resistance filtration (SRF was monitored during sludge conditioning as an important factor in sludge dewaterability. Furthermore, protein and polysaccharide concentrations were measured during the experiments. Results showed that the lowest SRF value contributed to −10°C in freezing process which showed a reducing trend by decreasing solution pH. In addition, results revealed that solution pH less than 3 caused a significant improvement in sludge dewatering; so the lowest SRF has been registered at pH = 2. By increasing current intensity from 0.5 to 1A, SRF values were reduced and then followed by an enhancement with increasing current intensity to 3.2 A. The lowest SRF value (6.1 × 104 m/kg was obtained at H2O2 = 30 mg/L which was the best conditions for sludge dewatering.

  10. Comparison of direct machine parameter optimization versus fluence optimization with sequential sequencing in IMRT of hypopharyngeal carcinoma

    International Nuclear Information System (INIS)

    Dobler, Barbara; Pohl, Fabian; Bogner, Ludwig; Koelbl, Oliver

    2007-01-01

    To evaluate the effects of direct machine parameter optimization in the treatment planning of intensity-modulated radiation therapy (IMRT) for hypopharyngeal cancer as compared to subsequent leaf sequencing in Oncentra Masterplan v1.5. For 10 hypopharyngeal cancer patients IMRT plans were generated in Oncentra Masterplan v1.5 (Nucletron BV, Veenendal, the Netherlands) for a Siemens Primus linear accelerator. For optimization the dose volume objectives (DVO) for the planning target volume (PTV) were set to 53 Gy minimum dose and 59 Gy maximum dose, in order to reach a dose of 56 Gy to the average of the PTV. For the parotids a median dose of 22 Gy was allowed and for the spinal cord a maximum dose of 35 Gy. The maximum DVO to the external contour of the patient was set to 59 Gy. The treatment plans were optimized with the direct machine parameter optimization ('Direct Step & Shoot', DSS, Raysearch Laboratories, Sweden) newly implemented in Masterplan v1.5 and the fluence modulation technique ('Intensity Modulation', IM) which was available in previous versions of Masterplan already. The two techniques were compared with regard to compliance to the DVO, plan quality, and number of monitor units (MU) required per fraction dose. The plans optimized with the DSS technique met the DVO for the PTV significantly better than the plans optimized with IM (p = 0.007 for the min DVO and p < 0.0005 for the max DVO). No significant difference could be observed for compliance to the DVO for the organs at risk (OAR) (p > 0.05). Plan quality, target coverage and dose homogeneity inside the PTV were superior for the plans optimized with DSS for similar dose to the spinal cord and lower dose to the normal tissue. The mean dose to the parotids was lower for the plans optimized with IM. Treatment plan efficiency was higher for the DSS plans with (901 ± 160) MU compared to (1151 ± 157) MU for IM (p-value < 0.05). Renormalization of the IM plans to the mean of the

  11. Geochemical imprint of depositional conditions on organic matter in laminated-Bioturbated interbeds from fine-grained marine sequences

    Science.gov (United States)

    Pratt, L.M.; Claypool, G.E.; King, J.D.

    1986-01-01

    Laminated organic-rich shales are interbedded at a scale of centimeters to a few meters with bioturbated organic-poor mudstones or limestones in some fine-grained marine sequences. We have analyzed the organic matter in pairs of laminated/bioturbated interbeds from Cretaceous and Devonian rocks deposited in epicontinental and oceanic settings for the purpose of studying the influence of depositional and early diagenetic environment on the organic geochemical properties of marine shales. Results of these analyses indicate that for rocks that are still in a diagenetic stage of thermal alteration, the relative abundance of biomarker compounds and specific biomarker indices can be useful indicators of depositional and early diagenetic conditions. Pristane/phytane ratios are generally highest for laminated rocks from epicontinental basins and appear to reflect the input of isoprenoid precursors more than oxygenated versus anoxic depositional conditions. The thermally immature laminated rocks are characterized by relatively high contents of 17??(H), 21??(H)-hopanes, hopenes, sterenes and diasterenes, and by strong predominance of the 22R over 22S homohopane isomers. Thermally immature bioturbated samples are characterized by absence of the ??,??-hopanes, by low contents of both saturated and unsaturated polycyclic hydrocarbons, and by slight or no predominance of the 22R over 22S homohopane isomers. There are less obvious compositional differences between the saturated hydrocarbons in the laminated and bioturbated units from the thermally mature sequences. For both the thermally mature and immature laminated samples, the degree of isomerization at the 22C position for hopanes and at the 20C position for steranes is generally consistent with the degree of thermal maturity interpreted from other properties of the organic matter. The bioturbated samples, however, exhibit inconsistent and anomalously high degrees of isomerization for the homohopanes, resulting either from

  12. Direct Numerical Simulation of Turbulent Multi-Stage Autoignition Relevant to Engine Conditions

    Science.gov (United States)

    Chen, Jacqueline

    2017-11-01

    Due to the unrivaled energy density of liquid hydrocarbon fuels combustion will continue to provide over 80% of the world's energy for at least the next fifty years. Hence, combustion needs to be understood and controlled to optimize combustion systems for efficiency to prevent further climate change, to reduce emissions and to ensure U.S. energy security. In this talk I will discuss recent progress in direct numerical simulations of turbulent combustion focused on providing fundamental insights into key `turbulence-chemistry' interactions that underpin the development of next generation fuel efficient, fuel flexible engines for transportation and power generation. Petascale direct numerical simulation (DNS) of multi-stage mixed-mode turbulent combustion in canonical configurations have elucidated key physics that govern autoignition and flame stabilization in engines and provide benchmark data for combustion model development under the conditions of advanced engines which operate near combustion limits to maximize efficiency and minimize emissions. Mixed-mode combustion refers to premixed or partially-premixed flames propagating into stratified autoignitive mixtures. Multi-stage ignition refers to hydrocarbon fuels with negative temperature coefficient behavior that undergo sequential low- and high-temperature autoignition. Key issues that will be discussed include: 1) the role of mixing in shear driven turbulence on the dynamics of multi-stage autoignition and cool flame propagation in diesel environments, 2) the role of thermal and composition stratification on the evolution of the balance of mixed combustion modes - flame propagation versus spontaneous ignition - which determines the overall combustion rate in autoignition processes, and 3) the role of cool flames on lifted flame stabilization. Finally prospects for DNS of turbulent combustion at the exascale will be discussed in the context of anticipated heterogeneous machine architectures. sponsored by DOE

  13. Main directions of providing of industrial enterprises effective development and conditions of their choice

    Directory of Open Access Journals (Sweden)

    Y. V. Zhuravlev

    2016-01-01

    Full Text Available Difficulties in managing the effective development of an industrial enterprise is largely due to the lack of complex tools to measure it, which is aggravated by the lack of identification of the factors that affect the food industry enterprises. In the article, we investigated directions of providing of industrial enterprises effective development and determined conditions of their choice depending on organizational assets and enterprise’s added value dynamics. For every possible combination, we offered certain mechanism of effective development: internal – by means of enterprise’s self-potential activation, and external – by means of deep, moderate or shallow integration. Deep integration means full merger of the enterprise and is recommended in case of critical level of enterprise’s potential. Moderate integration is implemented by purchase of controlling block of shares and is carried out in case of critical or high enterprise’s potential combined with growth of added value. Shallow integration can be used in any combination of resources and added value and is implemented on a contractual basis without institutional and legal change. The concept of directions of providing of industrial enterprises development, that we worked out, is of applicable character and can be used by industrial enterprises regardless field and specific character of industry. Implementation of offered measures will provide industrial enterprises effective development, which will help to form organizational assets base of Russian economics, which is a powerful driver of modernization of Russian industrial enterprises and economics as a whole.

  14. A direct numerical simulation of cool-flame affected autoignition in diesel engine-relevant conditions

    Energy Technology Data Exchange (ETDEWEB)

    Krisman, Alexander; Hawkes, Evatt Robert.; Talei, Mohsen; Bhagatwala, Ankit; Chen, Jacqueline H.

    2016-11-11

    In diesel engines, combustion is initiated by a two-staged autoignition that includes both low- and high-temperature chemistry. The location and timing of both stages of autoignition are important parameters that influence the development and stabilisation of the flame. In this study, a two-dimensional direct numerical simulation (DNS) is conducted to provide a fully resolved description of ignition at diesel engine-relevant conditions. The DNS is performed at a pressure of 40 atmospheres and at an ambient temperature of 900 K using dimethyl ether (DME) as the fuel, with a 30 species reduced chemical mechanism. At these conditions, similar to diesel fuel, DME exhibits two-stage ignition. The focus of this study is on the behaviour of the low-temperature chemistry (LTC) and the way in which it influences the high-temperature ignition. The results show that the LTC develops as a “spotty” first-stage autoignition in lean regions which transitions to a diffusively supported cool-flame and then propagates up the local mixture fraction gradient towards richer regions. The cool-flame speed is much faster than can be attributed to spatial gradients in first-stage ignition delay time in homogeneous reactors. The cool-flame causes a shortening of the second-stage ignition delay times compared to a homogeneous reactor and the shortening becomes more pronounced at richer mixtures. Multiple high-temperature ignition kernels are observed over a range of rich mixtures that are much richer than the homogeneous most reactive mixture and most kernels form much earlier than suggested by the homogeneous ignition delay time of the corresponding local mixture. Altogether, the results suggest that LTC can strongly influence both the timing and location in composition space of the high-temperature ignition.

  15. Optimum conditions of the synthesis of zeolite A by the direct hydrolysis of ethyl orthosilicate

    Energy Technology Data Exchange (ETDEWEB)

    Hino, R; Toki, K

    1975-11-01

    Synthesis of various types of zeolites has been reported using as a starting material silica sols, gels, silicates or silicate minerals, all of which are polymers of silicic acid. In this study Zeolite A was synthesized from ethyl orthosilicate which was probably a monomer at the beginning of hydrolysis. Optimum conditions of synthesis and factors which influence the formation of Zeolite A were examined. Ethyl orthosilicate was directly hydrolyzed by sodium aluminate solution in the presence of excess sodium hydroxide. After ultrasonic and mechanical stirring for an hour at 70/sup 0/C, the solution was kept in the air bath at 70/sup 0/C under atmospheric pressure for 48 approximately 120 hours. Zeolite A with high purity and crystallinity was obtained in a good yield from the starting mixture with the composition of 2 approximately 4.5 Na/sub 2/O . Al/sub 2/O/sub 3/ . 0.5 approximately 2 SiO/sub 2/ . 200 approximately 400 H/sub 2/O. Present method was effective for the synthesis of Zeolite A in the lower molar ratios of SiO/sub 2//Al/sub 2/O/sub 3/ as compared with the ordinary methods using silica or silicates. The species formed were also investigated by the optical, x-ray diffraction, DTA, TGA, IR and chemical methods.

  16. Modelling Geomechanical Heterogeneity of Rock Masses Using Direct and Indirect Geostatistical Conditional Simulation Methods

    Science.gov (United States)

    Eivazy, Hesameddin; Esmaieli, Kamran; Jean, Raynald

    2017-12-01

    An accurate characterization and modelling of rock mass geomechanical heterogeneity can lead to more efficient mine planning and design. Using deterministic approaches and random field methods for modelling rock mass heterogeneity is known to be limited in simulating the spatial variation and spatial pattern of the geomechanical properties. Although the applications of geostatistical techniques have demonstrated improvements in modelling the heterogeneity of geomechanical properties, geostatistical estimation methods such as Kriging result in estimates of geomechanical variables that are not fully representative of field observations. This paper reports on the development of 3D models for spatial variability of rock mass geomechanical properties using geostatistical conditional simulation method based on sequential Gaussian simulation. A methodology to simulate the heterogeneity of rock mass quality based on the rock mass rating is proposed and applied to a large open-pit mine in Canada. Using geomechanical core logging data collected from the mine site, a direct and an indirect approach were used to model the spatial variability of rock mass quality. The results of the two modelling approaches were validated against collected field data. The study aims to quantify the risks of pit slope failure and provides a measure of uncertainties in spatial variability of rock mass properties in different areas of the pit.

  17. Distributed adaptive asymptotically consensus tracking control of uncertain Euler-Lagrange systems under directed graph condition.

    Science.gov (United States)

    Wang, Wei; Wen, Changyun; Huang, Jiangshuai; Fan, Huijin

    2017-11-01

    In this paper, a backstepping based distributed adaptive control scheme is proposed for multiple uncertain Euler-Lagrange systems under directed graph condition. The common desired trajectory is allowed totally unknown by part of the subsystems and the linearly parameterized trajectory model assumed in currently available results is no longer needed. To compensate the effects due to unknown trajectory information, a smooth function of consensus errors and certain positive integrable functions are introduced in designing virtual control inputs. Besides, to overcome the difficulty of completely counteracting the coupling terms of distributed consensus errors and parameter estimation errors in the presence of asymmetric Laplacian matrix, extra information transmission of local parameter estimates are introduced among linked subsystem and adaptive gain technique is adopted to generate distributed torque inputs. It is shown that with the proposed distributed adaptive control scheme, global uniform boundedness of all the closed-loop signals and asymptotically output consensus tracking can be achieved. Copyright © 2017 ISA. Published by Elsevier Ltd. All rights reserved.

  18. Effect of operating conditions on energy efficiency for a small passive direct methanol fuel cell

    International Nuclear Information System (INIS)

    Chu Deryn; Jiang Rongzhong

    2006-01-01

    Energy conversion efficiency was studied in a direct methanol fuel cell (DMFC) with an air-breathing cathode using Nafion 117 as electrolyte membrane. The effect of operating conditions, such as methanol concentration, discharge voltage and temperature, on Faradic and energy conversion efficiencies was analyzed under constant voltage discharge with quantitative amount of fuel. Both of Faradic and energy conversion efficiencies decrease significantly with increasing methanol concentration and environmental temperature. The Faradic conversion efficiency can be as high as 94.8%, and the energy conversion efficiency can be as high as 23.9% if the environmental temperature is low enough (10 deg. C) under constant voltage discharge at 0.6 V with 3 M methanol for a DMFC bi-cell. Although higher temperature and higher methanol concentration can achieve higher discharge power, it will result in considerable losses of Faradic and energy conversion efficiencies for using Nafion electrolyte membrane. Development of alternative highly conductive membranes with significantly lower methanol crossover is necessary to avoid loss of Faradic conversion efficiency with temperature and with fuel concentration

  19. Onset condition of the off take from the stratified region to the branch with arbitrary direction

    International Nuclear Information System (INIS)

    Lee, Jae Young; Choo, Kyo Seong; Kim, Man Woong

    2004-01-01

    Two phase discharge from a stratified region through single or multiple branches has been studied considerably in the past two decades. The flow distribution in the header-feeder system of CANDU(Canada Deuterium and Uranium) reactors during accident scenario is one of good examples of these applications. Recently, the passive safety feature for PWR(Pressurized Water Reactor) introduce the concept of DVI(Direct Vessel Injection) for the emergency core make up. The expected water sweep out phenomena needs careful models including the curvature effect of down comer shell and the multi branches. It has been generally accepted that the onset condition of the off take follows the 2.5 power law, but recently, Lee et al. discussed that the experimental data produced large scattering to the 2.5 power law. Also, the effect of branch angle on the onset point of off take remains still as an unsolved problem. Hwang et al produced the CANDU specific branch angles of 0, +-90, +-36, +-72. The experimental results showed severe deviation from the 2.5 power law and needs mechanistic understanding on these phenomena. In the present paper, we try to develop a general model of onset point including the branch orientation

  20. Diagnostic Impact and Cost-effectiveness of Whole-Exome Sequencing for Ambulant Children With Suspected Monogenic Conditions.

    Science.gov (United States)

    Tan, Tiong Yang; Dillon, Oliver James; Stark, Zornitza; Schofield, Deborah; Alam, Khurshid; Shrestha, Rupendra; Chong, Belinda; Phelan, Dean; Brett, Gemma R; Creed, Emma; Jarmolowicz, Anna; Yap, Patrick; Walsh, Maie; Downie, Lilian; Amor, David J; Savarirayan, Ravi; McGillivray, George; Yeung, Alison; Peters, Heidi; Robertson, Susan J; Robinson, Aaron J; Macciocca, Ivan; Sadedin, Simon; Bell, Katrina; Oshlack, Alicia; Georgeson, Peter; Thorne, Natalie; Gaff, Clara; White, Susan M

    2017-09-01

    Optimal use of whole-exome sequencing (WES) in the pediatric setting requires an understanding of who should be considered for testing and when it should be performed to maximize clinical utility and cost-effectiveness. To investigate the impact of WES in sequencing-naive children suspected of having a monogenic disorder and evaluate its cost-effectiveness if WES had been available at different time points in their diagnostic trajectory. This prospective study was part of the Melbourne Genomics Health Alliance demonstration project. At the ambulatory outpatient clinics of the Victorian Clinical Genetics Services at the Royal Children's Hospital, Melbourne, Australia, children older than 2 years suspected of having a monogenic disorder were prospectively recruited from May 1 through November 30, 2015, by clinical geneticists after referral from general and subspecialist pediatricians. All children had nondiagnostic microarrays and no prior single-gene or panel sequencing. All children underwent singleton WES with targeted phenotype-driven analysis. The study examined the clinical utility of a molecular diagnosis and the cost-effectiveness of alternative diagnostic trajectories, depending on timing of WES. Of 61 children originally assessed, 44 (21 [48%] male and 23 [52%] female) aged 2 to 18 years (mean age at initial presentation, 28 months; range, 0-121 months) were recruited, and a diagnosis was achieved in 23 (52%) by singleton WES. The diagnoses were unexpected in 8 of 23 (35%), and clinical management was altered in 6 of 23 (26%). The mean duration of the diagnostic odyssey was 6 years, with each child having a mean of 19 tests and 4 clinical genetics and 4 nongenetics specialist consultations, and 26 (59%) underwent a procedure while under general anesthetic for diagnostic purposes. Economic analyses of the diagnostic trajectory identified that WES performed at initial tertiary presentation resulted in an incremental cost savings of A$9020 (US$6838) per

  1. Direct stacking of sequence-specific nuclease-induced mutations to produce high oleic and low linolenic soybean oil.

    Science.gov (United States)

    Demorest, Zachary L; Coffman, Andrew; Baltes, Nicholas J; Stoddard, Thomas J; Clasen, Benjamin M; Luo, Song; Retterath, Adam; Yabandith, Ann; Gamo, Maria Elena; Bissen, Jeff; Mathis, Luc; Voytas, Daniel F; Zhang, Feng

    2016-10-13

    The ability to modulate levels of individual fatty acids within soybean oil has potential to increase shelf-life and frying stability and to improve nutritional characteristics. Commodity soybean oil contains high levels of polyunsaturated linoleic and linolenic acid, which contribute to oxidative instability - a problem that has been addressed through partial hydrogenation. However, partial hydrogenation increases levels of trans-fatty acids, which have been associated with cardiovascular disease. Previously, we generated soybean lines with knockout mutations within fatty acid desaturase 2-1A (FAD2-1A) and FAD2-1B genes, resulting in oil with increased levels of monounsaturated oleic acid (18:1) and decreased levels of linoleic (18:2) and linolenic acid (18:3). Here, we stack mutations within FAD2-1A and FAD2-1B with mutations in fatty acid desaturase 3A (FAD3A) to further decrease levels of linolenic acid. Mutations were introduced into FAD3A by directly delivering TALENs into fad2-1a fad2-1b soybean plants. Oil from fad2-1a fad2-1b fad3a plants had significantly lower levels of linolenic acid (2.5 %), as compared to fad2-1a fad2-1b plants (4.7 %). Furthermore, oil had significantly lower levels of linoleic acid (2.7 % compared to 5.1 %) and significantly higher levels of oleic acid (82.2 % compared to 77.5 %). Transgene-free fad2-1a fad2-1b fad3a soybean lines were identified. The methods presented here provide an efficient means for using sequence-specific nucleases to stack quality traits in soybean. The resulting product comprised oleic acid levels above 80 % and linoleic and linolenic acid levels below 3 %.

  2. Direct DNA Extraction from Mycobacterium tuberculosis Frozen Stocks as a Reculture-Independent Approach to Whole-Genome Sequencing

    DEFF Research Database (Denmark)

    Bjorn-Mortensen, K; Zallet, J; Lillebaek, T

    2015-01-01

    Culturing before DNA extraction represents a major time-consuming step in whole-genome sequencing of slow-growing bacteria, such as Mycobacterium tuberculosis. We report a workflow to extract DNA from frozen isolates without reculturing. Prepared libraries and sequence data were comparable...... with results from recultured aliquots of the same stocks....

  3. Fungal communities in mycorrhizal roots of conifer seedlings in forest nurseries under different cultivation systems, assessed by morphotyping, direct sequencing and mycelial isolation.

    Science.gov (United States)

    Menkis, Audrius; Vasiliauskas, Rimvydas; Taylor, Andrew F S; Stenlid, Jan; Finlay, Roger

    2005-12-01

    Fungi colonising root tips of Pinus sylvestris and Picea abies grown under four different seedling cultivation systems were assessed by morphotyping, direct sequencing and isolation methods. Roots were morphotyped using two approaches: (1) 10% of the whole root system from 30 seedlings of each species and (2) 20 randomly selected tips per plant from 300 seedlings of each species. The first approach yielded 15 morphotypes, the second yielded 27, including 18 new morphotypes. The overall community consisted of 33 morphotypes. The level of mycorrhizal colonisation of roots determined by each approach was about 50%. The cultivation system had a marked effect on the level of mycorrhizal colonisation. In pine, the highest level of colonisation (48%) was observed in bare-root systems, while in spruce, colonisation was highest in polyethylene rolls (71%). Direct internal transcribed spacer ribosomal DNA sequencing and isolation detected a total of 93 fungal taxa, including 27 mycorrhizal. A total of 71 (76.3%) fungi were identified at least to a genus level. The overlap between the two methods was low. Only 13 (13.9%) of taxa were both sequenced and isolated, 47 (50.5%) were detected exclusively by sequencing and 33 (35.5%) exclusively by isolation. All isolated mycorrhizal fungi were also detected by direct sequencing. Characteristic mycorrhizas were Phialophora finlandia, Amphinema byssoides, Rhizopogon rubescens, Suillus luteus and Thelephora terrestris. There was a moderate similarity in mycorrhizal communities between pine and spruce and among different cultivation systems.

  4. First Complete Genomic Sequence of a Rabies Virus from the Republic of Tajikistan Obtained Directly from a Flinders Technology Associates Card

    OpenAIRE

    Goharriz, H.; Marston, D. A.; Sharifzoda, F.; Ellis, R. J.; Horton, D. L.; Khakimov, T.; Whatmore, A.; Khamroev, K.; Makhmadshoev, A. N.; Bazarov, M.; Fooks, A. R.; Banyard, A. C.

    2017-01-01

    ABSTRACT A brain homogenate derived from a rabid dog in the district of Tojikobod, Republic of Tajikistan, was applied to a Flinders Technology Associates (FTA) card. A full-genome sequence of rabies virus (RABV) was generated from the FTA card directly without extraction, demonstrating the utility of these cards for readily obtaining genetic data.

  5. First Complete Genomic Sequence of a Rabies Virus from the Republic of Tajikistan Obtained Directly from a Flinders Technology Associates Card.

    Science.gov (United States)

    Goharriz, H; Marston, D A; Sharifzoda, F; Ellis, R J; Horton, D L; Khakimov, T; Whatmore, A; Khamroev, K; Makhmadshoev, A N; Bazarov, M; Fooks, A R; Banyard, A C

    2017-07-06

    A brain homogenate derived from a rabid dog in the district of Tojikobod, Republic of Tajikistan, was applied to a Flinders Technology Associates (FTA) card. A full-genome sequence of rabies virus (RABV) was generated from the FTA card directly without extraction, demonstrating the utility of these cards for readily obtaining genetic data. © Crown copyright 2017.

  6. Plasma flow measurement using directional Langmuir probe under weakly ion-magnetized conditions

    Energy Technology Data Exchange (ETDEWEB)

    Nagaoka, Kenichi; Okamoto, Atsushi [Graduate School of Science, Nagoya Univ., Nagoya (Japan); Yoshimura, Shinji; Tanaka, Masayoshi Y. [National Inst. for Fusion Science, Toki, Gifu (Japan)

    2000-07-01

    It is both experimentally and theoretically demonstrated that ion flow velocity at an arbitrary angle with respect to the magnetic field can be measured with a directional Langmuir probe. Based on the symmetry argument, we show that the effect of magnetic field on directional probe current is exactly canceled in determining the ion flow velocity, and obtain the generalized relation between flow velocity and directional probe currents valid for any flowing direction. The absolute value of the flow velocity is determined by an in situ calibration method of the probe. The applicability limit of the present method to a strongly ion-magnetized plasma is experimentally examined. (author)

  7. 42 CFR 415.110 - Conditions for payment: Medically directed anesthesia services.

    Science.gov (United States)

    2010-10-01

    ... anesthesia services. 415.110 Section 415.110 Public Health CENTERS FOR MEDICARE & MEDICAID SERVICES... directed anesthesia services. (a) General payment rule. Medicare pays for the physician's medical direction of anesthesia services for one service or two through four concurrent anesthesia services furnished...

  8. Search Engine for Antimicrobial Resistance: A Cloud Compatible Pipeline and Web Interface for Rapidly Detecting Antimicrobial Resistance Genes Directly from Sequence Data.

    Science.gov (United States)

    Rowe, Will; Baker, Kate S; Verner-Jeffreys, David; Baker-Austin, Craig; Ryan, Jim J; Maskell, Duncan; Pearce, Gareth

    2015-01-01

    Antimicrobial resistance remains a growing and significant concern in human and veterinary medicine. Current laboratory methods for the detection and surveillance of antimicrobial resistant bacteria are limited in their effectiveness and scope. With the rapidly developing field of whole genome sequencing beginning to be utilised in clinical practice, the ability to interrogate sequencing data quickly and easily for the presence of antimicrobial resistance genes will become increasingly important and useful for informing clinical decisions. Additionally, use of such tools will provide insight into the dynamics of antimicrobial resistance genes in metagenomic samples such as those used in environmental monitoring. Here we present the Search Engine for Antimicrobial Resistance (SEAR), a pipeline and web interface for detection of horizontally acquired antimicrobial resistance genes in raw sequencing data. The pipeline provides gene information, abundance estimation and the reconstructed sequence of antimicrobial resistance genes; it also provides web links to additional information on each gene. The pipeline utilises clustering and read mapping to annotate full-length genes relative to a user-defined database. It also uses local alignment of annotated genes to a range of online databases to provide additional information. We demonstrate SEAR's application in the detection and abundance estimation of antimicrobial resistance genes in two novel environmental metagenomes, 32 human faecal microbiome datasets and 126 clinical isolates of Shigella sonnei. We have developed a pipeline that contributes to the improved capacity for antimicrobial resistance detection afforded by next generation sequencing technologies, allowing for rapid detection of antimicrobial resistance genes directly from sequencing data. SEAR uses raw sequencing data via an intuitive interface so can be run rapidly without requiring advanced bioinformatic skills or resources. Finally, we show that SEAR

  9. A statistic sensitive to deviations from the zero-loss condition in a sequence of material balances

    International Nuclear Information System (INIS)

    Sellinschegg, D.

    1982-01-01

    The CUMUFR (cumulative sum of standardized MUFresiduals) statistic is proposed to examine materials balance data for deviations from the zero-loss condition. The time series of MUF-residuals is shown to be a linear transformation of the MUF-time series. The MUF-residuals can directly be obtained by applying the transformation or they can be obtained, approximately, by the application of a Kalman filter to estimate the true state of MUF. A modified sequential test with power one is formulated for testing the CUMUFR statistic. The detection capability of the proposed examination procedure is demonstrated by an example, based on Monte Carlo simulations, where the materials balance of the chemical separation process in a reference reprocessing facility is considered. It is shown that abrupt as well as protracted loss patterns are detected with rather high probability when they occur after a zeroloss period

  10. Simple Moving Voltage Average Incremental Conductance MPPT Technique with Direct Control Method under Nonuniform Solar Irradiance Conditions

    Directory of Open Access Journals (Sweden)

    Amjad Ali

    2015-01-01

    Full Text Available A new simple moving voltage average (SMVA technique with fixed step direct control incremental conductance method is introduced to reduce solar photovoltaic voltage (VPV oscillation under nonuniform solar irradiation conditions. To evaluate and validate the performance of the proposed SMVA method in comparison with the conventional fixed step direct control incremental conductance method under extreme conditions, different scenarios were simulated. Simulation results show that in most cases SMVA gives better results with more stability as compared to traditional fixed step direct control INC with faster tracking system along with reduction in sustained oscillations and possesses fast steady state response and robustness. The steady state oscillations are almost eliminated because of extremely small dP/dV around maximum power (MP, which verify that the proposed method is suitable for standalone PV system under extreme weather conditions not only in terms of bus voltage stability but also in overall system efficiency.

  11. A SOM clustering pattern sequence-based next symbol prediction method for day-ahead direct electricity load and price forecasting

    International Nuclear Information System (INIS)

    Jin, Cheng Hao; Pok, Gouchol; Lee, Yongmi; Park, Hyun-Woo; Kim, Kwang Deuk; Yun, Unil; Ryu, Keun Ho

    2015-01-01

    Highlights: • A novel pattern sequence-based direct time series forecasting method was proposed. • Due to the use of SOM’s topology preserving property, only SOM can be applied. • SCPSNSP only deals with the cluster patterns not each specific time series value. • SCPSNSP performs better than recently developed forecasting algorithms. - Abstract: In this paper, we propose a new day-ahead direct time series forecasting method for competitive electricity markets based on clustering and next symbol prediction. In the clustering step, pattern sequence and their topology relations are obtained from self organizing map time series clustering. In the next symbol prediction step, with each cluster label in the pattern sequence represented as a pair of its topologically identical coordinates, artificial neural network is used to predict the topological coordinates of next day by training the relationship between previous daily pattern sequence and its next day pattern. According to the obtained topology relations, the nearest nonzero hits pattern is assigned to next day so that the whole time series values can be directly forecasted from the assigned cluster pattern. The proposed method was evaluated on Spanish, Australian and New York electricity markets and compared with PSF and some of the most recently published forecasting methods. Experimental results show that the proposed method outperforms the best forecasting methods at least 3.64%

  12. Analysis of scenarios for the direct disposal of spent nuclear fuel disposal conditions as expected in Germany

    International Nuclear Information System (INIS)

    Ashton, P.; Mehling, O.; Mohn, R.; Wingender, H.J.

    1990-01-01

    This report contains an investigation of aspects of the waste management of spent light water reactor fuel by direct disposal in a deep geological formation on land. The areas covered are: interim dry storage of spent fuel with three options of pre-conditioning; conditioning of spent fuel for final disposal in a salt dome repository; disposal of spent fuel (heat-generating waste) in a salt dome repository; disposal of medium and low-level radioactive wastes in the Konrad mine. Dose commitments, effluent discharges and potential incidents were not found to vary significantly for the various conditioning options/salt dome repository types. Due to uncertainty in the cost estimates, in particular the disposal cost estimates, the variation between the three conditioning options examined is not considered as being significant. The specific total costs for the direct disposal strategy are estimated to lie in the range ECU 600 to 700 per kg hm (basis 1988)

  13. Nanopore sequencing technology and tools for genome assembly: computational analysis of the current state, bottlenecks and future directions.

    Science.gov (United States)

    Senol Cali, Damla; Kim, Jeremie S; Ghose, Saugata; Alkan, Can; Mutlu, Onur

    2018-04-02

    Nanopore sequencing technology has the potential to render other sequencing technologies obsolete with its ability to generate long reads and provide portability. However, high error rates of the technology pose a challenge while generating accurate genome assemblies. The tools used for nanopore sequence analysis are of critical importance, as they should overcome the high error rates of the technology. Our goal in this work is to comprehensively analyze current publicly available tools for nanopore sequence analysis to understand their advantages, disadvantages and performance bottlenecks. It is important to understand where the current tools do not perform well to develop better tools. To this end, we (1) analyze the multiple steps and the associated tools in the genome assembly pipeline using nanopore sequence data, and (2) provide guidelines for determining the appropriate tools for each step. Based on our analyses, we make four key observations: (1) the choice of the tool for basecalling plays a critical role in overcoming the high error rates of nanopore sequencing technology. (2) Read-to-read overlap finding tools, GraphMap and Minimap, perform similarly in terms of accuracy. However, Minimap has a lower memory usage, and it is faster than GraphMap. (3) There is a trade-off between accuracy and performance when deciding on the appropriate tool for the assembly step. The fast but less accurate assembler Miniasm can be used for quick initial assembly, and further polishing can be applied on top of it to increase the accuracy, which leads to faster overall assembly. (4) The state-of-the-art polishing tool, Racon, generates high-quality consensus sequences while providing a significant speedup over another polishing tool, Nanopolish. We analyze various combinations of different tools and expose the trade-offs between accuracy, performance, memory usage and scalability. We conclude that our observations can guide researchers and practitioners in making conscious

  14. Uncooled EGR as a means of limiting wall-wetting under early direct injection conditions

    NARCIS (Netherlands)

    Boot, M.D.; Luijten, C.C.M.; Somers, L.M.T.; Eguz, U.; Erp, D.D.T.M. van; Albrecht, A.; Baert, R.S.G.

    2009-01-01

    Collision of injected fuel spray against the cylinder liner (wall-wetting) is one of the main hurdles that must be overcome in order for early direct injection Premixed Charge Compression Ignition (EDI PCCI) combustion to become a viable alternative for conventional DI diesel combustion. Preferably,

  15. Optimization of operating conditions in the early direct injection premixed charge compression ignition regime

    NARCIS (Netherlands)

    Boot, M.D.; Luijten, C.C.M.; Rijk, E.P.; Albrecht, B.A.; Baert, R.S.G.

    2009-01-01

    Early Direct Injection Premixed Charge Compression Ignition (EDI PCCI) is a widely researched combustion concept, which promises soot and CO2 emission levels of a spark-ignition (SI) and compression-ignition (CI) engine, respectively. Application of this concept to a conventional CI engine using a

  16. Effect of mutagen combined action on Chlamydomonas reinhardtii cells. I. Lethal effect dependence on the sequence of mutagen application and on cultivation conditions

    Energy Technology Data Exchange (ETDEWEB)

    Vlcek, D; Podstavkova, S; Dubovsky, J [Komenskeho Univ., Bratislava (Czechoslovakia). Prirodovedecka Fakulta

    1978-01-01

    The effect was investigated of single and combined actions of alkylnitrosourea derivatives (N-methyl-N-nitrosourea and N-ethyl-N-nitrosourea) and UV-radiation on the survival of cells of Chlamydomonas reinhardtii algae in dependence on the sequence of application of mutagens and on the given conditions of cultivation following mutagen activity. In particular, the single phases were investigated of the total lethal effect, i.e., the death of cells before division and their death after division. The most pronounced changes in dependence on the sequence of application of mutagens and on the given conditions of cultivation were noted in cell death before division. In dependence on the sequence of application of mutagens, the effect of the combined action on the survival of cells changed from an additive (alkylnitrosourea + UV-radiation) to a protective effect (UV-radiation + alkylnitrosourea).

  17. Molecular Biological Studies on the Biogenesis of Human Cholinesterases in vivo and as Directed by Cloned Cholinesterase DNA Sequences

    Science.gov (United States)

    1990-10-24

    species, was constructed using " lineup " and "profile." Sequences included human BCHE, Torpedo ACHE, Droscphila esterase-6 and rat lysophospholipase...in embryonic development. Prog. Histochem. Cytochem. 7: 1-52 (1975). 38 Layer, P.G.; Alber, R.; Rathjen, F.G. Sequential activation of

  18. Direct 16S rRNA gene sequencing of polymicrobial culture-negative samples with analysis of mixed chromatograms

    DEFF Research Database (Denmark)

    Hartmeyer, Gitte N; Justesen, Ulrik S

    2010-01-01

    Two cases involving polymicrobial culture-negative samples were investigated by 16S rRNA gene sequencing, with analysis of mixed chromatograms. Fusobacterium necrophorum, Prevotella intermedia and Streptococcus constellatus were identified from pleural fluid in a patient with Lemierre's syndrome...

  19. Installation of PMV Operation Program in DDC Controller and Air Conditioning Control Using PMV Directly as Set Point

    Science.gov (United States)

    Haramoto, Ken-Ichi

    In general, air conditioning control in a building is operated mainly by indoor air temperature control. Although the operators of the machine in the building accepted a claim for indoor air temperature presented by the building inhabitants, the indoor conditions have been often too cool or warm. Therefore, in an attempt to create better thermal environments, the author paid attention to the PMV that is a thermal comfort index. And then, the possibility of air conditioning control using the PMV directly as the set point was verified by employing actual equipment in an air conditioning testing room and an office building. Prior to the execution of this control, the operation program of the PMV was installed in a DDC controller for the air conditioning control. And information from indoor sensors and so on was inputted to the controller, and the computed PMV was used as the feedback variable.

  20. Liquid sprays and flow studies in the direct-injection diesel engine under motored conditions

    Science.gov (United States)

    Nguyen, Hung Lee; Carpenter, Mark H.; Ramos, Juan I.; Schock, Harold J.; Stegeman, James D.

    1988-01-01

    A two dimensional, implicit finite difference method of the control volume variety, a two equation model of turbulence, and a discrete droplet model were used to study the flow field, turbulence levels, fuel penetration, vaporization, and mixing in diesel engine environments. The model was also used to study the effects of engine speed, injection angle, spray cone angle, droplet distribution, and intake swirl angle on the flow field, spray penetration and vaporization, and turbulence in motored two-stroke diesel engines. It is shown that there are optimum conditions for injection, which depend on droplet distribution, swirl, spray cone angle, and injection angle. The optimum conditions result in good spray penetration and vaporization and in good fuel mixing. The calculation presented clearly indicates that internal combustion engine models can be used to assess, at least qualitatively, the effects of injection characteristics and engine operating conditions on the flow field and on the spray penetration and vaporization in diesel engines.

  1. Direct repeat sequences are essential for function of the cis-acting locus of transfer (clt) of Streptomyces phaeochromogenes plasmid pJV1.

    Science.gov (United States)

    Franco, Bernardo; González-Cerón, Gabriela; Servín-González, Luis

    2003-11-01

    The functionality of direct and inverted repeat sequences inside the cis acting locus of transfer (clt) of the Streptomyces plasmid pJV1 was determined by testing the effect of different deletions on plasmid transfer. The results show that the single most important element for pJV1 clt function is a series of evenly spaced 9 bp long direct repeats which match the consensus CCGCACA(C/G)(C/G), since their deletion caused a dramatic reduction in plasmid transfer. The presence of these repeats in the absence of any other clt sequences allowed plasmid transfer to occur at a frequency that was at least two orders of magnitude higher than that obtained in the complete absence of clt. A database search revealed regions with a similar organization, and in the same position, in Streptomyces plasmids pSN22 and pSLS, which have transfer proteins homologous to those of pJV1.

  2. Cathodal transcranial direct current stimulation (tDCS) applied to the left premotor cortex (PMC) stabilizes a newly learned motor sequence.

    Science.gov (United States)

    Focke, Jan; Kemmet, Sylvia; Krause, Vanessa; Keitel, Ariane; Pollok, Bettina

    2017-01-01

    While the primary motor cortex (M1) is involved in the acquisition the premotor cortex (PMC) has been related to over-night consolidation of a newly learned motor skill. The present study aims at investigating the possible contribution of the left PMC for the stabilization of a motor sequence immediately after acquisition as determined by susceptibility to interference. Thirty six healthy volunteers received anodal, cathodal and sham transcranial direct current stimulation (tDCS) to the left PMC either immediately prior to or during training on a serial reaction time task (SRTT) with the right hand. TDCS was applied for 10min, respectively. Reaction times were measured prior to training (t1), at the end of training (t2), and after presentation of an interfering random pattern (t3). Beyond interference from learning, the random pattern served as control condition in order to estimate general effects of tDCS on reaction times. TDCS applied during SRTT training did not result in any significant effects neither on acquisition nor on susceptibility to interference. In contrast to this, tDCS prior to SRTT training yielded an unspecific facilitation of reaction times at t2 independent of tDCS polarity. At t3, reduced susceptibility to interference was found following cathodal stimulation. The results suggest the involvement of the PMC in early consolidation and reveal a piece of evidence for the hypothesis that behavioral tDCS effects vary with the activation state of the stimulated area. Copyright © 2016. Published by Elsevier B.V.

  3. Thermal analysis of a direct evaporative cooling system enhancement with desiccant dehumidification for vehicular air conditioning

    International Nuclear Information System (INIS)

    Alahmer, Ali

    2016-01-01

    Highlights: • Thermal analysis was conducted to design a desiccant evaporative cooling system for vehicular air conditioning. • EC is more efficient than the conventional air conditioning when the gasoline price is more than 0.34 $/liter. • Drawbacks of evaporative cooler of increased weight and reduced COP. • A rotary desiccant dehumidifier with generation was combined with evaporative cooling to be more efficient. - Abstract: This manuscript analyzes the sub-systems of evaporative cooler (EC) combined with desiccant dehumidification and regeneration for automotive air conditioning purpose. The thermodynamic and psychometric analysis was conducted to design all evaporative cooling system components in terms of desiccant selection, regeneration process, compact heat exchanger and evaporative cooler. Moreover, the effect of the desiccant, heat exchanger and evaporative performances on the mass flow rate and water sprayed required for evaporative cooling system was investigated. The results show that the theoretical evaporative cooling design will achieve two main objectives: lower fuel consumption and less environmental pollutants. However, it has the two drawbacks in terms of increased weight and reduces the coefficient of performance (COP). The main remark is that evaporating cooling system is more efficient than the conventional air conditioning when the gasoline price is more than 0.34 $/liter.

  4. Digital image color analysis compared to direct dental CIE colorimeter assessment under different ambient conditions.

    Science.gov (United States)

    Knösel, Michael; Attin, Rengin; Jung, Klaus; Brunner, Edgar; Kubein-Meesenburg, Dietmar; Attin, Thomas

    2009-04-01

    To evaluate the concordance and repeatability of two in vivo methods for dental color assessment and to clarify the influence of different ambient light conditions and subject's head position on the assessed color variables. Color assessments were performed by two examiners on 16 arbitrarily selected subjects under two different, standardized conditions of illumination and at two different standardized head angulations. CIE (L*a*b*) data for upper and lower central incisors were recorded in two different ways: (1) by an intra-oral contact dental colorimeter and (2) by processing digital images for performing color calculation using Adobe Photoshop software. The influence of the different ambient conditions on both methods, as well as the concordance of measurements was analyzed statistically using several mixed linear models. Ambient light as a single factor had no significant influence on maxillary L*, a* and b* values, but it did have an effect on mandible assessments. Head angulation variation resulted in significant L* value differences using the photo method. The operator had a significant influence on values a* and b* for the photo method and on a* values for the colorimeter method. In fully lit ambient condition, the operator had a significant influence on the segregated L*, a*, and b* values. With dimmed lights, head angulation became significant, but not the operator. Evaluation of segregated L* values was error prone in both methods. Comparing both methods, deltaE values did not exceed 2.85 units, indicating that color differences between methods and recorded under varying ambient conditions were well below the sensitivity of the naked eye.

  5. Pseudogene of dihydrolipoyl succinyltransferase (E2k) found by PCR amplification and direct sequencing of rodent-human cell hybrid DNAs

    Energy Technology Data Exchange (ETDEWEB)

    Cai, X.; Ali, G.; Blass, J.P. [Cornell Univ. Medical College, White Plains, NY (United States); Szabo, P. [Cornell Univ. Medical College, New York, NY (United States); Tanzi, R.E. [Massachusetts General Hospital, Boston, MA (United States)

    1994-07-01

    Previous studies have indicated that the cDNA for the E2k component of the human {alpha}-ketoglutarate dehydrogenase complex (KGDHC) hybridized not only to a major locus on chromosome 14q24.3 in a region associated with familial Alzheimer`s disease and with Joseph-Machado disease, but also to another locus on chromosome 1p31. The authors now report that PCR of genomic DNA and direct sequencing indicated that the chromosome 1 locus is an intronless pseudogene. PCR of genomic DNA amplified E2k fragments from mouse-human cell hybrids containing human chromosome 1 DNA but not from hybrids containing human chromosome 14 DNA. The resulting amplicons were of comparable sizes to those when the cDNA was used to template. The direct sequencing of these amplicons confirmed the lack of introns and indicated a frame shift, which led to the presence of four termination codons early in the coding region. PCR followed by direct sequencing of the amplicons appears to be a convenient method for identifying intronless pseudogenes.

  6. Comparison of direct boiling method with commercial kits for extracting fecal microbiome DNA by Illumina sequencing of 16S rRNA tags.

    Science.gov (United States)

    Peng, Xin; Yu, Ke-Qiang; Deng, Guan-Hua; Jiang, Yun-Xia; Wang, Yu; Zhang, Guo-Xia; Zhou, Hong-Wei

    2013-12-01

    Low cost and high throughput capacity are major advantages of using next generation sequencing (NGS) techniques to determine metagenomic 16S rRNA tag sequences. These methods have significantly changed our view of microorganisms in the fields of human health and environmental science. However, DNA extraction using commercial kits has shortcomings of high cost and time constraint. In the present study, we evaluated the determination of fecal microbiomes using a direct boiling method compared with 5 different commercial extraction methods, e.g., Qiagen and MO BIO kits. Principal coordinate analysis (PCoA) using UniFrac distances and clustering showed that direct boiling of a wide range of feces concentrations gave a similar pattern of bacterial communities as those obtained from most of the commercial kits, with the exception of the MO BIO method. Fecal concentration by boiling method affected the estimation of α-diversity indices, otherwise results were generally comparable between boiling and commercial methods. The operational taxonomic units (OTUs) determined through direct boiling showed highly consistent frequencies with those determined through most of the commercial methods. Even those for the MO BIO kit were also obtained by the direct boiling method with high confidence. The present study suggested that direct boiling could be used to determine the fecal microbiome and using this method would significantly reduce the cost and improve the efficiency of the sample preparation for studying gut microbiome diversity. © 2013 Elsevier B.V. All rights reserved.

  7. Sequence assembly

    DEFF Research Database (Denmark)

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

    2009-01-01

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

  8. A direct comparison of MELCOR 1.8.3 and MAAP4 results for several PWR ampersand BWR accident sequences

    International Nuclear Information System (INIS)

    Leonard, M.T.; Ashbaugh, S.G.; Cole, R.K.; Bergeron, K.D.; Nagashima, K.

    1996-01-01

    This paper presents a comparison of calculations of severe accident progression for several postulated accident sequences for representative Pressurized Water Reactors (PWR) and Boiling Water Reactors (BWR) nuclear power plants performed with the MELCOR 1.8.3 and the MAAP4 computer codes. The PWR system examined in this study is a 1100 MWe system similar in design to a Westinghouse 3-loop plant with a large dry containment; the BWR is a 1100 MWe system similar in design to General Electric BWR/4 with a Mark I containment. A total of nine accident sequences were studied with both codes. Results of these calculations are compared to identify major differences in the timing of key events in the calculated accident progression or other important aspects of severe accident behavior, and to identify specific sources of the observed differences

  9. Microbial profiling of cpn60 universal target sequences in artificial mixtures of vaginal bacteria sampled by nylon swabs or self-sampling devices under different storage conditions.

    Science.gov (United States)

    Schellenberg, John J; Oh, Angela Yena; Hill, Janet E

    2017-05-01

    The vaginal microbiome is increasingly characterized by deep sequencing of universal genes. However, there are relatively few studies of how different specimen collection and sample storage and processing influence these molecular profiles. Here, we evaluate molecular microbial community profiles of samples collected using the HerSwab™ self-sampling device, compared to nylon swabs and under different storage conditions. In order to minimize technical variation, mixtures of 11 common vaginal bacteria in simulated vaginal fluid medium were sampled and DNA extracts prepared for massively parallel sequencing of the cpn60 universal target (UT). Three artificial mixtures imitating commonly observed vaginal microbiome profiles were easily distinguished and proportion of sequence reads correlated with the estimated proportion of the organism added to the artificial mixtures. Our results indicate that cpn60 UT amplicon sequencing quantifies the proportional abundance of member organisms in these artificial communities regardless of swab type or storage conditions, although some significant differences were observed between samples that were stored frozen and thawed prior to DNA extraction, compared to extractions from samples stored at room temperature for up to 7days. Our results indicate that an on-the-market device developed for infectious disease diagnostics may be appropriate for vaginal microbiome profiling, an approach that is increasingly facilitated by rapidly dropping deep sequencing costs. Copyright © 2017 Elsevier B.V. All rights reserved.

  10. Metallogenic geologic conditions and prospecting direction of sandstone type uranium mineralizations in Yili basin of Xinjiang

    International Nuclear Information System (INIS)

    Chen Daisheng; Wang Ruiying; Li Shengxiang; Zhang Kefang

    1994-09-01

    Yili basin is a Mesozoic down-warped basin superimposed on the late Paleozoic volcanic taphrogenic basin. Uranium mineralizations are hosted in the Middle-Lower Jurassic coal-bearing series. The depositions environment in the basin is turbulent in the east and relatively stable in the west. It is characterized by coarse-grained sequence with thin thickness in the eastern part and fine-grained with thick thickness in the western part. On the analytical basis of sedimentary facies indices, it is the first time to present a sedimentary model of 'alluvial fan-braided stream-(narrow) lakeshore delta-lacustrine facies and marsh facies' for the coal-bearing series. The authors have summarized the basic geologic features of U-mineralizations in the interlayer oxidation zone, analyzed the difference and cause of U-mineralizations between the south and north, as well as the east and west. The genetic mechanism of U-mineralizations in the basin is discussed. Finally, seven items of geologic prerequisites for the formation of in-situ leachable sandstone type uranium deposits have been suggested and the potential of sandstone type U-mineralizations in the basin has been evaluated. Four promising target areas are selected

  11. Enactment versus observation: item-specific and relational processing in goal-directed action sequences (and lists of single actions.

    Directory of Open Access Journals (Sweden)

    Janette Schult

    Full Text Available What are the memory-related consequences of learning actions (such as "apply the patch" by enactment during study, as compared to action observation? Theories converge in postulating that enactment encoding increases item-specific processing, but not the processing of relational information. Typically, in the laboratory enactment encoding is studied for lists of unrelated single actions in which one action execution has no overarching purpose or relation with other actions. In contrast, real-life actions are usually carried out with the intention to achieve such a purpose. When actions are embedded in action sequences, relational information provides efficient retrieval cues. We contrasted memory for single actions with memory for action sequences in three experiments. We found more reliance on relational processing for action-sequences than single actions. To what degree can this relational information be used after enactment versus after the observation of an actor? We found indicators of superior relational processing after observation than enactment in ordered pair recall (Experiment 1A and in emerging subjective organization of repeated recall protocols (recall runs 2-3, Experiment 2. An indicator of superior item-specific processing after enactment compared to observation was recognition (Experiment 1B, Experiment 2. Similar net recall suggests that observation can be as good a learning strategy as enactment. We discuss possible reasons why these findings only partly converge with previous research and theorizing.

  12. Studies of the Influence of Beam Profile and Cooling Conditions on the Laser Deposition of a Directionally-Solidified Superalloy

    Directory of Open Access Journals (Sweden)

    Shuo Yang

    2018-02-01

    Full Text Available In the laser deposition of single crystal and directionally-solidified superalloys, it is desired to form laser deposits with high volume fractions of columnar grains by suppressing the columnar-to-equiaxed transition efficiently. In this paper, the influence of beam profile (circular and square shapes and cooling conditions (natural cooling and forced cooling on the geometric morphology and microstructure of deposits were experimentally studied in the laser deposition of a directionally-solidified superalloy, IC10, and the mechanisms of influence were revealed through a numerical simulation of the thermal processes during laser deposition. The results show that wider and thinner deposits were obtained with the square laser beam than those with the circular laser beam, regardless of whether natural or forced cooling conditions was used. The heights and contact angles of deposits were notably increased due to the reduced substrate temperatures by the application of forced cooling for both laser beam profiles. Under natural cooling conditions, columnar grains formed epitaxially at both the center and the edges of the deposits with the square laser beam, but only at the center of the deposits with the circular laser beam; under forced cooling conditions, columnar grains formed at both the center and the edges of deposits regardless of the laser beam profile. The high ratios of thermal gradient and solidification velocity in the height direction of the deposits were favorable to forming deposits with higher volume fractions of columnar grains.

  13. Direct measurement of time dependent diffusion for Ag and Au under ambient conditions

    Energy Technology Data Exchange (ETDEWEB)

    Yoo, Pil Sun; Jo, Han Yeol; Kim, Tae Kyeong [Hankuk University of Foreign Studies, Yongin (Korea, Republic of)

    2014-12-15

    Time-dependent diffusion for Ag and Au metal atoms was measured using the scanning tunneling microscope break-junction technique in ambient conditions. We observed that Ag contacts do not form long single-atomic chains compared to Au contacts during the elongation of each metal electrode, and Ag atoms diffuse more quickly than Au atoms after metal contact rupture. This is consistent with previous results of molecular dynamic simulations. Further, we found a correlation between diffusion length and the evolution time on an atomic scale to reveal the time-dependent diffusion for Ag and Au metal atoms.

  14. Temporal sequencing of nicotine dependence and bipolar disorder in the national epidemiologic survey on alcohol and related conditions (NESARC)

    Science.gov (United States)

    Martínez-Ortega, José M.; Goldstein, Benjamin I.; Gutiérrez-Rojas, Luis; Sala, Regina; Wang, Shuai; Blanco, Carlos

    2013-01-01

    Bipolar disorder (BD) and nicotine dependence (ND) often co-occur. However, the mechanisms underlying this association remain unclear. We aimed to examine, for the first time in a national and representative sample, the magnitude and direction of the temporal relationship between BD and ND; and to compare, among individuals with lifetime ND and BD, the sociodemographic and clinical characteristics of individuals whose onset of ND preceded the onset of BD (ND-prior) with those whose onset of ND followed the onset of BD (BD-prior). The sample included individuals with lifetime BD type I or ND (n=7958) from the National Epidemiologic Survey on Alcohol and Related Conditions (NESARC, n=43093). Survival analyses and logistic regression models were computed to study the temporal association between ND and BD, and to compare ND-prior (n=135) and BD-prior (n=386) individuals. We found that ND predicted the onset of BD and BD also predicted the onset of ND. Furthermore, the risk of developing one disorder following the other one was greatest early in the course of illness. Most individuals with lifetime ND and BD were BD-prior (72.6%). BD-prior individuals had an earlier onset of BD and a higher number of manic episodes. By contrast, ND-prior individuals had an earlier onset of both daily smoking and ND, and an increased prevalence of alcohol use disorder. In conclusion, ND and BD predict the development of each other. The phenomenology and course of ND and BD varied significantly depending on which disorder had earlier onset. PMID:23582710

  15. Treatability studies with granular activated carbon (GAC) and sequencing batch reactor (SBR) system for textile wastewater containing direct dyes

    International Nuclear Information System (INIS)

    Sirianuntapiboon, Suntud; Sansak, Jutarat

    2008-01-01

    The GAC-SBR efficiency was decreased with the increase of dyestuff concentration or the decrease of bio-sludge concentration. The system showed the highest removal efficiency with synthetic textile wastewater (STWW) containing 40 mg/L direct red 23 or direct blue 201 under MLSS of 3000 mg/L and hydraulic retention time (HRT) of 7.5 days. But, the effluent NO 3 - was higher than that of the influent. Direct red 23 was more effective than direct blue 201 to repress the GAC-SBR system efficiency. The dyes removal efficiency of the system with STWW containing direct red 23 was reduced by 30% with the increase of direct red 23 from 40 mg/L to 160 mg/L. The system with raw textile wastewater (TWW) showed quite low BOD 5 TKN and dye removal efficiencies of only 64.7 ± 4.9% and 50.2 ± 6.9%, respectively. But its' efficiencies could be increased by adding carbon sources (BOD 5 ). The dye removal efficiency with TWW was increased by 30% and 20% by adding glucose (TWW + glucose) or Thai rice noodle wastewater (TWW + TRNWW), respectively. SRT of the systems were 28 ± 1 days and 31 ± 2 days with TWW + glucose and TWW + TRNWW, respectively

  16. Treatability studies with granular activated carbon (GAC) and sequencing batch reactor (SBR) system for textile wastewater containing direct dyes

    Energy Technology Data Exchange (ETDEWEB)

    Sirianuntapiboon, Suntud [Department of Environmental Technology, School of Energy Environment and Materials, King Mongkut' s University of Technology, Thonburi, Bangmod, Thung-kru, Bangkok 10140 (Thailand)], E-mail: suntud.sir@kmutt.ac.th; Sansak, Jutarat [Department of Environmental Technology, School of Energy Environment and Materials, King Mongkut' s University of Technology, Thonburi, Bangmod, Thung-kru, Bangkok 10140 (Thailand)

    2008-11-30

    The GAC-SBR efficiency was decreased with the increase of dyestuff concentration or the decrease of bio-sludge concentration. The system showed the highest removal efficiency with synthetic textile wastewater (STWW) containing 40 mg/L direct red 23 or direct blue 201 under MLSS of 3000 mg/L and hydraulic retention time (HRT) of 7.5 days. But, the effluent NO{sub 3}{sup -} was higher than that of the influent. Direct red 23 was more effective than direct blue 201 to repress the GAC-SBR system efficiency. The dyes removal efficiency of the system with STWW containing direct red 23 was reduced by 30% with the increase of direct red 23 from 40 mg/L to 160 mg/L. The system with raw textile wastewater (TWW) showed quite low BOD{sub 5} TKN and dye removal efficiencies of only 64.7 {+-} 4.9% and 50.2 {+-} 6.9%, respectively. But its' efficiencies could be increased by adding carbon sources (BOD{sub 5}). The dye removal efficiency with TWW was increased by 30% and 20% by adding glucose (TWW + glucose) or Thai rice noodle wastewater (TWW + TRNWW), respectively. SRT of the systems were 28 {+-} 1 days and 31 {+-} 2 days with TWW + glucose and TWW + TRNWW, respectively.

  17. Treatability studies with granular activated carbon (GAC) and sequencing batch reactor (SBR) system for textile wastewater containing direct dyes.

    Science.gov (United States)

    Sirianuntapiboon, Suntud; Sansak, Jutarat

    2008-11-30

    The GAC-SBR efficiency was decreased with the increase of dyestuff concentration or the decrease of bio-sludge concentration. The system showed the highest removal efficiency with synthetic textile wastewater (STWW) containing 40 mg/L direct red 23 or direct blue 201 under MLSS of 3,000 mg/L and hydraulic retention time (HRT) of 7.5 days. But, the effluent NO(3)(-) was higher than that of the influent. Direct red 23 was more effective than direct blue 201 to repress the GAC-SBR system efficiency. The dyes removal efficiency of the system with STWW containing direct red 23 was reduced by 30% with the increase of direct red 23 from 40 mg/L to 160 mg/L. The system with raw textile wastewater (TWW) showed quite low BOD(5) TKN and dye removal efficiencies of only 64.7+/-4.9% and 50.2+/-6.9%, respectively. But its' efficiencies could be increased by adding carbon sources (BOD(5)). The dye removal efficiency with TWW was increased by 30% and 20% by adding glucose (TWW+glucose) or Thai rice noodle wastewater (TWW+TRNWW), respectively. SRT of the systems were 28+/-1 days and 31+/-2 days with TWW+glucose and TWW+TRNWW, respectively.

  18. Direct approach for the fluctuation-dissipation theorem under nonequilibrium steady-state conditions

    Science.gov (United States)

    Komori, Kentaro; Enomoto, Yutaro; Takeda, Hiroki; Michimura, Yuta; Somiya, Kentaro; Ando, Masaki; Ballmer, Stefan W.

    2018-05-01

    The test mass suspensions of cryogenic gravitational-wave detectors such as the KAGRA project are tasked with extracting the heat deposited on the optics. These suspensions have a nonuniform temperature, requiring the calculation of thermal noise in nonequilibrium conditions. While it is not possible to describe the whole suspension system with one temperature, the local temperature at every point in the system is still well defined. We therefore generalize the application of the fluctuation-dissipation theorem to mechanical systems, pioneered by Saulson and Levin, to nonequilibrium conditions in which a temperature can only be defined locally. The result is intuitive in the sense that the thermal noise in the observed degree of freedom is given by averaging the temperature field, weighted by the dissipation density associated with that particular degree of freedom. After proving this theorem, we apply the result to examples of increasing complexity: a simple spring, the bending of a pendulum suspension fiber, and a model of the KAGRA cryogenic suspension. We conclude by outlining the application to nonequilibrium thermoelastic noise.

  19. The Solanum commersonii Genome Sequence Provides Insights into Adaptation to Stress Conditions and Genome Evolution of Wild Potato Relatives

    Science.gov (United States)

    Aversano, Riccardo; Contaldi, Felice; Ercolano, Maria Raffaella; Grosso, Valentina; Iorizzo, Massimo; Tatino, Filippo; Xumerle, Luciano; Dal Molin, Alessandra; Avanzato, Carla; Ferrarini, Alberto; Delledonne, Massimo; Sanseverino, Walter; Cigliano, Riccardo Aiese; Capella-Gutierrez, Salvador; Gabaldón, Toni; Frusciante, Luigi; Bradeen, James M.; Carputo, Domenico

    2015-01-01

    Here, we report the draft genome sequence of Solanum commersonii, which consists of ∼830 megabases with an N50 of 44,303 bp anchored to 12 chromosomes, using the potato (Solanum tuberosum) genome sequence as a reference. Compared with potato, S. commersonii shows a striking reduction in heterozygosity (1.5% versus 53 to 59%), and differences in genome sizes were mainly due to variations in intergenic sequence length. Gene annotation by ab initio prediction supported by RNA-seq data produced a catalog of 1703 predicted microRNAs, 18,882 long noncoding RNAs of which 20% are shown to target cold-responsive genes, and 39,290 protein-coding genes with a significant repertoire of nonredundant nucleotide binding site-encoding genes and 126 cold-related genes that are lacking in S. tuberosum. Phylogenetic analyses indicate that domesticated potato and S. commersonii lineages diverged ∼2.3 million years ago. Three duplication periods corresponding to genome enrichment for particular gene families related to response to salt stress, water transport, growth, and defense response were discovered. The draft genome sequence of S. commersonii substantially increases our understanding of the domesticated germplasm, facilitating translation of acquired knowledge into advances in crop stability in light of global climate and environmental changes. PMID:25873387

  20. Recent studies of transplutonium compounds: new directions and use of extreme conditions

    International Nuclear Information System (INIS)

    Peterson, J.R.; Begun, G.M.; Gibson, J.K.

    1987-01-01

    The number of bulk-phase compounds prepared and characterized for each of the transplutonium (TPu) elements drops off precipitously with increasing atomic number. However, efforts have been made to increase the number of TPu compounds known and also the range of investigative methods applied to their characterization. The results of a worldwide survey to determine the status of the preparation of new TPu compounds and/or the application of new investigative techniques to the study of such compounds in bulk will be presented. The focus will then shift to Oak Ridge projects: extreme conditions of pressure and/or temperature are being used for synthesis and for absorption and raman spectral studies; single crystals of trihalides are being grown for spectral and magnetic studies; new ternary chalcogenide-halide compounds are being characterized; vaporization thermodynamics of TPu compounds are being determined; and attempts to stabilize unusual oxidation states are being carried out

  1. A simple, flexible and efficient PCR-fusion/Gateway cloning procedure for gene fusion, site-directed mutagenesis, short sequence insertion and domain deletions and swaps

    Directory of Open Access Journals (Sweden)

    Etchells J Peter

    2009-10-01

    Full Text Available Abstract Background The progress and completion of various plant genome sequencing projects has paved the way for diverse functional genomic studies that involve cloning, modification and subsequent expression of target genes. This requires flexible and efficient procedures for generating binary vectors containing: gene fusions, variants from site-directed mutagenesis, addition of protein tags together with domain swaps and deletions. Furthermore, efficient cloning procedures, ideally high throughput, are essential for pyramiding of multiple gene constructs. Results Here, we present a simple, flexible and efficient PCR-fusion/Gateway cloning procedure for construction of binary vectors for a range of gene fusions or variants with single or multiple nucleotide substitutions, short sequence insertions, domain deletions and swaps. Results from selected applications of the procedure which include ORF fusion, introduction of Cys>Ser mutations, insertion of StrepII tag sequence and domain swaps for Arabidopsis secondary cell wall AtCesA genes are demonstrated. Conclusion The PCR-fusion/Gateway cloning procedure described provides an elegant, simple and efficient solution for a wide range of diverse and complicated cloning tasks. Through streamlined cloning of sets of gene fusions and modification variants into binary vectors for systematic functional studies of gene families, our method allows for efficient utilization of the growing sequence and expression data.

  2. BrAD-seq: Breath Adapter Directional sequencing: a streamlined, ultra-simple and fast library preparation protocol for strand specific mRNA library construction.

    Directory of Open Access Journals (Sweden)

    Brad Thomas Townsley

    2015-05-01

    Full Text Available Next Generation Sequencing (NGS is driving rapid advancement in biological understanding and RNA-sequencing (RNA-seq has become an indispensable tool for biology and medicine. There is a growing need for access to these technologies although preparation of NGS libraries remains a bottleneck to wider adoption. Here we report a novel method for the production of strand specific RNA-seq libraries utilizing inherent properties of double-stranded cDNA to capture and incorporate a sequencing adapter. Breath Adapter Directional sequencing (BrAD-seq reduces sample handling and requires far fewer enzymatic steps than most available methods to produce high quality strand-specific RNA-seq libraries. The method we present is optimized for 3-prime Digital Gene Expression (DGE libraries and can easily extend to full transcript coverage shotgun (SHO type strand-specific libraries and is modularized to accommodate a diversity of RNA and DNA input materials. BrAD-seq offers a highly streamlined and inexpensive option for RNA-seq libraries.

  3. Biodiesel production from Spirulina microalgae feedstock using direct transesterification near supercritical methanol condition.

    Science.gov (United States)

    Mohamadzadeh Shirazi, Hamed; Karimi-Sabet, Javad; Ghotbi, Cyrus

    2017-09-01

    Microalgae as a candidate for production of biodiesel, possesses a hard cell wall that prevents intracellular lipids leaving out from the cells. Direct or in situ supercritical transesterification has the potential for destruction of microalgae hard cell wall and conversion of extracted lipids to biodiesel that consequently reduces the total energy consumption. Response surface methodology combined with central composite design was applied to investigate process parameters including: Temperature, Time, Methanol-to-dry algae, Hexane-to-dry algae, and Moisture content. Thirty-two experiments were designed and performed in a batch reactor, and biodiesel efficiency between 0.44% and 99.32% was obtained. According to fatty acid methyl ester yields, a quadratic experimental model was adjusted and the significance of parameters was evaluated using analysis of variance (ANOVA). Effects of single and interaction parameters were also interpreted. In addition, the effect of supercritical process on the ultrastructure of microalgae cell wall using scanning electron spectrometry (SEM) was surveyed. Copyright © 2017 Elsevier Ltd. All rights reserved.

  4. Plausible Roles for RAGE in Conditions Exacerbated by Direct and Indirect (Secondhand) Smoke Exposure.

    Science.gov (United States)

    Lewis, Joshua B; Hirschi, Kelsey M; Arroyo, Juan A; Bikman, Benjamin T; Kooyman, David L; Reynolds, Paul R

    2017-03-17

    Approximately 1 billion people smoke worldwide, and the burden placed on society by primary and secondhand smokers is expected to increase. Smoking is the leading risk factor for myriad health complications stemming from diverse pathogenic programs. First- and second-hand cigarette smoke contains thousands of constituents, including several carcinogens and cytotoxic chemicals that orchestrate chronic inflammatory responses and destructive remodeling events. In the current review, we outline details related to compromised pulmonary and systemic conditions related to smoke exposure. Specifically, data are discussed relative to impaired lung physiology, cancer mechanisms, maternal-fetal complications, cardiometabolic, and joint disorders in the context of smoke exposure exacerbations. As a general unifying mechanism, the receptor for advanced glycation end-products (RAGE) and its signaling axis is increasingly considered central to smoke-related pathogenesis. RAGE is a multi-ligand cell surface receptor whose expression increases following cigarette smoke exposure. RAGE signaling participates in the underpinning of inflammatory mechanisms mediated by requisite cytokines, chemokines, and remodeling enzymes. Understanding the biological contributions of RAGE during cigarette smoke-induced inflammation may provide critically important insight into the pathology of lung disease and systemic complications that combine during the demise of those exposed.

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

    Science.gov (United States)

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

    2005-01-01

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

  6. A domain-decomposition method to implement electrostatic free boundary conditions in the radial direction for electric discharges

    Science.gov (United States)

    Malagón-Romero, A.; Luque, A.

    2018-04-01

    At high pressure electric discharges typically grow as thin, elongated filaments. In a numerical simulation this large aspect ratio should ideally translate into a narrow, cylindrical computational domain that envelops the discharge as closely as possible. However, the development of the discharge is driven by electrostatic interactions and, if the computational domain is not wide enough, the boundary conditions imposed to the electrostatic potential on the external boundary have a strong effect on the discharge. Most numerical codes circumvent this problem by either using a wide computational domain or by calculating the boundary conditions by integrating the Green's function of an infinite domain. Here we describe an accurate and efficient method to impose free boundary conditions in the radial direction for an elongated electric discharge. To facilitate the use of our method we provide a sample implementation. Finally, we apply the method to solve Poisson's equation in cylindrical coordinates with free boundary conditions in both radial and longitudinal directions. This case is of particular interest for the initial stages of discharges in long gaps or natural discharges in the atmosphere, where it is not practical to extend the simulation volume to be bounded by two electrodes.

  7. Investigation on the asymmetry of thermal condition and grain defect formation in the customary directional solidification process

    International Nuclear Information System (INIS)

    Ma, D; Wu, Q; Hollad, S; Bührig-Polaczek, A

    2012-01-01

    In the present study, the non-uniformity of the thermal condition and the corresponding grain defect formation in the customary Bridgman process were investigated. The casting clusters in radial alignment were directionally solidified in a Bridgman furnace. It was found that in the casting cluster, the shadow side facing the central rod was ineffectively heated in the hot zone and ineffectively cooled in the cooling zone during withdrawal, compared with the heater side facing the furnace heater. The metallographic examination of the simplified turbine blades exhibited that the platforms on the shadow side are very prone to stray grain formation, while the heater side reveals a markedly lower tendency for that. The asymmetric thermal condition causes the asymmetrical formation of these grain defects. This non-uniformity of the thermal condition should be minimized as far as possible, in order to effectively optimize the quality of the SC superalloy components.

  8. “Jump Start and Gain” Model for Dosage Compensation in Drosophila Based on Direct Sequencing of Nascent Transcripts

    Directory of Open Access Journals (Sweden)

    Francesco Ferrari

    2013-11-01

    Full Text Available Dosage compensation in Drosophila is mediated by the MSL complex, which increases male X-linked gene expression approximately 2-fold. The MSL complex preferentially binds the bodies of active genes on the male X, depositing H4K16ac with a 3′ bias. Two models have been proposed for the influence of the MSL complex on transcription: one based on promoter recruitment of RNA polymerase II (Pol II, and a second featuring enhanced transcriptional elongation. Here, we utilize nascent RNA sequencing to document dosage compensation during transcriptional elongation. We also compare X and autosomes from published data on paused and elongating polymerase in order to assess the role of Pol II recruitment. Our results support a model for differentially regulated elongation, starting with release from 5′ pausing and increasing through X-linked gene bodies. Our results highlight facilitated transcriptional elongation as a key mechanism for the coordinated regulation of a diverse set of genes.

  9. Present condition of uranium exploration and the prospecting direction in southwest China

    International Nuclear Information System (INIS)

    Ni Shijun; Zhang Chengjiang; Xu Zhengqi; Chen Youliang

    2012-01-01

    Southwest China is one of the important areas where uranium is distributed. After exploration and research of 50 years, the metallogenic conditions for uranium deposits in Southwest China have been studied more deeply. It is found that uranium ore in Southwest China has more complete types, less deposits and more mineral occurrences, and the amount of uranium resources is disproportionate to the area of Southwest China. Researches of years show that Southwest China is characterized by thick crust. thick sedimentary cover, weak crust-mantle interaction, weak deep flu id activity in shallow strata, strong dynamic formation in shallow strata and obvious deep geologic process on block mar- gins. In this paper, the control of deep geologic process and evolution in uranium metallogenesis in Southwest China is studied by employing new theories and thoughts on the fundamental concept that deep geologic process and evolution has important control on super-large scale deposits. The study focuses on the crust-mantle structure and evolution with uranium metallogenesis, structural and magmatic activity and deep fluid activity with uranium metallogenesis, and ore-con- trolling role of penetrating faults on block edges and inside the blocks. To offer theoretic basis for large-scale uranium deposit prospecting in Southwest China, the key research on uranium deposit in Southwest China in future should be on the deep geologic evolution and uranium metallogenesis in Western Qinling Region, the uranium metallogenesis of iron oxide copper gold deposits on Kangdian axis, the uranium metallogenesis in Yunnan-Guizhou contiguous area, the hydrothermal uranium metallogenesis in Eastern Tibet and Western Sichuan, and the connection between sandstone type uranium deposit and magmatic activity. Meanwhile, the above regions are also the key ones for uranium deposit prospecting in Southwest China in a rather long period in future. (authors)

  10. Improved annotation of 3' untranslated regions and complex loci by combination of strand-specific direct RNA sequencing, RNA-Seq and ESTs.

    Directory of Open Access Journals (Sweden)

    Nicholas J Schurch

    Full Text Available The reference annotations made for a genome sequence provide the framework for all subsequent analyses of the genome. Correct and complete annotation in addition to the underlying genomic sequence is particularly important when interpreting the results of RNA-seq experiments where short sequence reads are mapped against the genome and assigned to genes according to the annotation. Inconsistencies in annotations between the reference and the experimental system can lead to incorrect interpretation of the effect on RNA expression of an experimental treatment or mutation in the system under study. Until recently, the genome-wide annotation of 3' untranslated regions received less attention than coding regions and the delineation of intron/exon boundaries. In this paper, data produced for samples in Human, Chicken and A. thaliana by the novel single-molecule, strand-specific, Direct RNA Sequencing technology from Helicos Biosciences which locates 3' polyadenylation sites to within +/- 2 nt, were combined with archival EST and RNA-Seq data. Nine examples are illustrated where this combination of data allowed: (1 gene and 3' UTR re-annotation (including extension of one 3' UTR by 5.9 kb; (2 disentangling of gene expression in complex regions; (3 clearer interpretation of small RNA expression and (4 identification of novel genes. While the specific examples displayed here may become obsolete as genome sequences and their annotations are refined, the principles laid out in this paper will be of general use both to those annotating genomes and those seeking to interpret existing publically available annotations in the context of their own experimental data.

  11. Protective functions of credit unions in conditions of getting over the sequences of financial crisis in Ukraine

    OpenAIRE

    Duka, A.

    2009-01-01

    The theoretical and organizational bases of development of the credit unions is analyzed. The directions of activization of their development in Ukraine for reduction of crisis' influence are formulated

  12. Some properties of a granular activated carbon-sequencing batch reactor (GAC-SBR) system for treatment of textile wastewater containing direct dyes.

    Science.gov (United States)

    Sirianuntapiboon, Suntud; Sadahiro, Ohmomo; Salee, Paneeta

    2007-10-01

    Resting (living) bio-sludge from a domestic wastewater treatment plant was used as an adsorbent of both direct dyes and organic matter in a sequencing batch reactor (SBR) system. The dye adsorption capacity of the bio-sludge was not increased by acclimatization with direct dyes. The adsorption of Direct Red 23 and Direct Blue 201 onto the bio-sludge was almost the same. The resting bio-sludge showed higher adsorption capacity than the autoclaved bio-sludge. The resting bio-sludge that was acclimatized with synthetic textile wastewater (STWW) without direct dyes showed the highest Direct Blue 201, COD, and BOD(5) removal capacities of 16.1+/-0.4, 453+/-7, and 293+/-9 mg/g of bio-sludge, respectively. After reuse, the dye adsorption ability of deteriorated bio-sludge was recovered by washing with 0.1% sodium dodecyl sulfate (SDS) solution. The direct dyes in the STWW were also easily removed by a GAC-SBR system. The dye removal efficiencies were higher than 80%, even when the system was operated under a high organic loading of 0.36kgBOD(5)/m(3)-d. The GAC-SBR system, however, showed a low direct dye removal efficiency of only 57+/-2.1% with raw textile wastewater (TWW) even though the system was operated with an organic loading of only 0.083kgBOD(5)/m(3)-d. The dyes, COD, BOD(5), and total kjeldalh nitrogen removal efficiencies increased up to 76.0+/-2.8%, 86.2+/-0.5%, 84.2+/-0.7%, and 68.2+/-2.1%, respectively, when 0.89 g/L glucose (organic loading of 0.17kgBOD(5)/m(3)-d) was supplemented into the TWW.

  13. Did you say reference conditions? Ecological and socio-economic perspectives on the European Water Framework Directive

    International Nuclear Information System (INIS)

    Bouleau, Gabrielle; Pont, Didier

    2015-01-01

    Highlights: • Reference conditions refer to a stable state, ignoring non-linear and chaotic changes. • References were needed to set legally binding standards. • The DPSIR framework is based on a mitigation logic, which implies a stable reference. • Human activities do not equate pressures; Humans can create landscapes and ecosystems. • Setting goals for restoration requires a more adaptive management. - Abstract: Reference conditions are a key concept in the European Water Framework Directive (WFD). The WFD stipulates that the ecological status of a given water body shall be assessed by quantifying the deviation from a set of reference conditions that represent the stable state of an ecosystem in the absence of significant human disturbance. This concept is subject to criticism from several authors, particularly because underlying ecological concepts are weak and the distinction between natural variability and the effects of anthropogenic activities on ecosystem function will become increasingly artificial. In this paper, a sociologist and an aquatic ecologist examine the origin, successes and limits of the reference conditions concept and raise important questions about applying this concept in practice. We argue that this concept fitted specific needs from different institutions and stakeholders which promoted the WFD. Monitoring practices using this concept require some adaptations. Setting goals for restoration based on reference conditions is more problematic. A more adaptive management approach would be wiser

  14. Pyrroloindolone synthesis via a Cp*Co(III)-catalyzed redox-neutral directed C-H alkenylation/annulation sequence.

    Science.gov (United States)

    Ikemoto, Hideya; Yoshino, Tatsuhiko; Sakata, Ken; Matsunaga, Shigeki; Kanai, Motomu

    2014-04-09

    A unique synthetic utility of a Cp*Co(III) catalyst in comparison with related Cp*Rh(III) catalysts is described. A C2-selective indole alkenylation/annulation sequence proceeded smoothly with catalytic amount of a [Cp*Co(III)(C6H6)](PF6)2 complex and KOAc. Intramolecular addition of an alkenyl-Cp*Co species to a carbamoyl moiety gave pyrroloindolones in 58-89% yield in one pot. Clear difference was observed between the catalytic activity of the Cp*Co(III) complex and those of Cp*Rh(III) complexes, highlighting the unique nucleophilic activity of the organocobalt species. The Cp*Co(III) catalysis was also suitable for simple alkenylation process of N-carbamoyl indoles, and broad range of alkynes, including terminal alkynes, were applicable to give C2-alkenylated indoles in 50-99% yield. Mechanistic studies on C-H activation step under Cp*Co(III) catalysis with the aid of an acetate unit as well as evaluation of the difference between organo-Co(III) species and organo-Rh(III) species are also described.

  15. Integral Plus Resonant Sliding Mode Direct Power Control for VSC-HVDC Systems under Unbalanced Grid Voltage Conditions

    Directory of Open Access Journals (Sweden)

    Weipeng Yang

    2017-10-01

    Full Text Available An integral plus resonant sliding mode direct power control (IRSMC DPC strategy for voltage source converter high voltage direct current (VSC-HVDC systems under unbalanced grid voltage conditions is proposed in this paper. Through detailed instantaneous power flow analysis, a generalized power compensation method, by which the ratio between the amplitude of active and reactive power ripples can be controlled continuously, is obtained. This enables the system to provide flexible power control, so that the desired performance of the system on both the ac and dc sides can be attained under different operating conditions. When the grid voltage is unbalanced, one or both of the active and reactive power terms contain ripples, oscillating at twice the grid frequency, to obtain non-distorted ac current. A power controller consisting of the proportional, integral and resonant control laws is designed using the sliding mode control approach, to achieve accurate power control objective. Simulation studies on a two-terminal VSC-HVDC system using MATLAB/SIMULINK (R2013b, Mathworks, Natick, MA, USA are conducted to verify the effectiveness of the IRSMC DPC strategy. The results show that this strategy ensures satisfactory performance of the system over a wide range of operating conditions.

  16. A case report of aphallia with urorectal septum malformation sequence in a newborn: a very rarely seen condition

    Directory of Open Access Journals (Sweden)

    Sharma D

    2015-12-01

    Full Text Available Deepak Sharma,1 Ravinder Singh,2 Sweta Shastri3 1Department of Neonatology, Fernandez Hospital, Hyderabad, 2Department of Pediatrics, Civil Hospital, Hisar, Haryana, 3Department of Pathology, NKP Salve Medical College, Nagpur, Maharashtra, India Abstract: Aphallia (absence of penis is an extremely rare abnormality which has rarely been described in medical literature and can be part of the urorectal septum malformation sequence (URSMS. URSMS has hardly been reported in medical literature and includes the absence of perineal and anal openings in association with ambiguous genitalia and urogenital, colonic, and lumbosacral anomalies. This case report tells the importance of detailed examination of infants that are diagnosed with aphallia. We report a case of a newborn who was diagnosed as aphallia with the URSMS syndrome after birth. The neonate had an endocardial cushion defect (atrial septal defect and ventricular septal defect and bilateral agenesis of the kidney. The neonate succumbed to death secondary to hypoplastic lung leading to respiratory failure. Keywords: aphallia, urorectal septum malformation sequence, cloacal membrane, hindgut development, congenital aphallia, anorectal malformation

  17. Temporal direct numerical simulation of transitional natural-convection boundary layer under conditions of considerable external turbulence effects

    International Nuclear Information System (INIS)

    Abramov, Alexey G; Smirnov, Evgueni M; Goryachev, Valery D

    2014-01-01

    Results of direct numerical simulations for time-developing air natural-convection boundary layer are presented. Computations have been performed assuming periodicity conditions in both the directions parallel to the vertical isothermal hot plate. The contribution is mainly focused on understanding of laminar–turbulent transition peculiarities in the case of perturbation action of external turbulence that is modeled by isotropic disturbances initially introduced into the computational domain. Special attention is paid to identification and analysis of evolving three-dimensional vortices that clearly manifest themselves through the whole stages of laminar–turbulent transition in the boundary layer. A comparison of computed profiles of mean velocity, mean temperature and fluctuation characteristics for turbulent regimes of convection with experimental data is performed as well. (paper)

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

    Directory of Open Access Journals (Sweden)

    Prakash Radhakrishnan

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

  19. Optimal conditions in direct dimethyl ether synthesis from syngas utilizing a dual-type fluidized bed reactor

    International Nuclear Information System (INIS)

    Yousefi, Ahmad; Eslamloueyan, Reza; Kazerooni, Nooshin Moradi

    2017-01-01

    Concerns over environmental pollution and ever-increasing energy demand have urged the global community to tap clean-burning fuels among which dimethyl ether is a promising candidate for contribution in the transportation sector. Direct dimethyl ether synthesis from syngas, in which methanol production and dehydration take place simultaneously, is arguably the preferred route for large scale production. In this study, direct dimethyl ether synthesis is proposed in an industrial dual-type fluidized bed reactor. This configuration involves two fluidized bed reactors operating in different conditions. In the first catalytic reactor (water-cooled reactor), the synthesis gas is partly converted to methanol after being preheated by the reaction heat in the second reactor (gas-cooled reactor). A two-phase generalized comprehensive reactor model, comprised of the flow in three different regimes is applied and a smooth transition between flow regimes is provided based on the probabilistic averaging approach. The optimal operating conditions are sought by employing differential evolution algorithm as a robust optimization strategy. The dimethyl ether mole fraction is considered as the objective function during the optimization. The results show considerable dimethyl ether enhancement by 16% and 14% compared to the conventional direct dimethyl ether synthesis reactor and dual-type fixed bed dimethyl ether reactor arrangements, respectively. - Highlights: • Dual-type catalytic fluidized bed reactors for dimethyl ether synthesis is studied. • A two-phase comprehensive model comprised of flow in three regimes is used. • Probabilistic averaging approach is applied for smooth transitions between regimes. • Differential evolution method is employed to determine optimal operating conditions. • Production capacity is remarkably enhanced compared to conventional reactor.

  20. Development of a method for calculating steady-state equipment sensible heat ratio of direct expansion air conditioning units

    International Nuclear Information System (INIS)

    Xia Liang; Chan, M.Y.; Deng Shiming

    2008-01-01

    A complete set of calculation method for steady-state equipment sensible heat ratio (SHR) for a direct expansion (DX) cooling coil has been developed and reported. The method was based on the fundamentals of energy conservation and heat and mass transfer taking place in the DX cooling coil, and was experimentally validated using an experimental DX A/C rig. With the method developed, the effect of refrigerant evaporating temperature at fixed inlet air conditions on equipment SHR has been theoretically analyzed. The validated method can be useful in further studying the inherent operating characteristics of a DX air conditioning (A/C) unit and in developing suitable control strategies for achieving higher energy efficiency and better indoor thermal environment

  1. UGT1A1 (TA)n genotyping in sickle-cell disease: high resolution melting (HRM) curve analysis or direct sequencing, what is the best way?

    Science.gov (United States)

    Thomas, Vincent; Mazard, Blandine; Garcia, Caroline; Lacan, Philippe; Gagnieu, Marie-Claude; Joly, Philippe

    2013-09-23

    Minucci et al. have proposed in 2010 a rapid, simple and cost-effective HRM method on the LightCycler 480® apparatus (Roche) for the determination of the 6/6, 6/7 and 7/7 genotypes of the (TA)n UGT1A1 promoter polymorphism. However, they have not studied the n=5 and n=8 alleles which can be quite frequent in sickle-cell disease patients. The aim of our study was to test this HRM protocol to all the 10 possible (TA)n UGT1A1 genotypes (i.e. 5/5, 5/6, 5/7, 5/8, 6/6, 6/7, 6/8, 7/7, 7/8 and 8/8) by using our SCD cohort of patients. All genotypes could be unambiguously identified except 6/7 and 6/8 which give a similar HRM profile. For those two genotypes, the differentiation necessitates either a direct Sanger sequencing or a second PCR protocol followed by a 3% agarose gel migration. For the (TA)n UGT1A1 promoter genotyping of African patients, each lab has to wonder what is the best way between (i) direct Sanger sequencing of all patients and (ii) HRM protocol for all patients followed by a complementary analysis to differentiate the 6/7 and 6/8 genotypes. © 2013. Published by Elsevier B.V. All rights reserved.

  2. Directions of development for areas with unfavourable conditions for agricultural production, an example of the podlaskie voivodeship (Poland

    Directory of Open Access Journals (Sweden)

    Kazimierz Niewiadomski

    2012-01-01

    Full Text Available This paper is dedicated to the directions of development of rural areas, primarily agricultural areas of the Podlaskie voivodeship, which in light of current criteria has been qualified almost entirely as problem area (ONW. Results presented are culmination of research related to issues of problem areas primarily in the area of the Podlaskie voivodeship by the author of the herewith paper during last few years. In conclusion to the results of the research it can be said that the primary direction of the development of rural areas in the Podlaskie voivodeship will be modern, large-scale farms able to adjust to current conditions, in particular environmental and soil conditions. In problem areas these will be mostly farms focusing on production of cattle and milk, developing production based on very high share of grassland areas. Complementary role in relation to conventional agriculture will be fulfilled by farms developing organic farming and agro-touristic farms. More intensive development of conventional tourism in rural areas can be expected once new tourism products and services have been developed. Assessment of the current economic development parameters of the Podlaskie voivodeship does not point at the convergence with other regions and possibility of decreasing the distance between the Podlaskie voivodeship and average results for Poland in the near future. However, some positive trends in terms of convergence with other regions in Poland can be observed in agriculture, primarily due to relatively good results in production of cattle and milk.

  3. Cross-lagged relations between mentoring received from supervisors and employee OCBs: Disentangling causal direction and identifying boundary conditions.

    Science.gov (United States)

    Eby, Lillian T; Butts, Marcus M; Hoffman, Brian J; Sauer, Julia B

    2015-07-01

    Although mentoring has documented relationships with employee attitudes and outcomes of interest to organizations, neither the causal direction nor boundary conditions of the relationship between mentoring and organizational citizenship behaviors (OCBs) has been fully explored. On the basis of Social Learning Theory (SLT; Bandura, 1977, 1986), we predicted that mentoring received by supervisors would causally precede OCBs, rather than employee OCBs resulting in the receipt of more mentoring from supervisors. Results from cross-lagged data collected at 2 points in time from 190 intact supervisor-employee dyads supported our predictions; however, only for OCBs directed at individuals (OCB-Is) and not for OCBs directed at the organization (OCB-Os). Further supporting our theoretical rationale for expecting mentoring to precede OCBs, we found that coworker support operates as a substitute for mentoring in predicting OCB-Is. By contrast, no moderating effects were found for perceived organizational support. The results are discussed in terms of theoretical implications for mentoring and OCB research, as well as practical suggestions for enhancing employee citizenship behaviors. (c) 2015 APA, all rights reserved).

  4. Direct-to-consumer prescription drug advertising, 1989-1998. A content analysis of conditions, targets, inducements, and appeals.

    Science.gov (United States)

    Bell, R A; Kravitz, R L; Wilkes, M S

    2000-04-01

    We conducted a content analysis of consumer-targeted prescription drug advertisements to explore trends in prevalence, shifts in the medical conditions for which drugs are promoted, reliance on financial and nonmonetary inducements, and appeals used to attract public interest. We collected the drug advertisements appearing in 18 consumer magazines from 1989 through 1998. Two judges independently coded each advertisement and placed it in a category pertaining to the target audience, use of inducements, and product benefits (mean kappa=0.93). We employed descriptive statistics, cross-tabulations, and curve estimation procedures. A total of 320 distinct advertisements were identified, representing 101 brands and 14 medical conditions. New advertisement and brand introductions increased dramatically during this decade. Advertisements for drugs used for dermatologic, human immunodeficiency virus/acquired immune deficiency syndrome (HIV/AIDS), and obstetric/gynecologic conditions were most common. Almost all of the advertisements were aimed at the potential user of the drug, not third-party intermediaries such as parents and spouses. Although most advertisements were gender-neutral, women were more likely to be exclusively targeted. One eighth of the advertisements offered a monetary incentive (eg, a rebate or money-back guarantee), and one third made an offer of additional information in printed or audio/video form. The most common appeals used were effectiveness, symptom control, innovativeness, and convenience. Consumer-directed prescription drug advertising has increased dramatically during the past decade. The pharmaceutical industry is turning to this type of advertising to generate interest in its products. Our data may be useful to physicians who want to stay abreast of the treatments that are being directly marketed to their patients.

  5. Analysis of radionuclide behavior in a BWR Mark-II containment under severe accident management condition in low pressure sequence

    International Nuclear Information System (INIS)

    Funayama, Kyoko; Kajimoto, Mitsuhiro; Nagayoshi, Takuji; Tanaka, Nobuo

    1999-01-01

    In the Level 2 PSA program at INS/NUPEC, MELCOR1.8.3 is extensively applied to analyze radionuclide behavior of dominant sequences. In addition, the revised source terms provided in the NUREG-1465 report have been also discussed to examine the potential of the radionuclides release to the environment in the conventional siting criteria. In the present study, characteristics of source terms to the environment were examined comparing with results by the Hypothetical Accident (LOCA), NUREG-1465 and MELCOR1.8.3. calculation for a typical BWR with a Mark-II containment in order to assure conservatives of the Hypothetical Accident in Japan. Release fractions of iodine to the environment for the Hypothetical Accident and NUREG-1465, which used engineering models for predicting radionuclide behaviors, were about 10 -4 and 10 -6 of core inventory, respectively, while the best estimate MELCOR1.8.3 code predicted 10 -9 of iodine to the environment. The present study showed that the engineering models in the Hypothetical Accident or NUREG-1465 have large conservatives to estimate source term of iodine to the environment. (author)

  6. Illumina sequencing-based analysis of a microbial community enriched under anaerobic methane oxidation condition coupled to denitrification revealed coexistence of aerobic and anaerobic methanotrophs.

    Science.gov (United States)

    Siniscalchi, Luciene Alves Batista; Leite, Laura Rabelo; Oliveira, Guilherme; Chernicharo, Carlos Augusto Lemos; de Araújo, Juliana Calabria

    2017-07-01

    Methane is produced in anaerobic environments, such as reactors used to treat wastewaters, and can be consumed by methanotrophs. The composition and structure of a microbial community enriched from anaerobic sewage sludge under methane-oxidation condition coupled to denitrification were investigated. Denaturing gradient gel electrophoresis (DGGE) analysis retrieved sequences of Methylocaldum and Chloroflexi. Deep sequencing analysis revealed a complex community that changed over time and was affected by methane concentration. Methylocaldum (8.2%), Methylosinus (2.3%), Methylomonas (0.02%), Methylacidiphilales (0.45%), Nitrospirales (0.18%), and Methanosarcinales (0.3%) were detected. Despite denitrifying conditions provided, Nitrospirales and Methanosarcinales, known to perform anaerobic methane oxidation coupled to denitrification (DAMO) process, were in very low abundance. Results demonstrated that aerobic and anaerobic methanotrophs coexisted in the reactor together with heterotrophic microorganisms, suggesting that a diverse microbial community was important to sustain methanotrophic activity. The methanogenic sludge was a good inoculum to enrich methanotrophs, and cultivation conditions play a selective role in determining community composition.

  7. Direct Time Domain Numerical Analysis of Transient Behavior of a VLFS during Unsteady External Loads in Wave Condition

    Directory of Open Access Journals (Sweden)

    Yong Cheng

    2014-01-01

    Full Text Available The transient response of the VLFS subjected to arbitrary external load is systematically investigated by a direct time domain modal expansion method, in which the BEM solutions based on time domain Kelvin sources are used for hydrodynamic forces. In the analysis, the time domain free-surface Green functions with sufficient accuracy are rapidly evaluated in finite water depth by the interpolation-tabulation method, and the boundary integral equation with a quarter VLFS model is established taking advantage of symmetry of flow field and structure. The validity of the present method is verified by comparing with the time histories of vertical displacements of the VLFS during a mass drop and airplane landing and takeoff in still water conditions, respectively. Then the developed numerical scheme is used in wave conditions to study the combined action taking into account the mass drop/airplane landing/takeoff loads as well as incident wave action. It is found that the elevation of structural waves due to mass drop load can be significantly changed near the impact region, while the vertical motion of runway in wave conditions is dominant as compared with that only generated by airplane.

  8. Sustainable Change Sequence: a framework for developing behavior change interventions for patients with long-term conditions

    OpenAIRE

    Elwyn, Glyn; Marrin, Katy; Frosch, Dominick; White, James

    2014-01-01

    Objective\\ud \\ud Interactive interventions are increasingly advocated to support behavior change for patients who have long-term conditions. Such interventions are most likely to achieve behavior change when they are based on appropriate theoretical frameworks. Developers of interventions are faced with a diverse set of behavioral theories that do not specifically address intervention development. The aim of our work was to develop a framework to guide the developers of interactive healthcare...

  9. Beta band transcranial alternating (tACS and direct current stimulation (tDCS applied after initial learning facilitate retrieval of a motor sequence

    Directory of Open Access Journals (Sweden)

    Vanessa eKrause

    2016-01-01

    Full Text Available The primary motor cortex (M1 contributes to the acquisition and early consolidation of a motor sequence. Although the relevance of M1 excitability for motor learning has been supported, the significance of M1 oscillations remains an open issue. This study aims at investigating to what extent retrieval of a newly learned motor sequence can be differentially affected by motor-cortical transcranial alternating (tACS and direct current stimulation (tDCS. Alpha (10 Hz, beta (20 Hz or sham tACS was applied in 36 right-handers. Anodal or cathodal tDCS was applied in 30 right-handers. Participants learned an eight-digit serial reaction time task (SRTT; sequential vs. random with the right hand. Stimulation was applied to the left M1 after SRTT acquisition at rest for ten minutes. Reaction times were analyzed at baseline, end of acquisition, retrieval immediately after stimulation and reacquisition after eight further sequence repetitions.Reaction times during retrieval were significantly faster following 20 Hz tACS as compared to 10 Hz and sham tACS indicating a facilitation of early consolidation. TDCS yielded faster reaction times, too, independent of polarity. No significant differences between 20 Hz tACS and tDCS effects on retrieval were found suggesting that 20 Hz effects might be associated with altered motor-cortical excitability. Based on the behavioural modulation yielded by tACS and tDCS one might speculate that altered motor-cortical beta oscillations support early motor consolidation possibly associated with neuroplastic reorganization.

  10. Visually driven chaining of elementary swim patterns into a goal-directed motor sequence: a virtual reality study of zebrafish prey capture

    Science.gov (United States)

    Trivedi, Chintan A.; Bollmann, Johann H.

    2013-01-01

    Prey capture behavior critically depends on rapid processing of sensory input in order to track, approach, and catch the target. When using vision, the nervous system faces the problem of extracting relevant information from a continuous stream of input in order to detect and categorize visible objects as potential prey and to select appropriate motor patterns for approach. For prey capture, many vertebrates exhibit intermittent locomotion, in which discrete motor patterns are chained into a sequence, interrupted by short periods of rest. Here, using high-speed recordings of full-length prey capture sequences performed by freely swimming zebrafish larvae in the presence of a single paramecium, we provide a detailed kinematic analysis of first and subsequent swim bouts during prey capture. Using Fourier analysis, we show that individual swim bouts represent an elementary motor pattern. Changes in orientation are directed toward the target on a graded scale and are implemented by an asymmetric tail bend component superimposed on this basic motor pattern. To further investigate the role of visual feedback on the efficiency and speed of this complex behavior, we developed a closed-loop virtual reality setup in which minimally restrained larvae recapitulated interconnected swim patterns closely resembling those observed during prey capture in freely moving fish. Systematic variation of stimulus properties showed that prey capture is initiated within a narrow range of stimulus size and velocity. Furthermore, variations in the delay and location of swim triggered visual feedback showed that the reaction time of secondary and later swims is shorter for stimuli that appear within a narrow spatio-temporal window following a swim. This suggests that the larva may generate an expectation of stimulus position, which enables accelerated motor sequencing if the expectation is met by appropriate visual feedback. PMID:23675322

  11. Visually driven chaining of elementary swim patterns into a goal-directed motor sequence: a virtual reality study of zebrafish prey capture

    Directory of Open Access Journals (Sweden)

    Chintan A Trivedi

    2013-05-01

    Full Text Available Prey capture behavior critically depends on rapid processing of sensory input in order to track, approach and catch the target. When using vision, the nervous system faces the problem of extracting relevant information from a continuous stream of input in order to detect and categorize visible objects as potential prey and to select appropriate motor patterns for approach. For prey capture, many vertebrates exhibit intermittent locomotion, in which discrete motor patterns are chained into a sequence, interrupted by short periods of rest. Here, using high-speed recordings of full-length prey capture sequences performed by freely swimming zebrafish larvae in the presence of a single paramecium, we provide a detailed kinematic analysis of first and subsequent swim bouts during prey capture. Using Fourier analysis, we show that individual swim bouts represent an elementary motor pattern. Changes in orientation are directed towards the target on a graded scale and are implemented by an asymmetric tail bend component superimposed on this basic motor pattern. To further investigate the role of visual feedback on the efficiency and speed of this complex behavior, we developed a closed-loop virtual reality setup in which minimally restrained larvae recapitulated interconnected swim patterns closely resembling those observed during prey capture in freely moving fish. Systematic variation of stimulus properties showed that prey capture is initiated within a narrow range of stimulus size and velocity. Furthermore, variations in the delay and location of swim-triggered visual feedback showed that the reaction time of secondary and later swims is shorter for stimuli that appear within a narrow spatio-temporal window following a swim. This suggests that the larva may generate an expectation of stimulus position, which enables accelerated motor sequencing if the expectation is met by appropriate visual feedback.

  12. Avoidance versus use of neuromuscular blocking agents for improving conditions during tracheal intubation or direct laryngoscopy in adults and adolescents

    DEFF Research Database (Denmark)

    Lundstrøm, Lars Hyldborg; Duez, Christophe Hv; Nørskov, Anders Kehlet

    2017-01-01

    ) for adults and adolescents allocated to tracheal intubation with direct laryngoscopy. To look at various outcomes, conduct subgroup and sensitivity analyses, examine the role of bias, and apply trial sequential analysis (TSA) to examine the level of available evidence for this intervention. SEARCH METHODS......: We searched CENTRAL, MEDLINE, Embase, BIOSIS, International Web of Science, LILACS, advanced Google, CINAHL, and the following trial registries: Current Controlled Trials; ClinicalTrials.gov; and www.centerwatch.com, up to January 2017. We checked the reference lists of included trials and reviews...... the best conditions for tracheal intubation and may reduce the risk of upper airway discomfort or injury following tracheal intubation. Study results were characterized by indirectness, heterogeneity, and high or uncertain risk of bias concerning our primary outcome describing difficult tracheal intubation...

  13. Goal- and signal-directed incentive: conditioned approach, seeking, and consumption established with unsweetened alcohol in rats.

    Science.gov (United States)

    Krank, Marvin D; O'Neill, Susan; Squarey, Kyna; Jacob, Jackie

    2008-02-01

    Many theories of addictive behavior propose that cues signaling drug administration influence the likelihood of drug-taking and drug-seeking behavior. We investigated the behavioral impact of cues associated with unsweetened ethanol and their interaction with responding maintained by ethanol self-administration. Our goal was to establish the influence of such cues on ethanol seeking. The experiment used a matching contingency and saccharin-fading procedure to establish equal levels of responding to two spatially distinct levers using unsweetened 10% ethanol solution. After ethanol self-administration was established, a brief cue light located alternately over each lever location was either paired or unpaired (control) with the opportunity to consume the same ethanol solution. Finally, self-administration was re-established, and the effect of the cue was measured in a transfer design. The reaction to lights paired with the opportunity to ingest unsweetened ethanol had three main effects: (1) induction of operant behavior reinforced by ethanol, (2) stimulation of ethanol-seeking behavior (drinker entries), and (3) cue-directed approach and contact behavior (i.e. autoshaping or sign-tracking). Cue-directed behavior to the light interacted with choice behavior in a manner predicted by the location of the cue light, enhancing responding only when the approach response did not interfere with the operant response. These findings replicate and extend the effects of Pavlovian conditioning on ethanol-seeking and support-conditioned incentive theories of addictive behavior. Signals for ethanol influence spatial choice behavior and may be relevant to attentional bias shown to alcohol-associated stimuli in humans.

  14. Analysis of several hazardous conditions for large transfer and back-dilution sequences in Tank 241-SY-101

    International Nuclear Information System (INIS)

    CW Stewart; LA Mahoney; WB Barton

    2000-01-01

    The first transfer of 89 kgal of waste and back-dilution of 61 kgal of water in Hanford Tank 241-SY-101 was accomplished December 18--20, 1999. Limits were placed on the transfer and back-dilution volumes because of concerns about potential gas release, crust sinking, and degradation of mixer pump performance. Additional transfers and back-dilutions are being planned that will bring the total to 500 kgal, which should dissolve a large fraction of the solids in the tank and dilute it well beyond the point where significant gas retention can occur. This report provides the technical bases for removing the limits on transfer and back-dilution volume by evaluating the potential consequences of several postulated hazardous conditions in view of the results of the first campaign and results of additional analyses of waste behavior

  15. Analysis of several hazardous conditions for large transfer and back-dilution sequences in Tank 241-SY-101

    Energy Technology Data Exchange (ETDEWEB)

    CW Stewart; LA Mahoney; WB Barton

    2000-01-28

    The first transfer of 89 kgal of waste and back-dilution of 61 kgal of water in Hanford Tank 241-SY-101 was accomplished December 18--20, 1999. Limits were placed on the transfer and back-dilution volumes because of concerns about potential gas release, crust sinking, and degradation of mixer pump performance. Additional transfers and back-dilutions are being planned that will bring the total to 500 kgal, which should dissolve a large fraction of the solids in the tank and dilute it well beyond the point where significant gas retention can occur. This report provides the technical bases for removing the limits on transfer and back-dilution volume by evaluating the potential consequences of several postulated hazardous conditions in view of the results of the first campaign and results of additional analyses of waste behavior.

  16. Edaphic Conditions Regulate Denitrification Directly and Indirectly by Altering Denitrifier Abundance in Wetlands along the Han River, China.

    Science.gov (United States)

    Xiong, Ziqian; Guo, Laodong; Zhang, Quanfa; Liu, Guihua; Liu, Wenzhi

    2017-05-16

    Riparian wetlands play a critical role in retaining nitrogen (N) from upland runoff and improving river water quality, mainly through biological processes such as soil denitrification. However, the relative contribution of abiotic and biotic factors to riparian denitrification capacity remains elusive. Here we report the spatiotemporal dynamics of potential and unamended soil denitrification rates in 20 wetlands along the Han River, an important water source in central China. We also quantified the abundance of soil denitrifying microorganisms using nirK and nirS genes. Results showed that soil denitrification rates were significantly different between riparian and reservoir shoreline wetlands, but not between mountain and lowland wetlands. In addition, soil denitrification rates showed strong seasonality, with higher values in August (summer) and April (spring) but lower values in January (winter). The potential and unamended denitrification rates were positively correlated with edaphic conditions (moisture and carbon concentration), denitrifier abundance, and plant species richness. Path analysis further revealed that edaphic conditions could regulate denitrification rates both directly and indirectly through their effects on denitrifier abundance. Our findings highlight that not only environmental factors, but also biotic factors including denitrifying microorganisms and standing vegetation, play an important role in regulating denitrification rate and N removal capacity in riparian wetlands.

  17. Formation conditions, accumulation models and exploration direction of large-scale gas fields in Sinian-Cambrian, Sichuan Basin, China

    Directory of Open Access Journals (Sweden)

    Guoqi Wei

    2016-02-01

    Full Text Available According to comprehensive research on forming conditions including sedimentary facies, reservoirs, source rocks, and palaeo-uplift evolution of Sinian-Cambrian in Sichuan Basin, it is concluded that: (1 large-scale inherited palaeo-uplifts, large-scale intracratonic rifts, three widely-distributed high-quality source rocks, four widely-distributed karst reservoirs, and oil pyrolysis gas were all favorable conditions for large-scale and high-abundance accumulation; (2 diverse accumulation models were developed in different areas of the palaeo-uplift. In the core area of the inherited palaeo-uplift, “in-situ” pyrolysis accumulation model of paleo-reservoir was developed. On the other hand, in the slope area, pyrolysis accumulation model of dispersed liquid hydrocarbon was developed in the late stage structural trap; (3 there were different exploration directions in various areas of the palaeo-uplift. Within the core area of the palaeo-uplift, we mainly searched for the inherited paleo-structural trap which was also the foundation of lithological-strigraphic gas reservoirs. In the slope areas, we mainly searched for the giant structural trap formed in the Himalayan Period.

  18. Clinical and molecular characterization of a cohort of patients with novel nucleotide alterations of the Dystrophin gene detected by direct sequencing

    Directory of Open Access Journals (Sweden)

    Corti Stefania

    2011-03-01

    Full Text Available Abstract Background Duchenne and Becker Muscular dystrophies (DMD/BMD are allelic disorders caused by mutations in the dystrophin gene, which encodes a sarcolemmal protein responsible for muscle integrity. Deletions and duplications account for approximately 75% of mutations in DMD and 85% in BMD. The implementation of techniques allowing complete gene sequencing has focused attention on small point mutations and other mechanisms underlying complex rearrangements. Methods We selected 47 patients (41 families; 35 DMD, 6 BMD without deletions and duplications in DMD gene (excluded by multiplex ligation-dependent probe amplification and multiplex polymerase chain reaction analysis. This cohort was investigated by systematic direct sequence analysis to study sequence variation. We focused our attention on rare mutational events which were further studied through transcript analysis. Results We identified 40 different nucleotide alterations in DMD gene and their clinical correlates; altogether, 16 mutations were novel. DMD probands carried 9 microinsertions/microdeletions, 19 nonsense mutations, and 7 splice-site mutations. BMD patients carried 2 nonsense mutations, 2 splice-site mutations, 1 missense substitution, and 1 single base insertion. The most frequent stop codon was TGA (n = 10 patients, followed by TAG (n = 7 and TAA (n = 4. We also analyzed the molecular mechanisms of five rare mutational events. They are two frame-shifting mutations in the DMD gene 3'end in BMD and three novel splicing defects: IVS42: c.6118-3C>A, which causes a leaky splice-site; c.9560A>G, which determines a cryptic splice-site activation and c.9564-426 T>G, which creates pseudoexon retention within IVS65. Conclusion The analysis of our patients' sample, carrying point mutations or complex rearrangements in DMD gene, contributes to the knowledge on phenotypic correlations in dystrophinopatic patients and can provide a better understanding of pre-mRNA maturation defects

  19. On the effect of operating conditions in liquid-feed direct methanol fuel cells: A multiphysics modeling approach

    International Nuclear Information System (INIS)

    García-Salaberri, Pablo A.; Vera, Marcos

    2016-01-01

    A multiphysics model for liquid-feed Direct Methanol Fuel Cells is presented. The model accounts for two-dimensional (2D) across-the-channel anisotropic mass and charge transport in the anode and cathode Gas Diffusion Layers (GDLs), including the effect of GDL assembly compression and electrical contact resistances at the Bipolar Plate (BPP) and membrane interfaces. A one-dimensional (1D) across-the-membrane model is used to describe local species diffusion through the microporous layers, methanol/water crossover, proton transport, and electrochemical reactions, thereby coupling both GDL sub-models. The 2D/1D model is extended to the third dimension and supplemented with 1D descriptions of the flow channels to yield a 3D/1D + 1D model that is successfully validated. A parametric study is then conducted on the 2D/1D model to examine the effect of operating conditions on cell performance. The results show that an optimum methanol concentration exists that maximizes power output due to the trade-off between anode polarization and cathode mixed overpotential. For fixed methanol concentration, cell performance is largely affected by the oxygen supply rate, cell temperature, and liquid/gas saturation levels. There is also an optimal GDL compression due to the trade-off between ohmic and concentration losses, which strongly depends on BPP material and, more weakly, on the actual operating conditions. - Highlights: • A multiphysics model for liquid-feed DMFCs is presented. • GDL anisotropic transport, assembly compression, and ohmic contact resistances are considered. • The model is successfully validated against previous experimental data. • Optimum methanol concentrations, GDL compressions, and operating temperatures are reported. • Oxygen-starved conditions with spontaneous hydrogen evolution in the anode are also considered.

  20. Operating conditions of an open and direct solar thermal Brayton cycle with optimised cavity receiver and recuperator

    International Nuclear Information System (INIS)

    Le Roux, W.G.; Bello-Ochende, T.; Meyer, J.P.

    2011-01-01

    The small-scale open and direct solar thermal Brayton cycle with recuperator has several advantages, including low cost, low operation and maintenance costs and it is highly recommended. The main disadvantages of this cycle are the pressure losses in the recuperator and receiver, turbomachine efficiencies and recuperator effectiveness, which limit the net power output of such a system. The irreversibilities of the solar thermal Brayton cycle are mainly due to heat transfer across a finite temperature difference and fluid friction. In this paper, thermodynamic optimisation is applied to concentrate on these disadvantages in order to optimise the receiver and recuperator and to maximise the net power output of the system at various steady-state conditions, limited to various constraints. The effects of wind, receiver inclination, rim angle, atmospheric temperature and pressure, recuperator height, solar irradiance and concentration ratio on the optimum geometries and performance were investigated. The dynamic trajectory optimisation method was applied. Operating points of a standard micro-turbine operating at its highest compressor efficiency and a parabolic dish concentrator diameter of 16 m were considered. The optimum geometries, minimum irreversibility rates and maximum receiver surface temperatures of the optimised systems are shown. For an environment with specific conditions and constraints, there exists an optimum receiver and recuperator geometry so that the system produces maximum net power output. -- Highlights: → Optimum geometries exist such that the system produces maximum net power output. → Optimum operating conditions are shown. → Minimum irreversibility rates and minimum entropy generation rates are shown. → Net power output was described in terms of total entropy generation rate. → Effects such as wind, recuperator height and irradiance were investigated.

  1. Molecular modeling of directed self-assembly of block copolymers: Fundamental studies of processing conditions and evolutionary pattern design

    Science.gov (United States)

    Khaira, Gurdaman Singh

    Rapid progress in the semi-conductor industry has pushed for smaller feature sizes on integrated electronic circuits. Current photo-lithographic techniques for nanofabrication have reached their technical limit and are problematic when printing features small enough to meet future industrial requirements. "Bottom-up'' techniques, such as the directed self-assembly (DSA) of block copolymers (BCP), are the primary contenders to compliment current "top-down'' photo-lithography ones. For industrial requirements, the defect density from DSA needs to be less than 1 defect per 10 cm by 10 cm. Knowledge of both material synthesis and the thermodynamics of the self-assembly process are required before optimal operating conditions can be found to produce results adequate for industry. The work present in this thesis is divided into three chapters, each discussing various aspects of DSA as studied via a molecular model that contains the essential physics of BCP self-assembly. Though there are various types of guiding fields that can be used to direct BCPs over large wafer areas with minimum defects, this study focuses only on chemically patterned substrates. The first chapter addresses optimal pattern design by describing a framework where molecular simulations of various complexities are coupled with an advanced optimization technique to find a pattern that directs a target morphology. It demonstrates the first ever study where BCP self-assembly on a patterned substrate is optimized using a three-dimensional description of the block-copolymers. For problems pertaining to DSA, the methodology is shown to converge much faster than the traditional random search approach. The second chapter discusses the metrology of BCP thin films using TEM tomography and X-ray scattering techniques, such as CDSAXS and GISAXS. X-ray scattering has the advantage of being able to quickly probe the average structure of BCP morphologies over large wafer areas; however, deducing the BCP morphology

  2. Ranked solutions to a class of combinatorial optimizations—with applications in mass spectrometry based peptide sequencing and a variant of directed paths in random media

    Science.gov (United States)

    Doerr, Timothy P.; Alves, Gelio; Yu, Yi-Kuo

    2005-08-01

    Typical combinatorial optimizations are NP-hard; however, for a particular class of cost functions the corresponding combinatorial optimizations can be solved in polynomial time using the transfer matrix technique or, equivalently, the dynamic programming approach. This suggests a way to efficiently find approximate solutions-find a transformation that makes the cost function as similar as possible to that of the solvable class. After keeping many high-ranking solutions using the approximate cost function, one may then re-assess these solutions with the full cost function to find the best approximate solution. Under this approach, it is important to be able to assess the quality of the solutions obtained, e.g., by finding the true ranking of the kth best approximate solution when all possible solutions are considered exhaustively. To tackle this statistical issue, we provide a systematic method starting with a scaling function generated from the finite number of high-ranking solutions followed by a convergent iterative mapping. This method, useful in a variant of the directed paths in random media problem proposed here, can also provide a statistical significance assessment for one of the most important proteomic tasks-peptide sequencing using tandem mass spectrometry data. For directed paths in random media, the scaling function depends on the particular realization of randomness; in the mass spectrometry case, the scaling function is spectrum-specific.

  3. De novo transcriptome sequence assembly from coconut leaves and seeds with a focus on factors involved in RNA-directed DNA methylation.

    Science.gov (United States)

    Huang, Ya-Yi; Lee, Chueh-Pai; Fu, Jason L; Chang, Bill Chia-Han; Matzke, Antonius J M; Matzke, Marjori

    2014-09-04

    Coconut palm (Cocos nucifera) is a symbol of the tropics and a source of numerous edible and nonedible products of economic value. Despite its nutritional and industrial significance, coconut remains under-represented in public repositories for genomic and transcriptomic data. We report de novo transcript assembly from RNA-seq data and analysis of gene expression in seed tissues (embryo and endosperm) and leaves of a dwarf coconut variety. Assembly of 10 GB sequencing data for each tissue resulted in 58,211 total unigenes in embryo, 61,152 in endosperm, and 33,446 in leaf. Within each unigene pool, 24,857 could be annotated in embryo, 29,731 could be annotated in endosperm, and 26,064 could be annotated in leaf. A KEGG analysis identified 138, 138, and 139 pathways, respectively, in transcriptomes of embryo, endosperm, and leaf tissues. Given the extraordinarily large size of coconut seeds and the importance of small RNA-mediated epigenetic regulation during seed development in model plants, we used homology searches to identify putative homologs of factors required for RNA-directed DNA methylation in coconut. The findings suggest that RNA-directed DNA methylation is important during coconut seed development, particularly in maturing endosperm. This dataset will expand the genomics resources available for coconut and provide a foundation for more detailed analyses that may assist molecular breeding strategies aimed at improving this major tropical crop. Copyright © 2014 Huang et al.

  4. Gene Expressing and sRNA Sequencing Show That Gene Differentiation Associates with a Yellow Acer palmatum Mutant Leaf in Different Light Conditions.

    Science.gov (United States)

    Li, Shu-Shun; Li, Qian-Zhong; Rong, Li-Ping; Tang, Ling; Zhang, Bo

    2015-01-01

    Acer palmatum Thunb., like other maples, is a widely ornamental-use small woody tree for leaf shapes and colors. Interestingly, we found a yellow-leaves mutant "Jingling Huangfeng" turned to green when grown in shade or low-density light condition. In order to study the potential mechanism, we performed high-throughput sequencing and obtained 1,082 DEGs in leaves grown in different light conditions that result in A. palmatum significant morphological and physiological changes. A total of 989 DEGs were annotated and clustered, of which many DEGs were found associating with the photosynthesis activity and pigment synthesis. The expression of CHS and FDR gene was higher while the expression of FLS gene was lower in full-sunlight condition; this may cause more colorful substance like chalcone and anthocyanin that were produced in full-light condition, thus turning the foliage to yellow. Moreover, this is the first available miRNA collection which contains 67 miRNAs of A. palmatum, including 46 conserved miRNAs and 21 novel miRNAs. To get better understanding of which pathways these miRNAs involved, 102 Unigenes were found to be potential targets of them. These results will provide valuable genetic resources for further study on the molecular mechanisms of Acer palmatum leaf coloration.

  5. The effects of nicardipine or esmolol on the onset time of rocuronium and intubation conditions during rapid sequence induction: a randomized double-blind trial.

    Science.gov (United States)

    Lee, Ji Heui; Kim, Yunkwang; Lee, Kye Hyeok; Rim, Sung Kyu; Lee, Ji Yeon; Lee, Cheong

    2015-06-01

    The main aims of rapid sequence induction (RSI) are prompt and adequate muscle relaxation for tracheal intubation and hemodynamic stability during and after intubation. The purpose of the present study was to investigate the effects of nicardipine and esmolol on the action of rocuronium and intubation conditions during RSI. Adult patients (n = 82) were randomly allocated to one of three groups. One minute prior to the induction of sevoflurane-based general anesthesia, patients received 20 μg/kg of nicardipine (N group; n = 27) or 0.5 mg/kg of esmolol (E group; n = 27), or 5 ml of saline (C group; n = 28). Patients were assessed according to intubation conditions, the onset time of rocuronium, mean arterial pressure (MAP), and heart rate (HR) during RSI. The intubation conditions and score were significantly better in the C and N groups than in the E group (P rocuronium was shortened in the N group and prolonged in the E group when compared to the C group (P rocuronium and attenuated changes in MAP after intubation. Esmolol may disturb intubation conditions and the onset of action of rocuronium, despite being effective in alleviating responses of HR after RSI.

  6. Spray and evaporation characteristics of ethanol and gasoline direct injection in non-evaporating, transition and flash-boiling conditions

    International Nuclear Information System (INIS)

    Huang, Yuhan; Huang, Sheng; Huang, Ronghua; Hong, Guang

    2016-01-01

    Highlights: • Sprays can be considered as non-evaporating when vapour pressure is lower than 30 kPa. • Ethanol direct injection should only be applied in high temperature engine environment. • Gasoline spray collapses at lower fuel temperature (350 K) than ethanol spray does (360 K). • Flash-boiling does not occur when fuel temperature reaches boiling point until ΔT is 14 K. • Not only spray evaporation mode but also breakup mechanism change with fuel temperature. - Abstract: Ethanol direct injection plus gasoline port injection (EDI + GPI) represents a more efficient and flexible way to utilize ethanol fuel in spark ignition engines. To exploit the potentials of EDI, the mixture formation characteristics need to be investigated. In this study, the spray and evaporation characteristics of ethanol and gasoline fuels injected from a multi-hole injector were investigated by high speed Shadowgraphy imaging technique in a constant volume chamber. The experiments covered a wide range of fuel temperature from 275 K (non-evaporating) to 400 K (flash-boiling) which corresponded to cold start and running conditions in an engine. The spray transition process from normal-evaporating to flash-boiling was investigated in greater details than the existed studies. Results showed that ethanol and gasoline sprays demonstrated the same patterns in non-evaporating conditions. The sprays could be considered as non-evaporating when vapour pressure was lower than 30 kPa. Ethanol evaporated more slowly than gasoline did in low temperature environment, but they reached the similar evaporation rates when temperature was higher than 375 K. This suggested that EDI should only be applied in high temperature engine environment. For both ethanol and gasoline sprays, when the excess temperature was smaller than 4 K, the sprays behaved the same as the subcooled sprays did. The sprays collapsed when the excess temperature was 9 K. Flash-boiling did not occur until the excess temperature

  7. A preregistered, direct replication attempt of the retrieval-extinction effect in cued fear conditioning in rats.

    Science.gov (United States)

    Luyten, Laura; Beckers, Tom

    2017-10-01

    In 2009, Monfils and colleagues proposed a behavioral procedure that was said to result in a permanent attenuation of a previously established fear memory, thereby precluding a possible return of fear after extinction (Monfils, Cowansage, Klann, & LeDoux, 2009). By presenting a single retrieval trial one hour before standard extinction training, they found an enduring reduction of fear. The retrieval-extinction procedure holds great clinical potential, particularly for anxiety patients, but the findings are not undisputed, and several conceptual replications have failed to reproduce the effect. These failures have largely been attributed to small procedural differences. This preregistered study is the first endeavor to exactly replicate three key experiments of the original report by Monfils et al. (2009), thereby gauging the robustness of their seminal findings. Despite adhering to the original procedures as closely as possible, we did not find any evidence for reduced return of fear with the retrieval-extinction procedure relative to regular extinction training, as assessed through spontaneous recovery, reinstatement and renewal. Behavior of animals in the control condition (extinction only) was comparable to that in the original studies and provided an adequate baseline to reveal differences with the retrieval-extinction condition. Our null findings indicate that the effect sizes in the original paper may have been inflated and question the legitimacy of previously proposed moderators of the retrieval-extinction effect. We argue that direct experimental evaluation of purported moderators of the retrieval-extinction effect will be key to shed more light on its nature and prerequisites. Copyright © 2017 Elsevier Inc. All rights reserved.

  8. Detection of rifampin resistance patterns in Mycobacterium tuberculosis strains isolated in Iran by polymerase chain reaction-single-strand conformation polymorphism and direct sequencing methods

    Directory of Open Access Journals (Sweden)

    Bahram Nasr Isfahani

    2006-09-01

    Full Text Available Mutations in the rpoB locus confer conformational changes leading to defective binding of rifampin (RIF to rpoB and consequently resistance in Mycobacterium tuberculosis. Polymerase chain reaction-single-strand conformation polymorphism (PCR-SSCP was established as a rapid screening test for the detection of mutations in the rpoB gene, and direct sequencing has been unambiguously applied to characterize mutations. A total of 37 of Iranian isolates of M. tuberculosis, 16 sensitive and 21 resistant to RIF, were used in this study. A 193-bp region of the rpoB gene was amplified and PCR-SSCP patterns were determined by electrophoresis in 10% acrylamide gel and silver staining. Also, 21 samples of 193-bp rpoB amplicons with different PCR-SSCP patterns from RIFr and 10 from RIFs were sequenced. Seven distinguishable PCR-SSCP patterns were recognized in the 21 Iranian RIFr strains, while 15 out of 16 RIFs isolates demonstrated PCR-SSCP banding patterns similar to that of sensitive standard strain H37Rv. However one of the sensitive isolates demonstrated a different pattern. There were seen six different mutations in the amplified region of rpoB gene: codon 516(GAC/GTC, 523(GGG/GGT, 526(CAC/TAC, 531(TCG/TTG, 511(CTG/TTG, and 512(AGC/TCG. This study demonstrated the high specificity (93.8% and sensitivity (95.2% of PCR-SSCP method for detection of mutation in rpoB gene; 85.7% of RIFr strains showed a single mutation and 14.3% had no mutations. Three strains showed mutations caused polymorphism. Our data support the common notion that rifampin resistance genotypes are generally present mutations in codons 531 and 526, most frequently found in M. tuberculosis populations regardless of geographic origin.

  9. The diagnosis of inflammatory muscular and vascular conditions using MRT with STIR sequences. Diagnostik entzuendlicher Muskel- und Gefaesserkrankungen in der MRT mit STIR-Sequenzen

    Energy Technology Data Exchange (ETDEWEB)

    Beese, M.S. (Radiologische Klinik, Universitaetskrankenhaus Eppendorf, Hamburg (Germany)); Winkler, G. (Radiologische Klinik, Universitaetskrankenhaus Eppendorf, Hamburg (Germany) Neurologische Klinik, Universitaetskrankenhaus Eppendorf, Hamburg (Germany)); Nicolas, V. (Radiologische Klinik, Universitaetskrankenhaus Eppendorf, Hamburg (Germany)); Maas, R. (Radiologische Klinik, Universitaetskrankenhaus Eppendorf, Hamburg (Germany)); Kress, D. (Radiologische Klinik, Universitaetskrankenhaus Eppendorf, Hamburg (Germany)); Kunze, K. (Radiologische Klinik, Universitaetskrankenhaus Eppendorf, Hamburg (Germany) Neurologische Klinik, Universitaetskrankenhaus Eppendorf, Hamburg (Germany)); Buecheler, E. (Radiologische Klinik, Universitaetskrankenhaus Eppendorf, Hamburg (Germany))

    1993-06-01

    The role of MRT in the prebiopsy diagnosis of muscular and vascular inflammatory conditions was evaluated prospectively and an optimal method of examination was investigated. 92 patients with a suspected diagnosis of myositis (60 cases) or vasculitis (32 cases) were examined, in each case two extremities were studied using transverse T[sub 1] and T[sub 2] weighted SE sequences and double echo STIR sequences on a 0.5 Tesla (56 patients) or 1.5 Tesla magnet (36 patients; T5/S15 Gyroscan, Philips). The site of the biopsy depended on the MRT findings. In 41 patients the suspected diagnosis was confirmed histologically, in two patients an infective myositis was diagnosed on clinical grounds despite negative histology. MRT demonstrated muscle oedema in 86% of patients. There were negative findings after immuno-suppressive therapy (two patients), in focal myositis (3 out of 4 patients) and in one of 7 patients with untreated vasculitis. Amongst 49 patients in whom the suspected diagnosis could not be confirmed there was muscle oedema in 11 cases (9 neuropathies out of 22, two myopathies out of 10). Oedema indicated inflammatory muscular or vascular disease with a sensitivity of 97% (except in treated patients and for focal myositis). The number of false negative biopsies can be greatly reduced by the use of MRT. (orig.)

  10. Dual direction blower system powered by solar energy to reduce car cabin temperature in open parking condition

    Science.gov (United States)

    Hamdan, N. S.; Radzi, M. F. M.; Damanhuri, A. A. M.; Mokhtar, S. N.

    2017-10-01

    El-nino phenomenon that strikes Malaysia with temperature recorded more than 35°C can lead to extreme temperature rise in car cabin up to 80°C. Various problems will arise due to this extreme rising of temperature such as the occupant are vulnerable to heat stroke, emission of benzene gas that can cause cancer due to reaction of high temperature with interior compartments, and damage of compartments in the car. The current solution available to reduce car cabin temperature including tinted of window and portable heat rejection device that are available in the market. As an alternative to reduce car cabin temperature, this project modifies the car’s air conditioning blower motor into dual direction powered by solar energy and identifies its influence to temperature inside the car, parked under scorching sun. By reducing the car cabin temperature up to 10°C which equal to 14% of reduction in the car cabin temperature, this simple proposed system aims to provide comfort to users due to its capability in improving the quality of air and moisture in the car cabin.

  11. Overview of condition monitoring and operation control of electric power conversion systems in direct-drive wind turbines under faults

    Science.gov (United States)

    Huang, Shoudao; Wu, Xuan; Liu, Xiao; Gao, Jian; He, Yunze

    2017-09-01

    Electric power conversion system (EPCS), which consists of a generator and power converter, is one of the most important subsystems in a direct-drive wind turbine (DD-WT). However, this component accounts for the most failures (approximately 60% of the total number) in the entire DD-WT system according to statistical data. To improve the reliability of EPCSs and reduce the operation and maintenance cost of DD-WTs, numerous researchers have studied condition monitoring (CM) and fault diagnostics (FD). Numerous CM and FD techniques, which have respective advantages and disadvantages, have emerged. This paper provides an overview of the CM, FD, and operation control of EPCSs in DD-WTs under faults. After introducing the functional principle and structure of EPCS, this survey discusses the common failures in wind generators and power converters; briefly reviewed CM and FD methods and operation control of these generators and power converters under faults; and discussed the grid voltage faults related to EPCSs in DD-WTs. These theories and their related technical concepts are systematically discussed. Finally, predicted development trends are presented. The paper provides a valuable reference for developing service quality evaluation methods and fault operation control systems to achieve high-performance and high-intelligence DD-WTs.

  12. Experimental Investigation of an Automobile Air-Conditioning System using Integrated Brushless Direct Current Motor Rotary Compressor

    Directory of Open Access Journals (Sweden)

    Sukri M.F.

    2016-01-01

    Full Text Available The present study presents an experimental investigation on the effect of condenser air inlet temperature and dimensionless parameter of X on the performance of automobile air-conditioning (AAC system using integrated brushless direct current motor-rotary compressor and electronic expansion valve. The other components of AAC system are from original component of AAC system used for medium size passenger car. The experimental results showed that the increment of the condenser air inlet temperature and X caused an increase in condensing temperature, cooling capacity and compressor work, while decreasing the coefficient of performance (COP. Meanwhile, the evaporating temperature increase with the increment of condenser air inlet temperature, but decrease with decrement of X. In general, AAC system have to work at higher value of X in order to produce more cooling capacity, thereby increment in compressor work also occurs due to energy balance. However, at higher value of X, the COP of the system dropped due to dominant increase in compressor power, as opposed to a rise in cooling capacity. Due to this reason, the best operation of this compressor occurs at X = 4.96 for constant T5 (35ºC, or at T5 = 30ºC for constant X (4.96.

  13. Deemed Savings Estimates for Legacy Air Conditioning and WaterHeating Direct Load Control Programs in PJM Region

    Energy Technology Data Exchange (ETDEWEB)

    Goldman, Charles

    2007-03-01

    During 2005 and 2006, the PJM Interconnection (PJM) Load Analysis Subcommittee (LAS) examined ways to reduce the costs and improve the effectiveness of its existing measurement and verification (M&V) protocols for Direct Load Control (DLC) programs. The current M&V protocol requires that a PURPA-compliant Load Research study be conducted every five years for each Load-Serving Entity (LSE). The current M&V protocol is expensive to implement and administer particularly for mature load control programs, some of which are marginally cost-effective. There was growing evidence that some LSEs were mothballing or dropping their DLC programs in lieu of incurring the expense associated with the M&V. This project had several objectives: (1) examine the potential for developing deemed savings estimates acceptable to PJM for legacy air conditioning and water heating DLC programs, and (2) explore the development of a collaborative, regional, consensus-based approach for conducting monitoring and verification of load reductions for emerging load management technologies for customers that do not have interval metering capability.

  14. Whole-exome sequencing identified a homozygous FNBP4 mutation in a family with a condition similar to microphthalmia with limb anomalies.

    Science.gov (United States)

    Kondo, Yukiko; Koshimizu, Eriko; Megarbane, Andre; Hamanoue, Haruka; Okada, Ippei; Nishiyama, Kiyomi; Kodera, Hirofumi; Miyatake, Satoko; Tsurusaki, Yoshinori; Nakashima, Mitsuko; Doi, Hiroshi; Miyake, Noriko; Saitsu, Hirotomo; Matsumoto, Naomichi

    2013-07-01

    Microphthalmia with limb anomalies (MLA), also known as Waardenburg anophthalmia syndrome or ophthalmoacromelic syndrome, is a rare autosomal recessive disorder. Recently, we and others successfully identified SMOC1 as the causative gene for MLA. However, there are several MLA families without SMOC1 abnormality, suggesting locus heterogeneity in MLA. We aimed to identify a pathogenic mutation in one Lebanese family having an MLA-like condition without SMOC1 mutation by whole-exome sequencing (WES) combined with homozygosity mapping. A c.683C>T (p.Thr228Met) in FNBP4 was found as a primary candidate, drawing the attention that FNBP4 and SMOC1 may potentially modulate BMP signaling. Copyright © 2013 Wiley Periodicals, Inc.

  15. High-resolution sequence stratigraphy of lower Paleozoic sheet sandstones in central North America: The role of special conditions of cratonic interiors in development of stratal architecture

    Science.gov (United States)

    Runkel, Anthony C.; Miller, J.F.; McKay, R.M.; Palmer, A.R.; Taylor, John F.

    2007-01-01

    Well-known difficulties in applying sequence stratigraphic concepts to deposits that accumulated across slowly subsiding cratonic interior regions have limited our ability to interpret the history of continental-scale tectonism, oceanographic dynamics of epeiric seas, and eustasy. We used a multi-disciplinary approach to construct a high-resolution stratigraphic framework for lower Paleozoic strata in the cratonic interior of North America. Within this framework, these strata proved readily amenable to modern sequence stratigraphic techniques that were formulated based on successions along passive margins and in foreland basins, settings markedly different from the cratonic interior. Parasequences, parasequence stacking patterns, systems tracts, maximum flooding intervals, and sequence-bounding unconformities can be confidently recognized in the cratonic interior using mostly standard criteria for identification. The similarity of cratonic interior and foreland basin successions in size, geometry, constituent facies, and local stacking patterns of nearshore parasequences is especially striking. This similarity indicates that the fundamental processes that establish shoreface morphology and determine the stratal expression of retreat and progradation were likewise generally the same, despite marked differences in tectonism, physiography, and bathymetry between the two settings. Our results do not support the widespread perception that Paleozoic cratonic interior successions are so anomalous in stratal geometries, and constitute such a poor record of time, that they are poorly suited for modern sequence stratigraphic analyses. The particular arrangement of stratal elements in the cratonic interior succession we studied is no more anomalous or enigmatic than the variability in architecture that sets all sedimentary successions apart from one another. Thus, Paleozoic strata of the cratonic interior are most appropriately considered as a package that belongs in a

  16. A translational study of resistance emergence using sequential direct-acting antiviral agents for hepatitis C using ultra-deep sequencing.

    Science.gov (United States)

    Abe, Hiromi; Hayes, C Nelson; Hiraga, Nobuhiko; Imamura, Michio; Tsuge, Masataka; Miki, Daiki; Takahashi, Shoichi; Ochi, Hidenori; Chayama, Kazuaki

    2013-09-01

    Direct-acting antiviral agents (DAAs) against hepatitis C virus (HCV) have recently been developed and are ultimately hoped to replace interferon-based therapy. However, DAA monotherapy results in rapid emergence of resistant strains and DAAs must be used in combinations that present a high genetic barrier to resistance, although viral kinetics of multidrug-resistant strains remain poorly characterized. The aim of this study is to track the emergence and fitness of resistance using combinations of telaprevir and NS5A or NS5B inhibitors with genotype 1b clones. HCV-infected chimeric mice were treated with DAAs, and resistance was monitored using direct and ultra-deep sequencing. Combination therapy with telaprevir and BMS-788329 (NS5A inhibitor) reduced serum HCV RNA to undetectable levels. The presence of an NS3-V36A telaprevir resistance mutation resulted in poor response to telaprevir monotherapy but showed significant HCV reduction when telaprevir was combined with BMS-788329. However, a BMS-788329-resistant strain emerged at low frequency. Infection with a BMS-788329-resistant NS5A-L31V mutation rapidly resulted in gain of an additional NS5A-Y93A mutation that conferred telaprevir resistance during combination therapy. Infection with dual NS5AL31V/NS5AY93H mutations resulted in poor response to combination therapy and development of telaprevir resistance. Although HCV RNA became undetectable soon after the beginning of combination therapy with BMS-788329 and BMS-821095 (NS5B inhibitor), rebound with emergence of resistance against all three drugs occurred. Triple resistance also occurred following infection with the NS3V36A/NS5AL31V/NS5AY93H triple mutation. Resistant strains easily develop from cloned virus strains. Sequential use of DAAs should be avoided to prevent emergence of multidrug-resistant strains.

  17. Interference effects of transcranial direct current stimulation over the right frontal cortex and adrenergic system on conditioned fear.

    Science.gov (United States)

    Nasehi, Mohammad; Soltanpour, Reyhaneh; Ebrahimi-Ghiri, Mohaddeseh; Zarrabian, Shahram; Zarrindast, Mohammad-Reza

    2017-11-01

    The effects of pharmacological interventions on fear memory have widely been studied, but there are very few studies about the effects of brain electrical stimulation on fear memory function. Therefore, our aim was to determine whether anodal/cathodal transcranial direct current stimulation (tDCS) over the right frontal cortex would modify propranolol-induced contextual and auditory fear memory deficits, before or after training. The adult NMRI male mice were randomly assigned into three groups: the sham group, the anodal tDCS group, and the cathodal tDCS group. Fear memories were evaluated using a classical fear conditioning apparatus. While the anodal stimulation did not affect fear retrieval, post-training cathodal stimulation improved fear memory retrieval. Regardless of when propranolol (0.1 mg/kg) was administered, it impaired fear memory retrieval. However, when anodal stimulation and propranolol were applied prior to the training, contextual fear memory retrieval was increased and auditory fear memory was reversed. An enhanced contextual retrieval was also observed when propranolol was administered prior to the training and stimulation occurred after the training. Only when the stimulation occurred prior to the training and propranolol was administered after the training was there a selective improvement in contextual fear memory retrieval, leaving the auditory fear memory retrieval impaired. Interestingly, cathodal stimulation improved the effects of propranolol on auditory fear memory only when it occurred prior to the training. The results highlight possible improving effects for anodal/cathodal tDCS on propranolol-induced deficits on fear memories. The timing of the interventions related to the specific phases of memory formation is important in modulating fear behaviors.

  18. Directional RNA deep sequencing sheds new light on the transcriptional response of Anabaena sp. strain PCC 7120 to combined-nitrogen deprivation

    Directory of Open Access Journals (Sweden)

    Head Steven R

    2011-06-01

    Full Text Available Abstract Background Cyanobacteria are potential sources of renewable chemicals and biofuels and serve as model organisms for bacterial photosynthesis, nitrogen fixation, and responses to environmental changes. Anabaena (Nostoc sp. strain PCC 7120 (hereafter Anabaena is a multicellular filamentous cyanobacterium that can "fix" atmospheric nitrogen into ammonia when grown in the absence of a source of combined nitrogen. Because the nitrogenase enzyme is oxygen sensitive, Anabaena forms specialized cells called heterocysts that create a microoxic environment for nitrogen fixation. We have employed directional RNA-seq to map the Anabaena transcriptome during vegetative cell growth and in response to combined-nitrogen deprivation, which induces filaments to undergo heterocyst development. Our data provide an unprecedented view of transcriptional changes in Anabaena filaments during the induction of heterocyst development and transition to diazotrophic growth. Results Using the Illumina short read platform and a directional RNA-seq protocol, we obtained deep sequencing data for RNA extracted from filaments at 0, 6, 12, and 21 hours after the removal of combined nitrogen. The RNA-seq data provided information on transcript abundance and boundaries for the entire transcriptome. From these data, we detected novel antisense transcripts within the UTRs (untranslated regions and coding regions of key genes involved in heterocyst development, suggesting that antisense RNAs may be important regulators of the nitrogen response. In addition, many 5' UTRs were longer than anticipated, sometimes extending into upstream open reading frames (ORFs, and operons often showed complex structure and regulation. Finally, many genes that had not been previously identified as being involved in heterocyst development showed regulation, providing new candidates for future studies in this model organism. Conclusions Directional RNA-seq data were obtained that provide

  19. Directed International Technological Change and Climate Policy: New Methods for Identifying Robust Policies Under Conditions of Deep Uncertainty

    Science.gov (United States)

    Molina-Perez, Edmundo

    It is widely recognized that international environmental technological change is key to reduce the rapidly rising greenhouse gas emissions of emerging nations. In 2010, the United Nations Framework Convention on Climate Change (UNFCCC) Conference of the Parties (COP) agreed to the creation of the Green Climate Fund (GCF). This new multilateral organization has been created with the collective contributions of COP members, and has been tasked with directing over USD 100 billion per year towards investments that can enhance the development and diffusion of clean energy technologies in both advanced and emerging nations (Helm and Pichler, 2015). The landmark agreement arrived at the COP 21 has reaffirmed the key role that the GCF plays in enabling climate mitigation as it is now necessary to align large scale climate financing efforts with the long-term goals agreed at Paris 2015. This study argues that because of the incomplete understanding of the mechanics of international technological change, the multiplicity of policy options and ultimately the presence of climate and technological change deep uncertainty, climate financing institutions such as the GCF, require new analytical methods for designing long-term robust investment plans. Motivated by these challenges, this dissertation shows that the application of new analytical methods, such as Robust Decision Making (RDM) and Exploratory Modeling (Lempert, Popper and Bankes, 2003) to the study of international technological change and climate policy provides useful insights that can be used for designing a robust architecture of international technological cooperation for climate change mitigation. For this study I developed an exploratory dynamic integrated assessment model (EDIAM) which is used as the scenario generator in a large computational experiment. The scope of the experimental design considers an ample set of climate and technological scenarios. These scenarios combine five sources of uncertainty

  20. Advantages and Limitations of Direct PCR Amplification of Bacterial 16S-rDNA from Resected Heart Tissue or Swabs Followed by Direct Sequencing for Diagnosing Infective Endocarditis: A Retrospective Analysis in the Routine Clinical Setting

    Directory of Open Access Journals (Sweden)

    Daniela Maneg

    2016-01-01

    Full Text Available Infective endocarditis (IE is a life-threatening disease that is associated with high morbidity and mortality. Its long-term prognosis strongly depends on a timely and optimized antibiotic treatment. Therefore, identification of the causative pathogen is crucial and currently based on blood cultures followed by characterization and susceptibility testing of the isolate. However, antibiotic treatment starting prior to blood sampling or IE caused by fastidious or intracellular microorganisms may cause negative culture results. Here we investigate the additional diagnostic value of broad-range PCR in combination with direct sequencing on resected heart tissue or swabs in patients with tissue or swab culture-negative IE in a routine clinical setting. Sensitivity, specificity, and positive and negative predictive values of broad-range PCR from diagnostic material in our patients were 33.3%, 76.9%, 90.9%, and 14.3%, respectively. We identified a total of 20 patients (21.5% with tissue or culture-negative IE who profited by the additional application of broad-range PCR. We conclude that broad-range PCR on resected heart tissue or swabs is an important complementary diagnostic approach. It should be seen as an indispensable new tool for both the therapeutic and diagnostic management of culture-negative IE and we thus propose its possible inclusion in Duke’s diagnostic classification scheme.

  1. Advantages and Limitations of Direct PCR Amplification of Bacterial 16S-rDNA from Resected Heart Tissue or Swabs Followed by Direct Sequencing for Diagnosing Infective Endocarditis: A Retrospective Analysis in the Routine Clinical Setting.

    Science.gov (United States)

    Maneg, Daniela; Sponsel, Janina; Müller, Iris; Lohr, Benedikt; Penders, John; Madlener, Katharina; Hunfeld, Klaus-Peter

    2016-01-01

    Infective endocarditis (IE) is a life-threatening disease that is associated with high morbidity and mortality. Its long-term prognosis strongly depends on a timely and optimized antibiotic treatment. Therefore, identification of the causative pathogen is crucial and currently based on blood cultures followed by characterization and susceptibility testing of the isolate. However, antibiotic treatment starting prior to blood sampling or IE caused by fastidious or intracellular microorganisms may cause negative culture results. Here we investigate the additional diagnostic value of broad-range PCR in combination with direct sequencing on resected heart tissue or swabs in patients with tissue or swab culture-negative IE in a routine clinical setting. Sensitivity, specificity, and positive and negative predictive values of broad-range PCR from diagnostic material in our patients were 33.3%, 76.9%, 90.9%, and 14.3%, respectively. We identified a total of 20 patients (21.5%) with tissue or culture-negative IE who profited by the additional application of broad-range PCR. We conclude that broad-range PCR on resected heart tissue or swabs is an important complementary diagnostic approach. It should be seen as an indispensable new tool for both the therapeutic and diagnostic management of culture-negative IE and we thus propose its possible inclusion in Duke's diagnostic classification scheme.

  2. Direct protein-protein interaction between PLCγ1 and the bradykinin B2 receptor-Importance of growth conditions

    International Nuclear Information System (INIS)

    Duchene, Johan; Chauhan, Sharmila D.; Lopez, Frederic; Pecher, Christiane; Esteve, Jean-Pierre; Girolami, Jean-Pierre; Bascands, Jean-Loup; Schanstra, Joost P.

    2005-01-01

    Recently, we have described a novel protein-protein interaction between the G-protein coupled bradykinin B2 receptor and tyrosine phosphatase SHP-2 via an immunoreceptor tyrosine-based inhibition motif (ITIM) sequence located in the C-terminal part of the B2 receptor and the Src homology (SH2) domains of SHP-2. Here we show that phospholipase C (PLC)γ1, another SH2 domain containing protein, can also interact with this ITIM sequence. Using surface plasmon resonance analysis, we observed that PLCγ1 interacted with a peptide containing the phosphorylated form of the bradykinin B2 receptor ITIM sequence. In CHO cells expressing the wild-type B2 receptor, bradykinin-induced transient recruitment and activation of PLCγ1. Interestingly, this interaction was only observed in quiescent and not in proliferating cells. Mutation of the key ITIM residue abolished this interaction with and activation of PLCγ1. Finally we also identified bradykinin-induced PLCγ1 recruitment and activation in primary culture renal mesangial cells

  3. The directionality of the nuclear transport of the influenza A genome is driven by selective exposure of nuclear localization sequences on nucleoprotein

    Directory of Open Access Journals (Sweden)

    Panté Nelly

    2009-06-01

    Full Text Available Abstract Background Early in infection, the genome of the influenza A virus, consisting of eight complexes of RNA and proteins (termed viral ribonucleoproteins; vRNPs, enters the nucleus of infected cells for replication. Incoming vRNPs are imported into the nucleus of infected cells using at least two nuclear localization sequences on nucleoprotein (NP; NLS1 at the N terminus, and NLS2 in the middle of the protein. Progeny vRNP assembly occurs in the nucleus, and later in infection, these are exported from the nucleus to the cytoplasm. Nuclear-exported vRNPs are different from incoming vRNPs in that they are prevented from re-entering the nucleus. Why nuclear-exported vRNPs do not re-enter the nucleus is unknown. Results To test our hypothesis that the exposure of NLSs on the vRNP regulates the directionality of the nuclear transport of the influenza vRNPs, we immunolabeled the two NLSs of NP (NLS1 and NLS2 and analyzed their surface accessibility in cells infected with the influenza A virus. We found that the NLS1 epitope on NP was exposed throughout the infected cells, but the NLS2 epitope on NP was only exposed in the nucleus of the infected cells. Addition of the nuclear export inhibitor leptomycin B further revealed that NLS1 is no longer exposed in cytoplasmic NP and vRNPs that have already undergone nuclear export. Similar immunolabeling studies in the presence of leptomycin B and with cells transfected with the cDNA of NP revealed that the NLS1 on NP is hidden in nuclear exported-NP. Conclusion NLS1 mediates the nuclear import of newly-synthesized NP and incoming vRNPs. This NLS becomes hidden on nuclear-exported NP and nuclear-exported vRNPs. Thus the selective exposure of the NLS1 constitutes a critical mechanism to regulate the directionality of the nuclear transport of vRNPs during the influenza A viral life cycle.

  4. In silico site-directed mutagenesis informs species-specific predictions of chemical susceptibility derived from the Sequence Alignment to Predict Across Species Susceptibility (SeqAPASS) tool

    Science.gov (United States)

    The Sequence Alignment to Predict Across Species Susceptibility (SeqAPASS) tool was developed to address needs for rapid, cost effective methods of species extrapolation of chemical susceptibility. Specifically, the SeqAPASS tool compares the primary sequence (Level 1), functiona...

  5. Putting instruction sequences into effect

    NARCIS (Netherlands)

    Bergstra, J.A.

    2011-01-01

    An attempt is made to define the concept of execution of an instruction sequence. It is found to be a special case of directly putting into effect of an instruction sequence. Directly putting into effect of an instruction sequences comprises interpretation as well as execution. Directly putting into

  6. The genomic sequence of Exiguobacterium chiriqhucha str. N139 reveals a species that thrives in cold waters and extreme environmental conditions

    Directory of Open Access Journals (Sweden)

    Ana Gutiérrez-Preciado

    2017-04-01

    Full Text Available We report the genome sequence of Exiguobacterium chiriqhucha str. N139, isolated from a high-altitude Andean lake. Comparative genomic analyses of the Exiguobacterium genomes available suggest that our strain belongs to the same species as the previously reported E. pavilionensis str. RW-2 and Exiguobacterium str. GIC 31. We describe this species and propose the chiriqhucha name to group them. ‘Chiri qhucha’ in Quechua means ‘cold lake’, which is a common origin of these three cosmopolitan Exiguobacteria. The 2,952,588-bp E. chiriqhucha str. N139 genome contains one chromosome and three megaplasmids. The genome analysis of the Andean strain suggests the presence of enzymes that confer E. chiriqhucha str. N139 the ability to grow under multiple environmental extreme conditions, including high concentrations of different metals, high ultraviolet B radiation, scavenging for phosphorous and coping with high salinity. Moreover, the regulation of its tryptophan biosynthesis suggests that novel pathways remain to be discovered, and that these pathways might be fundamental in the amino acid metabolism of the microbial community from Laguna Negra, Argentina.

  7. Rapid Diagnostics of Onboard Sequences

    Science.gov (United States)

    Starbird, Thomas W.; Morris, John R.; Shams, Khawaja S.; Maimone, Mark W.

    2012-01-01

    Keeping track of sequences onboard a spacecraft is challenging. When reviewing Event Verification Records (EVRs) of sequence executions on the Mars Exploration Rover (MER), operators often found themselves wondering which version of a named sequence the EVR corresponded to. The lack of this information drastically impacts the operators diagnostic capabilities as well as their situational awareness with respect to the commands the spacecraft has executed, since the EVRs do not provide argument values or explanatory comments. Having this information immediately available can be instrumental in diagnosing critical events and can significantly enhance the overall safety of the spacecraft. This software provides auditing capability that can eliminate that uncertainty while diagnosing critical conditions. Furthermore, the Restful interface provides a simple way for sequencing tools to automatically retrieve binary compiled sequence SCMFs (Space Command Message Files) on demand. It also enables developers to change the underlying database, while maintaining the same interface to the existing applications. The logging capabilities are also beneficial to operators when they are trying to recall how they solved a similar problem many days ago: this software enables automatic recovery of SCMF and RML (Robot Markup Language) sequence files directly from the command EVRs, eliminating the need for people to find and validate the corresponding sequences. To address the lack of auditing capability for sequences onboard a spacecraft during earlier missions, extensive logging support was added on the Mars Science Laboratory (MSL) sequencing server. This server is responsible for generating all MSL binary SCMFs from RML input sequences. The sequencing server logs every SCMF it generates into a MySQL database, as well as the high-level RML file and dictionary name inputs used to create the SCMF. The SCMF is then indexed by a hash value that is automatically included in all command

  8. Transcriptome Profiling Using Single-Molecule Direct RNA Sequencing Approach for In-depth Understanding of Genes in Secondary Metabolism Pathways of Camellia sinensis

    Directory of Open Access Journals (Sweden)

    Qingshan Xu

    2017-07-01

    Full Text Available Characteristic secondary metabolites, including flavonoids, theanine and caffeine, are important components of Camellia sinensis, and their biosynthesis has attracted widespread interest. Previous studies on the biosynthesis of these major secondary metabolites using next-generation sequencing technologies limited the accurately prediction of full-length (FL splice isoforms. Herein, we applied single-molecule sequencing to pooled tea plant tissues, to provide a more complete transcriptome of C. sinensis. Moreover, we identified 94 FL transcripts and four alternative splicing events for enzyme-coding genes involved in the biosynthesis of flavonoids, theanine and caffeine. According to the comparison between long-read isoforms and assemble transcripts, we improved the quality and accuracy of genes sequenced by short-read next-generation sequencing technology. The resulting FL transcripts, together with the improved assembled transcripts and identified alternative splicing events, enhance our understanding of genes involved in the biosynthesis of characteristic secondary metabolites in C. sinensis.

  9. Reactivity of various leishmanial antigens in a direct agglutination test and their value in differentiating post-kala azar dermal leishmaniasis from leprosy and other skin conditions

    NARCIS (Netherlands)

    El Harith, A.; Chowdhury, S.; Al-Masum, A.; Semião-Santos, S.; Das, P. K.; Akhter, S.; Vetter, J. C.; Haq, I.

    1996-01-01

    A direct agglutination test (DAT) for the detection of post-kala azar dermal leishmaniasis (PKDL) was evaluated in conditions that simulate the disease clinically or immunologically. A reference strain of Leishmania donovani (LEM 1399), and antigen preparations from Leishmania isolates from

  10. Directionality of large-scale resting-state brain networks during eyes open and eyes closed conditions

    NARCIS (Netherlands)

    Zhang, Delong; Liang, Bishan; Wu, Xia; Wang, Zengjian; Xu, Pengfei; Chang, Song; Liu, Bo; Liu, Ming; Huang, Ruiwang

    2015-01-01

    The present study examined directional connections in the brain among resting-state networks (RSNs) when the participant had their eyes open (E0) or had their eyes closed (EC). The resting state fMRI data were collected from 20 healthy participants (9 males, 20.17 +/- 2.74 years) under the EO and EC

  11. Conditional Dependence between Response Time and Accuracy: An Overview of its Possible Sources and Directions for Distinguishing between Them

    Science.gov (United States)

    Bolsinova, Maria; Tijmstra, Jesper; Molenaar, Dylan; De Boeck, Paul

    2017-01-01

    With the widespread use of computerized tests in educational measurement and cognitive psychology, registration of response times has become feasible in many applications. Considering these response times helps provide a more complete picture of the performance and characteristics of persons beyond what is available based on response accuracy alone. Statistical models such as the hierarchical model (van der Linden, 2007) have been proposed that jointly model response time and accuracy. However, these models make restrictive assumptions about the response processes (RPs) that may not be realistic in practice, such as the assumption that the association between response time and accuracy is fully explained by taking speed and ability into account (conditional independence). Assuming conditional independence forces one to ignore that many relevant individual differences may play a role in the RPs beyond overall speed and ability. In this paper, we critically consider the assumption of conditional independence and the important ways in which it may be violated in practice from a substantive perspective. We consider both conditional dependences that may arise when all persons attempt to solve the items in similar ways (homogeneous RPs) and those that may be due to persons differing in fundamental ways in how they deal with the items (heterogeneous processes). The paper provides an overview of what we can learn from observed conditional dependences. We argue that explaining and modeling these differences in the RPs is crucial to increase both the validity of measurement and our understanding of the relevant RPs. PMID:28261136

  12. Directionality Effects of Aligned Wind and Wave Loads on a Y-Shape Semi-Submersible Floating Wind Turbine under Rated Operational Conditions

    Directory of Open Access Journals (Sweden)

    Shengtao Zhou

    2017-12-01

    Full Text Available The Y-shape (triangular semi-submersible foundation has been adopted by most of the built full-scale floating wind turbines, such as Windfloat, Fukushima Mirai and Shimpuu. Considering the non-fully-symmetrical shape and met-ocean condition, the foundation laying angle relative to wind/wave directions will not only influence the downtime and power efficiency of the floating turbine, but also the strength and fatigue safety of the whole structure. However, the dynamic responses induced by various aligned wind and wave load directions have scarcely been investigated comparatively before. In our study, the directionality effects are investigated by means of combined wind and wave tests and coupled multi-body simulations. By comparing the measured data in three load directions, it is found that the differences of platform motions are mainly derived from the wave loads and larger pitch motion can always be observed in one of the directions. To make certain the mechanism underlying the observed phenomena, a coupled multi-body dynamic model of the floating wind turbine is established and validated. The numerical results demonstrate that the second-order hydrodynamic forces contribute greatly to the directionality distinctions for surge and pitch, and the first-order hydrodynamic forces determine the variations of tower base bending moments and nacelle accelerations. These findings indicate the directionality effects should be predetermined comprehensively before installation at sea, which is important for the operation and maintenance of the Y-shape floating wind turbines.

  13. Spinning in different directions: western rock lobster larval condition varies with eddy polarity, but does their diet?

    OpenAIRE

    O'Rorke, R.; Jeffs, A. G.; Wang, M.; Waite, A. M.; Beckley, L. E.; Lavery, S. D.

    2015-01-01

    Larvae of the western rock lobster (Panulirus cygnus) that occur in the south-east Indian Ocean offshore of Western Australia have been found to be in poorer nutritional condition in anticyclonic compared with cyclonic mesoscale eddies. The reason for this is unknown, but culture-based experiments have shown that diet composition and water temperature are key determinants of phyllosoma health and survival. Whether differences in prey composition are the cause of poor phyllosoma co...

  14. Experimental evaluation of a direct air-cooled lithium bromide-water absorption prototype for solar air conditioning

    International Nuclear Information System (INIS)

    Gonzalez-Gil, A.; Izquierdo, M.; Marcos, J.D.; Palacios, E.

    2011-01-01

    A new direct air-cooled single-effect LiBr-H 2 O absorption prototype is described and proposed for use in solar cooling. As distinguishing aspects, it presents: an adiabatic absorber using flat-fan sheets; an air-cooling system that directly refrigerates both the condenser and the absorber and; the possibility of being operated also as a double-effect unit. A solar facility comprising a 48 m 2 field of flat-plate collectors was used to test the single-effect operation mode of the prototype. Results from an experimental campaign carried out in Madrid during summer 2010 are shown and operation parameters corresponding to two typical summer days are detailed. The prototype worked efficiently, with COP values around 0.6. Cooling power varied from 2 kW to 3.8 kW, which represented about 85% of the prototype's nominal capacity. Chilled water temperatures mostly ranged between 14 o C and 16 o C, although the lowest measured value was of 12.8 o C. Condensation and absorption temperatures were under 50 o C and 46 o C, respectively, even with outdoor temperatures of 40 o C. Driving water temperature ranged between 85 o C and 110 o C. As a mean, the system was able to meet 65% of the cooling demand corresponding to a room of 40 m 2 . No signs of crystallization were observed during about a hundred hours of operation. - Highlights: → A novel direct air-cooled single-effect absorption prototype is described. → Feasibility of air-cooled technology for LiBr-H 2 O absorption cooling is proved. → An adiabatic absorber using flat-fan sheets avoids crystallization of the solution. → A field of flat-plate collectors powers the chiller at temperatures from 85 to 110 o C. → The prototype works with thermal COP about 0.6.

  15. Direct quantification of human cytomegalovirus immediate-early and late mRNA levels in blood of lung transplant recipients by competitive nucleic acid sequence-based amplification

    NARCIS (Netherlands)

    Greijer, AE; Verschuuren, EAM; Harmsen, MC; Dekkers, CAJ; Adriaanse, HMA; The, TH; Middeldorp, JM

    The dynamics of active human cytomegalovirus (HCMV) infection was monitored by competitive nucleic acid sequence-based amplification (NASBA) assays for quantification of IE1 (UL123) and pp67 (UL65) mRNA expression levels In the blood of patients after lung transplantation. RNA was isolated from 339

  16. High mutation detection rate in the COL4A5 collagen gene in suspected Alport syndrome using PCR and direct DNA sequencing

    DEFF Research Database (Denmark)

    Martin, P; Heiskari, N; Zhou, J

    1998-01-01

    -amplified and sequenced from DNA of 50 randomly chosen patients with suspected Alport syndrome. Mutations were found in 41 patients, giving a mutation detection rate of 82%. Retrospective analysis of clinical data revealed that two of the cases might be autosomal. Although it could not be determined whether the remaining...

  17. Molecular characterization of long direct repeat (LDR) sequences expressing a stable mRNA encoding for a 35-amino-acid cell-killing peptide and a cis-encoded small antisense RNA in Escherichia coli.

    Science.gov (United States)

    Kawano, Mitsuoki; Oshima, Taku; Kasai, Hiroaki; Mori, Hirotada

    2002-07-01

    Genome sequence analyses of Escherichia coli K-12 revealed four copies of long repetitive elements. These sequences are designated as long direct repeat (LDR) sequences. Three of the repeats (LDR-A, -B, -C), each approximately 500 bp in length, are located as tandem repeats at 27.4 min on the genetic map. Another copy (LDR-D), 450 bp in length and nearly identical to LDR-A, -B and -C, is located at 79.7 min, a position that is directly opposite the position of LDR-A, -B and -C. In this study, we demonstrate that LDR-D encodes a 35-amino-acid peptide, LdrD, the overexpression of which causes rapid cell killing and nucleoid condensation of the host cell. Northern blot and primer extension analysis showed constitutive transcription of a stable mRNA (approximately 370 nucleotides) encoding LdrD and an unstable cis-encoded antisense RNA (approximately 60 nucleotides), which functions as a trans-acting regulator of ldrD translation. We propose that LDR encodes a toxin-antitoxin module. LDR-homologous sequences are not pre-sent on any known plasmids but are conserved in Salmonella and other enterobacterial species.

  18. Direct selection of expressed sequences on a YAC clone revealed proline-rich-like genes and BARE-1 sequences physically linked to the complex ¤Mla¤ powdery mildew resistance locus of barley (¤Hordeum vulgare¤ L.)

    DEFF Research Database (Denmark)

    Schwarz, G.; Michalek, W.; Jahoor, A.

    2002-01-01

    homology to the copia-like retroelement BA REI of barley, putatively involved in evolution of disease resistance loci. The high degree of clones representing barley rRNA sequences or false positives is a major disadvantage of direct selection of cDNAs in barley. (C) 2002 Elsevier Science Ireland Ltd. All...... gene. Of 22 selected cDNA clones, six were re-located on the YAC by southern analysis. Two of these clones are predicted to encode members of the hydroxyproline-rich glycoprotein and proline-rich protein gene families which have been implicated in plant defense response. Four sequences showed high...

  19. Optimum performance of the small scale open and direct solar thermal Brayton cycle at various environmental conditions and constraints

    Energy Technology Data Exchange (ETDEWEB)

    Le Roux, W.G.; Bello-Ochende, T.; Meyer, J.P. [Department of Mechanical and Aeronautical Engineering, University of Pretoria, (South Africa)

    2011-07-01

    The energy of the sun can be transformed into mechanical power through the use of concentrated solar power systems. The use of the Brayton cycle with recuperator has significant advantages but also raises issues such as pressure loss and low net power output which are mainly due to irreversibilities of heat transfer and fluid friction. The aim of this study is to optimize the system to generate maximum net power output. Thermodynamic and dynamic trajectory optimizations were performed on a dish concentrator and an off-the-shelf micro-turbine and the effects of wind, solar irradiance and other environmental conditions and constraints on the power output were analyzed. Results showed that the maximum power output is increased when wind decreases and irradiance increases; solar irradiance was found to have a more significant impact than wind. This study highlighted the factors which impact the power generation of concentrated solar power systems so that designers can take them into account.

  20. Direct generation of titanium dioxide nanoparticles dispersion under supercritical conditions for photocatalytic active thermoplastic surfaces for microbiological inactivation

    International Nuclear Information System (INIS)

    Zydziak, Nicolas; Zanin, Maria-Helena Ambrosio; Trick, Iris; Hübner, Christof

    2015-01-01

    Thermoplastic poly(propylene) (PP) and acrylonitrile-butadiene-styrene (ABS) surfaces were coated with silica based films via the sol–gel process, containing titanium dioxide (TiO 2 ) as photocatalyst. TiO 2 was previously synthesized via sol–gel and treated under supercritical conditions in water dispersions. The characterization of the TiO 2 dispersions was performed via disc centrifuge to determine the particle size and via Raman spectroscopy and X-Ray Diffraction (XRD) to characterize the crystallinity of TiO 2 . The synthesized TiO 2 dispersions and commercially available TiO 2 particles were incorporated in silica based films which were synthesized under acidic or basic conditions, leading to dense or porous films respectively. The morphology of the films was characterized via Scanning Electron Microscopy (SEM). The incorporation of synthesized TiO 2 in the coating led to photocatalytically more active thermoplastic surfaces than films formulated with commercially available TiO 2 as determined via dye discoloration test. A microbiological test performed with Sarcina lutea confirmed this result and showed an inactivation factor of 6 (99.9999%) after 24 h UV irradiation, for synthesized TiO 2 incorporated in acidic formulated silica layer on ABS surfaces. - Highlights: • We report about photocatalytic layers formulated on thermoplastic surfaces. • We synthesized silica layer and TiO 2 via sol–gel and supercritical treatment. • Amorphous, crystalline and commercial dispersions were generated and characterized. • The morphology of dense and porous photocatalytic layers is observed via SEM. • Discoloration and microbiological tests correlate activity and surface morphology

  1. Direct generation of titanium dioxide nanoparticles dispersion under supercritical conditions for photocatalytic active thermoplastic surfaces for microbiological inactivation

    Energy Technology Data Exchange (ETDEWEB)

    Zydziak, Nicolas, E-mail: nicolas.zydziak@kit.edu [Polymer Engineering Department, Fraunhofer Institute of Chemical Technology, Joseph-von-Fraunhofer-Str. 7, 76327 Pfinztal (Germany); Zanin, Maria-Helena Ambrosio [Laboratory of Chemical Processes and Particle Technology Bionanomanufacturing, Institute for Technological Research of the State of São Paulo – IPT, Av. Prof. Almeida Prado 532, Cidade Universitária, CEP 05508-901 São Paulo, SP (Brazil); Trick, Iris [Environmental Biotechnology and Bioprocess Engineering Department, Fraunhofer Institute for Interfacial Engineering and Biotechnology, Nobelstrasse 12, 70569 Stuttgart (Germany); Hübner, Christof [Polymer Engineering Department, Fraunhofer Institute of Chemical Technology, Joseph-von-Fraunhofer-Str. 7, 76327 Pfinztal (Germany)

    2015-03-01

    Thermoplastic poly(propylene) (PP) and acrylonitrile-butadiene-styrene (ABS) surfaces were coated with silica based films via the sol–gel process, containing titanium dioxide (TiO{sub 2}) as photocatalyst. TiO{sub 2} was previously synthesized via sol–gel and treated under supercritical conditions in water dispersions. The characterization of the TiO{sub 2} dispersions was performed via disc centrifuge to determine the particle size and via Raman spectroscopy and X-Ray Diffraction (XRD) to characterize the crystallinity of TiO{sub 2}. The synthesized TiO{sub 2} dispersions and commercially available TiO{sub 2} particles were incorporated in silica based films which were synthesized under acidic or basic conditions, leading to dense or porous films respectively. The morphology of the films was characterized via Scanning Electron Microscopy (SEM). The incorporation of synthesized TiO{sub 2} in the coating led to photocatalytically more active thermoplastic surfaces than films formulated with commercially available TiO{sub 2} as determined via dye discoloration test. A microbiological test performed with Sarcina lutea confirmed this result and showed an inactivation factor of 6 (99.9999%) after 24 h UV irradiation, for synthesized TiO{sub 2} incorporated in acidic formulated silica layer on ABS surfaces. - Highlights: • We report about photocatalytic layers formulated on thermoplastic surfaces. • We synthesized silica layer and TiO{sub 2} via sol–gel and supercritical treatment. • Amorphous, crystalline and commercial dispersions were generated and characterized. • The morphology of dense and porous photocatalytic layers is observed via SEM. • Discoloration and microbiological tests correlate activity and surface morphology.

  2. Lever conditioned stimulus-directed autoshaping induced by saccharin-ethanol unconditioned stimulus solution: effects of ethanol concentration and trial spacing.

    Science.gov (United States)

    Tomie, Arthur; Festa, Eugene D; Sparta, Dennis R; Pohorecky, Larissa A

    2003-05-01

    Two experiments were designed to evaluate whether brief access to a saccharin-ethanol solution would function as an effective unconditioned stimulus (US) in Pavlovian-autoshaping procedures. In these experiments, the insertion of a lever conditioned stimulus (CS) was followed by the brief presentation of a sipper tube containing saccharin-ethanol US solution. Experience with this Pavlovian-autoshaping procedure engendered lever CS-directed autoshaping conditioned responses (CRs) in all rats. In Experiment 1, the concentration of ethanol [0%, 2%, 4%, 6%, or 8% (vol./vol.)] in 0.1% saccharin was systematically increased within subjects across autoshaping sessions to evaluate the relation between a rat's drinking and lever pressing. In Experiment 2, the mean intertrial interval (ITI) duration (60, 90, 120 s) was systematically increased within subjects across autoshaping sessions to evaluate the effect of ITI duration on drinking and lever pressing. A pseudoconditioning control group received lever CS randomly with respect to the saccharin-ethanol US solution. In Experiment 1, lever-press autoshaping CRs developed in all rats, and the tendency of a rat to drink an ethanol concentration was predictive of the performance of lever-press autoshaping CRs. In Experiment 2, longer ITIs induced more lever CS-directed responding, and CS-US paired procedures yielded more lever CS-directed responding than that observed in CS-US random procedures. Saccharin-ethanol is an effective US in Pavlovian-autoshaping procedures, inducing more CS-directed responding than in pseudoconditioning controls receiving CS-US random procedures. More lever CS-directed responding was observed when there was more drinking of the saccharin-ethanol US solution (Experiment 1); when the CS and US were paired, rather than random (Experiment 2); and with longer mean ITI durations (Experiment 2). This pattern of results is consistent with the hypothesis that lever CS-directed responding reflects performance

  3. Towards an understanding of self-directed language as a mechanism of behavior change: A novel strategy for eliciting client language under laboratory conditions

    Directory of Open Access Journals (Sweden)

    Benjamin O. Ladd

    2018-06-01

    Full Text Available Introduction: Change talk (CT and sustain talk (ST are thought to reflect underlying motivation and be important mechanisms of behavior change (MOBCs. However, greater specificity and experimental rigor is needed to establish CT and ST as MOBCs. Testing the effects of self-directed language under laboratory conditions is one promising avenue. The current study presents a replication and extension of research examining the feasibility for using simulation tasks to elicit self-directed language. Methods: First-year college students (N=92 responded to the Collegiate Simulated Intoxication Digital Elicitation, a validated task for assessing decision-making in college drinking. Verbal responses elicited via free-response and structured interview formats were coded based on established definitions of CT and ST, with minor modifications to reflect the non-treatment context. Associations between self-directed language and alcohol use at baseline and eight months were examined. Additionally, this study examined whether a contextually-based measure of decision-making, behavioral willingness, mediated relationships between self-directed language and alcohol outcome. Results: Healthy talk and unhealthy talk independently were associated with baseline alcohol use across both elicitation formats. Only healthy talk during the free-response elicitation was associated with alcohol use at follow up; both healthy talk and unhealthy talk during the interview elicitation were associated with 8-month alcohol use. Behavioral willingness significantly mediated the relationship between percent healthy talk and alcohol outcome. Conclusions: Findings support the utility of studying self-directed language under laboratory conditions and suggest that such methods may provide a fruitful strategy to further understand the role of self-directed language as a MOBC. Keywords: Change talk, College students, Alcohol, Simulation task

  4. Initial discussion on ore-forming conditions and prospecting direction of volcanic type uranium deposits in the gangdise tectonic belt

    International Nuclear Information System (INIS)

    Zhao Baoguang; Wang Sili; Wang Qin; Sun Yue; Du Xiaolin; Chen Yuliang

    2010-01-01

    The most active volcanic activity in the Gangdise tectonic belt happened in early Cretaceous, Paleocene and Eocene, and Eocene is the most active period. The distribution of volcanic rock is controlled by latitudinal deep fault and deuteric longitudinal fault. Paleo-volcano was located at these structural compounds frequently. The volcanics which appeared near the merdional large scale pull-apart construction in Neogene is considered as land facies medium-acidic volcanics which brought by various kinds of volcanic basin. A large stream sediment anomaly (>6.8 x 10 -6 ) has been found at Cenozoic volcanics in south of CuoQin basin, and its areas amount to hundreds square kilometers. The uranium content of volcanics in Wuyu basin amounts to 20.0 x 10 -6 at most. It has favorable Ore-forming conditions for forming volcanic type uranium deposit due to the volcanic geologic environment, accompanying mineral, region feature of geochemistry and geophysical, volcanic-tectonic depression and so on. The major prospecting targets are the south of CuoQin basin and the Nanmulin district. (authors)

  5. Mineralogy, composition and PGM of chromitites from Pefki, Pindos ophiolite complex (NW Greece): evidence for progressively elevated fAs conditions in the upper mantle sequence

    Science.gov (United States)

    Kapsiotis, Argirios; Grammatikopoulos, Tassos A.; Tsikouras, Basilios; Hatzipanagiotou, Konstantin; Zaccarini, Federica; Garuti, Giorgio

    2011-01-01

    The Pindos ophiolite complex, located in the northwestern part of continental Greece, hosts various chromite deposits of both metallurgical (high-Cr) and refractory (high-Al) type. The Pefki chromitites are banded and sub-concordant to the surrounding serpentinized dunites. The Cr# [Cr/(Cr + Al)] of magnesiochromite varies between 0.75 and 0.79. The total PGE grade ranges from 105.9 up to 300.0 ppb. IPGE are higher than PPGE, typical of mantle hosted ophiolitic chromitites. The PGM assemblage in chromitites comprises anduoite, ruarsite, laurite, irarsite, sperrylite, hollingworthite, Os-Ru-Ir alloys including osmium and rutheniridosmine, Ru-bearing oxides, braggite, paolovite, platarsite, cooperite, vysotskite, and palladodymite. Iridarsenite and omeiite were also observed as exsolutions in other PGM. Rare electrum and native Ag are recovered in concentrates. This PGM assemblage is of great petrogenetic importance because it is significantly different from that commonly observed in podiform mantle-hosted and banded crustal-hosted ophiolitic chromitites. PGE chalcogenides of As and S are primary, and possibly crystallized directly from a progressively enriched in As boninitic melt before or during magnesiochromite precipitation. The presence of Ru-bearing oxides implies simultaneous desulfurization and dearsenication processes. Chemically zoned laurite and composite paolovite-electrum intergrowths are indicative of the relatively high mobility of certain PGE at low temperatures under locally oxidizing conditions. The PGM assemblage and chemistry, in conjunction with geological and petrologic data of the studied chromitites, indicate that it is characteristic of chromitites found within or close to the petrologic Moho. Furthermore, the strikingly different PGM assemblages between the high-Cr chromitites within the Pindos massif is suggestive of non-homogeneous group of ores.

  6. Deep nirS amplicon sequencing of San Francisco Bay sediments enables prediction of geography and environmental conditions from denitrifying community composition.

    Science.gov (United States)

    Lee, Jessica A; Francis, Christopher A

    2017-12-01

    Denitrification is a dominant nitrogen loss process in the sediments of San Francisco Bay. In this study, we sought to understand the ecology of denitrifying bacteria by using next-generation sequencing (NGS) to survey the diversity of a denitrification functional gene, nirS (encoding cytchrome-cd 1 nitrite reductase), along the salinity gradient of San Francisco Bay over the course of a year. We compared our dataset to a library of nirS sequences obtained previously from the same samples by standard PCR cloning and Sanger sequencing, and showed that both methods similarly demonstrated geography, salinity and, to a lesser extent, nitrogen, to be strong determinants of community composition. Furthermore, the depth afforded by NGS enabled novel techniques for measuring the association between environment and community composition. We used Random Forests modelling to demonstrate that the site and salinity of a sample could be predicted from its nirS sequences, and to identify indicator taxa associated with those environmental characteristics. This work contributes significantly to our understanding of the distribution and dynamics of denitrifying communities in San Francisco Bay, and provides valuable tools for the further study of this key N-cycling guild in all estuarine systems. © 2017 Society for Applied Microbiology and John Wiley & Sons Ltd.

  7. Detection and Resolution of Cryptosporidium Species and Species Mixtures by Genus-Specific Nested PCR-Restriction Fragment Length Polymorphism Analysis, Direct Sequencing, and Cloning ▿

    Science.gov (United States)

    Ruecker, Norma J.; Hoffman, Rebecca M.; Chalmers, Rachel M.; Neumann, Norman F.

    2011-01-01

    Molecular methods incorporating nested PCR-restriction fragment length polymorphism (RFLP) analysis of the 18S rRNA gene of Cryptosporidium species were validated to assess performance based on limit of detection (LoD) and for detecting and resolving mixtures of species and genotypes within a single sample. The 95% LoD was determined for seven species (Cryptosporidium hominis, C. parvum, C. felis, C. meleagridis, C. ubiquitum, C. muris, and C. andersoni) and ranged from 7 to 11 plasmid template copies with overlapping 95% confidence limits. The LoD values for genomic DNA from oocysts on microscope slides were 7 and 10 template copies for C. andersoni and C. parvum, respectively. The repetitive nested PCR-RFLP slide protocol had an LoD of 4 oocysts per slide. When templates of two species were mixed in equal ratios in the nested PCR-RFLP reaction mixture, there was no amplification bias toward one species over another. At high ratios of template mixtures (>1:10), there was a reduction or loss of detection of the less abundant species by RFLP analysis, most likely due to heteroduplex formation in the later cycles of the PCR. Replicate nested PCR was successful at resolving many mixtures of Cryptosporidium at template concentrations near or below the LoD. The cloning of nested PCR products resulted in 17% of the cloned sequences being recombinants of the two original templates. Limiting-dilution nested PCR followed by the sequencing of PCR products resulted in no sequence anomalies, suggesting that this method is an effective and accurate way to study the species diversity of Cryptosporidium, particularly for environmental water samples, in which mixtures of parasites are common. PMID:21498746

  8. Evaluation of Direct 16S rDNA Sequencing as a Metagenomics-based Approach to Screening Bacteria in Bottled Water

    DEFF Research Database (Denmark)

    Hansen, Trine; Skånseng, Beate; Hoorfar, Jeffrey

    2013-01-01

    Deliberate or accidental contamination of food, feed, and water supplies poses a threat to human health worldwide. A rapid and sensitive detection technique that could replace the current labor-intensive and time-consuming culture-based methods is highly desirable. In addition to species...... 2 B. cereus strains by the principal component plot, despite the close sequence resemblance. A linear correlation between the artificial contamination level and the relative amount of the Bacillus artificial contaminant in the metagenome was observed, and a relative amount value above 0.5 confirmed...

  9. Immunoglobulin variable region sequences of two human monoclonal antibodies directed to an onco-developmental carbohydrate antigen, lactotetraosylceramide (LcOse4Cer).

    Science.gov (United States)

    Yago, K; Zenita, K; Ohwaki, I; Harada, R; Nozawa, S; Tsukazaki, K; Iwamori, M; Endo, N; Yasuda, N; Okuma, M

    1993-11-01

    A human monoclonal antibody, 11-50, was generated and was shown to recognize an onco-developmental carbohydrate antigen, LcOse4Cer. The isotype of this antibody was IgM, lambda, similar to the previously known human anti-LcOse4 antibodies, such as IgMWOO and HMST-1. We raised a murine anti-idiotypic antibody G3 (IgG1, kappa) against 11-50, and tested its reactivity towards the affinity purified human polyclonal anti-LcOse4 antibodies prepared from pooled human sera using a Gal beta 1-->3GlcNAc beta-immobilized column. The results indicated that at least a part of the human polyclonal anti-LcOse4 antibodies shared the G3 idiotype with 11-50. We further analyzed the sequence of variable regions of the two anti-LcOse4 antibodies, 11-50 and HMST-1. Sequence analysis of the heavy chain variable regions indicated that the VH regions of these two antibodies were highly homologous to each other (93.5% at the nucleic acid level), and these antibodies utilized the germline genes VH1.9III and hv3005f3 as the VH segments, which are closely related germline genes of the VHIII family. It was noted that these germline VH genes are frequently utilized in fetal B cells. The JH region of both antibodies was encoded by the JH4 gene. For the light chain, the V lambda segments of the two antibodies were 96.3% homologous to each other at the nucleic acid level. The V lambda segments of both antibodies showed the highest homology to the rearranged V lambda gene called V lambda II.DS among reported V lambda genes, while the exact germline V lambda genes encoding the two antibodies were not yet registered in available sequence databanks. The amino acid sequences of the J lambda segments of both antibodies were identical. These results indicate that the two human antibodies recognizing the onco-developmental carbohydrate antigen Lc4 are encoded by the same or very homologous germline genes.

  10. Neuromodulation of conditioned placebo/nocebo in heat pain: anodal vs cathodal transcranial direct current stimulation to the right dorsolateral prefrontal cortex.

    Science.gov (United States)

    Egorova, Natalia; Yu, Rongjun; Kaur, Navneet; Vangel, Mark; Gollub, Randy L; Dougherty, Darin D; Kong, Jian; Camprodon, Joan A

    2015-07-01

    Placebo and nocebo play an important role in clinical practice and medical research. Modulating placebo/nocebo responses using noninvasive brain stimulation methods, such as transcranial direct current stimulation (tDCS), has the potential to harness these effects to therapeutic benefit in a clinical setting. In this study, we assessed the effect of anodal and cathodal tDCS over the right dorsolateral prefrontal cortex (rDLPFC) on conditioned placebo/nocebo cue response to heat pain. Two matched groups of healthy volunteers were subjected to an identical session of conditioning, during which low and high cues (abstract images) were associated with low and high pain levels, respectively. Twenty-minute 2-mA tDCS (either anodal or cathodal) over the rDLPFC was applied. The influence of tDCS current polarity (anodal vs cathodal) on placebo and nocebo was assessed, using subjects' pain ratings in response to identical pain preceded by the conditioned high or low cues. The duration of cue presentation varied to allow either fully conscious or subliminal processing. Significant placebo and nocebo effects in the anodal but not the cathodal group were elicited with the conditioning paradigm. This study provides evidence of a possibility to modulate the conditioned placebo and nocebo effect by changing the excitability of the rDLPFC using tDCS.

  11. Experimental analysis of a direct expansion solar assisted heat pump with integral storage tank for domestic water heating under zero solar radiation conditions

    International Nuclear Information System (INIS)

    Fernández-Seara, José; Piñeiro, Carolina; Alberto Dopazo, J.; Fernandes, F.; Sousa, Paulo X.B.

    2012-01-01

    Highlights: ► We analyze a direct expansion solar assisted heat pump under zero solar radiation. ► We determine the COP and equivalent seasonal performance factors (SPFe). ► We determine the main components’ performance under transient operating conditions. ► The Huang and Lee performance evaluation method provides a characteristic COP of 3.23. - Abstract: This paper deals with the experimental evaluation of the performance of a direct expansion solar assisted heat pump water heating (DX-SAHPWH) system working under zero solar radiation conditions at static heating operation mode of the storage tank. The DX-SAHPWH system includes two bare solar collectors as evaporator, a R134a rotary-type hermetic compressor, a thermostatic expansion valve and a helical coil condenser immersed in a 300 L water storage tank. The zero solar radiation and stable ambient air temperature working conditions were established by placing the solar collectors into a climate chamber. The analysis is based on experimental data taken from the DX-SAHPWH provided by the manufacturer and equipped with an appropriate data acquisition system. In the paper, the experimental facility, the data acquisition system and the experimental methodology are described. Performance parameters to evaluate the energy efficiency, such as COP and equivalent seasonal performance factors (SPFe) for the heating period, and the water thermal stratification in the storage tank are defined and obtained from the experimental data. Results from the experimental analysis under transient operating working conditions of the DX-SAHPWH system and its main components are shown and discussed. Lastly, the Huang and Lee DX-SAHPWH performance evaluation method was applied resulting in a characteristic COP of 3.23 for the DX-SAHPWH system evaluated under zero solar radiation condition.

  12. Direct detection of RNA in vitro and in situ by target-primed RCA: The impact of E. coli RNase III on the detection efficiency of RNA sequences distanced far from the 3'-end.

    Science.gov (United States)

    Merkiene, Egle; Gaidamaviciute, Edita; Riauba, Laurynas; Janulaitis, Arvydas; Lagunavicius, Arunas

    2010-08-01

    We improved the target RNA-primed RCA technique for direct detection and analysis of RNA in vitro and in situ. Previously we showed that the 3' --> 5' single-stranded RNA exonucleolytic activity of Phi29 DNA polymerase converts the target RNA into a primer and uses it for RCA initiation. However, in some cases, the single-stranded RNA exoribonucleolytic activity of the polymerase is hindered by strong double-stranded structures at the 3'-end of target RNAs. We demonstrate that in such hampered cases, the double-stranded RNA-specific Escherichia coli RNase III efficiently assists Phi29 DNA polymerase in converting the target RNA into a primer. These observations extend the target RNA-primed RCA possibilities to test RNA sequences distanced far from the 3'-end and customize this technique for the inner RNA sequence analysis.

  13. A directed approach for the identification of transcripts harbouring the spliced leader sequence and the effect of trans-splicing knockdown in Schistosoma mansoni

    Directory of Open Access Journals (Sweden)

    Marina de Moraes Mourao

    2013-09-01

    Full Text Available Schistosomiasis is a major neglected tropical disease caused by trematodes from the genus Schistosoma. Because schistosomes exhibit a complex life cycle and numerous mechanisms for regulating gene expression, it is believed that spliced leader (SL trans-splicing could play an important role in the biology of these parasites. The purpose of this study was to investigate the function of trans-splicing in Schistosoma mansoni through analysis of genes that may be regulated by this mechanism and via silencing SL-containing transcripts through RNA interference. Here, we report our analysis of SL transcript-enriched cDNA libraries from different S. mansoni life stages. Our results show that the trans-splicing mechanism is apparently not associated with specific genes, subcellular localisations or life stages. In cross-species comparisons, even though the sets of genes that are subject to SL trans-splicing regulation appear to differ between organisms, several commonly shared orthologues were observed. Knockdown of trans-spliced transcripts in sporocysts resulted in a systemic reduction of the expression levels of all tested trans-spliced transcripts; however, the only phenotypic effect observed was diminished larval size. Further studies involving the findings from this work will provide new insights into the role of trans-splicing in the biology of S. mansoni and other organisms. All Expressed Sequence Tags generated in this study were submitted to dbEST as five different libraries. The accessions for each library and for the individual sequences are as follows: (i adult worms of mixed sexes (LIBEST_027999: JZ139310 - JZ139779, (ii female adult worms (LIBEST_028000: JZ139780 - JZ140379, (iii male adult worms (LIBEST_028001: JZ140380 - JZ141002, (iv eggs (LIBEST_028002: JZ141003 - JZ141497 and (v schistosomula (LIBEST_028003: JZ141498 - JZ141974.

  14. Real-time tracking of tumor motions and deformations along the leaf travel direction with the aid of a synchronized dynamic MLC leaf sequencer

    International Nuclear Information System (INIS)

    Tacke, Martin; Nill, Simeon; Oelfke, Uwe

    2007-01-01

    Advanced radiotherapeutical techniques like intensity-modulated radiation therapy (IMRT) are based on an accurate knowledge of the location of the radiation target. An accurate dose delivery, therefore, requires a method to account for the inter- and intrafractional target motion and the target deformation occurring during the course of treatment. A method to compensate in real time for changes in the position and shape of the target is the use of a dynamic multileaf collimator (MLC) technique which can be devised to automatically arrange the treatment field according to real-time image information. So far, various approaches proposed for leaf sequencers have had to rely on a priori known target motion data and have aimed to optimize the overall treatment time. Since for a real-time dose delivery the target motion is not known a priori, the velocity range of the leading leaves is restricted by a safety margin to c x v max while the following leaves can travel with an additional maximum speed to compensate for the respective target movements. Another aspect to be considered is the tongue and groove effect. A uniform radiation field can only be achieved if the leaf movements are synchronized. The method presented in this note is the first to combine a synchronizing sequencer and real-time tracking with a dynamic MLC. The newly developed algorithm is capable of online optimizing the leaf velocities by minimizing the overall treatment time while at the same time it synchronizes the leaf trajectories in order to avoid the tongue and groove effect. The simultaneous synchronization is performed with the help of an online-calculated mid-time leaf trajectory which is common for all leaf pairs and which takes into account the real-time target motion and deformation information. (note)

  15. Real-time tracking of tumor motions and deformations along the leaf travel direction with the aid of a synchronized dynamic MLC leaf sequencer.

    Science.gov (United States)

    Tacke, Martin; Nill, Simeon; Oelfke, Uwe

    2007-11-21

    Advanced radiotherapeutical techniques like intensity-modulated radiation therapy (IMRT) are based on an accurate knowledge of the location of the radiation target. An accurate dose delivery, therefore, requires a method to account for the inter- and intrafractional target motion and the target deformation occurring during the course of treatment. A method to compensate in real time for changes in the position and shape of the target is the use of a dynamic multileaf collimator (MLC) technique which can be devised to automatically arrange the treatment field according to real-time image information. So far, various approaches proposed for leaf sequencers have had to rely on a priori known target motion data and have aimed to optimize the overall treatment time. Since for a real-time dose delivery the target motion is not known a priori, the velocity range of the leading leaves is restricted by a safety margin to c x v(max) while the following leaves can travel with an additional maximum speed to compensate for the respective target movements. Another aspect to be considered is the tongue and groove effect. A uniform radiation field can only be achieved if the leaf movements are synchronized. The method presented in this note is the first to combine a synchronizing sequencer and real-time tracking with a dynamic MLC. The newly developed algorithm is capable of online optimizing the leaf velocities by minimizing the overall treatment time while at the same time it synchronizes the leaf trajectories in order to avoid the tongue and groove effect. The simultaneous synchronization is performed with the help of an online-calculated mid-time leaf trajectory which is common for all leaf pairs and which takes into account the real-time target motion and deformation information.

  16. Analysis of Direct Outdoor Air Cooling Efficency for Combined Variable Air Volume Air-conditioning System in Stores in Cold Climates of China

    OpenAIRE

    Luo, Zhiwen

    2006-01-01

    Direct outdoor air cooling contributes a lot not only to the improvement of the indoor air quality but also to the energy saving. Its full use will reduce the water chiller’s running time especially in some stores where cooling load keeps much higher and longer than that in other buildings. A novel air-conditioning system named Combined Variable Air Volume system (CVAV), combining a normal AHU with a separate outdoor air supply system, was proposed firstly by the authors. The most attractive ...

  17. Frosting characteristics and heating performance of a direct-expansion solar-assisted heat pump for space heating under frosting conditions

    International Nuclear Information System (INIS)

    Huang, Wenzhu; Ji, Jie; Xu, Ning; Li, Guiqiang

    2016-01-01

    Highlights: • Frosting and heating performance of DX-SAHP under frosting conditions is investigated. • The conditions when DX-SAHP frosts are studied. • The frosting process is observed during 360 min of operating. • The effect of ambient temperature, relative humidity and solar irradiation is analyzed. - Abstract: Direct expansion solar-assisted heat pump system (DX-SAHP) is promising in energy saving applications, but the performance of DX-SAHP under frosting conditions is rarely reported in the published literatures. In this paper, a DX-SAHP system with bare solar collectors for space heating is designed and experimentally investigated in the enthalpy difference lab with a solar simulator. The system is tested under a range of frosting conditions, with the ambient temperatures from 7 °C to −3 °C, the relative humidities of 50%, 70% and 90% and the solar irradiances of 0 W/m"2, 100 W/m"2, 200 W/m"2 and 300 W/m"2. The conditions when the DX-SAHP system frosts are studied. Results show that solar irradiance as low as 100 W/m"2 can totally prevent frosting when the ambient temperature is above −3 °C and the relative humidity is 70%. Besides, the frosting process is observed to be slower than that of fin-and-tube heat exchangers. The evaporator is not seriously frosted and the system performance is not significantly influenced after 360 min of continuous operating. Moreover the effects of ambient parameters, including the ambient temperature and the relative humidity, especially solar irradiation, on the system performance are studied and analyzed. Solar irradiation can effectively prevent or retard frosting, and also improve the heating performance of the DX-SAHP system. The DX-SAHP system is proved to be applicable under frosting conditions.

  18. The application of strand invasion phenomenon, directed by peptide nucleic acid (PNA) and single-stranded DNA binding protein (SSB) for the recognition of specific sequences of human endogenous retroviral HERV-W family.

    Science.gov (United States)

    Machnik, Grzegorz; Bułdak, Łukasz; Ruczyński, Jarosław; Gąsior, Tomasz; Huzarska, Małgorzata; Belowski, Dariusz; Alenowicz, Magdalena; Mucha, Piotr; Rekowski, Piotr; Okopień, Bogusław

    2017-05-01

    The HERV-W family of human endogenous retroviruses represents a group of numerous sequences that show close similarity in genetic composition. It has been documented that some members of HERV-W-derived expression products are supposed to play significant role in humans' pathology, such as multiple sclerosis or schizophrenia. Other members of the family are necessary to orchestrate physiological processes (eg, ERVWE1 coding syncytin-1 that is engaged in syncytiotrophoblast formation). Therefore, an assay that would allow the recognition of particular form of HERV-W members is highly desirable. A peptide nucleic acid (PNA)-mediated technique for the discrimination between multiple sclerosis-associated retrovirus and ERVWE1 sequence has been developed. The assay uses a PNA probe that, being fully complementary to the ERVWE1 but not to multiple sclerosis-associated retrovirus (MSRV) template, shows high selective potential. Single-stranded DNA binding protein facilitates the PNA-mediated, sequence-specific formation of strand invasion complex and, consequently, local DNA unwinding. The target DNA may be then excluded from further analysis in any downstream process such as single-stranded DNA-specific exonuclease action. Finally, the reaction conditions have been optimized, and several PNA probes that are targeted toward distinct loci along whole HERV-W env sequences have been evaluated. We believe that PNA/single-stranded DNA binding protein-based application has the potential to selectively discriminate particular HERV-W molecules as they are at least suspected to play pathogenic role in a broad range of medical conditions, from psycho-neurologic disorders (multiple sclerosis and schizophrenia) and cancers (breast cancer) to that of an auto-immunologic background (psoriasis and lupus erythematosus). Copyright © 2016 John Wiley & Sons, Ltd.

  19. Relaxed damage threshold intensity conditions and nonlinear increase in the conversion efficiency of an optical parametric oscillator using a bi-directional pump geometry.

    Science.gov (United States)

    Norris, G; McConnell, G

    2010-03-01

    A novel bi-directional pump geometry that nonlinearly increases the nonlinear optical conversion efficiency of a synchronously pumped optical parametric oscillator (OPO) is reported. This bi-directional pumping method synchronizes the circulating signal pulse with two counter-propagating pump pulses within a linear OPO resonator. Through this pump scheme, an increase in nonlinear optical conversion efficiency of 22% was achieved at the signal wavelength, corresponding to a 95% overall increase in average power. Given an almost unchanged measured pulse duration of 260 fs under optimal performance conditions, this related to a signal wavelength peak power output of 18.8 kW, compared with 10 kW using the traditional single-pass geometry. In this study, a total effective peak intensity pump-field of 7.11 GW/cm(2) (corresponding to 3.55 GW/cm(2) from each pump beam) was applied to a 3 mm long periodically poled lithium niobate crystal, which had a damage threshold intensity of 4 GW/cm(2), without impairing crystal integrity. We therefore prove the application of this novel pump geometry provides opportunities for power-scaling of synchronously pumped OPO systems together with enhanced nonlinear conversion efficiency through relaxed damage threshold intensity conditions.

  20. Fundamental Evaluation of Adaptation and Human Capabilities in a Condition Using a System to Give a User an Artificial Oculomotor Function to Control Directions of Both Eyes Independently

    Directory of Open Access Journals (Sweden)

    Fumio Mizuno

    2011-10-01

    Full Text Available To investigate flexible adaptation of visual system, we developed a system to provide a user an artificial oculomotor function to control directions of both eyes. The system named “Virtual Chameleon” consists of two CCD cameras independently controlled and a head-mounted display. The user can control each tracking directions of two cameras with sensors set to both hands so that the user can get independent arbitrary view fields for both eyes. We performed fundamental experiments to evaluate capability to evaluate adaptation to use of Virtual Chameleon and effects on the user's capabilities. Eleven healthy volunteers with normal and corrected-to-normal vision participated in the experiments. The experiments were tests to find out each position of targets put in both side of a subject. In the experiments, a condition using Virtual Chameleon and a condition without it was adopted. We obtained accuracy rates and time intervals to find out target positions as experimental results. The experiments showed all of volunteers became able to actively control independent visual axes and correctly understood two different views by using Virtual Chameleon, even though two independent view fields yielded binocular rivalry to volunteers and binocular rivalry reduced human capabilities compared to cases without Virtual Chameleon.

  1. Ct shift: A novel and accurate real-time PCR quantification model for direct comparison of different nucleic acid sequences and its application for transposon quantifications.

    Science.gov (United States)

    Kolacsek, Orsolya; Pergel, Enikő; Varga, Nóra; Apáti, Ágota; Orbán, Tamás I

    2017-01-20

    There are numerous applications of quantitative PCR for both diagnostic and basic research. As in many other techniques the basis of quantification is that comparisons are made between different (unknown and known or reference) specimens of the same entity. When the aim is to compare real quantities of different species in samples, one cannot escape their separate precise absolute quantification. We have established a simple and reliable method for this purpose (Ct shift method) which combines the absolute and the relative approach. It requires a plasmid standard containing both sequences of amplicons to be compared (e.g. the target of interest and the endogenous control). It can serve as a reference sample with equal copies of templates for both targets. Using the ΔΔCt formula we can quantify the exact ratio of the two templates in each unknown sample. The Ct shift method has been successfully applied for transposon gene copy measurements, as well as for comparison of different mRNAs in cDNA samples. This study provides the proof of concept and introduces some potential applications of the method; the absolute nature of results even without the need for real reference samples can contribute to the universality of the method and comparability of different studies. Copyright © 2016 Elsevier B.V. All rights reserved.

  2. Distortion-free diffusion tensor imaging for evaluation of lumbar nerve roots: Utility of direct coronal single-shot turbo spin-echo diffusion sequence.

    Science.gov (United States)

    Sakai, Takayuki; Doi, Kunio; Yoneyama, Masami; Watanabe, Atsuya; Miyati, Tosiaki; Yanagawa, Noriyuki

    2018-06-01

    Diffusion tensor imaging (DTI) based on a single-shot echo planer imaging (EPI-DTI) is an established method that has been used for evaluation of lumbar nerve disorders in previous studies, but EPI-DTI has problems such as a long acquisition time, due to a lot of axial slices, and geometric distortion. To solve these problems, we attempted to apply DTI based on a single-shot turbo spin echo (TSE-DTI) with direct coronal acquisition. Our purpose in this study was to investigate whether TSE-DTI may be more useful for evaluation of lumbar nerve disorders than EPI-DTI. First, lumbar nerve roots of five healthy volunteers were evaluated for optimization of imaging parameters with TSE-DTI including b-values and the number of motion proving gradient (MPG) directions. Subsequently, optimized TSE-DTI was quantitatively compared with conventional EPI-DTI by using fractional anisotropy (FA) values and visual scores in subjective visual evaluation of tractography. Lumbar nerve roots of six patients, who had unilateral neurologic symptoms in one leg, were evaluated by the optimized TSE-DTI. TSE-DTI with b-value of 400 s/mm 2 and 32 diffusion-directions could reduce the image distortion compared with EPI-DTI, and showed that the average FA values on the symptomatic side for six patients were significantly lower than those on the non-symptomatic side (P DTI might show damaged areas of lumbar nerve roots without severe image distortion. TSE-DTI might improve the reproducibility in measurements of FA values for quantification of a nerve disorder, and would become a useful tool for diagnosis of low back pain. Copyright © 2018 Elsevier Inc. All rights reserved.

  3. Less work: more burnout? A comparison of working conditions and the risk of burnout by German physicians before and after the implementation of the EU Working Time Directive.

    Science.gov (United States)

    Richter, Astrid; Kostova, Petya; Baur, Xaver; Wegner, Ralf

    2014-02-01

    The present study is a 10-year comparison (1997 vs. 2007) of occupational and health aspects before and after the implementation of the European Working Time Directive on German hospital physicians. A major focus is whether the changes in working conditions are accompanied by a lower risk for burnout. Three hundred and twenty-eight physicians from the Medical Register of the city of Hamburg completed the survey in 1997 and 994 physicians in 2007. The response rates were 55.4 and 46.5 %, respectively. All participants filled in a 22-item version of the German translation of the Maslach Burnout Inventory. Results of multivariate covariance analyses are reported. The work of physicians has changed significantly within the 10-year period, for example, work time decreased by 4.5 h on average to 55.8 h per week in 2007. Junior physicians profited more from this development, but on-call duties increased for senior physicians in particular. The reduced hours were at the expense of fewer rests. Junior, as well as senior, physicians reported significantly higher rates on the burnout scale for emotional exhaustion (mean 21.8, SD 10.7) in the latter survey and senior physicians also on the depersonalization scale (mean 9.7, SD 6.3). Changes in working conditions in accordance with the European Working Time Directive are not accompanied by reduced strain and risk of burnout for physicians. Rather, our data argue for greater intensification in work, especially for senior physicians. Further studies are suggested in order to explore interventions for a sustainable improvement in the working conditions of physicians.

  4. New PN Even Balanced Sequences for Spread-Spectrum Systems

    Directory of Open Access Journals (Sweden)

    Inácio JAL

    2005-01-01

    Full Text Available A new class of pseudonoise even balanced (PN-EB binary spreading sequences is derived from existing classical odd-length families of maximum-length sequences, such as those proposed by Gold, by appending or inserting one extra-zero element (chip to the original sequences. The incentive to generate large families of PN-EB spreading sequences is motivated by analyzing the spreading effect of these sequences from a natural sampling point of view. From this analysis a new definition for PG is established, from which it becomes clear that very high processing gains (PGs can be achieved in band-limited direct-sequence spread-spectrum (DSSS applications by using spreading sequences with zero mean, given that certain conditions regarding spectral aliasing are met. To obtain large families of even balanced (i.e., equal number of ones and zeros sequences, two design criteria are proposed, namely the ranging criterion (RC and the generating ranging criterion (GRC. PN-EB sequences in the polynomial range are derived using these criteria, and it is shown that they exhibit secondary autocorrelation and cross-correlation peaks comparable to the sequences they are derived from. The methods proposed not only facilitate the generation of large numbers of new PN-EB spreading sequences required for CDMA applications, but simultaneously offer high processing gains and good despreading characteristics in multiuser SS scenarios with band-limited noise and interference spectra. Simulation results are presented to confirm the respective claims made.

  5. MR-sialography: optimisation and evaluation of an ultra-fast sequence in parallel acquisition technique and different functional conditions of salivary glands

    International Nuclear Information System (INIS)

    Habermann, C.R.; Cramer, M.C.; Aldefeld, D.; Weiss, F.; Kaul, M.G.; Adam, G.; Graessner, J.; Reitmeier, F.; Jaehne, M.; Petersen, K.U.

    2005-01-01

    Purpose: To optimise a fast sequence for MR-sialography and to compare a parallel and non-parallel acquisition technique. Additionally, the effect of oral stimulation regarding the image quality was evaluated. Material and Methods: All examinations were performed by using a 1.5-T superconducting system. After developing a sufficient sequence for MR-sialography, a single-shot turbo-spin-echo sequence (ss-TSE) with an acquisition time of 2.8 sec was used in transverse and oblique sagittal orientation in 27 healthy volunteers. All images were performed with and without parallel imaging technique. The assessment of the ductal system of the submandibular and parotid gland was performed using a 1 to 5 visual scale for each side separately. Images were evaluated by four independent experienced radiologists. For statistical evaluation, an ANOVA with post-hoc comparisons was used with an overall two-tailed significance level of P=.05. For evaluation of interobserver variability, an intraclass correlation was computed and correlation >.08 was determined to indicate a high correlation. Results: All parts of salivary excretal ducts could be visualised in all volunteers, with an overall rating for all ducts of 2.26 (SD±1.09). Between the four observers a high correlation could be obtained with an intraclass correlation of 0.9475. A significant influence regarding the slice angulations could not be obtained (p=0.74). In all healthy volunteers the visibility of excretory ducts improved significantly after oral application of a Sialogogum (p 2 =0.049). The use of a parallel imaging technique did not lead to an improvement of visualisation, showing a significant loss of image quality compared to an acquistion technique without parallel imaging (p 2 =0.013). Conclusion: The optimised ss-TSE MR-sialography seems to be a fast and sufficient technique for visualisation of excretory ducts of the main salivary glands, with no elaborate post-processing needed. To improve results of MR

  6. Comparative genomics and prediction of conditionally dispensable sequences in legume-infecting Fusarium oxysporum formae speciales facilitates identification of candidate effectors.

    Science.gov (United States)

    Williams, Angela H; Sharma, Mamta; Thatcher, Louise F; Azam, Sarwar; Hane, James K; Sperschneider, Jana; Kidd, Brendan N; Anderson, Jonathan P; Ghosh, Raju; Garg, Gagan; Lichtenzveig, Judith; Kistler, H Corby; Shea, Terrance; Young, Sarah; Buck, Sally-Anne G; Kamphuis, Lars G; Saxena, Rachit; Pande, Suresh; Ma, Li-Jun; Varshney, Rajeev K; Singh, Karam B

    2016-03-05

    Soil-borne fungi of the Fusarium oxysporum species complex cause devastating wilt disease on many crops including legumes that supply human dietary protein needs across many parts of the globe. We present and compare draft genome assemblies for three legume-infecting formae speciales (ff. spp.): F. oxysporum f. sp. ciceris (Foc-38-1) and f. sp. pisi (Fop-37622), significant pathogens of chickpea and pea respectively, the world's second and third most important grain legumes, and lastly f. sp. medicaginis (Fom-5190a) for which we developed a model legume pathosystem utilising Medicago truncatula. Focusing on the identification of pathogenicity gene content, we leveraged the reference genomes of Fusarium pathogens F. oxysporum f. sp. lycopersici (tomato-infecting) and F. solani (pea-infecting) and their well-characterised core and dispensable chromosomes to predict genomic organisation in the newly sequenced legume-infecting isolates. Dispensable chromosomes are not essential for growth and in Fusarium species are known to be enriched in host-specificity and pathogenicity-associated genes. Comparative genomics of the publicly available Fusarium species revealed differential patterns of sequence conservation across F. oxysporum formae speciales, with legume-pathogenic formae speciales not exhibiting greater sequence conservation between them relative to non-legume-infecting formae speciales, possibly indicating the lack of a common ancestral source for legume pathogenicity. Combining predicted dispensable gene content with in planta expression in the model legume-infecting isolate, we identified small conserved regions and candidate effectors, four of which shared greatest similarity to proteins from another legume-infecting ff. spp. We demonstrate that distinction of core and potential dispensable genomic regions of novel F. oxysporum genomes is an effective tool to facilitate effector discovery and the identification of gene content possibly linked to host

  7. Effects of Ginsenoside Rg1 on Learning and Memory in a Reward-directed Instrumental Conditioning Task in Chronic Restraint Stressed Rats.

    Science.gov (United States)

    Kezhu, Wang; Pan, Xu; Cong, Lu; Liming, Dong; Beiyue, Zhang; Jingwei, Lu; Yanyan, Yang; Xinmin, Liu

    2017-01-01

    Ginsenoside Rg1 is one of the major active ingredients of Panax ginseng and has showed notable improving learning and memory effects in several behavioral tasks, such as water maze, shuttle-box, and step-through, based on avoidance. However, there was no report about the role of Rg1 on the performance of reward-directed instrumental conditioning, which could reflect the adaptive capacity to ever-changing environments. Thus, in this study, the reward devaluation test and conditional visual discrimination task were conducted to study the ameliorating effects of Rg1 on cognitive deficits, especially the loss of adaptation capacity in chronic restraint stress (CRS) rat model. Our results showed that rat subjected to CRS became insensitive to the changes in outcome value, and it significantly harmed the rat's performance in conditional visual discrimination task. Moreover, the levels of BDNF, TrkB, and Erk phosphorylation were decreased in the prefrontal cortex of CRS rats. However, these changes were effectively reversed by Rg1 (5 and 10 mg/kg, i.p.). Therefore, it demonstrated that Rg1 has a good ability to improve learning and memory and also ameliorate impaired adaptive capacity induced by CRS. This amelioration effect of Rg1 might be mediated partially by BDNF/TrkB/Erk pathway in prefrontal cortex. Copyright © 2016 John Wiley & Sons, Ltd. Copyright © 2016 John Wiley & Sons, Ltd.

  8. Palaeolimnological assessment of the reference conditions and ecological status of lakes in Estonia - implications for the European Union Water Framework Directive

    Directory of Open Access Journals (Sweden)

    Heinsalu, Atko

    2009-12-01

    Full Text Available The European Union Water Framework Directive (WFD requires an assessment of reference conditions for lakes, i.e. the conditions expected with only minimal human impact on water bodies. Limnological monitoring records seldom go back more than a few decades and so rarely document the onset of human impact on lakes. Methods of palaeolimnological approaches especially fitted for the purposes of the WFD are described and two case studies, on lakes Rõuge Tõugjärv and Pappjärv, are presented. The palaeolimnological study of Rõuge Tõugjärv demonstrated that a commonly held belief that man-made eutrophication of Estonian lakes is a relatively modern matter of concern and is related to post-industrial population growth and intensification of agriculture is a misconception. The lakes, particularly those in rich soil areas, have been mediated by human impact over millennial time-scales. In many European countries it has been agreed that AD 1850 approximately represents the reference conditions for lakes. Our observations in Rõuge Tõugjärv showed that during that period anthropogenic disturbance on the lake was the greatest. Lake Pappjärv is an example of recent human influence on the aquatic ecosystem that has undergone severe degradation due to infiltration into the ground of a variety of substances from the local bitumen plant, mineral fertilizer storage tanks, and road service sand and salt mixing-grounds that have been accumulating in the lake since the 1950s.

  9. On the effect of injection timing on the ignition of lean PRF/air/EGR mixtures under direct dual fuel stratification conditions

    KAUST Repository

    Luong, Minh Bau; Sankaran, Ramanan; Yu, Gwang Hyeon; Chung, Suk-Ho; Yoo, Chun Sang

    2017-01-01

    The ignition characteristics of lean primary reference fuel (PRF)/air/exhaust gas recirculation (EGR) mixture under reactivity-controlled compression ignition (RCCI) and direct duel fuel stratification (DDFS) conditions are investigated by 2-D direct numerical simulations (DNSs) with a 116-species reduced chemistry of the PRF oxidation. The 2-D DNSs of the DDFS combustion are performed by varying the injection timing of iso-octane (i-C8H18) with a pseudo-iso-octane (PC8H18) model together with a novel compression heating model to account for the compression heating and expansion cooling effects of the piston motion in an engine cylinder. The PC8H18 model is newly developed to mimic the timing, duration, and cooling effects of the direct injection of i-C8H18 onto a premixed background charge of PRF/air/EGR mixture with composition inhomogeneities. It is found that the RCCI combustion exhibits a very high peak heat release rate (HRR) with a short combustion duration due to the predominance of the spontaneous ignition mode of combustion. However, the DDFS combustion has much lower peak HRR and longer combustion duration regardless of the fuel injection timing compared to those of the RCCI combustion, which is primarily attributed to the sequential injection of i-C8H18. It is also found that the ignition delay of the DDFS combustion features a non-monotonic behavior with increasing fuel-injection timing due to the different effect of fuel evaporation on the low-, intermediate-, and high-temperature chemistry of the PRF oxidation. The budget and Damköhler number analyses verify that although a mixed combustion mode of deflagration and spontaneous ignition exists during the early phase of the DDFS combustion, the spontaneous ignition becomes predominant during the main combustion, and hence, the spread-out of heat release rate in the DDFS combustion is mainly governed by the direct injection process of i-C8H18. Finally, a misfire is observed for the DDFS combustion when

  10. On the effect of injection timing on the ignition of lean PRF/air/EGR mixtures under direct dual fuel stratification conditions

    KAUST Repository

    Luong, Minh Bau

    2017-06-10

    The ignition characteristics of lean primary reference fuel (PRF)/air/exhaust gas recirculation (EGR) mixture under reactivity-controlled compression ignition (RCCI) and direct duel fuel stratification (DDFS) conditions are investigated by 2-D direct numerical simulations (DNSs) with a 116-species reduced chemistry of the PRF oxidation. The 2-D DNSs of the DDFS combustion are performed by varying the injection timing of iso-octane (i-C8H18) with a pseudo-iso-octane (PC8H18) model together with a novel compression heating model to account for the compression heating and expansion cooling effects of the piston motion in an engine cylinder. The PC8H18 model is newly developed to mimic the timing, duration, and cooling effects of the direct injection of i-C8H18 onto a premixed background charge of PRF/air/EGR mixture with composition inhomogeneities. It is found that the RCCI combustion exhibits a very high peak heat release rate (HRR) with a short combustion duration due to the predominance of the spontaneous ignition mode of combustion. However, the DDFS combustion has much lower peak HRR and longer combustion duration regardless of the fuel injection timing compared to those of the RCCI combustion, which is primarily attributed to the sequential injection of i-C8H18. It is also found that the ignition delay of the DDFS combustion features a non-monotonic behavior with increasing fuel-injection timing due to the different effect of fuel evaporation on the low-, intermediate-, and high-temperature chemistry of the PRF oxidation. The budget and Damköhler number analyses verify that although a mixed combustion mode of deflagration and spontaneous ignition exists during the early phase of the DDFS combustion, the spontaneous ignition becomes predominant during the main combustion, and hence, the spread-out of heat release rate in the DDFS combustion is mainly governed by the direct injection process of i-C8H18. Finally, a misfire is observed for the DDFS combustion when

  11. MR sialography: evaluation of an ultra-fast sequence in consideration of a parallel acquisition technique and different functional conditions in patients with salivary gland diseases

    International Nuclear Information System (INIS)

    Petridis, C.; Ries, T.; Cramer, M.C.; Graessner, J.; Petersen, K.U.; Reitmeier, F.; Jaehne, M.; Weiss, F.; Adam, G.; Habermann, C.R.

    2007-01-01

    Purpose: To evaluate an ultra-fast sequence for MR sialography requiring no post-processing and to compare the acquisition technique regarding the effect of oral stimulation with a parallel acquisition technique in patients with salivary gland diseases. Materials and Methods: 128 patients with salivary gland disease were prospectively examined using a 1.5-T superconducting system with a 30 mT/m maximum gradient capability and a maximum slew rate of 125 mT/m/sec. A single-shot turbo-spin-echo sequence (ss-TSE) with an acquisition time of 2.8 sec was used in transverse and oblique sagittal orientation. All images were obtained with and without a parallel imaging technique. The evaluation of the ductal system of the parotid and submandibular gland was performed using a visual scale of 1-5 for each side. The images were assessed by two independent experienced radiologists. An ANOVA with posthoc comparisons and an overall two tailed significance level of p=0.05 was used for the statistical evaluation. An intraclass correlation was computed to evaluate interobserver variability and a correlation of >0.8 was determined, thereby indicating a high correlation. Results: Depending on the diagnosed diseases and the absence of abruption of the ducts, all parts of excretory ducts were able to be visualized in all patients using the developed technique with an overall rating for all ducts of 2.70 (SD±0.89). A high correlation was achieved between the two observers with an intraclass correlation of 0.73. Oral application of a sialogogum improved the visibility of excretory ducts significantly (p<0.001). In contrast, the use of a parallel imaging technique led to a significant decrease in image quality (p=0,011). (orig.)

  12. 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...

  13. Evidence for an unorthodox firing sequence employed by the Berlin Painter : deciphering ancient ceramic firing conditions through high-resolution material characterization and replication

    NARCIS (Netherlands)

    Cianchetta, I.; Trentelman, K.; Maish, J.; Saunders, D.; Foran, B.; Walton, M.; Sciau, Ph.; Wang, T.; Pouyet, E.; Cotte, M.; Meirer, F.; Liu, Y.; Pianetta, P.; Mehta, A.

    2015-01-01

    XANES spectroscopy was used to complement the results previously obtained with Raman spectroscopy by the same group to determine the firing conditions used in the production of a single vessel painted by the Berlin Painter in the 5th century B.C. The vessel, part of the collection of the J. Paul

  14. Leaf area index estimation in a pine plantation with LAI-2000 under direct sunlight conditions: relationship with inventory and hydrologic variables

    International Nuclear Information System (INIS)

    Molina, A.; Campo, A. D. del

    2011-01-01

    LAI is a key factor in light and rainfall interception processes in forest stands and, for this reason, is called to play an important role in global change adaptive silviculture. Therefore, it is necessary to develop practical and operative methodologies to measure this parameter as well as simple relationships with other silviculture variables. This work has studied 1) the feasibility of LAI-2000 sensor in estimating LAI-stand when readings are taken under direct sunlight conditions; and 2) the ability of LAI in studying rainfall partitioned into throughfall (T) in an Aleppo pine stand after different thinning intensities, as well as its relationships to basal area, (G), cover (FCC), and tree density (D). Results showed that the angular correction scheme applied to LAI-2000 direct-sunlight readings stabilized them for different solar angles, allowing a better operational use of LAI-2000 in Mediterranean areas, where uniform overcast conditions are difficult to meet and predict. Forest cover showed the highest predictive ability of LAI (R 2 = 0.98; S = 0.28), then G (R 2 = 0.96; S = 0.43) and D (R 2 = 0.50; S = 0.28). In the hydrological plane, T increased with thinning intensity, being G the most explanatory variable (R 2 = 0.81; S = 3.07) and LAI the one that showed the poorest relation with it (R 2 = 0.69; S = 3.95). These results open a way for forest hydrologic modeling taking LAI as an input variable either estimated form LAI-2000 or deducted from inventory data. (Author) 36 refs.

  15. Optimizing the conditions for the microwave-assisted direct liquefaction of Ulva prolifera for bio-oil production using response surface methodology

    International Nuclear Information System (INIS)

    Liu, Junhai; Zhuang, Yingbin; Li, Yan; Chen, Limei; Guo, Jingxue; Li, Demao; Ye, Naihao

    2013-01-01

    Microwave-assisted direct liquefaction (MADL) of Ulva prolifera was performed in ethylene glycol (EG) using sulfuric acid (H 2 SO 4 ) as a catalyst. Response Surface Methodology (RSM) based on central composite rotatable design (CCRD) was employed to optimize the conditions of three independent variables (catalyst content, solvent-to-feedstock ratio and temperature) for the liquefaction yield. And the bio-oil was analyzed by elementary analysis, Fourier transform infrared spectroscopic analysis (FT-IR) and gas chromatography–mass spectrometry (GC–MS). The maximum liquefaction yield was 93.17%, which was obtained under a microwave power of 600 W for 30 min at 165 °C with a solvent-to-feedstock ratio of 18.87:1 and 4.93% sulfuric acid. The bio-oil was mainly composed of phthalic acid esters, alkenes and a fatty acid methyl ester with a long chain from C 16 to C 20 . - Highlights: • Ulva prolifera was converted to bio-oil through microwave-assisted direct liquefaction. • Response surface methodology was used to optimize the liquefaction technology. • A maximum liquefaction rate of 93.17 wt% bio-oil was obtained. • The bio-oil was composed of carboxylic acids and esters

  16. Blind sequence-length estimation of low-SNR cyclostationary sequences

    CSIR Research Space (South Africa)

    Vlok, JD

    2014-06-01

    Full Text Available Several existing direct-sequence spread spectrum (DSSS) detection and estimation algorithms assume prior knowledge of the symbol period or sequence length, although very few sequence-length estimation techniques are available in the literature...

  17. DC-bus voltage control of grid-connected voltage source converter by using space vector modulated direct power control under unbalanced network conditions

    DEFF Research Database (Denmark)

    Xiao, Lei; Huang, Shoudao; Lu, Kaiyuan

    2013-01-01

    Unbalanced grid voltage will cause large dc-bus voltage ripple and introduce high harmonic current components on the grid side. This will severely threaten the safety of the grid-connected voltage source converter (VSC) and consequently, affect the healthy operation condition of the load. In this......Unbalanced grid voltage will cause large dc-bus voltage ripple and introduce high harmonic current components on the grid side. This will severely threaten the safety of the grid-connected voltage source converter (VSC) and consequently, affect the healthy operation condition of the load....... In this study, a new proportional-integral-resonant (PI-RES) controller-based, space vector modulated direct power control topology is proposed to suppress the dc-bus voltage ripple and in the same time, controlling effectively the instantaneous power of the VSC. A special ac reactive power reference component...... is introduced in the controller, which is necessary in order to reduce the dc-bus voltage ripple and active power harmonics at the same time. The proposed control topology is implemented in the lab. Simulation and experimental results are provided to validate its performance and the analysis presented...

  18. Effect of operating conditions on direct liquefaction of low-lipid microalgae in ethanol-water co-solvent for bio-oil production

    International Nuclear Information System (INIS)

    Ji, Changhao; He, Zhixia; Wang, Qian; Xu, Guisheng; Wang, Shuang; Xu, Zhixiang; Ji, Hengsong

    2017-01-01

    Highlights: • Low-lipid microalgae was selected as feedstock for DL in ethanol-water co-solvent. • Operating conditions had great influence on product yields and conversion rate. • Bio-oil could be obtained from all three main components. • Ethanol and water showed obviously synergistic effect during the DL of microalgae. • Bio-oil composition from DL of microalgae was different from lignocellulose biomass. - Abstract: In this work, the direct liquefaction (DL) of low-lipid microalgae Spirulina was investigated in a 50 ml autoclave reactor with ethanol and water as co-solvent. The objective of this research was carried out to examine the effect of operating conditions such as reaction temperature, reaction time, solvent/microalgae (S/M) ratio and ethanol-water co-solvent (EWCS) composition on product distribution and bio-oil characterization. The results revealed that the optimal operating conditions for bio-oil yield and conversion rate were reaction temperature of 300 °C, reaction time of 45 min, ethanol content of 50 vol.% and S/M ratio of 40/4 ml/g, which gave the bio-oil yield of 59.5% and conversion rate of 94.73%. Conversion rate in EWCS was significantly higher than that in pure water or ethanol, suggesting the synergistic effect between ethanol and water during microalgae DL. Distinct difference in composition and relative content of compound among bio-oils in different solvents were observed by GC–MS and FT-IR. Compared with hydrothermal liquefaction, the most abundant compounds in bio-oil from both EWCS and pure ethanol were esters. The presence of ethanol could enhance the bio-oil yield and improve bio-oil quality by promoting the formation of esters.

  19. Droplet heat transfer and chemical reactions during direct containment heating

    International Nuclear Information System (INIS)

    Baker, L. Jr.

    1986-01-01

    A simplified model of heat transfer and chemical reaction has been adapted to evaluate the expected behavior of droplets containing unreacted Zircaloy and stainless steel moving through the containment atmosphere during postulated accidents involving direct containment heating. The model includes internal and external diffusive resistances to reaction. The results indicate that reactions will be incomplete for many conditions characteristic of direct containment heating sequences

  20. Optimization of culture conditions for biological hydrogen production by Citrobacter freundii CWBI952 in batch, sequenced-batch and semicontinuous operating mode

    Energy Technology Data Exchange (ETDEWEB)

    Hamilton, Christopher; Hiligsmann, Serge; Beckers, Laurent; Masset, Julien; Thonart, Philippe [Walloon Centre of Industrial Biology, Bd du Rectorat, 29, B.40 - P.70, B-4000 Liege (Belgium); Wilmotte, Annick [Center for Protein Engineering, Institute of Chemistry, B.6-P.14, B-4000 Liege (Belgium)

    2010-02-15

    Investigations were carried out to determine the effect of the pH, the nitrogen source, iron and the dilution rate (h{sup -1}) on fermentative hydrogen production from glucose by the newly isolated strain Citrobacter freundii CWBI952. The hydrogen production rate (HPR), hydrogen yield, biomass and soluble metabolites were monitored at 30 C in 100 mL serum bottles and in a 2.3 L bioreactor operated in batch, sequenced-batch and semicontinuous mode. The results indicate that hydrogen production activity, formate biosynthesis and glucose intake rates are very sensitive to the culture pH, and that additional formate bioconversion and production of hydrogen with lower biomass yields can be obtained at pH 5.9. In a further series of cultures casein peptone was replaced by (NH{sub 4}){sub 2}SO{sub 4}, a low cost alternative nitrogen source. The ammonia-based substitute was found to be suitable for H{sub 2} production when a concentration of 0.045 g/L FeSO{sub 4} was provided. Optimal overall performances (ca. an HPR of 33.2 mL H{sub 2}/L h and a yield of 0.83mol{sub H{sub 2}}/mol{sub glucose}) were obtained in the semicontinuous culture applying the previously optimized parameters for pH, nitrogen, and iron with a dilution rate of 0.012 h{sup -1} and degassing of biogas by N{sub 2} at a 28 mL/min flow rate. (author)

  1. Whole-body MRI in children: Would a 3D STIR sequence alone be sufficient for investigating common paediatric conditions? A comparative study

    Energy Technology Data Exchange (ETDEWEB)

    Merlini, Laura, E-mail: laura.merlini@hcuge.ch [Department of Radiology, Unit of Pediatric Radiology, University Hospital Rue Willy-Donzé 6, 1205 Geneva (Switzerland); Carpentier, Marc [Department of Epidemiology, University Hospital, Rue Gabrielle-Perret-Gentil 4, 1205 Geneva Switzerland (Switzerland); Ferrey, Solène; Anooshiravani, Mehrak [Department of Radiology, Unit of Pediatric Radiology, University Hospital Rue Willy-Donzé 6, 1205 Geneva (Switzerland); Poletti, Pierre-Alexandre [Department of Radiology, University Hospital, Rue Gabrielle-Perret-Gentil 4, 1205 Geneva (Switzerland); Hanquinet, Sylviane [Department of Radiology, Unit of Pediatric Radiology, University Hospital Rue Willy-Donzé 6, 1205 Geneva (Switzerland)

    2017-03-15

    Objectives: To test the performance of a single 3D IR T2-Weighted sequence compared to a Whole-body MRI protocol including DWI, T1-Weighted and STIR 3D IR (3S) in a pediatric population. Methods: Two radiologists (15 and 30 years of experience),reviewed WBMRIs: first the STIR alone and 2 weeks later the 3S protocol. The indications were variable. Only positive findings were explicitly reported. A third reader compared the results to gold standard (GS) exams specific for the pathology. Agreement between the two readers, sensitivity and positive predictive value of STIR were calculated. Results: fifty-four WBMRIs were included (16 suspected child abuse, 8 chronic recurrent multifocal osteomyelitis (CRMO), 11 lymphomas, 4 osteosarcomas, 9 neuroblastomas, 6 histiocytosis). The mean age was 6 years 10 months, range: 1 month to 15 years. Agreement between readers was of 0.87 [0.82–0.91] for 3D STIR, and 0.89 [0.83–0.93] for the 3S protocol. For reader 1 sensitivity of 3D STIR was 81.6% and of 3S 81.0%. For reader 2 it was 74.1% for 3D STIR and 74.7% for 3S. For both readers and for both protocols, the positive predictive value (PPV) depended on the type of disease (for example 100% histocytosis and osteosarcomas, >90% for child abuse, >85% CRMO but <70% for lymphoma and neuroblastoma). Conclusions: Sensitivities were not different between the 2 protocols, for each reader and were different between the 2 readers for each protocol.

  2. Whole-body MRI in children: Would a 3D STIR sequence alone be sufficient for investigating common paediatric conditions? A comparative study

    International Nuclear Information System (INIS)

    Merlini, Laura; Carpentier, Marc; Ferrey, Solène; Anooshiravani, Mehrak; Poletti, Pierre-Alexandre; Hanquinet, Sylviane

    2017-01-01

    Objectives: To test the performance of a single 3D IR T2-Weighted sequence compared to a Whole-body MRI protocol including DWI, T1-Weighted and STIR 3D IR (3S) in a pediatric population. Methods: Two radiologists (15 and 30 years of experience),reviewed WBMRIs: first the STIR alone and 2 weeks later the 3S protocol. The indications were variable. Only positive findings were explicitly reported. A third reader compared the results to gold standard (GS) exams specific for the pathology. Agreement between the two readers, sensitivity and positive predictive value of STIR were calculated. Results: fifty-four WBMRIs were included (16 suspected child abuse, 8 chronic recurrent multifocal osteomyelitis (CRMO), 11 lymphomas, 4 osteosarcomas, 9 neuroblastomas, 6 histiocytosis). The mean age was 6 years 10 months, range: 1 month to 15 years. Agreement between readers was of 0.87 [0.82–0.91] for 3D STIR, and 0.89 [0.83–0.93] for the 3S protocol. For reader 1 sensitivity of 3D STIR was 81.6% and of 3S 81.0%. For reader 2 it was 74.1% for 3D STIR and 74.7% for 3S. For both readers and for both protocols, the positive predictive value (PPV) depended on the type of disease (for example 100% histocytosis and osteosarcomas, >90% for child abuse, >85% CRMO but <70% for lymphoma and neuroblastoma). Conclusions: Sensitivities were not different between the 2 protocols, for each reader and were different between the 2 readers for each protocol.

  3. Alternating anoxic feast/aerobic famine condition for improving granular sludge formation in sequencing batch airlift reactor at reduced aeration rate.

    Science.gov (United States)

    Wan, Junfeng; Bessière, Yolaine; Spérandio, Mathieu

    2009-12-01

    In this study the influence of a pre-anoxic feast period on granular sludge formation in a sequencing batch airlift reactor is evaluated. Whereas a purely aerobic SBR was operated as a reference (reactor R2), another reactor (R1) was run with a reduced aeration rate and an alternating anoxic-aerobic cycle reinforced by nitrate feeding. The presence of pre-anoxic phase clearly improved the densification of aggregates and allowed granular sludge formation at reduced air flow rate (superficial air velocity (SAV)=0.63cms(-1)). A low sludge volume index (SVI(30)=45mLg(-1)) and a high MLSS concentration (9-10gL(-1)) were obtained in the anoxic/aerobic system compared to more conventional results for the aerobic reactor. A granular sludge was observed in the anoxic/aerobic system whilst only flocs were observed in the aerobic reference even when operated at a high aeration rate (SAV=2.83cms(-1)). Nitrification was maintained efficiently in the anoxic/aerobic system even when organic loading rate (OLR) was increased up to 2.8kgCODm(-3)d(-1). In the contrary nitrification was unstable in the aerobic system and dropped at high OLR due to competition between autotrophic and heterotrophic growth. The presence of a pre-anoxic period positively affected granulation process via different mechanisms: enhancing heterotrophic growth/storage deeper in the internal anoxic layer of granule, reducing the competition between autotrophic and heterotrophic growth. These processes help to develop dense granular sludge at a moderate aeration rate. This tends to confirm that oxygen transfer is the most limiting factor for granulation at reduced aeration. Hence the use of an alternative electron acceptor (nitrate or nitrite) should be encouraged during feast period for reducing energy demand of the granular sludge process.

  4. Stable symbiotic nitrogen fixation under water-deficit field conditions by a stress-tolerant alfalfa microsymbiont and its complete genome sequence.

    Science.gov (United States)

    Jozefkowicz, Cintia; Brambilla, Silvina; Frare, Romina; Stritzler, Margarita; Piccinetti, Carlos; Puente, Mariana; Berini, Carolina Andrea; Pérez, Pedro Reyes; Soto, Gabriela; Ayub, Nicolás

    2017-12-10

    We here characterized the stress-tolerant alfalfa microsymbiont Sinorhizobium meliloti B401. B401-treated plants showed high nitrogen fixation rates under humid and semiarid environments. The production of glycine betaine in isolated bacteroids positively correlated with low precipitation levels, suggesting that this compound acts as a critical osmoprotectant under field conditions. Genome analysis revealed that strain B401 contains alternative pathways for the biosynthesis and uptake of glycine betaine and its precursors. Such genomic information will offer substantial insight into the environmental physiology of this biotechnologically valuable nitrogen-fixing bacterium. Copyright © 2017 Elsevier B.V. All rights reserved.

  5. A nonsense mutation causing decreased levels of insulin receptor mRNA: Detection by a simplified technique for direct sequencing of genomic DNA amplified by the polymerase chain reaction

    International Nuclear Information System (INIS)

    Kadowaki, T.; Kadowaki, H.; Taylor, S.I.

    1990-01-01

    Mutations in the insulin receptor gene can render the cell resistant to the biological action of insulin. The authors have studied a patient with leprechaunism (leprechaun/Minn-1), a genetic syndrome associated with intrauterine growth retardation and extreme insulin resistance. Genomic DNA from the patient was amplified by the polymerase chain reaction catalyzed by Thermus aquaticus (Taq) DNA polymerase, and the amplified DNA was directly sequenced. A nonsense mutations was identified at codon 897 in exon 14 in the paternal allele of the patient's insulin receptor gene. Levels of insulin receptor mRNA are decreased to <10% of normal in Epstein-Barr virus-transformed lymphoblasts and cultured skin fibroblasts from this patient. Thus, this nonsense mutation appears to cause a decrease in the levels of insulin receptor mRNA. In addition, they have obtained indirect evidence that the patient's maternal allele of the insulin receptor gene contains a cis-acting dominant mutation that also decreases the level of mRNA, but by a different mechanism. The nucleotide sequence of the entire protein-coding domain and the sequences of the intron-exon boundaries for all 22 exons of the maternal allele were normal. Presumably, the mutation in the maternal allele maps elsewhere in the insulin receptor gene. Thus, they conclude that the patient is a compound heterozygote for two cis-acting dominant mutations in the insulin receptor gene: (i) a nonsense mutation in the paternal allel that reduces the level of insulin receptor mRNA and (ii) an as yet unidentified mutation in the maternal allele that either decreases the rate of transcription or decreases the stability of the mRNA

  6. Conditional sterility in plants

    Science.gov (United States)

    Meagher, Richard B.; McKinney, Elizabeth; Kim, Tehryung

    2010-02-23

    The present disclosure provides methods, recombinant DNA molecules, recombinant host cells containing the DNA molecules, and transgenic plant cells, plant tissue and plants which contain and express at least one antisense or interference RNA specific for a thiamine biosynthetic coding sequence or a thiamine binding protein or a thiamine-degrading protein, wherein the RNA or thiamine binding protein is expressed under the regulatory control of a transcription regulatory sequence which directs expression in male and/or female reproductive tissue. These transgenic plants are conditionally sterile; i.e., they are fertile only in the presence of exogenous thiamine. Such plants are especially appropriate for use in the seed industry or in the environment, for example, for use in revegetation of contaminated soils or phytoremediation, especially when those transgenic plants also contain and express one or more chimeric genes which confer resistance to contaminants.

  7. Site directed recombination

    Science.gov (United States)

    Jurka, Jerzy W.

    1997-01-01

    Enhanced homologous recombination is obtained by employing a consensus sequence which has been found to be associated with integration of repeat sequences, such as Alu and ID. The consensus sequence or sequence having a single transition mutation determines one site of a double break which allows for high efficiency of integration at the site. By introducing single or double stranded DNA having the consensus sequence flanking region joined to a sequence of interest, one can reproducibly direct integration of the sequence of interest at one or a limited number of sites. In this way, specific sites can be identified and homologous recombination achieved at the site by employing a second flanking sequence associated with a sequence proximal to the 3'-nick.

  8. Effect of beam condition in variable-shaped electron-beam direct writing for 0.25 μm and below

    International Nuclear Information System (INIS)

    Hirasawa, S.; Nakajima, K.; Tamura, T.; Aizaki, N.

    1993-01-01

    The effect of incident electron-beam conditions, which are acceleration voltage and beam blur of variable-shaped electron-beam direct writing, is investigated using the deposited energy distribution to realize a fine pattern of ≤0.25 μm in trilayer resist process. The deposited energy distribution is calculated using a three-dimensional Monte Carlo method. In a trilayer resist system, a thin bottom resist layer can be used, because the contrast value derived from the Monte Carlo calculation is independent of the bottom layer thickness. The beam blur of 0.05 μm does not degrade 0.25 μm line-and-space (L/S) patterns, but seriously degrades 0.1 μm L/S patterns. Higher acceleration voltage is effective for improving the contrast. At lower acceleration voltage, the slope of the deposited energy profile defined at the resist bottom is mainly influenced by electron scattering. On the other hand, at higher acceleration voltage, the slope of deposited energy profile mainly depends on the beam blur. The 0.1 μm L/S patterns are expected to be resolved at 30 kV when there is less than 0.02 μm beam blur with trilayer resist system. The possibility of using a single layer resist process for 0.1 μm L/S pattern will be barely realized at the conditions of 50 kV and 0.02 μm beam blur

  9. Sequence and transcriptional analysis of the genes responsible for curdlan biosynthesis in Agrobacterium sp. ATCC 31749 under simulated dissolved oxygen gradients conditions.

    Science.gov (United States)

    Zhang, Hong-Tao; Zhan, Xiao-Bei; Zheng, Zhi-Yong; Wu, Jian-Rong; Yu, Xiao-Bin; Jiang, Yun; Lin, Chi-Chung

    2011-07-01

    Expression at the mRNA level of ten selected genes in Agrobacterium sp. ATCC 31749 under various dissolved oxygen (DO) levels during curdlan fermentation related to electron transfer chain (ETC), tricarboxylic acid (TCA) cycle, peptidoglycan/lipopolysaccharide biosynthesis, and uridine diphosphate (UDP)-glucose biosynthesis were determined by qRT-PCR. Experiments were performed at DO levels of 30%, 50%, and 75%, as well as under low-oxygen conditions. The effect of high cell density on transcriptional response of the above genes under low oxygen was also studied. Besides cytochrome d (cyd A), the transcription levels of all the other genes were increased at higher DO and reached maximum at 50% DO. Under 75% DO, the transcriptional levels of all the genes were repressed. In addition, transcription levels of icd, sdh, cyo A, and fix N genes did not exhibit significant fluctuation with high cell density culture under low oxygen. These results suggested a mechanism for DO regulation of curdlan synthesis through regulation of transcriptional levels of ETCs, TCA, and UDP-glucose synthesis genes during curdlan fermentation. To our knowledge, this is the first report that DO concentration apparently regulates curdlan biosynthesis in Agrobacterium sp. ATCC 31749 providing essential lead for the optimization of the fermentation at the industrial scale.

  10. Is sequence awareness mandatory for perceptual sequence learning: An assessment using a pure perceptual sequence learning design.

    Science.gov (United States)

    Deroost, Natacha; Coomans, Daphné

    2018-02-01

    We examined the role of sequence awareness in a pure perceptual sequence learning design. Participants had to react to the target's colour that changed according to a perceptual sequence. By varying the mapping of the target's colour onto the response keys, motor responses changed randomly. The effect of sequence awareness on perceptual sequence learning was determined by manipulating the learning instructions (explicit versus implicit) and assessing the amount of sequence awareness after the experiment. In the explicit instruction condition (n = 15), participants were instructed to intentionally search for the colour sequence, whereas in the implicit instruction condition (n = 15), they were left uninformed about the sequenced nature of the task. Sequence awareness after the sequence learning task was tested by means of a questionnaire and the process-dissociation-procedure. The results showed that the instruction manipulation had no effect on the amount of perceptual sequence learning. Based on their report to have actively applied their sequence knowledge during the experiment, participants were subsequently regrouped in a sequence strategy group (n = 14, of which 4 participants from the implicit instruction condition and 10 participants from the explicit instruction condition) and a no-sequence strategy group (n = 16, of which 11 participants from the implicit instruction condition and 5 participants from the explicit instruction condition). Only participants of the sequence strategy group showed reliable perceptual sequence learning and sequence awareness. These results indicate that perceptual sequence learning depends upon the continuous employment of strategic cognitive control processes on sequence knowledge. Sequence awareness is suggested to be a necessary but not sufficient condition for perceptual learning to take place. Copyright © 2018 Elsevier B.V. All rights reserved.

  11. Algae and Partiele Removal in Direct Filtration of Biesbosch Water: Influence of Algal Characteristics, Oxidation and other Pre-treatment Conditions

    NARCIS (Netherlands)

    Petrusvenski, B.

    1996-01-01

    Direct flitration is an economicaily and environmentally attractive altemative to conventional treatment of impounded surface watei, provided that the waler bource is of appropriate quality, However, direct filtration has limited partiele and algae removal capacity. Problems related to algae and

  12. New Sequences with Low Correlation and Large Family Size

    Science.gov (United States)

    Zeng, Fanxin

    In direct-sequence code-division multiple-access (DS-CDMA) communication systems and direct-sequence ultra wideband (DS-UWB) radios, sequences with low correlation and large family size are important for reducing multiple access interference (MAI) and accepting more active users, respectively. In this paper, a new collection of families of sequences of length pn-1, which includes three constructions, is proposed. The maximum number of cyclically distinct families without GMW sequences in each construction is φ(pn-1)/n·φ(pm-1)/m, where p is a prime number, n is an even number, and n=2m, and these sequences can be binary or polyphase depending upon choice of the parameter p. In Construction I, there are pn distinct sequences within each family and the new sequences have at most d+2 nontrivial periodic correlation {-pm-1, -1, pm-1, 2pm-1,…,dpm-1}. In Construction II, the new sequences have large family size p2n and possibly take the nontrivial correlation values in {-pm-1, -1, pm-1, 2pm-1,…,(3d-4)pm-1}. In Construction III, the new sequences possess the largest family size p(d-1)n and have at most 2d correlation levels {-pm-1, -1,pm-1, 2pm-1,…,(2d-2)pm-1}. Three constructions are near-optimal with respect to the Welch bound because the values of their Welch-Ratios are moderate, WR_??_d, WR_??_3d-4 and WR_??_2d-2, respectively. Each family in Constructions I, II and III contains a GMW sequence. In addition, Helleseth sequences and Niho sequences are special cases in Constructions I and III, and their restriction conditions to the integers m and n, pm≠2 (mod 3) and n≅0 (mod 4), respectively, are removed in our sequences. Our sequences in Construction III include the sequences with Niho type decimation 3·2m-2, too. Finally, some open questions are pointed out and an example that illustrates the performance of these sequences is given.

  13. Log-balanced combinatorial sequences

    Directory of Open Access Journals (Sweden)

    Tomislav Došlic

    2005-01-01

    Full Text Available We consider log-convex sequences that satisfy an additional constraint imposed on their rate of growth. We call such sequences log-balanced. It is shown that all such sequences satisfy a pair of double inequalities. Sufficient conditions for log-balancedness are given for the case when the sequence satisfies a two- (or more- term linear recurrence. It is shown that many combinatorially interesting sequences belong to this class, and, as a consequence, that the above-mentioned double inequalities are valid for all of them.

  14. Genomic sequencing in clinical trials

    OpenAIRE

    Mestan, Karen K; Ilkhanoff, Leonard; Mouli, Samdeep; Lin, Simon

    2011-01-01

    Abstract Human genome sequencing is the process by which the exact order of nucleic acid base pairs in the 24 human chromosomes is determined. Since the completion of the Human Genome Project in 2003, genomic sequencing is rapidly becoming a major part of our translational research efforts to understand and improve human health and disease. This article reviews the current and future directions of clinical research with respect to genomic sequencing, a technology that is just beginning to fin...

  15. Biosensors for DNA sequence detection

    Science.gov (United States)

    Vercoutere, Wenonah; Akeson, Mark

    2002-01-01

    DNA biosensors are being developed as alternatives to conventional DNA microarrays. These devices couple signal transduction directly to sequence recognition. Some of the most sensitive and functional technologies use fibre optics or electrochemical sensors in combination with DNA hybridization. In a shift from sequence recognition by hybridization, two emerging single-molecule techniques read sequence composition using zero-mode waveguides or electrical impedance in nanoscale pores.

  16. Influence of swirl ratio on fuel distribution and cyclic variation under flash boiling conditions in a spark ignition direct injection gasoline engine

    International Nuclear Information System (INIS)

    Yang, Jie; Xu, Min; Hung, David L.S.; Wu, Qiang; Dong, Xue

    2017-01-01

    Highlights: • Influence of swirl on fuel distribution studied using laser induced fluorescence. • Gradient is sufficient for fuel spatial distribution variation analysis. • Close relation between fuel distribution and flame initiation/development. • Quantitative analysis shows high swirl suppresses variation of fuel distribution. • High order modes capable of identifying the distribution fluctuation patterns. - Abstract: One effective way of suppressing the cycle-to-cycle variation in engine is to design a combustion system that is robust to the root causes of engine variation over the entire engine working process. Flash boiling has been demonstrated as an ideal technique to produce stable fuel spray. But the generation of stable intake flow and fuel mixture remains challenging. In this study, to evaluate the capability of enhanced swirl flow to produce repeatable fuel mixture formation, the fuel distribution inside a single cylinder optical engine under two swirl ratios were measured using laser induced fluorescence technique. The swirl ratio was regulated by a swirl control valve installed in one of the intake ports. A 266 nm wavelength laser sheet from a frequency-quadrupled laser was directed into the optical engine through the quartz liner 15 mm below the tip of the spark plug. The fluorescence signal from the polycyclic aromatic hydrocarbon in gasoline was collected by applying a 320–420 nm band pass filter mounted in front of an intensified charge coupled device camera. Test results show that the in-cylinder fuel distribution is strongly influenced by the swirl ratio. Specifically, under high swirl condition, the fuel is mainly concentrated on the left side of the combustion chamber. While under the low swirl flow, fuel is distributed more randomly over the observing plane. This agrees well with the measurements of the stable flame location. Additionally, the cycle-to-cycle variation of the fuel distribution were analyzed. Results show that well

  17. Microarrays for global expression constructed with a low redundancy set of 27,500 sequenced cDNAs representing an array of developmental stages and physiological conditions of the soybean plant

    Directory of Open Access Journals (Sweden)

    Retzel Ernest

    2004-09-01

    Full Text Available Abstract Background Microarrays are an important tool with which to examine coordinated gene expression. Soybean (Glycine max is one of the most economically valuable crop species in the world food supply. In order to accelerate both gene discovery as well as hypothesis-driven research in soybean, global expression resources needed to be developed. The applications of microarray for determining patterns of expression in different tissues or during conditional treatments by dual labeling of the mRNAs are unlimited. In addition, discovery of the molecular basis of traits through examination of naturally occurring variation in hundreds of mutant lines could be enhanced by the construction and use of soybean cDNA microarrays. Results We report the construction and analysis of a low redundancy 'unigene' set of 27,513 clones that represent a variety of soybean cDNA libraries made from a wide array of source tissue and organ systems, developmental stages, and stress or pathogen-challenged plants. The set was assembled from the 5' sequence data of the cDNA clones using cluster analysis programs. The selected clones were then physically reracked and sequenced at the 3' end. In order to increase gene discovery from immature cotyledon libraries that contain abundant mRNAs representing storage protein gene families, we utilized a high density filter normalization approach to preferentially select more weakly expressed cDNAs. All 27,513 cDNA inserts were amplified by polymerase chain reaction. The amplified products, along with some repetitively spotted control or 'choice' clones, were used to produce three 9,728-element microarrays that have been used to examine tissue specific gene expression and global expression in mutant isolines. Conclusions Global expression studies will be greatly aided by the availability of the sequence-validated and low redundancy cDNA sets described in this report. These cDNAs and ESTs represent a wide array of developmental

  18. Electricity sequence control

    International Nuclear Information System (INIS)

    Shin, Heung Ryeol

    2010-03-01

    The contents of the book are introduction of control system, like classification and control signal, introduction of electricity power switch, such as push-button and detection switch sensor for induction type and capacitance type machinery for control, solenoid valve, expression of sequence and type of electricity circuit about using diagram, time chart, marking and term, logic circuit like Yes, No, and, or and equivalence logic, basic electricity circuit, electricity sequence control, added condition, special program control about choice and jump of program, motor control, extra circuit on repeat circuit, pause circuit in a conveyer, safety regulations and rule about classification of electricity disaster and protective device for insulation.

  19. PERSPECTIVE DIRECTIONS FOR THE DEVELOPMENT OF UKRAINIAN ANTI-CRISIS STRATEGY IN MODERN CONDITIONS OF AGGRAVATION OF THE SOCIO-ECONOMIC SITUATION

    Directory of Open Access Journals (Sweden)

    Yuriy Schedrin

    2017-11-01

    Full Text Available The article explores the prospects for the development of Ukraine’s anti-crisis strategy in the current conditions of aggravation of the socio-economic situation. The urgency of the researched subject – namely, the study of the potential directions for the development of the anti-crisis tools of Ukrainian state policy – is determined primarily by the seriousness of the problem, which should be overcome by means of these methods. The purpose of the article is to identify promising tools and mechanisms for an anti-crisis policy that can make a significant contribution to improving the current state of the socio-economic sphere in Ukraine. Its subject is anti-crisis tools and instruments, which could be used in Ukrainian scenario. It is noted that our state is at the stage of the permanent crisis and suffers from the consequences of both global and local crisis phenomena. The scientific novelty of the article is determined by the combination of economic, social, political, and legal approaches to the study of the current state of the Ukrainian economy. The methodology of the research is formed by the combination of economic and political methods of scientific activities, which are based on the principles of objectivism and systematic approach. The findings of scientific research and recommendations of some Ukrainian scientists regarding the necessary anti-crisis tools are considered as the sources for the article. The results of the study show that Ukraine suffers from a series of systemic problems and challenges, which are the main threat to the stability of the national economy. Among the most influential of them we can identify the low level of incomes of citizens, which is associated with the devaluation of the national currency and the increase in utility tariffs; high level of unemployment; shortage of foreign and domestic investments; the decline in production and exports, caused both by military operations in the Donbas and the loss

  20. Self- and other-directed forms of violence and their relationship with lifetime DSM-5 psychiatric disorders: Results from the National Epidemiologic Survey on Alcohol Related Conditions-III (NESARC-III).

    Science.gov (United States)

    Harford, Thomas C; Chen, Chiung M; Kerridge, Bradley T; Grant, Bridget F

    2018-04-01

    A combined history of violence toward self and others has been reported in clinical and incarcerated populations. Psychiatric disorders have been implicated as risk factors. This study examines the lifetime prevalence of this combined violence in the general population and its associations with DSM-5 psychiatric disorders in comparison with other- and self-directed violence. Data from the National Epidemiologic Survey on Alcohol and Related Conditions-III (NESARC-III) were analyzed, including 36,309 U.S. adults ages 18 and older. Violent behavior was defined by suicide attempts; recurrent suicidal behavior; gestures, threats, or self-mutilating behavior (self-directed); and multiple items of violence toward others (other-directed) in four categories: none, self-directed only, other-directed only, and combined self-/other-directed. Multinomial logistic regression examined these violence categories in association with sociodemographics and lifetime DSM-5 psychiatric disorders. Results show that approximately 18.1% of adults reported violent behavior, including self-directed only (4.4%), other-directed only (10.9%), and combined self- and other-directed violence (2.8%). DSM-5 psychiatric disorders significantly associated with the violence typology include alcohol, tobacco, cannabis, and other drug use disorders; mood disorders; posttraumatic stress disorder; and schizotypal, antisocial, and borderline personality disorders. Findings extend the clinical literature regarding the co-occurrence of self- and other-directed violent behaviors to the general population. Copyright © 2017 Elsevier B.V. All rights reserved.

  1. Accident Sequence Precursor Analysis for SGTR by Using Dynamic PSA Approach

    International Nuclear Information System (INIS)

    Lee, Han Sul; Heo, Gyun Young; Kim, Tae Wan

    2016-01-01

    In order to address this issue, this study suggests the sequence tree model to analyze accident sequence systematically. Using the sequence tree model, all possible scenarios which need a specific safety action to prevent the core damage can be identified and success conditions of safety action under complicated situation such as combined accident will be also identified. Sequence tree is branch model to divide plant condition considering the plant dynamics. Since sequence tree model can reflect the plant dynamics, arising from interaction of different accident timing and plant condition and from the interaction between the operator action, mitigation system, and the indicators for operation, sequence tree model can be used to develop the dynamic event tree model easily. Target safety action for this study is a feed-and-bleed (F and B) operation. A F and B operation directly cools down the reactor cooling system (RCS) using the primary cooling system when residual heat removal by the secondary cooling system is not available. In this study, a TLOFW accident and a TLOFW accident with LOCA were the target accidents. Based on the conventional PSA model and indicators, the sequence tree model for a TLOFW accident was developed. Based on the results of a sampling analysis and data from the conventional PSA model, the CDF caused by Sequence no. 26 can be realistically estimated. For a TLOFW accident with LOCA, second accident timings were categorized according to plant condition. Indicators were selected as branch point using the flow chart and tables, and a corresponding sequence tree model was developed. If sampling analysis is performed, practical accident sequences can be identified based on the sequence analysis. If a realistic distribution for the variables can be obtained for sampling analysis, much more realistic accident sequences can be described. Moreover, if the initiating event frequency under a combined accident can be quantified, the sequence tree model

  2. Combining direct and indirect tracking techniques to assess the impact of sub-Saharan conditions on cross-continental songbird migration

    DEFF Research Database (Denmark)

    Pedersen, Lykke; Fraser, Kevin C.; Kyser, T. Kurt

    2016-01-01

    Understanding how events throughout the annual cycle interact to influence individual fitness and hence population dynamics is crucial to optimize conservation strategies for migratory birds. Despite major advancements in technology, direct tracking devices for passerine songbirds are still limited...

  3. Survey of the transcriptome of Aspergillus oryzae via massively parallel mRNA sequencing

    OpenAIRE

    Wang, Bin; Guo, Guangwu; Wang, Chao; Lin, Ying; Wang, Xiaoning; Zhao, Mouming; Guo, Yong; He, Minghui; Zhang, Yong; Pan, Li

    2010-01-01

    Aspergillus oryzae, an important filamentous fungus used in food fermentation and the enzyme industry, has been shown through genome sequencing and various other tools to have prominent features in its genomic composition. However, the functional complexity of the A. oryzae transcriptome has not yet been fully elucidated. Here, we applied direct high-throughput paired-end RNA-sequencing (RNA-Seq) to the transcriptome of A. oryzae under four different culture conditions. With the high resoluti...

  4. Analysis of diverse direct arylation polymerization (DArP) conditions toward the efficient synthesis of polymers converging with stille polymers in organic solar cells

    DEFF Research Database (Denmark)

    Livi, Francesco; Gobalasingham, Nemal S.; Thompson, Barry C.

    2016-01-01

    Despite the emergence of direct arylation polymerization (DArP) as an alternative method to traditional cross-coupling routes like Stille polymerization, the exploration of DArP polymers in practical applications like polymer solar cells (PSCs) is limited. DArP polymers tend to have a reputation...... for being marginally inferior to Stille counterparts due to the increased presence of defects that result from unwanted side reactions in direct arylation, such as unselective C-H bond activation and homocoupling. We report ten DArP protocols across the three major classes of DArP to generate poly[(2,5-bis...... was synthesized in superheated THF with Cs2CO3, neodecanoic acid, and P(o-anisyl)3, it generated polymers of exceptional quality that performed comparably to Stille counterparts in both roll coated ITO-free and spin-coated ITO devices....

  5. Neonatal lesions of orbital frontal areas 11/13 in monkeys alter goal-directed behavior but spare fear conditioning and safety signal learning.

    Directory of Open Access Journals (Sweden)

    Andy M Kazama

    2014-03-01

    Full Text Available Recent studies in monkeys have demonstrated that damage to the lateral subfields of orbital frontal cortex (OFC areas 11/13 yields profound changes in flexible modulation of goal-directed behaviors and a lack in fear regulation. Yet, little consideration has been placed on its role in emotional and social development throughout life. The current study investigated the effects of neonatal lesions of the OFC on the flexible modulation of goal-directed behaviors and fear responses in monkeys. Infant monkeys received neonatal lesions of OFC areas 11/13 or sham-lesions during the first post-natal week. Modulation of goal-directed behaviors was measured with a devaluation task at 3-4 years and 6-7 years. Modulation of fear reactivity by safety signals was assessed with the AX+/BX- potentiated-startle paradigm at 6-7 years. Similar to adult-onset OFC lesions, selective neonatal lesions of OFC areas 11/13 yielded a failure to modulate behavioral responses guided by changes in reward value, but spared the ability to modulate fear responses in the presence of safety signals. These results suggest that these areas play a critical role in the development of behavioral adaptation during goal-directed behaviors, but not, or less so, in the development of the ability to process emotionally salient stimuli and to modulate emotional reactivity using environmental contexts, which could be supported by other OFC subfields, such as the most ventromedial subfields (i.e. areas 14/25. Given similar impaired decision-making abilities and spared modulation of fear followed both neonatal lesions of either OFC areas 11 and 13 or amygdala (Kazama et al., 2012; Kazama & Bachevalier, 2013, the present results suggest that interactions between these two neural structures play a critical role in the development of behavioral adaptation; an ability essential for the self-regulation of emotion and behavior that assures the maintenance of successful social relationships.

  6. Direct measurement of glucose profiles in immobilized yeast gels with a pH-insensitive micro-electrode under anaerobic conditions

    NARCIS (Netherlands)

    Cronenberg, C.C.H.; Heuvel, van den J.C.; Ottengraf, S.P.P.

    1993-01-01

    A 10 µm glucose sensor was developed based on a glucose oxidase coated Pt-electrode inserted in a capillary shaft. The internal buffer medium effected in a glucose response that was insensitive for the external pH. The sensor was successfully utilized at pH 4 under anaerobic conditions in gel

  7. Static multiplicities in heterogeneous azeotropic distillation sequences

    DEFF Research Database (Denmark)

    Esbjerg, Klavs; Andersen, Torben Ravn; Jørgensen, Sten Bay

    1998-01-01

    In this paper the results of a bifurcation analysis on heterogeneous azeotropic distillation sequences are given. Two sequences suitable for ethanol dehydration are compared: The 'direct' and the 'indirect' sequence. It is shown, that the two sequences, despite their similarities, exhibit very...... different static behavior. The method of Petlyuk and Avet'yan (1971), Bekiaris et al. (1993), which assumes infinite reflux and infinite number of stages, is extended to and applied on heterogeneous azeotropic distillation sequences. The predictions are substantiated through simulations. The static sequence...

  8. Amino-terminal domain of the v-fms oncogene product includes a functional signal peptide that directs synthesis of a transforming glycoprotein in the absence of feline leukemia virus gag sequences

    International Nuclear Information System (INIS)

    Wheeler, E.F.; Roussel, M.F.; Hampe, A.; Walker, M.H.; Fried, V.A.; Look, A.T.; Rettenmier, C.W.; Sherr, C.J.

    1986-01-01

    The nucleotide sequence of a 5' segment of the human genomic c-fms proto-oncogene suggested that recombination between feline leukemia virus and feline c-fms sequences might have occurred in a region encoding the 5' untranslated portion of c-fms mRNA. The polyprotein precursor gP180/sup gag-fms/ encoded by the McDonough strain of feline sarcoma virus was therefore predicted to contain 34 v-fms-coded amino acids derived from sequences of the c-fms gene that are not ordinarily translated from the proto-oncogene mRNA. The (gP180/sup gag-fms/) polyprotein was cotranslationally cleaved near the gag-fms junction to remove its gag gene-coded portion. Determination of the amino-terminal sequence of the resulting v-fms-coded glycoprotein, gp120/sup v-fms/, showed that the site of proteolysis corresponded to a predicted signal peptidase cleavage site within the c-fms gene product. Together, these analyses suggested that the linked gag sequences may not be necessary for expression of a biologically active v-fms gene product. The gag-fms sequences of feline sarcoma virus strain McDonough and the v-fms sequences alone were inserted into a murine retroviral vector containing a neomycin resistance gene. The authors conclude that a cryptic hydrophobic signal peptide sequence in v-fms was unmasked by gag deletion, thereby allowing the correct orientation and transport of the v-fms was unmasked by gag deletion, thereby allowing the correct orientation and transport of the v-fms gene product within membranous organelles. It seems likely that the proteolytic cleavage of gP180/gag-fms/ is mediated by signal peptidase and that the amino termini of gp140/sup v-fms/ and the c-fms gene product are identical

  9. Amino-terminal domain of the v-fms oncogene product includes a functional signal peptide that directs synthesis of a transforming glycoprotein in the absence of feline leukemia virus gag sequences

    Energy Technology Data Exchange (ETDEWEB)

    Wheeler, E.F.; Roussel, M.F.; Hampe, A.; Walker, M.H.; Fried, V.A.; Look, A.T.; Rettenmier, C.W.; Sherr, C.J.

    1986-08-01

    The nucleotide sequence of a 5' segment of the human genomic c-fms proto-oncogene suggested that recombination between feline leukemia virus and feline c-fms sequences might have occurred in a region encoding the 5' untranslated portion of c-fms mRNA. The polyprotein precursor gP180/sup gag-fms/ encoded by the McDonough strain of feline sarcoma virus was therefore predicted to contain 34 v-fms-coded amino acids derived from sequences of the c-fms gene that are not ordinarily translated from the proto-oncogene mRNA. The (gP180/sup gag-fms/) polyprotein was cotranslationally cleaved near the gag-fms junction to remove its gag gene-coded portion. Determination of the amino-terminal sequence of the resulting v-fms-coded glycoprotein, gp120/sup v-fms/, showed that the site of proteolysis corresponded to a predicted signal peptidase cleavage site within the c-fms gene product. Together, these analyses suggested that the linked gag sequences may not be necessary for expression of a biologically active v-fms gene product. The gag-fms sequences of feline sarcoma virus strain McDonough and the v-fms sequences alone were inserted into a murine retroviral vector containing a neomycin resistance gene. The authors conclude that a cryptic hydrophobic signal peptide sequence in v-fms was unmasked by gag deletion, thereby allowing the correct orientation and transport of the v-fms was unmasked by gag deletion, thereby allowing the correct orientation and transport of the v-fms gene product within membranous organelles. It seems likely that the proteolytic cleavage of gP180/gag-fms/ is mediated by signal peptidase and that the amino termini of gp140/sup v-fms/ and the c-fms gene product are identical.

  10. Comparative evaluation of direct thrombin and factor Xa inhibitors with antiplatelet agents under flow and static conditions: an in vitro flow chamber model.

    Directory of Open Access Journals (Sweden)

    Kazuya Hosokawa

    Full Text Available Dabigatran and rivaroxaban are novel oral anticoagulants that specifically inhibit thrombin and factor Xa, respectively. The aim of this study is to elucidate antithrombotic properties of these anticoagulant agents under arterial and venous shear conditions. Whole blood samples treated with dabigatran or rivaroxaban at 250, 500, and 1000 nM, with/without aspirin and AR-C66096, a P2Y12 antagonist, were perfused over a microchip coated with collagen and tissue thromboplastin at shear rates of 240 and 600 s(-1. Fibrin-rich platelet thrombus formation was quantified by monitoring flow pressure changes. Dabigatran at higher concentrations (500 and 1000 nM potently inhibited thrombus formation at both shear rates, whereas 1000 nM of rivaroxaban delayed, but did not completely inhibit, thrombus formation. Dual antiplatelet agents weakly suppressed thrombus formation at both shear rates, but intensified the anticoagulant effects of dabigatran and rivaroxaban. The anticoagulant effects of dabigatran and rivaroxaban were also evaluated under static conditions using thrombin generation (TG assay. In platelet-poor plasma, dabigatran at 250 and 500 nM efficiently prolonged the lag time (LT and moderately reduce peak height (PH of TG, whereas rivaroxaban at 250 nM efficiently prolonged LT and reduced PH of TG. In platelet-rich plasma, however, both anticoagulants efficiently delayed LT and reduced PH of TG. Our results suggest that dabigatran and rivaroxaban may exert distinct antithrombotic effects under flow conditions, particularly in combination with dual antiplatelet therapy.

  11. DIRECTIONS, CONDITIONS, AND RISKS OF IMPLEMENTATION OF THE TRANSPORT MEGA-PROJECTS “NORTH-SOUTH” AND “EAST-WEST” UNDER THE NEW GEOPOLITICAL REALITIES

    Directory of Open Access Journals (Sweden)

    A. K. Tulokhonov

    2017-01-01

    Full Text Available The paper discusses the prospect of the development of Russia’s transport infrastructure mega-projects in the context of the Eurasian Economic Union and the Shanghai Cooperation Organization formation. The paper focuses on the country’s interests in the area of influence of the Silk and the Tea Roads. Economic cooperation with the countries of the Asia-Pacific region on the Trans-Siberian Railway-Mongolia-China direction, with diversification of transport routes to all four oceans and five continents, is the most effective policy for Russia.

  12. PCR-based assays versus direct sequencing for evaluating the effect of KRAS status on anti-EGFR treatment response in colorectal cancer patients: a systematic review and meta-analysis.

    Directory of Open Access Journals (Sweden)

    Lianfeng Shan

    Full Text Available The survival rate of colorectal cancer (CRC patients carrying wild-type KRAS is significantly increased by combining anti-EGFR monoclonal antibody (mAb with standard chemotherapy. However, conflicting data exist in both the wild-type KRAS and mutant KRAS groups, which strongly challenge CRC anti-EGFR treatment. Here we conducted a meta-analysis in an effort to provide more reliable information regarding anti-EGFR treatment in CRC patients.We searched full reports of randomized clinical trials using Medline, the American Society of Clinical Oncology (ASCO, and the European Society for Medical Oncology (ESMO. Two investigators independently screened the published literature according to our inclusive and exclusive criteria and the relative data were extracted. We used Review Manager 5.2 software to analyze the data.The addition of anti-EGFR mAb to standard chemotherapy significantly improved both progression-free survival (PFS and median overall survival (mOS in the wild-type KRAS group; hazard ratios (HRs for PFS and mOS were 0.70 [95% confidence interval (CI, 0.58-0.84] and 0.83 [95% CI, 0.75-0.91], respectively. In sub-analyses of the wild-type KRAS group, when PCR-based assays are employed, PFS and mOS notably increase: the HRs were 0.74 [95% CI, 0.62-0.88] and 0.87 [95% CI, 0.78-0.96], respectively. In sub-analyses of the mutant KRAS group, neither PCR-based assays nor direct sequencing enhance PFS or mOS.Our data suggest that PCR-based assays with high sensitivity and specificity allow accurate identification of patients with wild-type KRAS and thus increase PFS and mOS. Furthermore, such assays liberate patients with mutant KRAS from unnecessary drug side effects, and provide them an opportunity to receive appropriate treatment. Thus, establishing a precise standard reference test will substantially optimize CRC-targeted therapies.

  13. Rate in template-directed polymer synthesis.

    Science.gov (United States)

    Saito, Takuya

    2014-06-01

    We discuss the temporal efficiency of template-directed polymer synthesis, such as DNA replication and transcription, under a given template string. To weigh the synthesis speed and accuracy on the same scale, we propose a template-directed synthesis (TDS) rate, which contains an expression analogous to that for the Shannon entropy. Increasing the synthesis speed accelerates the TDS rate, but the TDS rate is lowered if the produced sequences are diversified. We apply the TDS rate to some production system models and investigate how the balance between the speed and the accuracy is affected by changes in the system conditions.

  14. Pd/Nb2O5/SiO2 catalyst for the direct hydrodeoxygenation of biomass-related compounds to liquid alkanes under mild conditions.

    Science.gov (United States)

    Shao, Yi; Xia, Qineng; Liu, Xiaohui; Lu, Guanzhong; Wang, Yanqin

    2015-05-22

    A simple Pd-loaded Nb2 O5 /SiO2 catalyst was prepared for the hydrodeoxygenation of biomass-related compounds to alkanes under mild conditions. Niobium oxide dispersed in silica (Nb2 O5 /SiO2 ) as the support was prepared by the sol-gel method and characterized by various techniques, including N2 adsorption, XRD, NH3 temperature-programmed desorption (TPD), TEM, and energy-dispersive X-ray spectroscopy (EDAX) atomic mapping. The characterization results showed that the niobium oxide species were amorphous and well dispersed in silica. Compared to commercial Nb2 O5 , Nb2 O5 /SiO2 has significantly more active niobium oxide species exposed on the surface. Under mild conditions (170 °C, 2.5 MPa), Pd/10 %Nb2 O5 /SiO2 was effective for the hydrodeoxygenation reactions of 4-(2-furyl)-3-buten-2-one (aldol adduct of furfural with acetone), palmitic acid, tristearin, and diphenyl ether (model compounds of microalgae oils, vegetable oils, and lignin), which gave high yields (>94 %) of alkanes with little CC bond cleavage. More importantly, owing to the significant promotion effect of NbOx species on CO bond cleavage and the mild reaction conditions, the CC cleavage was considerably restrained, and the catalyst showed an excellent activity and stability for the hydrodeoxygenation of palmitic acid with almost no decrease in hexadecane yield (94-95 %) in a 150 h time-on-stream test. © 2015 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  15. A persistent Holocene wetting trend in arid central Asia, with wettest conditions in the late Holocene, revealed by multi-proxy analyses of loess-paleosol sequences in Xinjiang, China

    Science.gov (United States)

    Chen, Fahu; Jia, Jia; Chen, Jianhui; Li, Guoqiang; Zhang, Xiaojian; Xie, Haichao; Xia, Dunsheng; Huang, Wei; An, Chengbang

    2016-08-01

    There are significant differences in the interpretation of the moisture (precipitation) history of arid central Asia (ACA) during the Holocene, as inferred on one hand from speleothem oxygen isotope records, and on the other from lake sediments. Here we present the results of measurements of climatically-sensitive magnetic properties and soil color from four well-dated loess-paleosol sequences from the northern slopes of the Tienshan Mountains and the Yili River valley, Xinjiang, China, in the core area of ACA. Our results demonstrate that the characteristic Holocene paleosol, indicating relatively moist conditions, generally formed after ∼6 ka (1 ka = 1000 cal yr BP) in the study region, and that the accumulation of unweathered loess prevailed during the early Holocene, indicating a dry climate at that time. The magnetic proxies further reveal a trend of generally increasing moisture since the Last Glacial Maximum, with the wettest climate occurring during the late Holocene. This trend of increasing moisture during the Holocene is representative of the Xinjiang region and possibly of the whole of the core area of ACA, and is in marked contrast both to the mid-Holocene moisture maximum observed in the East Asian summer monsoon region and to the general decrease in the strength of the Indian summer monsoon since the early Holocene. Our findings are supported by the results of a climate simulation which indicate a trend of increasing summer and winter precipitation during the Holocene in the core area of ACA, caused mainly by an increase in the strength of the westerlies effected by an increasing latitudinal insolation gradient and by a negative trend of the Arctic Oscillation (AO) or North Atlantic Oscillation (NAO).

  16. Air conditioning in a CINEMAXX cinema. Innovative solution involving a screw compressor and direct evaporation; Klimatisierung in einem CINEMAXX-Kino. Innovative Loesung mit Schraubenverdichter und Direktverdampfung

    Energy Technology Data Exchange (ETDEWEB)

    Anon.

    2001-03-01

    The new CINEMAXX cinema building in the Trier city centre has fully glazed walls and a modern air conditioning system. The system was installed by local organisations. Its key components are two Comer-Dorin screw compressors. [German] Im Trierer Stadtzentrum befindet sich ein neues CINEMAXX-Kino, hinter dessen glaeserner Fassade die Klimaanlage diskret verborgen bleibt. Oertliche Firmen der Branche konnten die Ausschreibung der Klimaanlage zu ihren Gunsten entscheiden und mit Erfahrung und handwerklichem Koennen unter Verwendung zweier Comer-Dorin-Schraubenverdichter eine nachahmenswerte Loesung planen und installieren. (orig.)

  17. Effects of the pyrethroid insecticide cypermethrin on a freshwater community studied under field conditions. II. Direct and indirect effects on the species composition

    DEFF Research Database (Denmark)

    Wendt-Rasch, Lina; Friberg-Jensen, Ursula; Woin, Per

    2003-01-01

    species were calculated using inverse regression and revealed that copepod nauplii were the most sensitive (NEC=0.01 microg/l) of the crustacean groups examined. The observed alterations of the species composition of the autotrophic communities as well as of the rotifers were most likely caused indirectly...... cypermethrin concentrations, ranging from 0.01 to 6 microg/l. This paper is the second in a series of two and describes the effects on the species composition of the crustacean, rotifer, periphyton and phytoplankton communities. Multivariate ordination technique (redundancy analysis (RDA) combined with Monte...... Carlo permutation tests) showed that exposure to cypermethrin caused significant changes in the species composition of the communities. Changes in the structure of the communities were observed following exposure to a nominal concentration of 0.13 microg cypermethrin per litre above. The direct acute...

  18. Transformation of a Water Slug in Free Fall Under the Conditions of Exposure to an Air Flow Orthogonal to the Direction of the Slug Motion

    Science.gov (United States)

    Volkov, R. S.; Zabelin, M. V.; Kuznetsov, G. V.; Strizhak, P. A.

    2016-07-01

    An experimental study has been made of the influence of an orthogonal (side) air flow propagating with a velocity to 5 m/s on the phases of transformation of a water slug with an initial volume of 0.05-0.5 liter in free fall from a height of 3 m. Use was made of Phantom V411 and Phantom Miro M310 high-speed video cameras and a Tema Automotive software system with the function of continuous tracking. The laws of retardation of the phases of transformation of the water slug from the instant of formation to that of formation of a droplet cloud under the action of the air flow orthogonal to the direction of the slug motion, and also of the deceleration, removal, and destruction of the droplets and fragments of water separating from the slug surface, have been established.

  19. Advantageous direct quantification of viable closely related probiotics in petit-suisse cheeses under in vitro gastrointestinal conditions by Propidium Monoazide--qPCR.

    Directory of Open Access Journals (Sweden)

    Martha Lissete Morales Villarreal

    Full Text Available Species-specific Quantitative Real Time PCR (qPCR alone and combined with the use of propidium monoazide (PMA were used along with the plate count method to evaluate the survival of the probiotic strains Lactobacillus acidophilus La-5 and Bifidobacterium animalis subsp. lactis Bb-12, and the bacteriocinogenic and potentially probiotic strain Lactobacillus sakei subsp. sakei 2a in synbiotic (F1 and probiotic (F2 petit-suisse cheeses exposed throughout shelf-life to in vitro simulated gastrointestinal tract conditions. The three strains studied showed a reduction in their viability after the 6 h assay. Bb-12 displayed the highest survival capacity, above 72.6 and 74.6% of the initial populations, respectively, by plate count and PMA-qPCR, maintaining population levels in the range or above 6 log CFU/g. The prebiotic mix of inulin and FOS did not offer any additional protection for the strains against the simulated gastrointestinal environment. The microorganisms' populations were comparable among the three methods at the initial time of the assay, confirming the presence of mainly viable and culturable cells. However, with the intensification of the stress induced throughout the various stages of the in vitro test, the differences among the methods increased. The qPCR was not a reliable enumeration method for the quantification of intact bacterial populations, mixed with large numbers of injured and dead bacteria, as confirmed by the scanning electron microscopy results. Furthermore, bacteria plate counts were much lower (P<0.05 than with the PMA-qPCR method, suggesting the accumulation of stressed or dead microorganisms unable to form colonies. The use of PMA overcame the qPCR inability to differentiate between dead and alive cells. The combination of PMA and species-specific qPCR in this study allowed a quick and unequivocal way of enumeration of viable closely related species incorporated into probiotic and synbiotic petit-suisse cheeses and

  20. Improving outcomes in patients with coexisting multimorbid conditions-the development and evaluation of the combined diabetes and renal control trial (C-DIRECT): study protocol.

    Science.gov (United States)

    Griva, Konstadina; Mooppil, Nandakumar; Khoo, Eric; Lee, Vanessa Yin Woan; Kang, Augustine Wee Cheng; Newman, Stanton P

    2015-02-12

    Diabetes mellitus (DM) is the most common cause of end-stage renal disease (ESRD). Patients with diabetes on dialysis have worse clinical outcomes and increased psychological burden. The need to manage the combined treatment demands for both conditions is particularly challenging yet there is paucity of data of the barriers preventing optimal management to combined therapy for diabetes and kidney failure. The study aims to explore needs of patients and develop an intervention to enable people with diabetes and ESRD to better manage both their conditions. A two-phase study comprising a mixed method observational study (phase I) and a feasibility trial (phase II). Phase I will seek to document outcomes and needs of the population (patients with DM-ESRD) and seek input on preferred delivery/implementation for the programme. Data will be collected with in-depth interviews with patients, caregivers and healthcare providers (N=50), and from a questionnaire-based survey (N=170). Phase 2 will build on these data to design and test the feasibility of a practical, low-intensity, clinic-integrated intervention using a self-management paradigm. The intervention will primarily seek to support behavioural change so as to improve adherence and clinical outcomes for DM as well as for ESRD. For the feasibility trial, we will be evaluating acceptability, retention and completion rates of the programme. The study protocol has been approved by the local ethics committee and written informed consent is required from every participant. Findings will be disseminated through journals, conferences and will be used to create a fully manualised intervention (materials) and training course for facilitators. Published by the BMJ Publishing Group Limited. For permission to use (where not already granted under a licence) please go to http://group.bmj.com/group/rights-licensing/permissions.

  1. Hygroscopic properties of atmospheric aerosol particles over the Eastern Mediterranean: implications for regional direct radiative forcing under clean and polluted conditions

    Directory of Open Access Journals (Sweden)

    M. Stock

    2011-05-01

    Full Text Available This work examines the effect of direct radiative forcing of aerosols in the eastern Mediterranean troposphere as a function of air mass composition, particle size distribution and hygroscopicity, and relative humidity (RH. During intensive field measurements on the island of Crete, Greece, the hygroscopic properties of atmospheric particles were determined using a Hygroscopicity Tandem Differential Mobility Analyzer (H-TDMA and a Hygroscopicity Differential Mobility Analyzer-Aerodynamic Particle Sizer (H-DMA-APS. Similar to former studies, the H-TDMA identified three hygroscopic sub-fractions of particles in the sub-μm range: a more hygroscopic group, a less hygroscopic group and a nearly hydrophobic particle group. The average hygroscopic particle growth factors at 90 % RH were a significant function of particle mobility diameter (Dp: 1.42 (± 0.05 at 30 nm compared to 1.63 (± 0.07 at 250 nm. The H-DMA-APS identified up to three hygroscopic sub-fractions at mobility diameters of 1.0 and 1.2 μm. The data recorded between 12 August and 20 October 2005 were classified into four distinct synoptic-scale air mass types distinguishing between different regions of origin (western Mediterranean vs. the Aegean Sea as well as the degree of continental pollution (marine vs. continentally influenced. The hygroscopic properties of particles with diameter Dp≥150 nm showed the most pronounced dependency on air mass origin, with growth factors in marine air masses exceeding those in continentally influenced air masses. Particle size distributions and hygroscopic growth factors were used to calculate aerosol light scattering coefficients at ambient RH using a Mie model. A main result was the pronounced enhancement of particle scattering over the eastern Mediterranean due to hygroscopic growth, both in the marine and continentally influenced air masses. When RH reached its summer daytime values around 70

  2. Heat pump control method based on direct measurement of evaporation pressure to improve energy efficiency and indoor air temperature stability at a low cooling load condition

    International Nuclear Information System (INIS)

    Park, Young Sung; Jeong, Ji Hwan; Ahn, Byoung Ha

    2014-01-01

    Highlights: • New heat pump control method was developed. • Experimental investigation on performance of heat pump with various control method. • New control method appeared to improve the stability of indoor air temperature. • New control method appeared to have a potential to reduce power consumption. - Abstract: The control systems of conventional heat pumps have an input of refrigerant temperature at the evaporator outlet to maintain superheat at proper level. In order to develop a control method that can be used to achieve better indoor thermal comfort and energy efficiency at a low cooling load condition than the current control method, a new method of the evaporation pressure control based on the evaporator outlet pressure reading (EPCP) was developed. The changes in the stability of indoor air temperature and power consumption were measured while changing the compressor frequency in accordance with the new control method. Compared with the evaporation pressure control based on the evaporator outlet temperature reading, the EPCP control method appeared to improve the stability of room air temperature or occupant thermal comfort significantly

  3. Rapid Polymer Sequencer

    Science.gov (United States)

    Stolc, Viktor (Inventor); Brock, Matthew W (Inventor)

    2013-01-01

    Method and system for rapid and accurate determination of each of a sequence of unknown polymer components, such as nucleic acid components. A self-assembling monolayer of a selected substance is optionally provided on an interior surface of a pipette tip, and the interior surface is immersed in a selected liquid. A selected electrical field is impressed in a longitudinal direction, or in a transverse direction, in the tip region, a polymer sequence is passed through the tip region, and a change in an electrical current signal is measured as each polymer component passes through the tip region. Each of the measured changes in electrical current signals is compared with a database of reference electrical change signals, with each reference signal corresponding to an identified polymer component, to identify the unknown polymer component with a reference polymer component. The nanopore preferably has a pore inner diameter of no more than about 40 nm and is prepared by heating and pulling a very small section of a glass tubing.

  4. Sequence Tree Modeling for Combined Accident and Feed-and-Bleed Operation

    International Nuclear Information System (INIS)

    Kim, Bo Gyung; Kang Hyun Gook; Yoon, Ho Joon

    2016-01-01

    In order to address this issue, this study suggests the sequence tree model to analyze accident sequence systematically. Using the sequence tree model, all possible scenarios which need a specific safety action to prevent the core damage can be identified and success conditions of safety action under complicated situation such as combined accident will be also identified. Sequence tree is branch model to divide plant condition considering the plant dynamics. Since sequence tree model can reflect the plant dynamics, arising from interaction of different accident timing and plant condition and from the interaction between the operator action, mitigation system, and the indicators for operation, sequence tree model can be used to develop the dynamic event tree model easily. Target safety action for this study is a feed-and-bleed (F and B) operation. A F and B operation directly cools down the reactor cooling system (RCS) using the primary cooling system when residual heat removal by the secondary cooling system is not available. In this study, a TLOFW accident and a TLOFW accident with LOCA were the target accidents. Based on the conventional PSA model and indicators, the sequence tree model for a TLOFW accident was developed. If sampling analysis is performed, practical accident sequences can be identified based on the sequence analysis. If a realistic distribution for the variables can be obtained for sampling analysis, much more realistic accident sequences can be described. Moreover, if the initiating event frequency under a combined accident can be quantified, the sequence tree model can translate into a dynamic event tree model based on the sampling analysis results

  5. Sequence Tree Modeling for Combined Accident and Feed-and-Bleed Operation

    Energy Technology Data Exchange (ETDEWEB)

    Kim, Bo Gyung; Kang Hyun Gook [KAIST, Daejeon (Korea, Republic of); Yoon, Ho Joon [Khalifa University of Science, Abu Dhabi (United Arab Emirates)

    2016-05-15

    In order to address this issue, this study suggests the sequence tree model to analyze accident sequence systematically. Using the sequence tree model, all possible scenarios which need a specific safety action to prevent the core damage can be identified and success conditions of safety action under complicated situation such as combined accident will be also identified. Sequence tree is branch model to divide plant condition considering the plant dynamics. Since sequence tree model can reflect the plant dynamics, arising from interaction of different accident timing and plant condition and from the interaction between the operator action, mitigation system, and the indicators for operation, sequence tree model can be used to develop the dynamic event tree model easily. Target safety action for this study is a feed-and-bleed (F and B) operation. A F and B operation directly cools down the reactor cooling system (RCS) using the primary cooling system when residual heat removal by the secondary cooling system is not available. In this study, a TLOFW accident and a TLOFW accident with LOCA were the target accidents. Based on the conventional PSA model and indicators, the sequence tree model for a TLOFW accident was developed. If sampling analysis is performed, practical accident sequences can be identified based on the sequence analysis. If a realistic distribution for the variables can be obtained for sampling analysis, much more realistic accident sequences can be described. Moreover, if the initiating event frequency under a combined accident can be quantified, the sequence tree model can translate into a dynamic event tree model based on the sampling analysis results.

  6. Deep recurrent conditional random field network for protein secondary prediction

    DEFF Research Database (Denmark)

    Johansen, Alexander Rosenberg; Sønderby, Søren Kaae; Sønderby, Casper Kaae

    2017-01-01

    Deep learning has become the state-of-the-art method for predicting protein secondary structure from only its amino acid residues and sequence profile. Building upon these results, we propose to combine a bi-directional recurrent neural network (biRNN) with a conditional random field (CRF), which...... of the labels for all time-steps. We condition the CRF on the output of biRNN, which learns a distributed representation based on the entire sequence. The biRNN-CRF is therefore close to ideally suited for the secondary structure task because a high degree of cross-talk between neighboring elements can...

  7. Primate amygdala neurons evaluate the progress of self-defined economic choice sequences.

    Science.gov (United States)

    Grabenhorst, Fabian; Hernadi, Istvan; Schultz, Wolfram

    2016-10-12

    The amygdala is a prime valuation structure yet its functions in advanced behaviors are poorly understood. We tested whether individual amygdala neurons encode a critical requirement for goal-directed behavior: the evaluation of progress during sequential choices. As monkeys progressed through choice sequences toward rewards, amygdala neurons showed phasic, gradually increasing responses over successive choice steps. These responses occurred in the absence of external progress cues or motor preplanning. They were often specific to self-defined sequences, typically disappearing during instructed control sequences with similar reward expectation. Their build-up rate reflected prospectively the forthcoming choice sequence, suggesting adaptation to an internal plan. Population decoding demonstrated a high-accuracy progress code. These findings indicate that amygdala neurons evaluate the progress of planned, self-defined behavioral sequences. Such progress signals seem essential for aligning stepwise choices with internal plans. Their presence in amygdala neurons may inform understanding of human conditions with amygdala dysfunction and deregulated reward pursuit.

  8. Comparative analysis of sequences from PT 2013

    DEFF Research Database (Denmark)

    Mikkelsen, Susie Sommer

    Sheatfish and not EHNV. Generally, mistakes occurred at the ends of the sequences. This can be due to several factors. One is that the sequence has not been trimmed of the sequence primer sites. Another is the lack of quality control of the chromatogram. Finally, sequencing in just one direction can result...... diseases in Europe. As part of the EURL proficiency test for fish diseases it is required to sequence any RANA virus isolates found in any of the samples. It is also highly recommended to sequence the ISA virus to determine whether it be HPRΔ or HPR0. Furthermore, it is recommended that any VHSV and IHNV...... isolates be genotyped. As part of the evaluation of the proficiency results it was decided this year to look into the quality and similarity of the sequence results for selected viruses. Ampoule III in the proficiency test 2013 contained an EHNV isolate. The EURL received 43 sequences from 41 laboratories...

  9. Shotgun protein sequencing.

    Energy Technology Data Exchange (ETDEWEB)

    Faulon, Jean-Loup Michel; Heffelfinger, Grant S.

    2009-06-01

    A novel experimental and computational technique based on multiple enzymatic digestion of a protein or protein mixture that reconstructs protein sequences from sequences of overlapping peptides is described in this SAND report. This approach, analogous to shotgun sequencing of DNA, is to be used to sequence alternative spliced proteins, to identify post-translational modifications, and to sequence genetically engineered proteins.

  10. [Complete genome sequencing and sequence analysis of BCG Tice].

    Science.gov (United States)

    Wang, Zhiming; Pan, Yuanlong; Wu, Jun; Zhu, Baoli

    2012-10-04

    The objective of this study is to obtain the complete genome sequence of Bacillus Calmette-Guerin Tice (BCG Tice), in order to provide more information about the molecular biology of BCG Tice and design more reasonable vaccines to prevent tuberculosis. We assembled the data from high-throughput sequencing with SOAPdenovo software, with many contigs and scaffolds obtained. There are many sequence gaps and physical gaps remained as a result of regional low coverage and low quality. We designed primers at the end of contigs and performed PCR amplification in order to link these contigs and scaffolds. With various enzymes to perform PCR amplification, adjustment of PCR reaction conditions, and combined with clone construction to sequence, all the gaps were finished. We obtained the complete genome sequence of BCG Tice and submitted it to GenBank of National Center for Biotechnology Information (NCBI). The genome of BCG Tice is 4334064 base pairs in length, with GC content 65.65%. The problems and strategies during the finishing step of BCG Tice sequencing are illuminated here, with the hope of affording some experience to those who are involved in the finishing step of genome sequencing. The microarray data were verified by our results.

  11. Multimodal sequence learning.

    Science.gov (United States)

    Kemény, Ferenc; Meier, Beat

    2016-02-01

    While sequence learning research models complex phenomena, previous studies have mostly focused on unimodal sequences. The goal of the current experiment is to put implicit sequence learning into a multimodal context: to test whether it can operate across different modalities. We used the Task Sequence Learning paradigm to test whether sequence learning varies across modalities, and whether participants are able to learn multimodal sequences. Our results show that implicit sequence learning is very similar regardless of the source modality. However, the presence of correlated task and response sequences was required for learning to take place. The experiment provides new evidence for implicit sequence learning of abstract conceptual representations. In general, the results suggest that correlated sequences are necessary for implicit sequence learning to occur. Moreover, they show that elements from different modalities can be automatically integrated into one unitary multimodal sequence. Copyright © 2015 Elsevier B.V. All rights reserved.

  12. Sequence Read Archive (SRA)

    Data.gov (United States)

    U.S. Department of Health & Human Services — The Sequence Read Archive (SRA) stores raw sequencing data from the next generation of sequencing platforms including Roche 454 GS System®, Illumina Genome...

  13. Metagenomic Sequencing of an In Vitro-Simulated Microbial Community

    Energy Technology Data Exchange (ETDEWEB)

    Morgan, Jenna L.; Darling, Aaron E.; Eisen, Jonathan A.

    2009-12-01

    Background: Microbial life dominates the earth, but many species are difficult or even impossible to study under laboratory conditions. Sequencing DNA directly from the environment, a technique commonly referred to as metagenomics, is an important tool for cataloging microbial life. This culture-independent approach involves collecting samples that include microbes in them, extracting DNA from the samples, and sequencing the DNA. A sample may contain many different microorganisms, macroorganisms, and even free-floating environmental DNA. A fundamental challenge in metagenomics has been estimating the abundance of organisms in a sample based on the frequency with which the organism's DNA was observed in reads generated via DNA sequencing. Methodology/Principal Findings: We created mixtures of ten microbial species for which genome sequences are known. Each mixture contained an equal number of cells of each species. We then extracted DNA from the mixtures, sequenced the DNA, and measured the frequency with which genomic regions from each organism was observed in the sequenced DNA. We found that the observed frequency of reads mapping to each organism did not reflect the equal numbers of cells that were known to be included in each mixture. The relative organism abundances varied significantly depending on the DNA extraction and sequencing protocol utilized. Conclusions/Significance: We describe a new data resource for measuring the accuracy of metagenomic binning methods, created by in vitro-simulation of a metagenomic community. Our in vitro simulation can be used to complement previous in silico benchmark studies. In constructing a synthetic community and sequencing its metagenome, we encountered several sources of observation bias that likely affect most metagenomic experiments to date and present challenges for comparative metagenomic studies. DNA preparation methods have a particularly profound effect in our study, implying that samples prepared with

  14. The Influence of a Mouthpiece-Based Topography Measurement Device on Electronic Cigarette User's Plasma Nicotine Concentration, Heart Rate, and Subjective Effects Under Directed and Ad Libitum Use Conditions.

    Science.gov (United States)

    Spindle, Tory R; Hiler, Marzena M; Breland, Alison B; Karaoghlanian, Nareg V; Shihadeh, Alan L; Eissenberg, Thomas

    2017-04-01

    Electronic cigarettes e-cigarettes aerosolize a liquid solution often containing nicotine. e-cigarette nicotine delivery may be influenced by user puffing behaviors ("puff topography"). E-cigarette puff topography can be recorded using mouthpiece-based computerized systems. The present study sought to examine the extent to which these systems influence e-cigarette nicotine delivery and other e-cigarette associated acute effects under ad libitum use conditions. Plasma nicotine concentration, heart rate, and subjective effects were assessed in 29 experienced e-cigarette users using their preferred e-cigarette battery and liquid (≥12mg/mL nicotine) in two sessions differing only by the presence of a mouthpiece-based device. In both sessions, participants completed a directed e-cigarette use bout (10 puffs, 30-s interpuff interval) and a 90-min ad libitum bout. Puff topography was recorded in the session with the topography mouthpiece. Plasma nicotine, heart rate, and subjective effects, aside from "Did the e-cigarette Taste Good?" were independent of topography measurement (higher mean taste ratings were observed in the no topography condition). Mean (SEM) plasma nicotine concentration following the ad libitum bout was 34.3ng/mL (4.9) in the no topography condition and 35.7ng/mL (4.3) in the topography condition. Longer puff durations, longer interpuff intervals, and larger puff volumes were observed in the ad libitum relative to the directed bout. E-cigarette use significantly increased plasma nicotine concentration and heart rate while suppressing abstinence symptoms. These effects did not differ when a topography mouthpiece was present. Future studies using ad libitum e-cigarette use bouts would facilitate understanding of e-cigarette toxicant yield. No prior study has examined whether mouthpiece-based topography recording devices influence e-cigarette associated nicotine delivery, heart rate, or subjective effects under ad libitum conditions or assessed ad

  15. Question-answer sequences in survey interviews

    NARCIS (Netherlands)

    Dijkstra, W.; Ongena, Y.P.

    2006-01-01

    Interaction analysis was used to analyze a total of 14,265 question-answer sequences of (Q-A Sequences) 80 questions that originated from two face-to-face and three telephone surveys. The analysis was directed towards the causes and effects of particular interactional problems. Our results showed

  16. Bacterial identification and subtyping using DNA microarray and DNA sequencing.

    Science.gov (United States)

    Al-Khaldi, Sufian F; Mossoba, Magdi M; Allard, Marc M; Lienau, E Kurt; Brown, Eric D

    2012-01-01

    The era of fast and accurate discovery of biological sequence motifs in prokaryotic and eukaryotic cells is here. The co-evolution of direct genome sequencing and DNA microarray strategies not only will identify, isotype, and serotype pathogenic bacteria, but also it will aid in the discovery of new gene functions by detecting gene expressions in different diseases and environmental conditions. Microarray bacterial identification has made great advances in working with pure and mixed bacterial samples. The technological advances have moved beyond bacterial gene expression to include bacterial identification and isotyping. Application of new tools such as mid-infrared chemical imaging improves detection of hybridization in DNA microarrays. The research in this field is promising and future work will reveal the potential of infrared technology in bacterial identification. On the other hand, DNA sequencing by using 454 pyrosequencing is so cost effective that the promise of $1,000 per bacterial genome sequence is becoming a reality. Pyrosequencing technology is a simple to use technique that can produce accurate and quantitative analysis of DNA sequences with a great speed. The deposition of massive amounts of bacterial genomic information in databanks is creating fingerprint phylogenetic analysis that will ultimately replace several technologies such as Pulsed Field Gel Electrophoresis. In this chapter, we will review (1) the use of DNA microarray using fluorescence and infrared imaging detection for identification of pathogenic bacteria, and (2) use of pyrosequencing in DNA cluster analysis to fingerprint bacterial phylogenetic trees.

  17. Developing an inverted Barrovian sequence; insights from monazite petrochronology

    Science.gov (United States)

    Mottram, Catherine M.; Warren, Clare J.; Regis, Daniele; Roberts, Nick M. W.; Harris, Nigel B. W.; Argles, Tom W.; Parrish, Randall R.

    2014-10-01

    In the Himalayan region of Sikkim, the well-developed inverted metamorphic sequence of the Main Central Thrust (MCT) zone is folded, thus exposing several transects through the structure that reached similar metamorphic grades at different times. In-situ LA-ICP-MS U-Th-Pb monazite ages, linked to pressure-temperature conditions via trace-element reaction fingerprints, allow key aspects of the evolution of the thrust zone to be understood for the first time. The ages show that peak metamorphic conditions were reached earliest in the structurally highest part of the inverted metamorphic sequence, in the Greater Himalayan Sequence (GHS) in the hanging wall of the MCT. Monazite in this unit grew over a prolonged period between ∼37 and 16 Ma in the southerly leading-edge of the thrust zone and between ∼37 and 14.5 Ma in the northern rear-edge of the thrust zone, at peak metamorphic conditions of ∼790 °C and 10 kbar. Monazite ages in Lesser Himalayan Sequence (LHS) footwall rocks show that identical metamorphic conditions were reached ∼4-6 Ma apart along the ∼60 km separating samples along the MCT transport direction. Upper LHS footwall rocks reached peak metamorphic conditions of ∼655 °C and 9 kbar between ∼21 and 16 Ma in the more southerly-exposed transect and ∼14.5-12 Ma in the northern transect. Similarly, lower LHS footwall rocks reached peak metamorphic conditions of ∼580 °C and 8.5 kbar at ∼16 Ma in the south, and 9-10 Ma in the north. In the southern transect, the timing of partial melting in the GHS hanging wall (∼23-19.5 Ma) overlaps with the timing of prograde metamorphism (∼21 Ma) in the LHS footwall, confirming that the hanging wall may have provided the heat necessary for the metamorphism of the footwall. Overall, the data provide robust evidence for progressively downwards-penetrating deformation and accretion of original LHS footwall material to the GHS hanging wall over a period of ∼5 Ma. These processes appear to have

  18. SEQUENCING OF FLAX LIS-1 INSERTION SITE IN THE ALBIDUM GENOTYPE

    Directory of Open Access Journals (Sweden)

    Jana Žiarovská

    2012-12-01

    Full Text Available The paper presents a methodology of identifying the insertion site of LIS-1-1 (Linum Insertion Sequence 1 element in flax Albidum variety when growing under the in vitro combined with environmental stress conditions. Abiotic stress was induced by a reduced nutrient content in a growth medium. The LIS-1 insertion site amplification was reaLIS-1ed using the forward LIS-L: 5'-GGG CAG TTT AAC TGT AAC GAA - 3 'and revers LIS-R: 5'-GCT TGG ATT TAG ACT TGG CAA C - 3' primers by PCR. PCR product was sequenced by direct sequencing method to proove the nucleotide sequence for matching with database LIS-1 sequence. A comparison has been matched with the sequence of the amplified segment in the database for all nucleotides except the 11-position in the 5'-3 ' direction, where instead of the three adenine pair is a couple in the Albidum variety. Changes caused by mobile elements or insertion sequences result in common flax in variability that can be used for the purposes of development of effective marker identification or environment based markers development.

  19. Integrated sequence analysis. Final report

    International Nuclear Information System (INIS)

    Andersson, K.; Pyy, P.

    1998-02-01

    The NKS/RAK subprojet 3 'integrated sequence analysis' (ISA) was formulated with the overall objective to develop and to test integrated methodologies in order to evaluate event sequences with significant human action contribution. The term 'methodology' denotes not only technical tools but also methods for integration of different scientific disciplines. In this report, we first discuss the background of ISA and the surveys made to map methods in different application fields, such as man machine system simulation software, human reliability analysis (HRA) and expert judgement. Specific event sequences were, after the surveys, selected for application and testing of a number of ISA methods. The event sequences discussed in the report were cold overpressure of BWR, shutdown LOCA of BWR, steam generator tube rupture of a PWR and BWR disturbed signal view in the control room after an external event. Different teams analysed these sequences by using different ISA and HRA methods. Two kinds of results were obtained from the ISA project: sequence specific and more general findings. The sequence specific results are discussed together with each sequence description. The general lessons are discussed under a separate chapter by using comparisons of different case studies. These lessons include areas ranging from plant safety management (design, procedures, instrumentation, operations, maintenance and safety practices) to methodological findings (ISA methodology, PSA,HRA, physical analyses, behavioural analyses and uncertainty assessment). Finally follows a discussion about the project and conclusions are presented. An interdisciplinary study of complex phenomena is a natural way to produce valuable and innovative results. This project came up with structured ways to perform ISA and managed to apply the in practice. The project also highlighted some areas where more work is needed. In the HRA work, development is required for the use of simulators and expert judgement as

  20. Green's theorem and Gorenstein sequences

    OpenAIRE

    Ahn, Jeaman; Migliore, Juan C.; Shin, Yong-Su

    2016-01-01

    We study consequences, for a standard graded algebra, of extremal behavior in Green's Hyperplane Restriction Theorem. First, we extend his Theorem 4 from the case of a plane curve to the case of a hypersurface in a linear space. Second, assuming a certain Lefschetz condition, we give a connection to extremal behavior in Macaulay's theorem. We apply these results to show that $(1,19,17,19,1)$ is not a Gorenstein sequence, and as a result we classify the sequences of the form $(1,a,a-2,a,1)$ th...

  1. Multihospital Occurrence of Pan-Resistant Klebsiella pneumoniae Sequence Type 147 with an ISEcp1-Directed blaOXA-181 Insertion in the mgrB Gene in the United Arab Emirates.

    Science.gov (United States)

    Sonnevend, Ágnes; Ghazawi, Akela; Hashmey, Rayhan; Haidermota, Aliasgher; Girgis, Safinaz; Alfaresi, Mubarak; Omar, Mohammed; Paterson, David L; Zowawi, Hosam M; Pál, Tibor

    2017-07-01

    The emergence of pan-resistant Klebsiella pneumoniae strains is an increasing concern. In the present study, we describe a cluster of 9 pan-resistant K. pneumoniae sequence type 147 (ST147) isolates encountered in 4 patients over nearly 1 year in 3 hospitals of the United Arab Emirates (UAE). The isolates exhibited highly similar genotypes. All produced chromosomally encoded OXA-181, and the majority also produced the NDM-5 carbapenemase. As with the previously described single isolate from the UAE, MS6671, the mgrB was disrupted by a functional, IS Ecp1 -driven bla OXA-181 insertion causing resistance to carbapenems. The mutation was successfully complemented with an intact mgrB gene, indicating that it was responsible for colistin resistance. bla NDM-5 was located within a resistance island of an approximately 100-kb IncFII plasmid carrying ermB , mph (A), bla TEM-1B , rmtB , bla NDM-5 , sul1 , aadA2 , and dfrA12 resistance genes. Sequencing this plasmid (pABC143-NDM) revealed that its backbone was nearly identical to that of plasmid pMS6671E from which several resistance genes, including bla NDM-5 , had been deleted. More extensive similarities of the backbone and the resistance island were found between pABC143C-NDM and the bla NDM-5 -carrying IncFII plasmids of two K. pneumoniae ST147 isolates from South Korea, one of which was colistin resistant, and both also produced OXA-181. Notably, one of these strains was isolated from a patient transferred from the UAE. Our data show that this pan-resistant clone has an alarming capacity to maintain itself over an extended period of time and is even likely to be transmitted internationally. Copyright © 2017 American Society for Microbiology.

  2. Nonparametric combinatorial sequence models.

    Science.gov (United States)

    Wauthier, Fabian L; Jordan, Michael I; Jojic, Nebojsa

    2011-11-01

    This work considers biological sequences that exhibit combinatorial structures in their composition: groups of positions of the aligned sequences are "linked" and covary as one unit across sequences. If multiple such groups exist, complex interactions can emerge between them. Sequences of this kind arise frequently in biology but methodologies for analyzing them are still being developed. This article presents a nonparametric prior on sequences which allows combinatorial structures to emerge and which induces a posterior distribution over factorized sequence representations. We carry out experiments on three biological sequence families which indicate that combinatorial structures are indeed present and that combinatorial sequence models can more succinctly describe them than simpler mixture models. We conclude with an application to MHC binding prediction which highlights the utility of the posterior distribution over sequence representations induced by the prior. By integrating out the posterior, our method compares favorably to leading binding predictors.

  3. Viral metagenomics: Analysis of begomoviruses by illumina high-throughput sequencing

    KAUST Repository

    Idris, Ali

    2014-03-12

    Traditional DNA sequencing methods are inefficient, lack the ability to discern the least abundant viral sequences, and ineffective for determining the extent of variability in viral populations. Here, populations of single-stranded DNA plant begomoviral genomes and their associated beta- and alpha-satellite molecules (virus-satellite complexes) (genus, Begomovirus; family, Geminiviridae) were enriched from total nucleic acids isolated from symptomatic, field-infected plants, using rolling circle amplification (RCA). Enriched virus-satellite complexes were subjected to Illumina-Next Generation Sequencing (NGS). CASAVA and SeqMan NGen programs were implemented, respectively, for quality control and for de novo and reference-guided contig assembly of viral-satellite sequences. The authenticity of the begomoviral sequences, and the reproducibility of the Illumina-NGS approach for begomoviral deep sequencing projects, were validated by comparing NGS results with those obtained using traditional molecular cloning and Sanger sequencing of viral components and satellite DNAs, also enriched by RCA or amplified by polymerase chain reaction. As the use of NGS approaches, together with advances in software development, make possible deep sequence coverage at a lower cost; the approach described herein will streamline the exploration of begomovirus diversity and population structure from naturally infected plants, irrespective of viral abundance. This is the first report of the implementation of Illumina-NGS to explore the diversity and identify begomoviral-satellite SNPs directly from plants naturally-infected with begomoviruses under field conditions. 2014 by the authors; licensee MDPI, Basel, Switzerland.

  4. Viral Metagenomics: Analysis of Begomoviruses by Illumina High-Throughput Sequencing

    Directory of Open Access Journals (Sweden)

    Ali Idris

    2014-03-01

    Full Text Available Traditional DNA sequencing methods are inefficient, lack the ability to discern the least abundant viral sequences, and ineffective for determining the extent of variability in viral populations. Here, populations of single-stranded DNA plant begomoviral genomes and their associated beta- and alpha-satellite molecules (virus-satellite complexes (genus, Begomovirus; family, Geminiviridae were enriched from total nucleic acids isolated from symptomatic, field-infected plants, using rolling circle amplification (RCA. Enriched virus-satellite complexes were subjected to Illumina-Next Generation Sequencing (NGS. CASAVA and SeqMan NGen programs were implemented, respectively, for quality control and for de novo and reference-guided contig assembly of viral-satellite sequences. The authenticity of the begomoviral sequences, and the reproducibility of the Illumina-NGS approach for begomoviral deep sequencing projects, were validated by comparing NGS results with those obtained using traditional molecular cloning and Sanger sequencing of viral components and satellite DNAs, also enriched by RCA or amplified by polymerase chain reaction. As the use of NGS approaches, together with advances in software development, make possible deep sequence coverage at a lower cost; the approach described herein will streamline the exploration of begomovirus diversity and population structure from naturally infected plants, irrespective of viral abundance. This is the first report of the implementation of Illumina-NGS to explore the diversity and identify begomoviral-satellite SNPs directly from plants naturally-infected with begomoviruses under field conditions.

  5. Genome Sequence Databases (Overview): Sequencing and Assembly

    Energy Technology Data Exchange (ETDEWEB)

    Lapidus, Alla L.

    2009-01-01

    From the date its role in heredity was discovered, DNA has been generating interest among scientists from different fields of knowledge: physicists have studied the three dimensional structure of the DNA molecule, biologists tried to decode the secrets of life hidden within these long molecules, and technologists invent and improve methods of DNA analysis. The analysis of the nucleotide sequence of DNA occupies a special place among the methods developed. Thanks to the variety of sequencing technologies available, the process of decoding the sequence of genomic DNA (or whole genome sequencing) has become robust and inexpensive. Meanwhile the assembly of whole genome sequences remains a challenging task. In addition to the need to assemble millions of DNA fragments of different length (from 35 bp (Solexa) to 800 bp (Sanger)), great interest in analysis of microbial communities (metagenomes) of different complexities raises new problems and pushes some new requirements for sequence assembly tools to the forefront. The genome assembly process can be divided into two steps: draft assembly and assembly improvement (finishing). Despite the fact that automatically performed assembly (or draft assembly) is capable of covering up to 98% of the genome, in most cases, it still contains incorrectly assembled reads. The error rate of the consensus sequence produced at this stage is about 1/2000 bp. A finished genome represents the genome assembly of much higher accuracy (with no gaps or incorrectly assembled areas) and quality ({approx}1 error/10,000 bp), validated through a number of computer and laboratory experiments.

  6. Long sequence correlation coprocessor

    Science.gov (United States)

    Gage, Douglas W.

    1994-09-01

    A long sequence correlation coprocessor (LSCC) accelerates the bitwise correlation of arbitrarily long digital sequences by calculating in parallel the correlation score for 16, for example, adjacent bit alignments between two binary sequences. The LSCC integrated circuit is incorporated into a computer system with memory storage buffers and a separate general purpose computer processor which serves as its controller. Each of the LSCC's set of sequential counters simultaneously tallies a separate correlation coefficient. During each LSCC clock cycle, computer enable logic associated with each counter compares one bit of a first sequence with one bit of a second sequence to increment the counter if the bits are the same. A shift register assures that the same bit of the first sequence is simultaneously compared to different bits of the second sequence to simultaneously calculate the correlation coefficient by the different counters to represent different alignments of the two sequences.

  7. Roles of repetitive sequences

    Energy Technology Data Exchange (ETDEWEB)

    Bell, G.I.

    1991-12-31

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

  8. Anomaly Detection in Sequences

    Data.gov (United States)

    National Aeronautics and Space Administration — We present a set of novel algorithms which we call sequenceMiner, that detect and characterize anomalies in large sets of high-dimensional symbol sequences that...

  9. DNA sequencing conference, 2

    Energy Technology Data Exchange (ETDEWEB)

    Cook-Deegan, R.M. [Georgetown Univ., Kennedy Inst. of Ethics, Washington, DC (United States); Venter, J.C. [National Inst. of Neurological Disorders and Strokes, Bethesda, MD (United States); Gilbert, W. [Harvard Univ., Cambridge, MA (United States); Mulligan, J. [Stanford Univ., CA (United States); Mansfield, B.K. [Oak Ridge National Lab., TN (United States)

    1991-06-19

    This conference focused on DNA sequencing, genetic linkage mapping, physical mapping, informatics and bioethics. Several were used to study this sequencing and mapping. This article also discusses computer hardware and software aiding in the mapping of genes.

  10. sequenceMiner algorithm

    Data.gov (United States)

    National Aeronautics and Space Administration — Detecting and describing anomalies in large repositories of discrete symbol sequences. sequenceMiner has been open-sourced! Download the file below to try it out....

  11. Direct Extraction of InP/GaAsSb/InP DHBT Equivalent-Circuit Elements From S-Parameters Measured at Cut-Off and Normal Bias Conditions

    DEFF Research Database (Denmark)

    Johansen, Tom Keinicke; Leblanc, Rémy; Poulain, Julien

    2016-01-01

    A unique direct parameter extraction method for the small-signal equivalent-circuit model of InP/GaAsSb/InP double heterojunction bipolar transistors (DHBTs) is presented. $S$-parameters measured at cut-off bias are used, at first, to extract the distribution factor $X_{0}$ for the base-collector......A unique direct parameter extraction method for the small-signal equivalent-circuit model of InP/GaAsSb/InP double heterojunction bipolar transistors (DHBTs) is presented. $S$-parameters measured at cut-off bias are used, at first, to extract the distribution factor $X_{0}$ for the base......-collector capacitance at zero collector current and the collector-to-emitter overlap capacitance $C_{ceo}$ present in InP DHBT devices. Low-frequency $S$-parameters measured at normal bias conditions then allows the extraction of the external access resistances $R_{bx}$, $R_{e}$, and $R_{cx}$ as well as the intrinsic...

  12. Direct identification by matrix-assisted laser desorption ionization-time of flight mass spectrometry (MALDI-TOF MS from positive blood culture bottles: An opportunity to customize growth conditions for fastidious organisms causing bloodstream infections

    Directory of Open Access Journals (Sweden)

    Megha Sharma

    2017-01-01

    Full Text Available Culture-negative bacteraemia has been an enigmatic entity with respect to its aetiological agents. In an attempt to actively identify those positive blood cultures that escape isolation and detection on routine workflow, an additional step of MALDI-TOF MS (matrix-assisted laser desorption ionization-time of flight mass spectrometry based detection was carried out directly from the flagged blood culture bottles. Blood samples from 200 blood culture bottles that beeped positive with automated (BACTEC system and showed no growth of organism on routine culture media, were subjected to analysis by MALDI-TOF MS. Forty seven of the 200 (23.5% bacterial aetiology could be established by bottle-based method. Based on these results, growth on culture medium could be achieved for the isolates by providing special growth conditions to the fastidious organisms. Direct identification by MALDI-TOF MS from BACTEC-positive bottles provided an opportunity to isolate those fastidious organisms that failed to grow on routine culture medium by providing them with necessary alterations in growth environment.

  13. Direct identification by matrix-assisted laser desorption ionization-time of flight mass spectrometry (MALDI-TOF MS) from positive blood culture bottles: An opportunity to customize growth conditions for fastidious organisms causing bloodstream infections.

    Science.gov (United States)

    Sharma, Megha; Gautam, Vikas; Mahajan, Monika; Rana, Sudesh; Majumdar, Manasi; Ray, Pallab

    2017-10-01

    Culture-negative bacteraemia has been an enigmatic entity with respect to its aetiological agents. In an attempt to actively identify those positive blood cultures that escape isolation and detection on routine workflow, an additional step of MALDI-TOF MS (matrix-assisted laser desorption ionization-time of flight mass spectrometry) based detection was carried out directly from the flagged blood culture bottles. Blood samples from 200 blood culture bottles that beeped positive with automated (BACTEC) system and showed no growth of organism on routine culture media, were subjected to analysis by MALDI-TOF MS. Forty seven of the 200 (23.5%) bacterial aetiology could be established by bottle-based method. Based on these results, growth on culture medium could be achieved for the isolates by providing special growth conditions to the fastidious organisms. Direct identification by MALDI-TOF MS from BACTEC-positive bottles provided an opportunity to isolate those fastidious organisms that failed to grow on routine culture medium by providing them with necessary alterations in growth environment.

  14. MR-sialography: optimisation and evaluation of an ultra-fast sequence in parallel acquisition technique and different functional conditions of salivary glands; MR-Sialographie: Optimierung und Bewertung ultraschneller Sequenzen mit paralleler Bildgebung und oraler Stimulation

    Energy Technology Data Exchange (ETDEWEB)

    Habermann, C.R.; Cramer, M.C.; Aldefeld, D.; Weiss, F.; Kaul, M.G.; Adam, G. [Radiologisches Zentrum, Klinik und Poliklinik fuer Diagnostische und Interventionelle Radiologie, Universitaetsklinikum Hamburg-Eppendorf (Germany); Graessner, J. [Siemens Medical Systems, Hamburg (Germany); Reitmeier, F.; Jaehne, M. [Kopf- und Hautzentrum, Klinik und Poliklinik fuer Hals-, Nasen- und Ohrenheilkunde, Universitaetsklinikum Hamburg-Eppendorf (Germany); Petersen, K.U. [Zentrum fuer Psychosoziale Medizin, Klinik und Poliklinik fuer Psychiatrie und Psychotherapie, Universitaetsklinikum Hamburg-Eppendorf (Germany)

    2005-04-01

    Purpose: To optimise a fast sequence for MR-sialography and to compare a parallel and non-parallel acquisition technique. Additionally, the effect of oral stimulation regarding the image quality was evaluated. Material and Methods: All examinations were performed by using a 1.5-T superconducting system. After developing a sufficient sequence for MR-sialography, a single-shot turbo-spin-echo sequence (ss-TSE) with an acquisition time of 2.8 sec was used in transverse and oblique sagittal orientation in 27 healthy volunteers. All images were performed with and without parallel imaging technique. The assessment of the ductal system of the submandibular and parotid gland was performed using a 1 to 5 visual scale for each side separately. Images were evaluated by four independent experienced radiologists. For statistical evaluation, an ANOVA with post-hoc comparisons was used with an overall two-tailed significance level of P=.05. For evaluation of interobserver variability, an intraclass correlation was computed and correlation >.08 was determined to indicate a high correlation. Results: All parts of salivary excretal ducts could be visualised in all volunteers, with an overall rating for all ducts of 2.26 (SD{+-}1.09). Between the four observers a high correlation could be obtained with an intraclass correlation of 0.9475. A significant influence regarding the slice angulations could not be obtained (p=0.74). In all healthy volunteers the visibility of excretory ducts improved significantly after oral application of a Sialogogum (p<0.001; {eta}{sup 2}=0.049). The use of a parallel imaging technique did not lead to an improvement of visualisation, showing a significant loss of image quality compared to an acquistion technique without parallel imaging (p<0.001; {eta}{sup 2}=0.013). Conclusion: The optimised ss-TSE MR-sialography seems to be a fast and sufficient technique for visualisation of excretory ducts of the main salivary glands, with no elaborate post

  15. Multipliers on Generalized Mixed Norm Sequence Spaces

    Directory of Open Access Journals (Sweden)

    Oscar Blasco

    2014-01-01

    Full Text Available Given 1≤p,q≤∞ and sequences of integers (nkk and (nk′k such that nk≤nk′≤nk+1, the generalized mixed norm space ℓℐ(p,q is defined as those sequences (ajj such that ((∑j∈Ik‍|aj|p1/pk∈ℓq where Ik={j∈ℕ0 s.t. nk≤jconditions for a sequence λ=(λjj to belong to the space of multipliers (ℓℐ(r,s,ℓ(u,v, for different sequences ℐ and of intervals in ℕ0, are determined.

  16. Robustness analysis of chiller sequencing control

    International Nuclear Information System (INIS)

    Liao, Yundan; Sun, Yongjun; Huang, Gongsheng

    2015-01-01

    Highlights: • Uncertainties with chiller sequencing control were systematically quantified. • Robustness of chiller sequencing control was systematically analyzed. • Different sequencing control strategies were sensitive to different uncertainties. • A numerical method was developed for easy selection of chiller sequencing control. - Abstract: Multiple-chiller plant is commonly employed in the heating, ventilating and air-conditioning system to increase operational feasibility and energy-efficiency under part load condition. In a multiple-chiller plant, chiller sequencing control plays a key role in achieving overall energy efficiency while not sacrifices the cooling sufficiency for indoor thermal comfort. Various sequencing control strategies have been developed and implemented in practice. Based on the observation that (i) uncertainty, which cannot be avoided in chiller sequencing control, has a significant impact on the control performance and may cause the control fail to achieve the expected control and/or energy performance; and (ii) in current literature few studies have systematically addressed this issue, this paper therefore presents a study on robustness analysis of chiller sequencing control in order to understand the robustness of various chiller sequencing control strategies under different types of uncertainty. Based on the robustness analysis, a simple and applicable method is developed to select the most robust control strategy for a given chiller plant in the presence of uncertainties, which will be verified using case studies

  17. The RNA world, automatic sequences and oncogenetics

    Energy Technology Data Exchange (ETDEWEB)

    Tahir Shah, K

    1993-04-01

    We construct a model of the RNA world in terms of naturally evolving nucleotide sequences assuming only Crick-Watson base pairing and self-cleaving/splicing capability. These sequences have the following properties. (1) They are recognizable by an automation (or automata). That is, to each k-sequence, there exist a k-automation which accepts, recognizes or generates the k-sequence. These are known as automatic sequences. Fibonacci and Morse-Thue sequences are the most natural outcome of pre-biotic chemical conditions. (2) Infinite (resp. large) sequences are self-similar (resp. nearly self-similar) under certain rewrite rules and consequently give rise to fractal (resp.fractal-like) structures. Computationally, such sequences can also be generated by their corresponding deterministic parallel re-write system, known as a DOL system. The self-similar sequences are fixed points of their respective rewrite rules. Some of these automatic sequences have the capability that they can read or ``accept`` other sequences while others can detect errors and trigger error-correcting mechanisms. They can be enlarged and have block and/or palindrome structure. Linear recurring sequences such as Fibonacci sequence are simply Feed-back Shift Registers, a well know model of information processing machines. We show that a mutation of any rewrite rule can cause a combinatorial explosion of error and relates this to oncogenetical behavior. On the other hand, a mutation of sequences that are not rewrite rules, leads to normal evolutionary change. Known experimental results support our hypothesis. (author). Refs.

  18. The RNA world, automatic sequences and oncogenetics

    International Nuclear Information System (INIS)

    Tahir Shah, K.

    1993-04-01

    We construct a model of the RNA world in terms of naturally evolving nucleotide sequences assuming only Crick-Watson base pairing and self-cleaving/splicing capability. These sequences have the following properties. 1) They are recognizable by an automation (or automata). That is, to each k-sequence, there exist a k-automation which accepts, recognizes or generates the k-sequence. These are known as automatic sequences. Fibonacci and Morse-Thue sequences are the most natural outcome of pre-biotic chemical conditions. 2) Infinite (resp. large) sequences are self-similar (resp. nearly self-similar) under certain rewrite rules and consequently give rise to fractal (resp.fractal-like) structures. Computationally, such sequences can also be generated by their corresponding deterministic parallel re-write system, known as a DOL system. The self-similar sequences are fixed points of their respective rewrite rules. Some of these automatic sequences have the capability that they can read or 'accept' other sequences while others can detect errors and trigger error-correcting mechanisms. They can be enlarged and have block and/or palindrome structure. Linear recurring sequences such as Fibonacci sequence are simply Feed-back Shift Registers, a well know model of information processing machines. We show that a mutation of any rewrite rule can cause a combinatorial explosion of error and relates this to oncogenetical behavior. On the other hand, a mutation of sequences that are not rewrite rules, leads to normal evolutionary change. Known experimental results support our hypothesis. (author). Refs

  19. Habits as action sequences: hierarchical action control and changes in outcome value.

    Science.gov (United States)

    Dezfouli, Amir; Lingawi, Nura W; Balleine, Bernard W

    2014-11-05

    Goal-directed action involves making high-level choices that are implemented using previously acquired action sequences to attain desired goals. Such a hierarchical schema is necessary for goal-directed actions to be scalable to real-life situations, but results in decision-making that is less flexible than when action sequences are unfolded and the decision-maker deliberates step-by-step over the outcome of each individual action. In particular, from this perspective, the offline revaluation of any outcomes that fall within action sequence boundaries will be invisible to the high-level planner resulting in decisions that are insensitive to such changes. Here, within the context of a two-stage decision-making task, we demonstrate that this property can explain the emergence of habits. Next, we show how this hierarchical account explains the insensitivity of over-trained actions to changes in outcome value. Finally, we provide new data that show that, under extended extinction conditions, habitual behaviour can revert to goal-directed control, presumably as a consequence of decomposing action sequences into single actions. This hierarchical view suggests that the development of action sequences and the insensitivity of actions to changes in outcome value are essentially two sides of the same coin, explaining why these two aspects of automatic behaviour involve a shared neural structure. © 2014 The Author(s) Published by the Royal Society. All rights reserved.

  20. Advantages of genome sequencing by long-read sequencer using SMRT technology in medical area.

    Science.gov (United States)

    Nakano, Kazuma; Shiroma, Akino; Shimoji, Makiko; Tamotsu, Hinako; Ashimine, Noriko; Ohki, Shun; Shinzato, Misuzu; Minami, Maiko; Nakanishi, Tetsuhiro; Teruya, Kuniko; Satou, Kazuhito; Hirano, Takashi

    2017-07-01

    PacBio RS II is the first commercialized third-generation DNA sequencer able to sequence a single molecule DNA in real-time without amplification. PacBio RS II's sequencing technology is novel and unique, enabling the direct observation of DNA synthesis by DNA polymerase. PacBio RS II confers four major advantages compared to other sequencing technologies: long read lengths, high consensus accuracy, a low degree of bias, and simultaneous capability of epigenetic characterization. These advantages surmount the obstacle of sequencing genomic regions such as high/low G+C, tandem repeat, and interspersed repeat regions. Moreover, PacBio RS II is ideal for whole genome sequencing, targeted sequencing, complex population analysis, RNA sequencing, and epigenetics characterization. With PacBio RS II, we have sequenced and analyzed the genomes of many species, from viruses to humans. Herein, we summarize and review some of our key genome sequencing projects, including full-length viral sequencing, complete bacterial genome and almost-complete plant genome assemblies, and long amplicon sequencing of a disease-associated gene region. We believe that PacBio RS II is not only an effective tool for use in the basic biological sciences but also in the medical/clinical setting.

  1. Target selection for direct marketing.

    NARCIS (Netherlands)

    Bult, Jan Roelf

    1993-01-01

    In this thesis we concentrated on the use ol direct mail for targeting potential buyers. The major characteristics that influences the success of a plomotional direct mail campaign are the of-fbr,the communication elements, the timing or sequence of these communication elements, and the list of

  2. A Unified Theoretical Framework for Cognitive Sequencing.

    Science.gov (United States)

    Savalia, Tejas; Shukla, Anuj; Bapi, Raju S

    2016-01-01

    The capacity to sequence information is central to human performance. Sequencing ability forms the foundation stone for higher order cognition related to language and goal-directed planning. Information related to the order of items, their timing, chunking and hierarchical organization are important aspects in sequencing. Past research on sequencing has emphasized two distinct and independent dichotomies: implicit vs. explicit and goal-directed vs. habits. We propose a theoretical framework unifying these two streams. Our proposal relies on brain's ability to implicitly extract statistical regularities from the stream of stimuli and with attentional engagement organizing sequences explicitly and hierarchically. Similarly, sequences that need to be assembled purposively to accomplish a goal require engagement of attentional processes. With repetition, these goal-directed plans become habits with concomitant disengagement of attention. Thus, attention and awareness play a crucial role in the implicit-to-explicit transition as well as in how goal-directed plans become automatic habits. Cortico-subcortical loops basal ganglia-frontal cortex and hippocampus-frontal cortex loops mediate the transition process. We show how the computational principles of model-free and model-based learning paradigms, along with a pivotal role for attention and awareness, offer a unifying framework for these two dichotomies. Based on this framework, we make testable predictions related to the potential influence of response-to-stimulus interval (RSI) on developing awareness in implicit learning tasks.

  3. A Unified Theoretical Framework for Cognitive Sequencing

    Directory of Open Access Journals (Sweden)

    Tejas Savalia

    2016-11-01

    Full Text Available The capacity to sequence information is central to human performance. Sequencing ability forms the foundation stone for higher order cognition related to language and goal-directed planning. Information related to the order of items, their timing, chunking and hierarchical organization are important aspects in sequencing. Past research on sequencing has emphasized two distinct and independent dichotomies: implicit versus explicit and goal-directed versus habits. We propose a theoretical framework unifying these two streams. Our proposal relies on brain's ability to implicitly extract statistical regularities from the stream of stimuli and with attentional engagement organizing sequences explicitly and hierarchically. Similarly, sequences that need to be assembled purposively to accomplish a goal require engagement of attentional processes. With repetition, these goal-directed plans become habits with concomitant disengagement of attention. Thus attention and awareness play a crucial role in the implicit-to-explicit transition as well as in how goal-directed plans become automatic habits. Cortico-subcortical loops ─ basal ganglia-frontal cortex and hippocampus-frontal cortex loops ─ mediate the transition process. We show how the computational principles of model-free and model-based learning paradigms, along with a pivotal role for attention and awareness, offer a unifying framework for these two dichotomies. Based on this framework, we make testable predictions related to the potential influence of response-to-stimulus interval (RSI on developing awareness in implicit learning tasks.

  4. Progress in strategies for sequence diversity library creation for ...

    African Journals Online (AJOL)

    As the simplest technique of protein engineering, directed evolution has been ... An experiment of directed evolution comprises mutant libraries creation and ... evolution, sequence diversity creation, novel strategy, computational design, ...

  5. Integrated sequence analysis. Final report

    Energy Technology Data Exchange (ETDEWEB)

    Andersson, K.; Pyy, P

    1998-02-01

    The NKS/RAK subprojet 3 `integrated sequence analysis` (ISA) was formulated with the overall objective to develop and to test integrated methodologies in order to evaluate event sequences with significant human action contribution. The term `methodology` denotes not only technical tools but also methods for integration of different scientific disciplines. In this report, we first discuss the background of ISA and the surveys made to map methods in different application fields, such as man machine system simulation software, human reliability analysis (HRA) and expert judgement. Specific event sequences were, after the surveys, selected for application and testing of a number of ISA methods. The event sequences discussed in the report were cold overpressure of BWR, shutdown LOCA of BWR, steam generator tube rupture of a PWR and BWR disturbed signal view in the control room after an external event. Different teams analysed these sequences by using different ISA and HRA methods. Two kinds of results were obtained from the ISA project: sequence specific and more general findings. The sequence specific results are discussed together with each sequence description. The general lessons are discussed under a separate chapter by using comparisons of different case studies. These lessons include areas ranging from plant safety management (design, procedures, instrumentation, operations, maintenance and safety practices) to methodological findings (ISA methodology, PSA,HRA, physical analyses, behavioural analyses and uncertainty assessment). Finally follows a discussion about the project and conclusions are presented. An interdisciplinary study of complex phenomena is a natural way to produce valuable and innovative results. This project came up with structured ways to perform ISA and managed to apply the in practice. The project also highlighted some areas where more work is needed. In the HRA work, development is required for the use of simulators and expert judgement as

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

    Energy Technology Data Exchange (ETDEWEB)

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

    2007-11-15

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

  7. A measurement of disorder in binary sequences

    Science.gov (United States)

    Gong, Longyan; Wang, Haihong; Cheng, Weiwen; Zhao, Shengmei

    2015-03-01

    We propose a complex quantity, AL, to characterize the degree of disorder of L-length binary symbolic sequences. As examples, we respectively apply it to typical random and deterministic sequences. One kind of random sequences is generated from a periodic binary sequence and the other is generated from the logistic map. The deterministic sequences are the Fibonacci and Thue-Morse sequences. In these analyzed sequences, we find that the modulus of AL, denoted by |AL | , is a (statistically) equivalent quantity to the Boltzmann entropy, the metric entropy, the conditional block entropy and/or other quantities, so it is a useful quantitative measure of disorder. It can be as a fruitful index to discern which sequence is more disordered. Moreover, there is one and only one value of |AL | for the overall disorder characteristics. It needs extremely low computational costs. It can be easily experimentally realized. From all these mentioned, we believe that the proposed measure of disorder is a valuable complement to existing ones in symbolic sequences.

  8. Mixed Sequence Reader: A Program for Analyzing DNA Sequences with Heterozygous Base Calling

    Science.gov (United States)

    Chang, Chun-Tien; Tsai, Chi-Neu; Tang, Chuan Yi; Chen, Chun-Houh; Lian, Jang-Hau; Hu, Chi-Yu; Tsai, Chia-Lung; Chao, Angel; Lai, Chyong-Huey; Wang, Tzu-Hao; Lee, Yun-Shien

    2012-01-01

    The direct sequencing of PCR products generates heterozygous base-calling fluorescence chromatograms that are useful for identifying single-nucleotide polymorphisms (SNPs), insertion-deletions (indels), short tandem repeats (STRs), and paralogous genes. Indels and STRs can be easily detected using the currently available Indelligent or ShiftDetector programs, which do not search reference sequences. However, the detection of other genomic variants remains a challenge due to the lack of appropriate tools for heterozygous base-calling fluorescence chromatogram data analysis. In this study, we developed a free web-based program, Mixed Sequence Reader (MSR), which can directly analyze heterozygous base-calling fluorescence chromatogram data in .abi file format using comparisons with reference sequences. The heterozygous sequences are identified as two distinct sequences and aligned with reference sequences. Our results showed that MSR may be used to (i) physically locate indel and STR sequences and determine STR copy number by searching NCBI reference sequences; (ii) predict combinations of microsatellite patterns using the Federal Bureau of Investigation Combined DNA Index System (CODIS); (iii) determine human papilloma virus (HPV) genotypes by searching current viral databases in cases of double infections; (iv) estimate the copy number of paralogous genes, such as β-defensin 4 (DEFB4) and its paralog HSPDP3. PMID:22778697

  9. Crash sequence based risk matrix for motorcycle crashes.

    Science.gov (United States)

    Wu, Kun-Feng; Sasidharan, Lekshmi; Thor, Craig P; Chen, Sheng-Yin

    2018-04-05

    included in this study, weighted to represent 338,655 motorcyclists involved in traffic crashes in three years (2011-2013)(NHTSA, 2013). The top five most frequent and severe types of crash sequences were identified, accounting for 23 percent of all the motorcycle crashes included in the study, and they are (1) run-off-road crashes on the right, and hitting roadside objects, (2) cross-median crashes, and rollover, (3) left-turn oncoming crashes, and head-on, (4) crossing over (passing through) or turning into opposite direction at intersections, and (5) side-impacted. In addition to crash sequences, several other factors were also identified to have effects on crash severity: use of helmet, presence of horizontal curves, alcohol consumption, road surface condition, roadway functional class, and nighttime condition. Copyright © 2018 Elsevier Ltd. All rights reserved.

  10. Direct Democracy

    DEFF Research Database (Denmark)

    Beramendi, Virginia; Ellis, Andrew; Kaufman, Bruno

    While many books on direct democracy have a regional or national approach, or simply focus on one of the many mechanisms associated with direct democracy, this Handbook delves into a global comparison of direct democracy mechanisms, including referendums, citizens' initiatives, agenda initiatives...... learned. In addition, the uniquely comprehensive world survey outlines direct democracy provisions in 214 countries and territories and indicates which, if any, of these provisions are used by each country or territory at both the national and sub-national levels. Furthermore, the world survey includes...

  11. Sequences for Student Investigation

    Science.gov (United States)

    Barton, Jeffrey; Feil, David; Lartigue, David; Mullins, Bernadette

    2004-01-01

    We describe two classes of sequences that give rise to accessible problems for undergraduate research. These problems may be understood with virtually no prerequisites and are well suited for computer-aided investigation. The first sequence is a variation of one introduced by Stephen Wolfram in connection with his study of cellular automata. The…

  12. Directing 101.

    Science.gov (United States)

    Pintoff, Ernest

    Providing an introduction to anyone considering directing as a field of study or career, this book takes a broad look at the process of directing and encourages students and professionals alike to look outside of the movie industry for inspiration. Chapters in the book discuss selecting and acquiring material; budgeting and financing; casting and…

  13. Sequence History Update Tool

    Science.gov (United States)

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

    2008-01-01

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

  14. Protecting genomic sequence anonymity with generalization lattices.

    Science.gov (United States)

    Malin, B A

    2005-01-01

    Current genomic privacy technologies assume the identity of genomic sequence data is protected if personal information, such as demographics, are obscured, removed, or encrypted. While demographic features can directly compromise an individual's identity, recent research demonstrates such protections are insufficient because sequence data itself is susceptible to re-identification. To counteract this problem, we introduce an algorithm for anonymizing a collection of person-specific DNA sequences. The technique is termed DNA lattice anonymization (DNALA), and is based upon the formal privacy protection schema of k -anonymity. Under this model, it is impossible to observe or learn features that distinguish one genetic sequence from k-1 other entries in a collection. To maximize information retained in protected sequences, we incorporate a concept generalization lattice to learn the distance between two residues in a single nucleotide region. The lattice provides the most similar generalized concept for two residues (e.g. adenine and guanine are both purines). The method is tested and evaluated with several publicly available human population datasets ranging in size from 30 to 400 sequences. Our findings imply the anonymization schema is feasible for the protection of sequences privacy. The DNALA method is the first computational disclosure control technique for general DNA sequences. Given the computational nature of the method, guarantees of anonymity can be formally proven. There is room for improvement and validation, though this research provides the groundwork from which future researchers can construct genomics anonymization schemas tailored to specific datasharing scenarios.

  15. Compressing DNA sequence databases with coil

    Directory of Open Access Journals (Sweden)

    Hendy Michael D

    2008-05-01

    Full Text Available Abstract Background Publicly available DNA sequence databases such as GenBank are large, and are growing at an exponential rate. The sheer volume of data being dealt with presents serious storage and data communications problems. Currently, sequence data is usually kept in large "flat files," which are then compressed using standard Lempel-Ziv (gzip compression – an approach which rarely achieves good compression ratios. While much research has been done on compressing individual DNA sequences, surprisingly little has focused on the compression of entire databases of such sequences. In this study we introduce the sequence database compression software coil. Results We have designed and implemented a portable software package, coil, for compressing and decompressing DNA sequence databases based on the idea of edit-tree coding. coil is geared towards achieving high compression ratios at the expense of execution time and memory usage during compression – the compression time represents a "one-off investment" whose cost is quickly amortised if the resulting compressed file is transmitted many times. Decompression requires little memory and is extremely fast. We demonstrate a 5% improvement in compression ratio over state-of-the-art general-purpose compression tools for a large GenBank database file containing Expressed Sequence Tag (EST data. Finally, coil can efficiently encode incremental additions to a sequence database. Conclusion coil presents a compelling alternative to conventional compression of flat files for the storage and distribution of DNA sequence databases having a narrow distribution of sequence lengths, such as EST data. Increasing compression levels for databases having a wide distribution of sequence lengths is a direction for future work.

  16. Direct numerical simulations of exhaust gas recirculation effect on multistage autoignition in the negative temperature combustion regime for stratified HCCI flow conditions by using H2O2 addition

    Science.gov (United States)

    El-Asrag, Hossam A.; Ju, Yiguang

    2013-04-01

    Direct numerical simulations (DNSs) of a stratified flow in a homogeneous compression charge ignition (HCCI) engine are performed to investigate the exhaust gas recirculation (EGR) and temperature/mixture stratification effects on the autoignition of synthetic dimethyl ether (DME) in the negative temperature combustion region. Detailed chemistry for a DME/air mixture is employed and solved by a hybrid multi-time scale (HMTS) algorithm to reduce the computational cost. The effect of ? to mimic the EGR effect on autoignition are studied. The results show that adding ? enhances autoignition by rapid OH radical pool formation (34-46% reduction in ignition delay time) and changes the ignition heat release rates at different ignition stages. Sensitivity analysis is performed and the important reactions pathways affecting the autoignition are specified. The DNS results show that the scales introduced by thermal and mixture stratifications have a strong effect after the low temperature chemistry (LTC) ignition especially at the locations of high scalar dissipation rates. Compared to homogenous ignition, stratified ignitions show similar first autoignition delay times, but 18% reduction in the second and third ignition delay times. The results also show that molecular transport plays an important role in stratified low temperature ignition, and that the scalar mixing time scale is strongly affected by local ignition in the stratified flow. Two ignition-kernel propagation modes are observed: a wave-like, low-speed, deflagrative mode and a spontaneous, high-speed, ignition mode. Three criteria are introduced to distinguish these modes by different characteristic time scales and Damkhöler numbers using a progress variable conditioned by an ignition kernel indicator. The low scalar dissipation rate flame front is characterized by high displacement speeds and high mixing Damkhöler number. The proposed criteria are applied successfully at the different ignition stages and

  17. Thermal management and performance evaluation of a dual bi-directional, soft-switched IGBT-based inverter for the 1st autonomous microgrid power system in Taiwan under various operating conditions

    Science.gov (United States)

    Chang, Tien-Chan; Fuh, Yiin-Kuen; Lu, Hong-Yi; Tu, Sheng-Xun

    2016-06-01

    The thermal management of the inverter system is of great importance since very high voltage/current will be switched intermittently and/or continuously and high temperature is excruciably detrimental to the service life of electronics, especially for the switching devices such as insulated gate bipolar transistor (IGBT). In this study, a newly developed dual bi-directional IGBT-based inverter in conjunction with autonomous microgrid system is investigated with particular focus on the thermal management and performance evaluation under various operation conditions. Locally enhanced heat transfer approach such as oblique orientation and heat dissipating materials are experimentally investigated. The studied inverter system is initially packaged by a galvanized steel plate (size 62 × 48 × 18 cm) and the switching power is set in the range of 0.5-3 kW. The module is operated at the switching and pulse frequencies of 60 Hz and 20 kHz, respectively. The adoption of heat dissipating material in either paste or film form had experimentally shown to possess the flexibility tailoring heat transfer performance locally. Experimental studies of heat dissipating film with various hotspot scenarios showed that the temperature difference can be appreciably reduced as much as 13.1 and 15.4 °C, respectively with facilitation of one- and two-layers of heat dissipating film. From the measurement results, the measured peak temperature is highly dominated by the thickness of heat dissipating film, showing the dominance of thickness-dependent thermal resistance and resultant heat accumulation phenomena.

  18. Sequence complexity and work extraction

    International Nuclear Information System (INIS)

    Merhav, Neri

    2015-01-01

    We consider a simplified version of a solvable model by Mandal and Jarzynski, which constructively demonstrates the interplay between work extraction and the increase of the Shannon entropy of an information reservoir which is in contact with a physical system. We extend Mandal and Jarzynski’s main findings in several directions: first, we allow sequences of correlated bits rather than just independent bits. Secondly, at least for the case of binary information, we show that, in fact, the Shannon entropy is only one measure of complexity of the information that must increase in order for work to be extracted. The extracted work can also be upper bounded in terms of the increase in other quantities that measure complexity, like the predictability of future bits from past ones. Third, we provide an extension to the case of non-binary information (i.e. a larger alphabet), and finally, we extend the scope to the case where the incoming bits (before the interaction) form an individual sequence, rather than a random one. In this case, the entropy before the interaction can be replaced by the Lempel–Ziv (LZ) complexity of the incoming sequence, a fact that gives rise to an entropic meaning of the LZ complexity, not only in information theory, but also in physics. (paper)

  19. HIV Sequence Compendium 2015

    Energy Technology Data Exchange (ETDEWEB)

    Foley, Brian Thomas [Los Alamos National Lab. (LANL), Los Alamos, NM (United States); Leitner, Thomas Kenneth [Los Alamos National Lab. (LANL), Los Alamos, NM (United States); Apetrei, Cristian [Univ. of Pittsburgh, PA (United States); Hahn, Beatrice [Univ. of Pennsylvania, Philadelphia, PA (United States); Mizrachi, Ilene [National Center for Biotechnology Information, Bethesda, MD (United States); Mullins, James [Univ. of Washington, Seattle, WA (United States); Rambaut, Andrew [Univ. of Edinburgh, Scotland (United Kingdom); Wolinsky, Steven [Northwestern Univ., Evanston, IL (United States); Korber, Bette Tina Marie [Los Alamos National Lab. (LANL), Los Alamos, NM (United States)

    2015-10-05

    This compendium is an annual printed summary of the data contained in the HIV sequence database. We try to present a judicious selection of the data in such a way that it is of maximum utility to HIV researchers. Each of the alignments attempts to display the genetic variability within the different species, groups and subtypes of the virus. This compendium contains sequences published before January 1, 2015. Hence, though it is published in 2015 and called the 2015 Compendium, its contents correspond to the 2014 curated alignments on our website. The number of sequences in the HIV database is still increasing. In total, at the end of 2014, there were 624,121 sequences in the HIV Sequence Database, an increase of 7% since the previous year. This is the first year that the number of new sequences added to the database has decreased compared to the previous year. The number of near complete genomes (>7000 nucleotides) increased to 5834 by end of 2014. However, as in previous years, the compendium alignments contain only a fraction of these. A more complete version of all alignments is available on our website, http://www.hiv.lanl.gov/ content/sequence/NEWALIGN/align.html As always, we are open to complaints and suggestions for improvement. Inquiries and comments regarding the compendium should be addressed to seq-info@lanl.gov.

  20. Mapping sequences by parts

    Directory of Open Access Journals (Sweden)

    Guziolowski Carito

    2007-09-01

    Full Text Available Abstract Background: We present the N-map method, a pairwise and asymmetrical approach which allows us to compare sequences by taking into account evolutionary events that produce shuffled, reversed or repeated elements. Basically, the optimal N-map of a sequence s over a sequence t is the best way of partitioning the first sequence into N parts and placing them, possibly complementary reversed, over the second sequence in order to maximize the sum of their gapless alignment scores. Results: We introduce an algorithm computing an optimal N-map with time complexity O (|s| × |t| × N using O (|s| × |t| × N memory space. Among all the numbers of parts taken in a reasonable range, we select the value N for which the optimal N-map has the most significant score. To evaluate this significance, we study the empirical distributions of the scores of optimal N-maps and show that they can be approximated by normal distributions with a reasonable accuracy. We test the functionality of the approach over random sequences on which we apply artificial evolutionary events. Practical Application: The method is illustrated with four case studies of pairs of sequences involving non-standard evolutionary events.

  1. The Colliding Beams Sequencer

    International Nuclear Information System (INIS)

    Johnson, D.E.; Johnson, R.P.

    1989-01-01

    The Colliding Beam Sequencer (CBS) is a computer program used to operate the pbar-p Collider by synchronizing the applications programs and simulating the activities of the accelerator operators during filling and storage. The Sequencer acts as a meta-program, running otherwise stand alone applications programs, to do the set-up, beam transfers, acceleration, low beta turn on, and diagnostics for the transfers and storage. The Sequencer and its operational performance will be described along with its special features which include a periodic scheduler and command logger. 14 refs., 3 figs

  2. Phylogenetic Trees From Sequences

    Science.gov (United States)

    Ryvkin, Paul; Wang, Li-San

    In this chapter, we review important concepts and approaches for phylogeny reconstruction from sequence data.We first cover some basic definitions and properties of phylogenetics, and briefly explain how scientists model sequence evolution and measure sequence divergence. We then discuss three major approaches for phylogenetic reconstruction: distance-based phylogenetic reconstruction, maximum parsimony, and maximum likelihood. In the third part of the chapter, we review how multiple phylogenies are compared by consensus methods and how to assess confidence using bootstrapping. At the end of the chapter are two sections that list popular software packages and additional reading.

  3. Directing Creativity

    DEFF Research Database (Denmark)

    Darsø, Lotte; Ibbotson, Piers

    2008-01-01

    In this article we argue that leaders facing complex challenges can learn from the arts, specifically that leaders can learn by examining how theatre directors direct creativity through creative constraints. We suggest that perceiving creativity as a boundary phenomenon is helpful for directing it....... Like leaders, who are caught in paradoxical situations where they have to manage production and logistics simultaneously with making space for creativity and innovation, theatre directors need to find the delicate balance between on one hand renewal of perceptions, acting and interaction...... and on the other hand getting ready for the opening night. We conclude that the art of directing creativity is linked to developing competencies of conscious presence, attention and vigilance, whereas the craft of directing creativity concerns communication, framing and choice....

  4. Direct Heat

    Energy Technology Data Exchange (ETDEWEB)

    Lienau, P J

    1990-01-01

    Potential resources and applications of earth heat in the form of geothermal energy are large. United States direct uses amount to 2,100 MWt thermal and worldwide 8,850 MWt above a reference temperature of 35 degrees Celsius. Space and district heating are the major direct uses of geothermal energy. Equipment employed in direct use projects is of standard manufacture and includes downhole and circulation pumps, transmission and distribution pipelines, heat exchangers and convectors, heat pumps and chillers. Direct uses of earth heat discussed are space and district heating, greenhouse heating and fish farming, process and industrial applications. The economic feasibility of direct use projects is governed by site specific factors such as location of user and resource, resource quality, system load factor and load density, as well as financing. Examples are presented of district heating in Klamath Falls, and Elko. Further developments of direct uses of geothermal energy will depend on matching user needs to the resource, and improving load factors and load density.

  5. Attentional load and implicit sequence learning.

    Science.gov (United States)

    Shanks, David R; Rowland, Lee A; Ranger, Mandeep S

    2005-06-01

    A widely employed conceptualization of implicit learning hypothesizes that it makes minimal demands on attentional resources. This conjecture was investigated by comparing learning under single-task and dual-task conditions in the sequential reaction time (SRT) task. Participants learned probabilistic sequences, with dual-task participants additionally having to perform a counting task using stimuli that were targets in the SRT display. Both groups were then tested for sequence knowledge under single-task (Experiments 1 and 2) or dual-task (Experiment 3) conditions. Participants also completed a free generation task (Experiments 2 and 3) under inclusion or exclusion conditions to determine if sequence knowledge was conscious or unconscious in terms of its access to intentional control. The experiments revealed that the secondary task impaired sequence learning and that sequence knowledge was consciously accessible. These findings disconfirm both the notion that implicit learning is able to proceed normally under conditions of divided attention, and that the acquired knowledge is inaccessible to consciousness. A unitary framework for conceptualizing implicit and explicit learning is proposed.

  6. Gomphid DNA sequence data

    Data.gov (United States)

    U.S. Environmental Protection Agency — DNA sequence data for several genetic loci. This dataset is not publicly accessible because: It's already publicly available on GenBank. It can be accessed through...

  7. Yeast genome sequencing:

    DEFF Research Database (Denmark)

    Piskur, Jure; Langkjær, Rikke Breinhold

    2004-01-01

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

  8. Directed polymers versus directed percolation

    Science.gov (United States)

    Halpin-Healy, Timothy

    1998-10-01

    Universality plays a central role within the rubric of modern statistical mechanics, wherein an insightful continuum formulation rises above irrelevant microscopic details, capturing essential scaling behaviors. Nevertheless, occasions do arise where the lattice or another discrete aspect can constitute a formidable legacy. Directed polymers in random media, along with its close sibling, directed percolation, provide an intriguing case in point. Indeed, the deep blood relation between these two models may have sabotaged past efforts to fully characterize the Kardar-Parisi-Zhang universality class, to which the directed polymer belongs.

  9. Dynamic Sequence Assignment.

    Science.gov (United States)

    1983-12-01

    D-136 548 DYNAMIIC SEQUENCE ASSIGNMENT(U) ADVANCED INFORMATION AND 1/2 DECISION SYSTEMS MOUNTAIN YIELW CA C A 0 REILLY ET AL. UNCLSSIIED DEC 83 AI/DS...I ADVANCED INFORMATION & DECISION SYSTEMS Mountain View. CA 94040 84 u ,53 V,..’. Unclassified _____ SCURITY CLASSIFICATION OF THIS PAGE REPORT...reviews some important heuristic algorithms developed for fas- ter solution of the sequence assignment problem. 3.1. DINAMIC MOGRAMUNIG FORMULATION FOR

  10. HIV Sequence Compendium 2010

    Energy Technology Data Exchange (ETDEWEB)

    Kuiken, Carla [Los Alamos National Lab. (LANL), Los Alamos, NM (United States); Foley, Brian [Los Alamos National Lab. (LANL), Los Alamos, NM (United States); Leitner, Thomas [Los Alamos National Lab. (LANL), Los Alamos, NM (United States); Apetrei, Christian [Univ. of Pittsburgh, PA (United States); Hahn, Beatrice [Univ. of Alabama, Tuscaloosa, AL (United States); Mizrachi, Ilene [National Center for Biotechnology Information, Bethesda, MD (United States); Mullins, James [Univ. of Washington, Seattle, WA (United States); Rambaut, Andrew [Univ. of Edinburgh, Scotland (United Kingdom); Wolinsky, Steven [Northwestern Univ., Evanston, IL (United States); Korber, Bette [Los Alamos National Lab. (LANL), Los Alamos, NM (United States)

    2010-12-31

    This compendium is an annual printed summary of the data contained in the HIV sequence database. In these compendia we try to present a judicious selection of the data in such a way that it is of maximum utility to HIV researchers. Each of the alignments attempts to display the genetic variability within the different species, groups and subtypes of the virus. This compendium contains sequences published before January 1, 2010. Hence, though it is called the 2010 Compendium, its contents correspond to the 2009 curated alignments on our website. The number of sequences in the HIV database is still increasing exponentially. In total, at the time of printing, there were 339,306 sequences in the HIV Sequence Database, an increase of 45% since last year. The number of near complete genomes (>7000 nucleotides) increased to 2576 by end of 2009, reflecting a smaller increase than in previous years. However, as in previous years, the compendium alignments contain only a small fraction of these. Included in the alignments are a small number of sequences representing each of the subtypes and the more prevalent circulating recombinant forms (CRFs) such as 01 and 02, as well as a few outgroup sequences (group O and N and SIV-CPZ). Of the rarer CRFs we included one representative each. A more complete version of all alignments is available on our website, http://www.hiv.lanl.gov/content/sequence/NEWALIGN/align.html. Reprints are available from our website in the form of both HTML and PDF files. As always, we are open to complaints and suggestions for improvement. Inquiries and comments regarding the compendium should be addressed to seq-info@lanl.gov.

  11. General LTE Sequence

    OpenAIRE

    Billal, Masum

    2015-01-01

    In this paper,we have characterized sequences which maintain the same property described in Lifting the Exponent Lemma. Lifting the Exponent Lemma is a very powerful tool in olympiad number theory and recently it has become very popular. We generalize it to all sequences that maintain a property like it i.e. if p^{\\alpha}||a_k and p^\\b{eta}||n, then p^{{\\alpha}+\\b{eta}}||a_{nk}.

  12. Pairwise Sequence Alignment Library

    Energy Technology Data Exchange (ETDEWEB)

    2015-05-20

    Vector extensions, such as SSE, have been part of the x86 CPU since the 1990s, with applications in graphics, signal processing, and scientific applications. Although many algorithms and applications can naturally benefit from automatic vectorization techniques, there are still many that are difficult to vectorize due to their dependence on irregular data structures, dense branch operations, or data dependencies. Sequence alignment, one of the most widely used operations in bioinformatics workflows, has a computational footprint that features complex data dependencies. The trend of widening vector registers adversely affects the state-of-the-art sequence alignment algorithm based on striped data layouts. Therefore, a novel SIMD implementation of a parallel scan-based sequence alignment algorithm that can better exploit wider SIMD units was implemented as part of the Parallel Sequence Alignment Library (parasail). Parasail features: Reference implementations of all known vectorized sequence alignment approaches. Implementations of Smith Waterman (SW), semi-global (SG), and Needleman Wunsch (NW) sequence alignment algorithms. Implementations across all modern CPU instruction sets including AVX2 and KNC. Language interfaces for C/C++ and Python.

  13. Spontaneous direct and reverse osmosis

    International Nuclear Information System (INIS)

    Valitov, N.Kh.

    1996-01-01

    It has been ascertained experimentally that in the course of separation of CsCl, KCl, NaCl aqueous solutions by semi-permeable membrane from distilled water the direct and then reverse osmosis are observed. The same sequence is observed in case of separation of CsCl aqueous solutions from NaCl of different concentrations. The reason for the direct and reverse osmosis has been explained. 5 refs.; 3 figs. 1 tab

  14. Boundary conditions for the numerical solution of elliptic equations in exterior regions

    International Nuclear Information System (INIS)

    Bayliss, A.; Gunzburger, M.; Turkel, E.

    1982-01-01

    Elliptic equations in exterior regions frequently require a boundary condition at infinity to ensure the well-posedness of the problem. Examples of practical applications include the Helmholtz equation and Laplace's equation. Computational procedures based on a direct discretization of the elliptic problem require the replacement of the condition at infinity by a boundary condition on a finite artificial surface. Direct imposition of the condition at infinity along the finite boundary results in large errors. A sequence of boundary conditions is developed which provides increasingly accurate approximations to the problem in the infinite domain. Estimates of the error due to the finite boundary are obtained for several cases. Computations are presented which demonstrate the increased accuracy that can be obtained by the use of the higher order boundary conditions. The examples are based on a finite element formulation but finite difference methods can also be used

  15. Direct marketing

    Directory of Open Access Journals (Sweden)

    Čičić Muris

    2002-01-01

    Full Text Available Direct Marketing (DM is usually treated as unworthy activity, with actions at the edge of legality and activities minded cheating. Despite obvious problems regarding ethics and privacy threat, DM with its size, importance and role in a concept of integrated marketing communication deserves respect and sufficient analysis and review

  16. Adaptive Processing for Sequence Alignment

    KAUST Repository

    Zidan, Mohammed A.; Bonny, Talal; Salama, Khaled N.

    2012-01-01

    Disclosed are various embodiments for adaptive processing for sequence alignment. In one embodiment, among others, a method includes obtaining a query sequence and a plurality of database sequences. A first portion of the plurality of database sequences is distributed to a central processing unit (CPU) and a second portion of the plurality of database sequences is distributed to a graphical processing unit (GPU) based upon a predetermined splitting ratio associated with the plurality of database sequences, where the database sequences of the first portion are shorter than the database sequences of the second portion. A first alignment score for the query sequence is determined with the CPU based upon the first portion of the plurality of database sequences and a second alignment score for the query sequence is determined with the GPU based upon the second portion of the plurality of database sequences.

  17. Adaptive Processing for Sequence Alignment

    KAUST Repository

    Zidan, Mohammed A.

    2012-01-26

    Disclosed are various embodiments for adaptive processing for sequence alignment. In one embodiment, among others, a method includes obtaining a query sequence and a plurality of database sequences. A first portion of the plurality of database sequences is distributed to a central processing unit (CPU) and a second portion of the plurality of database sequences is distributed to a graphical processing unit (GPU) based upon a predetermined splitting ratio associated with the plurality of database sequences, where the database sequences of the first portion are shorter than the database sequences of the second portion. A first alignment score for the query sequence is determined with the CPU based upon the first portion of the plurality of database sequences and a second alignment score for the query sequence is determined with the GPU based upon the second portion of the plurality of database sequences.

  18. On site DNA barcoding by nanopore sequencing.

    Directory of Open Access Journals (Sweden)

    Michele Menegon

    Full Text Available Biodiversity research is becoming increasingly dependent on genomics, which allows the unprecedented digitization and understanding of the planet's biological heritage. The use of genetic markers i.e. DNA barcoding, has proved to be a powerful tool in species identification. However, full exploitation of this approach is hampered by the high sequencing costs and the absence of equipped facilities in biodiversity-rich countries. In the present work, we developed a portable sequencing laboratory based on the portable DNA sequencer from Oxford Nanopore Technologies, the MinION. Complementary laboratory equipment and reagents were selected to be used in remote and tough environmental conditions. The performance of the MinION sequencer and the portable laboratory was tested for DNA barcoding in a mimicking tropical environment, as well as in a remote rainforest of Tanzania lacking electricity. Despite the relatively high sequencing error-rate of the MinION, the development of a suitable pipeline for data analysis allowed the accurate identification of different species of vertebrates including amphibians, reptiles and mammals. In situ sequencing of a wild frog allowed us to rapidly identify the species captured, thus confirming that effective DNA barcoding in the field is possible. These results open new perspectives for real-time-on-site DNA sequencing thus potentially increasing opportunities for the understanding of biodiversity in areas lacking conventional laboratory facilities.

  19. Chromosomal Conditions

    Science.gov (United States)

    ... and more. Stony Point, NY 10980 Close X Home > Complications & Loss > Birth defects & other health conditions > Chromosomal conditions Chromosomal conditions ... Disorders See also: Genetic counseling , Your family health history Last reviewed: February, 2013 ... labor & premature birth The newborn intensive care unit (NICU) Birth defects & ...

  20. Main sequence mass loss

    International Nuclear Information System (INIS)

    Brunish, W.M.; Guzik, J.A.; Willson, L.A.; Bowen, G.

    1987-01-01

    It has been hypothesized that variable stars may experience mass loss, driven, at least in part, by oscillations. The class of stars we are discussing here are the δ Scuti variables. These are variable stars with masses between about 1.2 and 2.25 M/sub θ/, lying on or very near the main sequence. According to this theory, high rotation rates enhance the rate of mass loss, so main sequence stars born in this mass range would have a range of mass loss rates, depending on their initial rotation velocity and the amplitude of the oscillations. The stars would evolve rapidly down the main sequence until (at about 1.25 M/sub θ/) a surface convection zone began to form. The presence of this convective region would slow the rotation, perhaps allowing magnetic braking to occur, and thus sharply reduce the mass loss rate. 7 refs

  1. Next-generation sequencing

    DEFF Research Database (Denmark)

    Rieneck, Klaus; Bak, Mads; Jønson, Lars

    2013-01-01

    , Illumina); several millions of PCR sequences were analyzed. RESULTS: The results demonstrated the feasibility of diagnosing the fetal KEL1 or KEL2 blood group from cell-free DNA purified from maternal plasma. CONCLUSION: This method requires only one primer pair, and the large amount of sequence...... information obtained allows well for statistical analysis of the data. This general approach can be integrated into current laboratory practice and has numerous applications. Besides DNA-based predictions of blood group phenotypes, platelet phenotypes, or sickle cell anemia, and the determination of zygosity...

  2. Weak contractions via $\\lambda$-sequences

    OpenAIRE

    Agyingi, Collins Amburo; Gaba, Yaé Ulrich

    2018-01-01

    In this note, we discuss common fixed point for a family of self mapping defined on a metric type space and satisfying a weakly contractive condition. In our development, we make use of the $\\lambda$-sequence approach and also of a certain class of real valued maps. We derive some implications for self-mappings on quasi-pseudometric type spaces.

  3. Biological sequence analysis

    DEFF Research Database (Denmark)

    Durbin, Richard; Eddy, Sean; Krogh, Anders Stærmose

    This book provides an up-to-date and tutorial-level overview of sequence analysis methods, with particular emphasis on probabilistic modelling. Discussed methods include pairwise alignment, hidden Markov models, multiple alignment, profile searches, RNA secondary structure analysis, and phylogene...

  4. THE RHIC SEQUENCER

    International Nuclear Information System (INIS)

    VAN ZEIJTS, J.; DOTTAVIO, T.; FRAK, B.; MICHNOFF, R.

    2001-01-01

    The Relativistic Heavy Ion Collider (RHIC) has a high level asynchronous time-line driven by a controlling program called the ''Sequencer''. Most high-level magnet and beam related issues are orchestrated by this system. The system also plays an important task in coordinated data acquisition and saving. We present the program, operator interface, operational impact and experience

  5. Twin anemia polycythemia sequence

    NARCIS (Netherlands)

    Slaghekke, Femke

    2014-01-01

    In this thesis we describe that Twin Anemia Polycythemia Sequence (TAPS) is a form of chronic feto-fetal transfusion in monochorionic (identical) twins based on a small amount of blood transfusion through very small anastomoses. For the antenatal diagnosis of TAPS, Middle Cerebral Artery – Peak

  6. simple sequence repeat (SSR)

    African Journals Online (AJOL)

    In the present study, 78 mapped simple sequence repeat (SSR) markers representing 11 linkage groups of adzuki bean were evaluated for transferability to mungbean and related Vigna spp. 41 markers amplified characteristic bands in at least one Vigna species. The transferability percentage across the genotypes ranged ...

  7. Bordism, stable homotopy and adams spectral sequences

    CERN Document Server

    Kochman, Stanley O

    1996-01-01

    This book is a compilation of lecture notes that were prepared for the graduate course "Adams Spectral Sequences and Stable Homotopy Theory" given at The Fields Institute during the fall of 1995. The aim of this volume is to prepare students with a knowledge of elementary algebraic topology to study recent developments in stable homotopy theory, such as the nilpotence and periodicity theorems. Suitable as a text for an intermediate course in algebraic topology, this book provides a direct exposition of the basic concepts of bordism, characteristic classes, Adams spectral sequences, Brown-Peter

  8. Safety Assessment of Advanced Imaging Sequences I: Measurements

    DEFF Research Database (Denmark)

    Jensen, Jørgen Arendt; Rasmussen, Morten Fischer; Pihl, Michael Johannes

    2016-01-01

    intensity measurement program. The approach can measure and store data for a full imaging sequence in 3.8 to 8.2 s per spatial position. Based on Ispta, MI, and probe surface temperature, the method gives the ability to determine whether a sequence is within US FDA limits, or alternatively indicate how......A method for rapid measurement of intensities (Ispta), mechanical index (MI), and probe surface temperature for any ultrasound scanning sequence is presented. It uses the scanner’s sampling capability to give an accurate measurement of the whole imaging sequence for all emissions to yield the true...... measurement system (Onda Corporation, Sunnyvale, CA, USA). Four different sequences have been measured: a fixed focus emission, a duplex sequence containing B-mode and flow emissions, a vector flow sequence with B-mode and flow emissions in 17 directions, and finally a synthetic aperture (SA) duplex flow...

  9. Sequence Selection and Performance in DS/CDMA Systems

    Directory of Open Access Journals (Sweden)

    Jefferson Santos Ambrosio

    2016-03-01

    Full Text Available In this work key concepts on coding division multiple access (CDMA communication systems have been discussed. The sequence selection impact on the performance and capacity of direct sequence CDMA (DS/CDMA systems under AWGN and increasing system loading, as well as under multiple antennas channels was investigated.

  10. Gene mining a marama bean expressed sequence tags (ESTs ...

    African Journals Online (AJOL)

    The authors reported the identification of genes associated with embryonic development and microsatellite sequences. The future direction will entail characterization of these genes using gene over-expression and mutant assays. Key words: Namibia, simple sequence repeats (SSR), data mining, homology searches, ...

  11. No effects of transcranial DLPFC stimulation on implicit task sequence learning and consolidation.

    Science.gov (United States)

    Savic, Branislav; Cazzoli, Dario; Müri, René; Meier, Beat

    2017-08-29

    Neurostimulation of the dorsolateral prefrontal cortex (DLPFC) can modulate performance in cognitive tasks. In a recent study, however, transcranial direct current stimulation (tDCS) of the DLPFC did not affect implicit task sequence learning and consolidation in a paradigm that involved bimanual responses. Because bimanual performance increases the coupling between homologous cortical areas of the hemispheres and left and right DLPFC were stimulated separately the null findings may have been due to the bimanual setup. The aim of the present study was to test the effect of neuro-stimulation on sequence learning in a uni-manual setup. For this purpose two experiments were conducted. In Experiment 1, the DLPFC was stimulated with tDCS. In Experiment 2 the DLPFC was stimulated with transcranial magnetic stimulation (TMS). In both experiments, consolidation was measured 24 hours later. The results showed that sequence learning was present in all conditions and sessions, but it was not influenced by stimulation. Likewise, consolidation of sequence learning was robust across sessions, but it was not influenced by stimulation. These results replicate and extend previous findings. They indicate that established tDCS and TMS protocols on the DLPFC do not influence implicit task sequence learning and consolidation.

  12. Targeted sequencing of plant genomes

    Science.gov (United States)

    Mark D. Huynh

    2014-01-01

    Next-generation sequencing (NGS) has revolutionized the field of genetics by providing a means for fast and relatively affordable sequencing. With the advancement of NGS, wholegenome sequencing (WGS) has become more commonplace. However, sequencing an entire genome is still not cost effective or even beneficial in all cases. In studies that do not require a whole-...

  13. Almost convergence of triple sequences

    OpenAIRE

    Ayhan Esi; M.Necdet Catalbas

    2013-01-01

    In this paper we introduce and study the concepts of almost convergence and almost Cauchy for triple sequences. Weshow that the set of almost convergent triple sequences of 0's and 1's is of the first category and also almost everytriple sequence of 0's and 1's is not almost convergent.Keywords: almost convergence, P-convergent, triple sequence.

  14. A few Smarandache Integer Sequences

    OpenAIRE

    Ibstedt, Henry

    2010-01-01

    This paper deals with the analysis of a few Smarandache Integer Sequences which first appeared in Properties or the Numbers, F. Smarandache, University or Craiova Archives, 1975. The first four sequences are recurrence generated sequences while the last three are concatenation sequences.

  15. Renewable energy act. How did the framework conditions in the amendment 2012 change? Direct marketing of electric power and modifications in the biogas sector; Erneuerbare-Energien-Gesetz. Wie haben sich die Rahmenbedingungen in der Novelle 2012 geaendert? Strom-Direktvermarktungen und Veraenderungen in der Biogasbranche

    Energy Technology Data Exchange (ETDEWEB)

    Kipper, Bernd-Ruediger

    2013-06-01

    On 1 January 2012, the EEG 2012 and some other legal texts became effective. The author of the contribution under consideration reports on the changing framework conditions in the amendment 2012. In particular, the direct marketing of electric power and the modifications in the biogas sector are considered.

  16. THE USE OF A FACTORIAL DESIGN TO EVALUATE THE PHYSICAL STABILITY OF TABLETS PREPARED BY DIRECT COMPRESSION .2. SELECTION OF EXCIPIENTS SUITABLE FOR USE UNDER TROPICAL STORAGE-CONDITIONS

    NARCIS (Netherlands)

    BOS, CE; BOLHUIS, GK; LERK, CF; DEBOER, JH; DUINEVELD, CAA; SMILDE, AK; DOORNBOS, DA

    1991-01-01

    A factorial design has been used to study the influence of disintegrant concentration, storage temperature and relative humidity upon storage on the physical stability of tablets prepared by direct compression. Tablets prepared from a binary mixture of a filler-binder and a disintegrant were stored

  17. Aspects of coverage in medical DNA sequencing

    Directory of Open Access Journals (Sweden)

    Wilson Richard K

    2008-05-01

    Full Text Available Abstract Background DNA sequencing is now emerging as an important component in biomedical studies of diseases like cancer. Short-read, highly parallel sequencing instruments are expected to be used heavily for such projects, but many design specifications have yet to be conclusively established. Perhaps the most fundamental of these is the redundancy required to detect sequence variations, which bears directly upon genomic coverage and the consequent resolving power for discerning somatic mutations. Results We address the medical sequencing coverage problem via an extension of the standard mathematical theory of haploid coverage. The expected diploid multi-fold coverage, as well as its generalization for aneuploidy are derived and these expressions can be readily evaluated for any project. The resulting theory is used as a scaling law to calibrate performance to that of standard BAC sequencing at 8× to 10× redundancy, i.e. for expected coverages that exceed 99% of the unique sequence. A differential strategy is formalized for tumor/normal studies wherein tumor samples are sequenced more deeply than normal ones. In particular, both tumor alleles should be detected at least twice, while both normal alleles are detected at least once. Our theory predicts these requirements can be met for tumor and normal redundancies of approximately 26× and 21×, respectively. We explain why these values do not differ by a factor of 2, as might intuitively be expected. Future technology developments should prompt even deeper sequencing of tumors, but the 21× value for normal samples is essentially a constant. Conclusion Given the assumptions of standard coverage theory, our model gives pragmatic estimates for required redundancy. The differential strategy should be an efficient means of identifying potential somatic mutations for further study.

  18. Direct Reactions

    Energy Technology Data Exchange (ETDEWEB)

    Austern, N. [University of Pittsburgh, Pittsburgh, PA (United States)

    1963-01-15

    In order to give a unified presentation of one point of view, these lectures are devoted only to a detailed development of the standard theories of direct reactions, starting from basic principles. Discussion is given of the present status of the theories, of the techniques used for practical calculation, and of possible future developments. The direct interaction (DI) aspects of a reaction are those which involve only a few of the many degrees of freedom of a nucleus. In fact the minimum number of degrees of freedom which must be involved in a reaction are those required to describe the initial and final channels, and DI studies typically consider these degrees of freedom and no others. Because of this simplicity DI theories may be worked out in painstaking detail. DI processes concern only part of the wave function for a problem. The other part involves complicated excitations of many degrees of freedom, and gives the compound nucleus (CN) effects. While it is extremely interesting to learn how to separate DI and CN effects in an orderly manner, if they are both present in a reaction, no suitable method has yet been found. Instead, current work stresses the kinds of reactions and the kinds of final states in which DI effects dominate and in which CN effects may almost be forgotten. The DI cross-sections which are studied are often extremely large, comparable to elastic scattering cross-sections. (author)

  19. Allele Re-sequencing Technologies

    DEFF Research Database (Denmark)

    Byrne, Stephen; Farrell, Jacqueline Danielle; Asp, Torben

    2013-01-01

    The development of next-generation sequencing technologies has made sequencing an affordable approach for detection of genetic variations associated with various traits. However, the cost of whole genome re-sequencing still remains too high to be feasible for many plant species with large...... alternative to whole genome re-sequencing to identify causative genetic variations in plants. One challenge, however, will be efficient bioinformatics strategies for data handling and analysis from the increasing amount of sequence information....

  20. Miscellaneous conditions

    International Nuclear Information System (INIS)

    Berquist, T.H.; Hoffman, A.D.

    1989-01-01

    This paper reports on numerous conditions (systemic diseases, metabolic diseases, etc.) that may also affect the foot and ankle. In many cases, imaging of the foot and ankle is not performed for primary diagnostic purposes. However, radiographic changes do occur with these conditions. Therefore, it is important to be aware of radiographic abnormalities that these diseases may cause in the foot and ankle

  1. Future direction of direct writing

    Science.gov (United States)

    Kim, Nam-Soo; Han, Kenneth N.

    2010-11-01

    Direct write technology using special inks consisting of finely dispersed metal nanoparticles in liquid is receiving an undivided attention in recent years for its wide range of applicability in modern electronic industry. The application of this technology covers radio frequency identification-tag (RFID-tag), flexible-electronics, organic light emitting diodes (OLED) display, e-paper, antenna, bumpers used in flip-chip, underfilling, frit, miniresistance applications and biological uses, artificial dental applications and many more. In this paper, the authors have reviewed various direct write technologies on the market and discussed their advantages and shortfalls. Emphasis has given on microdispensing deposition write (MDDW), maskless mesoscale materials deposition (M3D), and ink-jet technologies. All of these technologies allow printing various patterns without employing a mask or a resist with an enhanced speed with the aid of computer. MDDW and M3D are capable of drawing patterns in three-dimension and MDDW, in particular, is capable of writing nanoinks with high viscosity. However, it is still far away for direct write to be fully implemented in the commercial arena. One of the hurdles to overcome is in manufacturing conductive inks which are chemically and physically stable, capable of drawing patterns with acceptable conductivity, and also capable of drawing patterns with acceptable adhesiveness with the substrates. The authors have briefly discussed problems involved in manufacturing nanometal inks to be used in various writing devices. There are numerous factors to be considered in manufacturing such inks. They are reducing agents, concentrations, oxidation, compact ability allowing good conductivity, and stability in suspension.

  2. Legal boundary conditions for direct marketing of 'green current' according to EEG 2012; Rechtliche Rahmenbedingungen fuer die Direktvermarktung von ''Gruenstrom'' nach dem EEG 2012

    Energy Technology Data Exchange (ETDEWEB)

    Breuer, Daniel [Landgericht Koeln (Germany); Osborne Clarke, Koeln (Germany). Bereich Energierecht

    2012-07-01

    The new direct marketing regime of the EEG 2012 provides incentives for operators of renewables-based systems to leave the fixed reimbursement scheme and integrate their systems in the markets, especially in the context of marketing of regulating power. However, it remains to be seen if this will reduce the cost of regulating energy supply, or at least keep it at the current level. In any case, plant operators should be careful in choosing their direct marketers and other partners and consultants. Simultaneous supply of regulating power is attractive especially for controllable and in some cases also for fluctuating renewable energy sources. This does comply with the priority principle and also with the prohibition of double marketing as is clearly stated in SEction 8 No. 3a.

  3. Influence of different flow conditions on the occurrence and behavior of potentially hazardous organic xenobiotics in the influent and effluent of a municipal sewage treatment plant in Germany: an effect-directed approach

    Energy Technology Data Exchange (ETDEWEB)

    Faber, Peter [University of Trier (Germany). Department of Hydrology; Max-Planck-Institute for Chemistry, Mainz (Germany). Particle Chemistry Dept.; Bierl, Reinhard [University of Trier (Germany). Department of Hydrology

    2012-12-15

    Flow conditions in the sewer systems are particularly important for the chemical and toxicological characteristics of raw and treated wastewater. Nevertheless, this topic has not been thoroughly investigated to date. In this study, composite wastewater samples were taken daily from the influent and effluent of a municipal sewage treatment plant. Polarity-based fractionation of the samples was carried out through sequential solid phase extractions. Biological testing of single and recombinant fractions was performed using bioluminescence inhibition assay according to DIN EN ISO 11348-2. Selected compounds (pharmaceuticals and polycyclic aromatic hydrocarbons) were also included in the chemical analysis by liquid chromatography coupled with tandem mass spectrometry and gas chromatography coupled with mass spectrometry. By analyzing different flow conditions, this study clarifies how these fractions contribute to the total toxicity of organic substances in wastewater. Additionally, it demonstrates the extent to which the potentially hazardous effects of the fractions can be reduced at the examined sewage treatment plant. Summarizing, medium to highly polar organic compounds were particularly relevant for the total toxicity of organic xenobiotics. For rising wastewater flow under wet weather conditions, we observed a significant decrease in the overall toxicity of the organic pollutants and specifically in the toxic effects of the moderately polar fraction 2. The results provide the starting point for an important risk assessment regarding the occurrence and behavior of potentially toxic xenobiotics by differentiated polarity in municipal wastewater for varying flow conditions. (orig.)

  4. Multilocus Sequence Typing

    OpenAIRE

    Belén, Ana; Pavón, Ibarz; Maiden, Martin C.J.

    2009-01-01

    Multilocus sequence typing (MLST) was first proposed in 1998 as a typing approach that enables the unambiguous characterization of bacterial isolates in a standardized, reproducible, and portable manner using the human pathogen Neisseria meningitidis as the exemplar organism. Since then, the approach has been applied to a large and growing number of organisms by public health laboratories and research institutions. MLST data, shared by investigators over the world via the Internet, have been ...

  5. Achalasia Carcinoma Sequence

    OpenAIRE

    Makmun, Dadang

    2001-01-01

    We report a case of carcinoma of the esophagus in a 58 years old woman with achalasia, who has been diagnosed since 30 years ago, which initiated by surgical treatment (myotomy) and the symptoms recurred since 3 years ago. According to the progress of the disease, Malignancy was strongly suspected due to prolonged stasis and mucosal irritation caused by achalasia (achalasia carcinoma sequence). Because of these contributing factors for the development of serious complications such as Malignan...

  6. Sequencing BPS spectra

    Energy Technology Data Exchange (ETDEWEB)

    Gukov, Sergei [Walter Burke Institute for Theoretical Physics, California Institute of Technology,1200 E California Blvd, Pasadena, CA 91125 (United States); Max-Planck-Institut für Mathematik,Vivatsgasse 7, D-53111 Bonn (Germany); Nawata, Satoshi [Walter Burke Institute for Theoretical Physics, California Institute of Technology,1200 E California Blvd, Pasadena, CA 91125 (United States); Centre for Quantum Geometry of Moduli Spaces, University of Aarhus,Nordre Ringgade 1, DK-8000 (Denmark); Saberi, Ingmar [Walter Burke Institute for Theoretical Physics, California Institute of Technology,1200 E California Blvd, Pasadena, CA 91125 (United States); Stošić, Marko [CAMGSD, Departamento de Matemática, Instituto Superior Técnico,Av. Rovisco Pais, 1049-001 Lisbon (Portugal); Mathematical Institute SANU,Knez Mihajlova 36, 11000 Belgrade (Serbia); Sułkowski, Piotr [Walter Burke Institute for Theoretical Physics, California Institute of Technology,1200 E California Blvd, Pasadena, CA 91125 (United States); Faculty of Physics, University of Warsaw,ul. Pasteura 5, 02-093 Warsaw (Poland)

    2016-03-02

    This paper provides both a detailed study of color-dependence of link homologies, as realized in physics as certain spaces of BPS states, and a broad study of the behavior of BPS states in general. We consider how the spectrum of BPS states varies as continuous parameters of a theory are perturbed. This question can be posed in a wide variety of physical contexts, and we answer it by proposing that the relationship between unperturbed and perturbed BPS spectra is described by a spectral sequence. These general considerations unify previous applications of spectral sequence techniques to physics, and explain from a physical standpoint the appearance of many spectral sequences relating various link homology theories to one another. We also study structural properties of colored HOMFLY homology for links and evaluate Poincaré polynomials in numerous examples. Among these structural properties is a novel “sliding” property, which can be explained by using (refined) modular S-matrix. This leads to the identification of modular transformations in Chern-Simons theory and 3d N=2 theory via the 3d/3d correspondence. Lastly, we introduce the notion of associated varieties as classical limits of recursion relations of colored superpolynomials of links, and study their properties.

  7. Sequencing BPS spectra

    International Nuclear Information System (INIS)

    Gukov, Sergei; Nawata, Satoshi; Saberi, Ingmar; Stošić, Marko; Sułkowski, Piotr

    2016-01-01

    This paper provides both a detailed study of color-dependence of link homologies, as realized in physics as certain spaces of BPS states, and a broad study of the behavior of BPS states in general. We consider how the spectrum of BPS states varies as continuous parameters of a theory are perturbed. This question can be posed in a wide variety of physical contexts, and we answer it by proposing that the relationship between unperturbed and perturbed BPS spectra is described by a spectral sequence. These general considerations unify previous applications of spectral sequence techniques to physics, and explain from a physical standpoint the appearance of many spectral sequences relating various link homology theories to one another. We also study structural properties of colored HOMFLY homology for links and evaluate Poincaré polynomials in numerous examples. Among these structural properties is a novel “sliding” property, which can be explained by using (refined) modular S-matrix. This leads to the identification of modular transformations in Chern-Simons theory and 3d N=2 theory via the 3d/3d correspondence. Lastly, we introduce the notion of associated varieties as classical limits of recursion relations of colored superpolynomials of links, and study their properties.

  8. Image sequence analysis

    CERN Document Server

    1981-01-01

    The processing of image sequences has a broad spectrum of important applica­ tions including target tracking, robot navigation, bandwidth compression of TV conferencing video signals, studying the motion of biological cells using microcinematography, cloud tracking, and highway traffic monitoring. Image sequence processing involves a large amount of data. However, because of the progress in computer, LSI, and VLSI technologies, we have now reached a stage when many useful processing tasks can be done in a reasonable amount of time. As a result, research and development activities in image sequence analysis have recently been growing at a rapid pace. An IEEE Computer Society Workshop on Computer Analysis of Time-Varying Imagery was held in Philadelphia, April 5-6, 1979. A related special issue of the IEEE Transactions on Pattern Anal­ ysis and Machine Intelligence was published in November 1980. The IEEE Com­ puter magazine has also published a special issue on the subject in 1981. The purpose of this book ...

  9. Estimating Outdoor Illumination Conditions Based on Detection of Dynamic Shadows

    DEFF Research Database (Denmark)

    Madsen, Claus B.; Lal, Brajesh Behari

    2013-01-01

    into the image stream to achieve realistic Augmented Reality where the shading and the shadowing of virtual objects is consistent with the real scene. Other techniques require the presence of a known object, a light probe, in the scene for estimating illumination. The technique proposed here works in general......The paper proposes a technique for estimation outdoor illumination conditions in terms of sun and sky radiances directly from pixel values of dynamic shadows detected in video sequences produved by a commercial stereo camera. The technique is applied to the rendering of virtual object...

  10. Chaotic generation of PN sequences : a VLSI implementation

    NARCIS (Netherlands)

    Dornbusch, A.; Pineda de Gyvez, J.

    1999-01-01

    Generation of repeatable pseudo-random sequences with chaotic analog electronics is not feasible using standard circuit topologies. Component variation caused by imperfect fabrication causes the same divergence of output sequences as does varying initial conditions. By quantizing the output of a

  11. Tauberian theorems for Abel summability of sequences of fuzzy numbers

    Science.gov (United States)

    Yavuz, Enes; ćoşkun, Hüsamettin

    2015-09-01

    We give some conditions under which Abel summable sequences of fuzzy numbers are convergent. As corollaries we obtain the results given in [E. Yavuz, Ö. Talo, Abel summability of sequences of fuzzy numbers, Soft computing 2014, doi: 10.1007/s00500-014-1563-7].

  12. Sufficiency of Bell's conditions

    Energy Technology Data Exchange (ETDEWEB)

    Gutkowski, D; Masotto, G [Istituto di Matematica della Universita di Palermo (Italy); Valdes, M V

    1979-04-11

    It is shown that, if the results of measurements of spin components of two-spin one-half particles coupled to a singlet state with respect to n=3 directions satisfy Bell's conditions, then these results are compatible with a local hidden-variable theory. The previous statement is extended to the case n=4.

  13. SNAD: sequence name annotation-based designer

    Directory of Open Access Journals (Sweden)

    Gorbalenya Alexander E

    2009-08-01

    Full Text Available Abstract Background A growing diversity of biological data is tagged with unique identifiers (UIDs associated with polynucleotides and proteins to ensure efficient computer-mediated data storage, maintenance, and processing. These identifiers, which are not informative for most people, are often substituted by biologically meaningful names in various presentations to facilitate utilization and dissemination of sequence-based knowledge. This substitution is commonly done manually that may be a tedious exercise prone to mistakes and omissions. Results Here we introduce SNAD (Sequence Name Annotation-based Designer that mediates automatic conversion of sequence UIDs (associated with multiple alignment or phylogenetic tree, or supplied as plain text list into biologically meaningful names and acronyms. This conversion is directed by precompiled or user-defined templates that exploit wealth of annotation available in cognate entries of external databases. Using examples, we demonstrate how this tool can be used to generate names for practical purposes, particularly in virology. Conclusion A tool for controllable annotation-based conversion of sequence UIDs into biologically meaningful names and acronyms has been developed and placed into service, fostering links between quality of sequence annotation, and efficiency of communication and knowledge dissemination among researchers.

  14. Harnessing Whole Genome Sequencing in Medical Mycology.

    Science.gov (United States)

    Cuomo, Christina A

    2017-01-01

    Comparative genome sequencing studies of human fungal pathogens enable identification of genes and variants associated with virulence and drug resistance. This review describes current approaches, resources, and advances in applying whole genome sequencing to study clinically important fungal pathogens. Genomes for some important fungal pathogens were only recently assembled, revealing gene family expansions in many species and extreme gene loss in one obligate species. The scale and scope of species sequenced is rapidly expanding, leveraging technological advances to assemble and annotate genomes with higher precision. By using iteratively improved reference assemblies or those generated de novo for new species, recent studies have compared the sequence of isolates representing populations or clinical cohorts. Whole genome approaches provide the resolution necessary for comparison of closely related isolates, for example, in the analysis of outbreaks or sampled across time within a single host. Genomic analysis of fungal pathogens has enabled both basic research and diagnostic studies. The increased scale of sequencing can be applied across populations, and new metagenomic methods allow direct analysis of complex samples.

  15. Foundations of Sequence-to-Sequence Modeling for Time Series

    OpenAIRE

    Kuznetsov, Vitaly; Mariet, Zelda

    2018-01-01

    The availability of large amounts of time series data, paired with the performance of deep-learning algorithms on a broad class of problems, has recently led to significant interest in the use of sequence-to-sequence models for time series forecasting. We provide the first theoretical analysis of this time series forecasting framework. We include a comparison of sequence-to-sequence modeling to classical time series models, and as such our theory can serve as a quantitative guide for practiti...

  16. Implicitly Defined Neural Networks for Sequence Labeling

    Science.gov (United States)

    2017-07-31

    ularity has soared for the Long Short - Term Memory (LSTM) (Hochreiter and Schmidhuber, 1997) and vari- ants such as Gated Recurrent Unit (GRU) (Cho et...610. Sepp Hochreiter and Jürgen Schmidhuber. 1997. Long short - term memory . Neural computation 9(8):1735– 1780. Zhiheng Huang, Wei Xu, and Kai Yu. 2015...network are coupled together, in order to improve perfor- mance on complex, long -range dependencies in either direction of a sequence. We contrast our

  17. Novel expressed sequence tag- simple sequence repeats (EST ...

    African Journals Online (AJOL)

    Using different bioinformatic criteria, the SUCEST database was used to mine for simple sequence repeat (SSR) markers. Among 42,189 clusters, 1,425 expressed sequence tag- simple sequence repeats (EST-SSRs) were identified in silico. Trinucleotide repeats were the most abundant SSRs detected. Of 212 primer pairs ...

  18. Linear Co-occurrence Rate Networks (L-CRNs) for Sequence Labeling

    NARCIS (Netherlands)

    Zhu, Zhemin; Hiemstra, Djoerd; Apers, Peter M.G.

    2014-01-01

    Sequence labeling has wide applications in natural language processing and speech processing. Popular sequence labeling models suffer from some known problems. Hidden Markov models (HMMs) are generative models and they cannot encode transition features; Conditional Markov models (CMMs) suffer from

  19. Infinite sequences and series

    CERN Document Server

    Knopp, Konrad

    1956-01-01

    One of the finest expositors in the field of modern mathematics, Dr. Konrad Knopp here concentrates on a topic that is of particular interest to 20th-century mathematicians and students. He develops the theory of infinite sequences and series from its beginnings to a point where the reader will be in a position to investigate more advanced stages on his own. The foundations of the theory are therefore presented with special care, while the developmental aspects are limited by the scope and purpose of the book. All definitions are clearly stated; all theorems are proved with enough detail to ma

  20. Fast global sequence alignment technique

    KAUST Repository

    Bonny, Mohamed Talal; Salama, Khaled N.

    2011-01-01

    fast alignment algorithm, called 'Alignment By Scanning' (ABS), to provide an approximate alignment of two DNA sequences. We compare our algorithm with the wellknown sequence alignment algorithms, the 'GAP' (which is heuristic) and the 'Needleman

  1. Next-Generation Sequencing Platforms

    Science.gov (United States)

    Mardis, Elaine R.

    2013-06-01

    Automated DNA sequencing instruments embody an elegant interplay among chemistry, engineering, software, and molecular biology and have built upon Sanger's founding discovery of dideoxynucleotide sequencing to perform once-unfathomable tasks. Combined with innovative physical mapping approaches that helped to establish long-range relationships between cloned stretches of genomic DNA, fluorescent DNA sequencers produced reference genome sequences for model organisms and for the reference human genome. New types of sequencing instruments that permit amazing acceleration of data-collection rates for DNA sequencing have been developed. The ability to generate genome-scale data sets is now transforming the nature of biological inquiry. Here, I provide an historical perspective of the field, focusing on the fundamental developments that predated the advent of next-generation sequencing instruments and providing information about how these instruments work, their application to biological research, and the newest types of sequencers that can extract data from single DNA molecules.

  2. Identification of succinimide sites in proteins by N-terminal sequence analysis after alkaline hydroxylamine cleavage.

    Science.gov (United States)

    Kwong, M. Y.; Harris, R. J.

    1994-01-01

    Under favorable conditions, Asp or Asn residues can undergo rearrangement to a succinimide (cyclic imide), which may also serve as an intermediate for deamidation and/or isoaspartate formation. Direct identification of such succinimides by peptide mapping is hampered by their lability at neutral and alkaline pH. We determined that incubation in 2 M hydroxylamine, 0.2 M Tris buffer, pH 9, for 2 h at 45 degrees C will specifically cleave on the C-terminal side of succinimides without cleavage at Asn-Gly bonds; yields are typically approximately 50%. N-terminal sequence analysis can then be used to identify an internal sequence generated by cleavage of the succinimide, hence identifying the succinimide site. PMID:8142891

  3. Conditions promoting and restraining agronomic effectiveness of water-insoluble phosphate sources, in particular phosphate rock (PR): I. Indices of phosphate rock use opportunity (PRUOIS) and of phosphate rock suitability for direct use (PRSIDU)

    International Nuclear Information System (INIS)

    Borlan, Z.; Gavriluta, I.; Soare, M.; Stefanescu, D.; Alexandrescu, A.

    2002-01-01

    Several issues of phosphate rock (PR) use are discussed in this paper. Maize for green fodder (Zea mays L) and ryegrass (Lolium multiflorum Lam.) were grown in 7 kg of dry soil and in small pots of 1.25 kg dry soil capacity, respectively, on several base unsaturated soils belonging to Hapludoll and Hapludalf soil groups. The amount of phosphate rock (PR) to apply was based on experimental data considering soil adsorbed acidity (Ah), humus content (H 2 ), cation exchange capacity (T), sum of exchangeable bases (SEB) and mobile (easily soluble) phosphate content (P A L) in the soil. The factors were combined in a rock phosphate use, opportunity index of the soil (PRUOIS): PRUOIS=(A h *H 2 *100)/SEB*10 0.0245*P AL Rock phosphate suitability for direct use was evaluated by means of the rate of PR-P dissolution (PRPRS) in a 0.6% ammonium heptamolybdate in 0.01M calcium chloride solution (ppm P) and by carbonate content (%CaCO 3 ) in PR. Both of these parameters combined provided a phosphate rock suitability index for direct use (PRSIDU): PRSIDU [ppmP/min]=PRPRS*(1-0.03*CaCO 3 ) Water insoluble P sources studied were PR from Kola-Russia, Morocco, Kneifiss-Siria, El Hassa-Jordan, Gafsa- Tunisia, North-Carolina (USA), and Arad-Israel. All PRs were compared with TSP applied at the same rate of P. Neither PRUOIS or PRSIDU considered separately could satisfactorily explain the variance of PR efficiency. An index obtained by multiplicative combination of PRUOIS x PRSIDU did correlate significantly with indices on the agronomic efficiency of PR. (author)

  4. Tournaments, oriented graphs and football sequences

    Directory of Open Access Journals (Sweden)

    Pirzada S.

    2017-08-01

    Full Text Available Consider the result of a soccer league competition where n teams play each other exactly once. A team gets three points for each win and one point for each draw. The total score obtained by each team vi is called the f-score of vi and is denoted by fi. The sequences of all f-scores [fi]i=1n$\\left[ {{\\rm{f}}_{\\rm{i}} } \\right]_{{\\rm{i}} = 1}^{\\rm{n}} $ arranged in non-decreasing order is called the f-score sequence of the competition. We raise the following problem: Which sequences of non-negative integers in non-decreasing order is a football sequence, that is the outcome of a soccer league competition. We model such a competition by an oriented graph with teams represented by vertices in which the teams play each other once, with an arc from team u to team v if and only if u defeats v. We obtain some necessary conditions for football sequences and some characterizations under restrictions.

  5. Extended sequence diagram for human system interaction

    International Nuclear Information System (INIS)

    Hwang, Jong Rok; Choi, Sun Woo; Ko, Hee Ran; Kim, Jong Hyun

    2012-01-01

    Unified Modeling Language (UML) is a modeling language in the field of object oriented software engineering. The sequence diagram is a kind of interaction diagram that shows how processes operate with one another and in what order. It is a construct of a message sequence chart. It depicts the objects and classes involved in the scenario and the sequence of messages exchanged between the objects needed to carry out the functionality of the scenario. This paper proposes the Extended Sequence Diagram (ESD), which is capable of depicting human system interaction for nuclear power plants, as well as cognitive process of operators analysis. In the conventional sequence diagram, there is a limit to only identify the activities of human and systems interactions. The ESD is extended to describe operators' cognitive process in more detail. The ESD is expected to be used as a task analysis method for describing human system interaction. The ESD can also present key steps causing abnormal operations or failures and diverse human errors based on cognitive condition

  6. Use of amplicon sequencing to improve sensitivity in PCR-based detection of microbial pathogen in environmental samples.

    Science.gov (United States)

    Saingam, Prakit; Li, Bo; Yan, Tao

    2018-06-01

    DNA-based molecular detection of microbial pathogens in complex environments is still plagued by sensitivity, specificity and robustness issues. We propose to address these issues by viewing them as inadvertent consequences of requiring specific and adequate amplification (SAA) of target DNA molecules by current PCR methods. Using the invA gene of Salmonella as the model system, we investigated if next generation sequencing (NGS) can be used to directly detect target sequences in false-negative PCR reaction (PCR-NGS) in order to remove the SAA requirement from PCR. False-negative PCR and qPCR reactions were first created using serial dilutions of laboratory-prepared Salmonella genomic DNA and then analyzed directly by NGS. Target invA sequences were detected in all false-negative PCR and qPCR reactions, which lowered the method detection limits near the theoretical minimum of single gene copy detection. The capability of the PCR-NGS approach in correcting false negativity was further tested and confirmed under more environmentally relevant conditions using Salmonella-spiked stream water and sediment samples. Finally, the PCR-NGS approach was applied to ten urban stream water samples and detected invA sequences in eight samples that would be otherwise deemed Salmonella negative. Analysis of the non-target sequences in the false-negative reactions helped to identify primer dime-like short sequences as the main cause of the false negativity. Together, the results demonstrated that the PCR-NGS approach can significantly improve method sensitivity, correct false-negative detections, and enable sequence-based analysis for failure diagnostics in complex environmental samples. Copyright © 2018 Elsevier B.V. All rights reserved.

  7. The advantages of SMRT sequencing

    OpenAIRE

    Roberts, Richard J; Carneiro, Mauricio O; Schatz, Michael C

    2013-01-01

    Of the current next-generation sequencing technologies, SMRT sequencing is sometimes overlooked. However, attributes such as long reads, modified base detection and high accuracy make SMRT a useful technology and an ideal approach to the complete sequencing of small genomes.

  8. Region segmentation along image sequence

    International Nuclear Information System (INIS)

    Monchal, L.; Aubry, P.

    1995-01-01

    A method to extract regions in sequence of images is proposed. Regions are not matched from one image to the following one. The result of a region segmentation is used as an initialization to segment the following and image to track the region along the sequence. The image sequence is exploited as a spatio-temporal event. (authors). 12 refs., 8 figs

  9. Aquatic conditions

    Science.gov (United States)

    Warren E. Heilman

    1999-01-01

    This publication provides citizens, private and public organizations, scientists, and others with information about the aquatic conditions in or near national forests in the Ozark-Ouachita Highlands: the Mark Twain in Missouri, the Ouachita in Arkansas and Oklahoma, and the Ozark-St. Francis National Forests in Arkansas. This report includes water quality analyses...

  10. Robustness of ancestral sequence reconstruction to phylogenetic uncertainty.

    Science.gov (United States)

    Hanson-Smith, Victor; Kolaczkowski, Bryan; Thornton, Joseph W

    2010-09-01

    Ancestral sequence reconstruction (ASR) is widely used to formulate and test hypotheses about the sequences, functions, and structures of ancient genes. Ancestral sequences are usually inferred from an alignment of extant sequences using a maximum likelihood (ML) phylogenetic algorithm, which calculates the most likely ancestral sequence assuming a probabilistic model of sequence evolution and a specific phylogeny--typically the tree with the ML. The true phylogeny is seldom known with certainty, however. ML methods ignore this uncertainty, whereas Bayesian methods incorporate it by integrating the likelihood of each ancestral state over a distribution of possible trees. It is not known whether Bayesian approaches to phylogenetic uncertainty improve the accuracy of inferred ancestral sequences. Here, we use simulation-based experiments under both simplified and empirically derived conditions to compare the accuracy of ASR carried out using ML and Bayesian approaches. We show that incorporating phylogenetic uncertainty by integrating over topologies very rarely changes the inferred ancestral state and does not improve the accuracy of the reconstructed ancestral sequence. Ancestral state reconstructions are robust to uncertainty about the underlying tree because the conditions that produce phylogenetic uncertainty also make the ancestral state identical across plausible trees; conversely, the conditions under which different phylogenies yield different inferred ancestral states produce little or no ambiguity about the true phylogeny. Our results suggest that ML can produce accurate ASRs, even in the face of phylogenetic uncertainty. Using Bayesian integration to incorporate this uncertainty is neither necessary nor beneficial.

  11. PN Sequence Preestimator Scheme for DS-SS Signal Acquisition Using Block Sequence Estimation

    Directory of Open Access Journals (Sweden)

    Sang Kyu Park

    2005-03-01

    Full Text Available An m-sequence (PN sequence preestimator scheme for direct-sequence spread spectrum (DS-SS signal acquisition by using block sequence estimation (BSE is proposed and analyzed. The proposed scheme consists of an estimator and a verifier which work according to the PN sequence chip clock, and provides not only the enhanced chip estimates with a threshold decision logic and one-chip error correction among the first m received chips, but also the reliability check of the estimates with additional decision logic. The probabilities of the estimator and verifier operations are calculated. With these results, the detection, the false alarm, and the missing probabilities of the proposed scheme are derived. In addition, using a signal flow graph, the average acquisition time is calculated. The proposed scheme can be used as a preestimator and easily implemented by changing the internal signal path of a generally used digital matched filter (DMF correlator or any other correlator that has a lot of sampling data memories for sampled PN sequence. The numerical results show rapid acquisition performance in a relatively good CNR.

  12. Phylogenomics of Phrynosomatid Lizards: Conflicting Signals from Sequence Capture versus Restriction Site Associated DNA Sequencing

    Science.gov (United States)

    Leaché, Adam D.; Chavez, Andreas S.; Jones, Leonard N.; Grummer, Jared A.; Gottscho, Andrew D.; Linkem, Charles W.

    2015-01-01

    Sequence capture and restriction site associated DNA sequencing (RADseq) are popular methods for obtaining large numbers of loci for phylogenetic analysis. These methods are typically used to collect data at different evolutionary timescales; sequence capture is primarily used for obtaining conserved loci, whereas RADseq is designed for discovering single nucleotide polymorphisms (SNPs) suitable for population genetic or phylogeographic analyses. Phylogenetic questions that span both “recent” and “deep” timescales could benefit from either type of data, but studies that directly compare the two approaches are lacking. We compared phylogenies estimated from sequence capture and double digest RADseq (ddRADseq) data for North American phrynosomatid lizards, a species-rich and diverse group containing nine genera that began diversifying approximately 55 Ma. Sequence capture resulted in 584 loci that provided a consistent and strong phylogeny using concatenation and species tree inference. However, the phylogeny estimated from the ddRADseq data was sensitive to the bioinformatics steps used for determining homology, detecting paralogs, and filtering missing data. The topological conflicts among the SNP trees were not restricted to any particular timescale, but instead were associated with short internal branches. Species tree analysis of the largest SNP assembly, which also included the most missing data, supported a topology that matched the sequence capture tree. This preferred phylogeny provides strong support for the paraphyly of the earless lizard genera Holbrookia and Cophosaurus, suggesting that the earless morphology either evolved twice or evolved once and was subsequently lost in Callisaurus. PMID:25663487

  13. Direct thermal dyes

    Science.gov (United States)

    Ehlinger, Edward

    1990-07-01

    Direct thermal dyes are members of a class of compounds referred to in the imaging industry as color formers or leuco dyes. The oldest members of that class have simple triarylmethane structures, and have been employed for years in various dyeing applications. More complex triarylmethane compounds, such as phthalides and fluorans, are now used in various imaging systems to produce color. Color is derived from all of these compounds via the same mechanism, on a molecular level. That is, an event of activation produces a highly resonating cationic system whose interaction with incident light produces reflected light of a specific color. The activation event in the case of a direct thermal system is the creation of a melt on the paper involving dye and an acidic developer. The three major performance parameters in a thermal system are background color, image density, and image stability. The three major dye physical parameters affecting thermal performance are chemical constituency, purity, and particle size. Those dyes having the best combination of characteristics which can also be manufactured economically dominate the marketplace. Manufacturing high performance dyes for the thermal market involves multi-step, convergent reaction sequences performed on large scale. Intermediates must be manufactured at the right time, and at the right quality to be useful.

  14. Minimum degree and density of binary sequences

    DEFF Research Database (Denmark)

    Brandt, Stephan; Müttel, J.; Rautenbach, D.

    2010-01-01

    For d,k∈N with k ≤ 2d, let g(d,k) denote the infimum density of binary sequences (x)∈{0,1} which satisfy the minimum degree condition σ(x+) ≥ k for all i∈Z with xi=1. We reduce the problem of computing g(d,k) to a combinatorial problem related to the generalized k-girth of a graph G w