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Sample records for direct sequencing results

  1. Direct, rapid RNA sequence analysis

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

    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

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

    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.

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

    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.

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

    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.

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

    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.

  7. Snake Genome Sequencing: Results and Future Prospects.

    Kerkkamp, Harald M I; Kini, R Manjunatha; Pospelov, Alexey S; Vonk, Freek J; Henkel, Christiaan V; Richardson, Michael K

    2016-12-01

    Snake genome sequencing is in its infancy-very much behind the progress made in sequencing the genomes of humans, model organisms and pathogens relevant to biomedical research, and agricultural species. We provide here an overview of some of the snake genome projects in progress, and discuss the biological findings, with special emphasis on toxinology, from the small number of draft snake genomes already published. We discuss the future of snake genomics, pointing out that new sequencing technologies will help overcome the problem of repetitive sequences in assembling snake genomes. Genome sequences are also likely to be valuable in examining the clustering of toxin genes on the chromosomes, in designing recombinant antivenoms and in studying the epigenetic regulation of toxin gene expression.

  8. Snake Genome Sequencing: Results and Future Prospects

    Harald M. I. Kerkkamp

    2016-12-01

    Full Text Available Snake genome sequencing is in its infancy—very much behind the progress made in sequencing the genomes of humans, model organisms and pathogens relevant to biomedical research, and agricultural species. We provide here an overview of some of the snake genome projects in progress, and discuss the biological findings, with special emphasis on toxinology, from the small number of draft snake genomes already published. We discuss the future of snake genomics, pointing out that new sequencing technologies will help overcome the problem of repetitive sequences in assembling snake genomes. Genome sequences are also likely to be valuable in examining the clustering of toxin genes on the chromosomes, in designing recombinant antivenoms and in studying the epigenetic regulation of toxin gene expression.

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

    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

  10. Constructing and sampling directed graphs with given degree sequences

    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)

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

    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

  12. Deep-sequencing protocols influence the results obtained in small-RNA sequencing.

    Joern Toedling

    Full Text Available Second-generation sequencing is a powerful method for identifying and quantifying small-RNA components of cells. However, little attention has been paid to the effects of the choice of sequencing platform and library preparation protocol on the results obtained. We present a thorough comparison of small-RNA sequencing libraries generated from the same embryonic stem cell lines, using different sequencing platforms, which represent the three major second-generation sequencing technologies, and protocols. We have analysed and compared the expression of microRNAs, as well as populations of small RNAs derived from repetitive elements. Despite the fact that different libraries display a good correlation between sequencing platforms, qualitative and quantitative variations in the results were found, depending on the protocol used. Thus, when comparing libraries from different biological samples, it is strongly recommended to use the same sequencing platform and protocol in order to ensure the biological relevance of the comparisons.

  13. Sequencing results of pncA gene at JALMA

    First page Back Continue Last page Overview Graphics. Sequencing results of pncA gene at JALMA. Red colour indicates novel mutations, Blue colour indicates the novel mutations reported at the same codon earlier also.

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

    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

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

    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.

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

    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.

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

    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.

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

    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.

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

    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.

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

    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.

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

    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.

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

    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.

  3. IRIS PRA preliminary results and future direction

    Finnicum, D.J.; Kling, C.L.; Carelli, M.D.

    2004-01-01

    Westinghouse is currently conducting the pre-application licensing of the International Reactor Innovative and Secure (IRIS) on behalf of the IRIS Consortium. One of the key aspects of the IRIS design is the concept of safety-by-design. The PRA (Probabilistic Risk Analysis) is being used as an integral part of the design process. As part of this effort, a PRA of the initial design was generated to address 2 key areas. First, the IRIS PRA supported the evaluation of IRIS design issues by providing a solid risk basis for design and analyses required for the pre-licensing evaluation of the IRIS design. The PRA provides the tool for quantifying the benefit of the safety-by-design approach. Second, the current PRA task is beginning the preparation of the more complete PRA analyses and documentation eventually required for Design Certification. One of the key risk-related goals for IRIS is to reduce the EPZ (Emergency Protection Zone) to within the exclusion area by demonstrating that the off-site doses are consistent with the US Protective Action Guidelines (PAGs) for initiation of emergency response so that the required protective actions would be limited to the exclusion area. The results of the preliminary PRA indicated a core damage frequency of 1.2 E-08 for internal initiators. This is a very good result but much work is needed to meet the ambitious goal of no emergency response. The next phase of the PRA analyses will involve a two-fold expansion of the PRA. First, as the design and analyses approach a greater level of detail, the assumptions used for the initial PRA will be reviewed and the models will be revised as needed to reflect the improved knowledge of the system design and performance. Furthermore, as the full plant design advances, the PRA will be expanded to incorporate risk associated with external challenges such as seismic and fire, and to address low power and shutdowns modes of operation. As with the initial work, the PRA will serve as a tool to

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

    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...

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

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

    2017-12-01

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

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

    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.

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

    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.

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

    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...

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

    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.

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

    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.

  11. The Accident Sequence Precursor program: Methods improvements and current results

    Minarick, J.W.; Manning, F.M.; Harris, J.D.

    1987-01-01

    Changes in the US NRC Accident Sequence Precursor program methods since the initial program evaluations of 1969-81 operational events are described, along with insights from the review of 1984-85 events. For 1984-85, the number of significant precursors was consistent with the number observed in 1980-81, dominant sequences associated with significant events were reasonably consistent with PRA estimates for BWRs, but lacked the contribution due to small-break LOCAs previously observed and predicted in PWRs, and the frequency of initiating events and non-recoverable system failures exhibited some reduction compared to 1980-81. Operational events which provide information concerning additional PRA modeling needs are also described

  12. Results of the event sequence reliability benchmark exercise

    Silvestri, E.

    1990-01-01

    The Event Sequence Reliability Benchmark Exercise is the fourth of a series of benchmark exercises on reliability and risk assessment, with specific reference to nuclear power plant applications, and is the logical continuation of the previous benchmark exercises on System Analysis Common Cause Failure and Human Factors. The reference plant is the Nuclear Power Plant at Grohnde Federal Republic of Germany a 1300 MW PWR plant of KWU design. The specific objective of the Exercise is to model, to quantify and to analyze such event sequences initiated by the occurrence of a loss of offsite power that involve the steam generator feed. The general aim is to develop a segment of a risk assessment, which ought to include all the specific aspects and models of quantification, such as common canal failure, Human Factors and System Analysis, developed in the previous reliability benchmark exercises, with the addition of the specific topics of dependences between homologous components belonging to different systems featuring in a given event sequence and of uncertainty quantification, to end up with an overall assessment of: - the state of the art in risk assessment and the relative influences of quantification problems in a general risk assessment framework. The Exercise has been carried out in two phases, both requiring modelling and quantification, with the second phase adopting more restrictive rules and fixing certain common data, as emerged necessary from the first phase. Fourteen teams have participated in the Exercise mostly from EEC countries, with one from Sweden and one from the USA. (author)

  13. New paleomagnetic and paleointensity results from late pliocene volcanic sequences from southern Georgia (Caucasus)

    Calvo-Rathert, Manuel; Bogalo, Maria-Felicidad; Carrancho, Angel; Villalain, Juan Jose [Universidad de Burgos, Burgos (Spain). Departamento de Fisica, EPS; Goguichaichvili, Avto [Universidad Nacional Autonoma de Mexico, Morelia (Mexico). Laboratorio de Magnetismo Natural, Instituto de Geofisica; Vegas-Tubia, Nestor [Universidad del Pais Vasco, Bilbao (Spain). Departamento de Geodinamica; Sologashvili, Jemal [Ivane Javakhishvili State University of Tbilisi, Tbilisi (Georgia). Department of Geophysics

    2009-07-01

    Complete text of publication follows. Paleomagnetic and rock-magnetic experiments were carried out on 21 basaltic lava flows belonging to four different sequences of late Pliocene age from southern Georgia (Caucasus): Dmanisi (11 flows), Diliska (5 flows), Kvemo Orozmani (5 flows), and Zemo Karabulaki (3 flows). Paleomagnetic analysis generally showed the presence of a single component (mainly in the Dmanisi sequence) but also two more or less superimposed components in several other cases. All sites except one clearly displayed a normal-polarity characteristic component. Rock-magnetic experiments included measurement of thermomagnetic curves and hysteresis parameters. Susceptibility-versus-temperature curves measured in argon atmosphere on whole-rock powdered samples yielded low-Ti titanomagnetite as main carrier of remanence, although a lower T{sub C}-component was also observed in several cases. Both reversible and non-reversible k-T curves were measured. A pilot paleointensity study was performed with the Coe (1967) method on two samples of each of those sites considered suitable after interpretation of rock-magnetic and paleomagnetic data from all sites. The pilot study showed that reliable paleointensity results were mainly obtained from sites of the Dmanisi sequence. This thick sequence of basaltic lava flows records the upper end of the normal-polarity Olduvai subchron, a fact confirmed by {sup 40}Ar/{sup 39}Ar dating of the uppermost lava flow and overlying volcanogenic ashes, which yields ages of 1.8 to 1.85 My. A second paleointensity experiment was carried out only on samples belonging to the Dmanisi sequence. Preliminary results show that paleointensities often are low, their values lying between 10 and 20 muT in many cases. For comparison, present day field is 47 muT. The Dmanisi sequence of lava flows directly underlies the Dmanisi paleoanthropologic site, in which the end of the Olduvai subchron is recorded.

  14. European external quality control study on the competence of laboratories to recognize rare sequence variants resulting in unusual genotyping results.

    Márki-Zay, János; Klein, Christoph L; Gancberg, David; Schimmel, Heinz G; Dux, László

    2009-04-01

    Depending on the method used, rare sequence variants adjacent to the single nucleotide polymorphism (SNP) of interest may cause unusual or erroneous genotyping results. Because such rare variants are known for many genes commonly tested in diagnostic laboratories, we organized a proficiency study to assess their influence on the accuracy of reported laboratory results. Four external quality control materials were processed and sent to 283 laboratories through 3 EQA organizers for analysis of the prothrombin 20210G>A mutation. Two of these quality control materials contained sequence variants introduced by site-directed mutagenesis. One hundred eighty-nine laboratories participated in the study. When samples gave a usual result with the method applied, the error rate was 5.1%. Detailed analysis showed that more than 70% of the failures were reported from only 9 laboratories. Allele-specific amplification-based PCR had a much higher error rate than other methods (18.3% vs 2.9%). The variants 20209C>T and [20175T>G; 20179_20180delAC] resulted in unusual genotyping results in 67 and 85 laboratories, respectively. Eighty-three (54.6%) of these unusual results were not recognized, 32 (21.1%) were attributed to technical issues, and only 37 (24.3%) were recognized as another sequence variant. Our findings revealed that some of the participating laboratories were not able to recognize and correctly interpret unusual genotyping results caused by rare SNPs. Our study indicates that the majority of the failures could be avoided by improved training and careful selection and validation of the methods applied.

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

    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...

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

    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...

  17. Perceived ambiguity as a barrier to intentions to learn genome sequencing results.

    Taber, Jennifer M; Klein, William M P; Ferrer, Rebecca A; Han, Paul K J; Lewis, Katie L; Biesecker, Leslie G; Biesecker, Barbara B

    2015-10-01

    Many variants that could be returned from genome sequencing may be perceived as ambiguous-lacking reliability, credibility, or adequacy. Little is known about how perceived ambiguity influences thoughts about sequencing results. Participants (n = 494) in an NIH genome sequencing study completed a baseline survey before sequencing results were available. We examined how perceived ambiguity regarding sequencing results and individual differences in medical ambiguity aversion and tolerance for uncertainty were associated with cognitions and intentions concerning sequencing results. Perceiving sequencing results as more ambiguous was associated with less favorable cognitions about results and lower intentions to learn and share results. Among participants low in tolerance for uncertainty or optimism, greater perceived ambiguity was associated with lower intentions to learn results for non-medically actionable diseases; medical ambiguity aversion did not moderate any associations. Results are consistent with the phenomenon of "ambiguity aversion" and may influence whether people learn and communicate genomic information.

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

    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.

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

    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.

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

    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...

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

    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.

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

    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...

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

    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.

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

    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.

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

    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...

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

    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

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

    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

  8. Portero versus portador: Spanish interpretation of genomic terminology during whole exome sequencing results disclosure.

    Gutierrez, Amanda M; Robinson, Jill O; Statham, Emily E; Scollon, Sarah; Bergstrom, Katie L; Slashinski, Melody J; Parsons, Donald W; Plon, Sharon E; McGuire, Amy L; Street, Richard L

    2017-11-01

    Describe modifications to technical genomic terminology made by interpreters during disclosure of whole exome sequencing (WES) results. Using discourse analysis, we identified and categorized interpretations of genomic terminology in 42 disclosure sessions where Spanish-speaking parents received their child's WES results either from a clinician using a medical interpreter, or directly from a bilingual physician. Overall, 76% of genomic terms were interpreted accordantly, 11% were misinterpreted and 13% were omitted. Misinterpretations made by interpreters and bilingual physicians included using literal and nonmedical terminology to interpret genomic concepts. Modifications to genomic terminology made during interpretation highlight the need to standardize bilingual genomic lexicons. We recommend Spanish terms that can be used to refer to genomic concepts.

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

    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.

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

    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.)

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

    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

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

    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.

  13. Results from the DCH-1 [Direct Containment Heating] experiment

    Tarbell, W.W.; Brockmann, J.E.; Pilch, M.; Ross, J.E.; Oliver, M.S.; Lucero, D.A.; Kerley, T.E.; Arellano, F.E.; Gomez, R.D.

    1987-05-01

    The DCH-1 (Direct Containment Heating) test was the first experiment performed in the Surtsey Direct Heating Test Facility. The test involved 20 kg of molten core debris simulant ejected into a 1:10 scale model of the Zion reactor cavity. The melt was produced by a metallothermic reaction of iron oxide and aluminum powders to yield molten iron and alumina. The cavity model was placed so that the emerging debris propagated directly upwards along the vertical centerline of the chamber. Results from the experiment showed that the molten material was ejected from the caviity as a cloud of particles and aerosol. The dispersed debris caused a rapid pressurization of the 103-m 3 chamber atmosphere. Peak pressure from the six transducers ranged from 0.09 to 0.13 MPa (13.4 to 19.4 psig) above the initial value in the chamber. Posttest debris collection yielded 11.6 kg of material outside the cavity, of which approximately 1.6 kg was attributed to the uptake of oxygen by the iron particles. Mechanical sieving of the recovered debris showed a lognormal size distribution with a mass mean size of 0.55 mm. Aerosol measurements indicated a subsantial portion (2 to 16%) of the ejected mass was in the size range less than 10 m aerodynamic equivalent diameter

  14. From verbal prefixes to direction/result markers in Romance

    Patrizia Cordin

    2011-12-01

    Full Text Available In this paper I analyze verb-locative constructions in Romance. Even though not allowed in standard Romance languages, which have maintained and codified the classical Latin prefix system, these constructions are widely attested in non standard varieties, that are scarcely (or not at all regularized. In this paper I deal in particular with a northern Italian variety, Trentino, where locatives, combining with some classes of verbs (unaccusative verbs and transitive activity verbs can express not only concrete direction and metaphorical direction, but also aspect (the result of an activity or the progress of a process; in other words, they can express an abstract, more grammaticalized feature of direction. In fact, Trentino verb-locative constructions can express a specific phase of the development of an event, often the result (end-point of an activity, or the start-point, or the progress, or the intensity of the activity itself. I argue that in Trentino (and in other similar dialectal varieties locatives can function as grammatical markers both for arguments (in combination with motion verbs and for aspect (in combination with verbs involving the feature of an abstract path. In a more general context, I note that locatives in combination of verbs function as goal/result markers in those varieties that tend to spell out markers of functional elements, frequently generating a repetition (doubling of the same feature. Finally, I compare Romance and Germanic constructions, noting that diachronic, grammatical and typological differences (with particular reference to Talmy's distinction between verb-framed languages and satellite languages confirm the independence of Romance verb-locative constructions.

  15. Cenozoic global sea level, sequences, and the New Jersey transect: Results from coastal plain and continental slope drilling

    Miller, K.G.; Mountain, Gregory S.; Browning, J.V.; Kominz, M.; Sugarman, P.J.; Christie-Blick, N.; Katz, M.E.; Wright, J.D.

    1998-01-01

    The New Jersey Sea Level Transect was designed to evaluate the relationships among global sea level (eustatic) change, unconformity-bounded sequences, and variations in subsidence, sediment supply, and climate on a passive continental margin. By sampling and dating Cenozoic strata from coastal plain and continental slope locations, we show that sequence boundaries correlate (within ??0.5 myr) regionally (onshore-offshore) and interregionally (New Jersey-Alabama-Bahamas), implicating a global cause. Sequence boundaries correlate with ??18O increases for at least the past 42 myr, consistent with an ice volume (glacioeustatic) control, although a causal relationship is not required because of uncertainties in ages and correlations. Evidence for a causal connection is provided by preliminary Miocene data from slope Site 904 that directly link ??18O increases with sequence boundaries. We conclude that variation in the size of ice sheets has been a primary control on the formation of sequence boundaries since ~42 Ma. We speculate that prior to this, the growth and decay of small ice sheets caused small-amplitude sea level changes (changes on mid-ocean ridges. Although our results are consistent with the general number and timing of Paleocene to middle Miocene sequences published by workers at Exxon Production Research Company, our estimates of sea level amplitudes are substantially lower than theirs. Lithofacies patterns within sequences follow repetitive, predictable patterns: (1) coastal plain sequences consist of basal transgressive sands overlain by regressive highstand silts and quartz sands; and (2) although slope lithofacies variations are subdued, reworked sediments constitute lowstand deposits, causing the strongest, most extensive seismic reflections. Despite a primary eustatic control on sequence boundaries, New Jersey sequences were also influenced by changes in tectonics, sediment supply, and climate. During the early to middle Eocene, low siliciclastic and

  16. How do providers discuss the results of pediatric exome sequencing with families?

    Walser, Sarah A; Werner-Lin, Allison; Mueller, Rebecca; Miller, Victoria A; Biswas, Sawona; Bernhardt, Barbara A

    2017-09-01

    This study provides preliminary data on the process and content of returning results from exome sequencing offered to children through one of the Clinical Sequencing Exploratory Research (CSER) projects. We recorded 25 sessions where providers returned diagnostic and secondary sequencing results to families. Data interpretation utilized inductive thematic analysis. Typically, providers followed a results report and discussed diagnostic findings using technical genomic and sequencing concepts. We identified four provider processes for returning results: teaching genetic concepts; assessing family response; personalizing findings; and strengthening patient-provider relationships. Sessions should reflect family interest in medical management and next steps, and minimize detailed genomic concepts. As the scope and complexity of sequencing increase, the traditional information-laden counseling model requires revision.

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

    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.

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

    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.

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

    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.)

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

    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.

  1. Partial sequence homogenization in the 5S multigene families may generate sequence chimeras and spurious results in phylogenetic reconstructions.

    Galián, José A; Rosato, Marcela; Rosselló, Josep A

    2014-03-01

    Multigene families have provided opportunities for evolutionary biologists to assess molecular evolution processes and phylogenetic reconstructions at deep and shallow systematic levels. However, the use of these markers is not free of technical and analytical challenges. Many evolutionary studies that used the nuclear 5S rDNA gene family rarely used contiguous 5S coding sequences due to the routine use of head-to-tail polymerase chain reaction primers that are anchored to the coding region. Moreover, the 5S coding sequences have been concatenated with independent, adjacent gene units in many studies, creating simulated chimeric genes as the raw data for evolutionary analysis. This practice is based on the tacitly assumed, but rarely tested, hypothesis that strict intra-locus concerted evolution processes are operating in 5S rDNA genes, without any empirical evidence as to whether it holds for the recovered data. The potential pitfalls of analysing the patterns of molecular evolution and reconstructing phylogenies based on these chimeric genes have not been assessed to date. Here, we compared the sequence integrity and phylogenetic behavior of entire versus concatenated 5S coding regions from a real data set obtained from closely related plant species (Medicago, Fabaceae). Our results suggest that within arrays sequence homogenization is partially operating in the 5S coding region, which is traditionally assumed to be highly conserved. Consequently, concatenating 5S genes increases haplotype diversity, generating novel chimeric genotypes that most likely do not exist within the genome. In addition, the patterns of gene evolution are distorted, leading to incorrect haplotype relationships in some evolutionary reconstructions.

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

    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)

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

    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.

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

    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.

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

    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

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

    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.  

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

    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.

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

    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

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

    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).

  10. INTEGRATED GEOREFERENCING OF STEREO IMAGE SEQUENCES CAPTURED WITH A STEREOVISION MOBILE MAPPING SYSTEM – APPROACHES AND PRACTICAL RESULTS

    H. Eugster

    2012-07-01

    Full Text Available Stereovision based mobile mapping systems enable the efficient capturing of directly georeferenced stereo pairs. With today's camera and onboard storage technologies imagery can be captured at high data rates resulting in dense stereo sequences. These georeferenced stereo sequences provide a highly detailed and accurate digital representation of the roadside environment which builds the foundation for a wide range of 3d mapping applications and image-based geo web-services. Georeferenced stereo images are ideally suited for the 3d mapping of street furniture and visible infrastructure objects, pavement inspection, asset management tasks or image based change detection. As in most mobile mapping systems, the georeferencing of the mapping sensors and observations – in our case of the imaging sensors – normally relies on direct georeferencing based on INS/GNSS navigation sensors. However, in urban canyons the achievable direct georeferencing accuracy of the dynamically captured stereo image sequences is often insufficient or at least degraded. Furthermore, many of the mentioned application scenarios require homogeneous georeferencing accuracy within a local reference frame over the entire mapping perimeter. To achieve these demands georeferencing approaches are presented and cost efficient workflows are discussed which allows validating and updating the INS/GNSS based trajectory with independently estimated positions in cases of prolonged GNSS signal outages in order to increase the georeferencing accuracy up to the project requirements.

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

    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.

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

    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.

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

    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.

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

    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.

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

    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.

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

    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.

  17. Violence Directed against Teachers: Results from a National Survey

    Mcmahon, Susan D.; Martinez, Andrew; Espelage, Dorothy; Rose, Chad; Reddy, Linda A.; Lane, Kathleen; Anderman, Eric M.; Reynolds, Cecil R.; Jones, Abraham; Brown, Veda

    2014-01-01

    Teachers in U.S. schools report high rates of victimization, yet previous studies focus on select types of victimization and student perpetrators, which may underestimate the extent of the problem. This national study was based on work conducted by the American Psychological Association Classroom Violence Directed Against Teachers Task Force and…

  18. Direct structural parameter identification by modal test results

    Chen, J.-C.; Kuo, C.-P.; Garba, J. A.

    1983-01-01

    A direct identification procedure is proposed to obtain the mass and stiffness matrices based on the test measured eigenvalues and eigenvectors. The method is based on the theory of matrix perturbation in which the correct mass and stiffness matrices are expanded in terms of analytical values plus a modification matrix. The simplicity of the procedure enables real time operation during the structural testing.

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

    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.

  20. Alien Species and the Water Framework Directive - Questionnaire Results

    VANDEKERKHOVE JOCHEN; CARDOSO Ana

    2010-01-01

    Alien species constitute a major pressure in aquatic environments, both ecologically and economically. This recognition has initiated a debate on the role of alien species in ecological status classifications. We distributed a questionnaire to review how EU Member States (MSs) deal with alien species in their national status assessments under the Water Framework Directive (WFD). The questionnaire was filled and returned by 23 EU MSs and Norway. Analysis of the questionnaire returns and referr...

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

    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

  2. Direct drive: Simulations and results from the National Ignition Facility

    Radha, P. B., E-mail: rbah@lle.rochester.edu; Hohenberger, M.; Edgell, D. H.; Marozas, J. A.; Marshall, F. J.; Michel, D. T.; Rosenberg, M. J.; Seka, W.; Shvydky, A.; Boehly, T. R.; Collins, T. J. B.; Campbell, E. M.; Craxton, R. S.; Delettrez, J. A.; Froula, D. H.; Goncharov, V. N.; Hu, S. X.; Knauer, J. P.; McCrory, R. L.; McKenty, P. W. [Laboratory for Laser Energetics, University of Rochester, Rochester, New York 14623 (United States); and others

    2016-05-15

    Direct-drive implosion physics is being investigated at the National Ignition Facility. The primary goal of the experiments is twofold: to validate modeling related to implosion velocity and to estimate the magnitude of hot-electron preheat. Implosion experiments indicate that the energetics is well-modeled when cross-beam energy transfer (CBET) is included in the simulation and an overall multiplier to the CBET gain factor is employed; time-resolved scattered light and scattered-light spectra display the correct trends. Trajectories from backlit images are well modeled, although those from measured self-emission images indicate increased shell thickness and reduced shell density relative to simulations. Sensitivity analyses indicate that the most likely cause for the density reduction is nonuniformity growth seeded by laser imprint and not laser-energy coupling. Hot-electron preheat is at tolerable levels in the ongoing experiments, although it is expected to increase after the mitigation of CBET. Future work will include continued model validation, imprint measurements, and mitigation of CBET and hot-electron preheat.

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

    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

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

    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.

  5. Internal event analysis for Laguna Verde Unit 1 Nuclear Power Plant. Accident sequence quantification and results

    Huerta B, A.; Aguilar T, O.; Nunez C, A.; Lopez M, R.

    1994-01-01

    The Level 1 results of Laguna Verde Nuclear Power Plant PRA are presented in the I nternal Event Analysis for Laguna Verde Unit 1 Nuclear Power Plant, CNSNS-TR 004, in five volumes. The reports are organized as follows: CNSNS-TR 004 Volume 1: Introduction and Methodology. CNSNS-TR4 Volume 2: Initiating Event and Accident Sequences. CNSNS-TR 004 Volume 3: System Analysis. CNSNS-TR 004 Volume 4: Accident Sequence Quantification and Results. CNSNS-TR 005 Volume 5: Appendices A, B and C. This volume presents the development of the dependent failure analysis, the treatment of the support system dependencies, the identification of the shared-components dependencies, and the treatment of the common cause failure. It is also presented the identification of the main human actions considered along with the possible recovery actions included. The development of the data base and the assumptions and limitations in the data base are also described in this volume. The accident sequences quantification process and the resolution of the core vulnerable sequences are presented. In this volume, the source and treatment of uncertainties associated with failure rates, component unavailabilities, initiating event frequencies, and human error probabilities are also presented. Finally, the main results and conclusions for the Internal Event Analysis for Laguna Verde Nuclear Power Plant are presented. The total core damage frequency calculated is 9.03x 10-5 per year for internal events. The most dominant accident sequences found are the transients involving the loss of offsite power, the station blackout accidents, and the anticipated transients without SCRAM (ATWS). (Author)

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

    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

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

    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.

  8. Lynch syndrome patients' views of and preferences for return of results following whole exome sequencing.

    Hitch, Kelly; Joseph, Galen; Guiltinan, Jenna; Kianmahd, Jessica; Youngblom, Janey; Blanco, Amie

    2014-08-01

    Whole exome sequencing (WES) uses next generation sequencing technology to provide information on nearly all functional, protein-coding regions in an individual's genome. Due to the vast amount of information and incidental findings that can be generated from this technology, patient preferences must be investigated to help clinicians consent and return results to patients. Patients (n = 19) who were previously clinically diagnosed with Lynch syndrome, but received uninformative negative Lynch syndrome genetic results through traditional molecular testing methods participated in semi-structured interviews after WES testing but before return of results to explore their views of WES and preferences for return of results. Analyses of interview results found that nearly all participants believed that the benefits of receiving all possible results generated from WES outweighed the undesirable effects. The majority of participants conveyed that relative to coping with a cancer diagnosis, information generated from WES would be manageable. Importantly, participants' experience with Lynch syndrome influenced their notions of genetic determinism, tolerance for uncertain results, and family communication plans. Participants would prefer to receive WES results in person from a genetic counselor or medical geneticist so that an expert could help explain the meaning and implications of the potentially large quantity and range of complicated results. These results underscore the need to study various populations with regard to the clinical use of WES in order to effectively and empathetically communicate the possible implications of this new technology and return results.

  9. 13-colour photometry of pre-main sequence stars: preliminary report and results

    Chavarria-K, C; de Lara, E [Universidad Nacional Autonoma de Mexico, Mexico City. Inst. de Astronomia

    1981-01-01

    Broad (UBVRI) and intermediate (13-colour) band photometry of 160 stars selected mainly from the Herbig Rao catalogue are being carried on currently, mainly to complement the published data of these stars in the optical window (for example shortward of the Balmer and longward of the Paschen discontinuities). The 13-colour photometric system and its applications to pre-main sequences stars are briefly discussed. First results are presented.

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

    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

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

    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...

  12. Dispositional optimism and perceived risk interact to predict intentions to learn genome sequencing results.

    Taber, Jennifer M; Klein, William M P; Ferrer, Rebecca A; Lewis, Katie L; Biesecker, Leslie G; Biesecker, Barbara B

    2015-07-01

    Dispositional optimism and risk perceptions are each associated with health-related behaviors and decisions and other outcomes, but little research has examined how these constructs interact, particularly in consequential health contexts. The predictive validity of risk perceptions for health-related information seeking and intentions may be improved by examining dispositional optimism as a moderator, and by testing alternate types of risk perceptions, such as comparative and experiential risk. Participants (n = 496) had their genomes sequenced as part of a National Institutes of Health pilot cohort study (ClinSeq®). Participants completed a cross-sectional baseline survey of various types of risk perceptions and intentions to learn genome sequencing results for differing disease risks (e.g., medically actionable, nonmedically actionable, carrier status) and to use this information to change their lifestyle/health behaviors. Risk perceptions (absolute, comparative, and experiential) were largely unassociated with intentions to learn sequencing results. Dispositional optimism and comparative risk perceptions interacted, however, such that individuals higher in optimism reported greater intentions to learn all 3 types of sequencing results when comparative risk was perceived to be higher than when it was perceived to be lower. This interaction was inconsistent for experiential risk and absent for absolute risk. Independent of perceived risk, participants high in dispositional optimism reported greater interest in learning risks for nonmedically actionable disease and carrier status, and greater intentions to use genome information to change their lifestyle/health behaviors. The relationship between risk perceptions and intentions may depend on how risk perceptions are assessed and on degree of optimism. (c) 2015 APA, all rights reserved.

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

    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....

  14. The role of 3D volumetric MR sequences in diagnosing intraventricular neurocysticercosis: preliminar results

    Francisco Edward Frota Mont'Alverne Filho

    2011-02-01

    Full Text Available OBJECTIVE: The purpose of this paper was to investigate the role of two three-dimensional magnetic resonance (MRI sequences: enhanced spoiled gradient recalled echo (SPGR, and fast imaging employing steady-state acquisition (FIESTA in the evaluation of intraventricular neurocysticercosis cysts and scolices. METHOD: Seven neurocysticercosis patients suspected of presenting intraventricular lesions were evaluated by magnetic resonance imaging using enhanced SPGR, and FIESTA. RESULTS: Enhanced SPGR detected eight cystic lesions, with scolices in four. Contrast enhancement was observed in three cysts. FIESTA also detected eight cystic lesions with the presence of scolices in seven of those cystic lesions. Four patients presented parenchymal involvement, while the remaining three presented the racemose form. CONCLUSION: FIESTA and SPGR are sequences that can detect intraventricular cysts of neurocysticercosis, and FIESTA also is good for the detection of the scolex. Considering this information we suggest that FIESTA and SPGR should be included in the MRI protocol for the investigation of intraventricular neurocysticercosis.

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

    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).

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

    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.

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

    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

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

    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%

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

    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

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

    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.

  1. Clinical providers' experiences with returning results from genomic sequencing: an interview study.

    Wynn, Julia; Lewis, Katie; Amendola, Laura M; Bernhardt, Barbara A; Biswas, Sawona; Joshi, Manasi; McMullen, Carmit; Scollon, Sarah

    2018-05-08

    Current medical practice includes the application of genomic sequencing (GS) in clinical and research settings. Despite expanded use of this technology, the process of disclosure of genomic results to patients and research participants has not been thoroughly examined and there are no established best practices. We conducted semi-structured interviews with 21 genetic and non-genetic clinicians returning results of GS as part of the NIH funded Clinical Sequencing Exploratory Research (CSER) Consortium projects. Interviews focused on the logistics of sessions, participant/patient reactions and factors influencing them, how the sessions changed with experience, and resources and training recommended to return genomic results. The length of preparation and disclosure sessions varied depending on the type and number of results and their implications. Internal and external databases, online resources and result review meetings were used to prepare. Respondents reported that participants' reactions were variable and ranged from enthusiasm and relief to confusion and disappointment. Factors influencing reactions were types of results, expectations and health status. A recurrent challenge was managing inflated expectations about GS. Other challenges included returning multiple, unanticipated and/or uncertain results and navigating a rare diagnosis. Methods to address these challenges included traditional genetic counseling techniques and modifying practice over time in order to provide anticipatory guidance and modulate expectations. Respondents made recommendations to improve access to genomic resources and genetic referrals to prepare future providers as the uptake of GS increases in both genetic and non-genetic settings. These findings indicate that returning genomic results is similar to return of results in traditional genetic testing but is magnified by the additional complexity and potential uncertainty of the results. Managing patient expectations, initially

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

    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.

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

    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.

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

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

    2007-01-01

    dose to 95% of the PTV (D 95 ) of the DSS plans, resulted in similar target coverage and dose to the parotids for both strategies, at the cost of a significantly higher dose to the normal tissue and maximum dose to the target. The relative volume of the PTV receiving 107% or more of the prescription dose V 107 increased to 35.5% ± 20.0% for the IM plan as compared to a mean of 0.9% ± 0.9% for the DSS plan. The direct machine parameter optimization is a major improvement compared to the fluence modulation with subsequent leaf sequencing in Oncentra Masterplan v1.5. The resulting dose distribution complies better with the DVO and better plan quality is achieved for identical specification of DVO. An additional asset is the reduced number of MU as compared to IM

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

    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

  6. Directional atherectomy for treatment of restenosis within coronary stents: clinical, angiographic and histologic results

    B.H. Strauss (Bradley); V.A.W.M. Umans (Victor); R-J. van Suylen (Robert-Jan); P.J. de Feyter (Pim); J. Marco (Jean); G. Robertson; J. Renkin; G.R. Heyndrickx (Guy); V.D. Vuzevski (Vojislav); F.T.B. Bosman (Fré); P.W.J.C. Serruys (Patrick)

    1992-01-01

    textabstractAbstract OBJECTIVES: The safety and long-term results of directional coronary atherectomy in stented coronary arteries were determined. In addition, tissue studies were performed to characterize the development of restenosis. METHODS: Directional coronary atherectomy was performed in

  7. Highly conserved intragenic HSV-2 sequences: Results from next-generation sequencing of HSV-2 UL and US regions from genital swabs collected from 3 continents.

    Johnston, Christine; Magaret, Amalia; Roychoudhury, Pavitra; Greninger, Alexander L; Cheng, Anqi; Diem, Kurt; Fitzgibbon, Matthew P; Huang, Meei-Li; Selke, Stacy; Lingappa, Jairam R; Celum, Connie; Jerome, Keith R; Wald, Anna; Koelle, David M

    2017-10-01

    Understanding the variability in circulating herpes simplex virus type 2 (HSV-2) genomic sequences is critical to the development of HSV-2 vaccines. Genital lesion swabs containing ≥ 10 7 log 10 copies HSV DNA collected from Africa, the USA, and South America underwent next-generation sequencing, followed by K-mer based filtering and de novo genomic assembly. Sites of heterogeneity within coding regions in unique long and unique short (U L _U S ) regions were identified. Phylogenetic trees were created using maximum likelihood reconstruction. Among 46 samples from 38 persons, 1468 intragenic base-pair substitutions were identified. The maximum nucleotide distance between strains for concatenated U L_ U S segments was 0.4%. Phylogeny did not reveal geographic clustering. The most variable proteins had non-synonymous mutations in < 3% of amino acids. Unenriched HSV-2 DNA can undergo next-generation sequencing to identify intragenic variability. The use of clinical swabs for sequencing expands the information that can be gathered directly from these specimens. Copyright © 2017 Elsevier Inc. All rights reserved.

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

    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...

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

    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.

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

    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.

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

    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. ...

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

    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 %.

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

    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

  14. Adaptive Optics Facility: control strategy and first on-sky results of the acquisition sequence

    Madec, P.-Y.; Kolb, J.; Oberti, S.; Paufique, J.; La Penna, P.; Hackenberg, W.; Kuntschner, H.; Argomedo, J.; Kiekebusch, M.; Donaldson, R.; Suarez, M.; Arsenault, R.

    2016-07-01

    The Adaptive Optics Facility is an ESO project aiming at converting Yepun, one of the four 8m telescopes in Paranal, into an adaptive telescope. This is done by replacing the current conventional secondary mirror of Yepun by a Deformable Secondary Mirror (DSM) and attaching four Laser Guide Star (LGS) Units to its centerpiece. In the meantime, two Adaptive Optics (AO) modules have been developed incorporating each four LGS WaveFront Sensors (WFS) and one tip-tilt sensor used to control the DSM at 1 kHz frame rate. The four LGS Units and one AO module (GRAAL) have already been assembled on Yepun. Besides the technological challenge itself, one critical area of AOF is the AO control strategy and its link with the telescope control, including Active Optics used to shape M1. Another challenge is the request to minimize the overhead due to AOF during the acquisition phase of the observation. This paper presents the control strategy of the AOF. The current control of the telescope is first recalled, and then the way the AO control makes the link with the Active Optics is detailed. Lab results are used to illustrate the expected performance. Finally, the overall AOF acquisition sequence is presented as well as first results obtained on sky with GRAAL.

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

    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.

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

    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.

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

    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.

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

    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...

  19. Preferences for learning different types of genome sequencing results among young breast cancer patients: Role of psychological and clinical factors.

    Kaphingst, Kimberly A; Ivanovich, Jennifer; Lyons, Sarah; Biesecker, Barbara; Dresser, Rebecca; Elrick, Ashley; Matsen, Cindy; Goodman, Melody

    2018-01-29

    The growing importance of genome sequencing means that patients will increasingly face decisions regarding what results they would like to learn. The present study examined psychological and clinical factors that might affect these preferences. 1,080 women diagnosed with breast cancer at age 40 or younger completed an online survey. We assessed their interest in learning various types of genome sequencing results: risk of preventable disease or unpreventable disease, cancer treatment response, uncertain meaning, risk to relatives' health, and ancestry/physical traits. Multivariable logistic regression was used to examine whether being "very" interested in each result type was associated with clinical factors: BRCA1/2 mutation status, prior genetic testing, family history of breast cancer, and psychological factors: cancer recurrence worry, genetic risk worry, future orientation, health information orientation, and genome sequencing knowledge. The proportion of respondents who were very interested in learning each type of result ranged from 16% to 77%. In all multivariable models, those who were very interested in learning a result type had significantly higher knowledge about sequencing benefits, greater genetic risks worry, and stronger health information orientation compared to those with less interest (p-values psychological factors. Shared decision-making approaches that increase knowledge about genome sequencing and incorporate patient preferences for health information and learning about genetic risks may help support patients' informed choices about learning different types of sequencing results. © Society of Behavioral Medicine 2018.

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

    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.

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

    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. Characterization of Request Sequences for List Accessing Problem and New Theoretical Results for MTF Algorithm

    Mohanty, Rakesh; Sharma, Burle; Tripathy, Sasmita

    2011-01-01

    List Accessing Problem is a well studied research problem in the context of linear search. Input to the list accessing problem is an unsorted linear list of distinct elements along with a sequence of requests, where each request is an access operation on an element of the list. A list accessing algorithm reorganizes the list while processing a request sequence on the list in order to minimize the access cost. Move-To-Front algorithm has been proved to be the best performing list accessing onl...

  3. Determination of errors in derived magnetic field directions in geosynchronous orbit: results from a statistical approach

    Chen, Yue; Cunningham, Gregory; Henderson, Michael

    2016-09-01

    This study aims to statistically estimate the errors in local magnetic field directions that are derived from electron directional distributions measured by Los Alamos National Laboratory geosynchronous (LANL GEO) satellites. First, by comparing derived and measured magnetic field directions along the GEO orbit to those calculated from three selected empirical global magnetic field models (including a static Olson and Pfitzer 1977 quiet magnetic field model, a simple dynamic Tsyganenko 1989 model, and a sophisticated dynamic Tsyganenko 2001 storm model), it is shown that the errors in both derived and modeled directions are at least comparable. Second, using a newly developed proxy method as well as comparing results from empirical models, we are able to provide for the first time circumstantial evidence showing that derived magnetic field directions should statistically match the real magnetic directions better, with averaged errors ˜ 5°. In addition, our results suggest that the errors in derived magnetic field directions do not depend much on magnetospheric activity, in contrast to the empirical field models. Finally, as applications of the above conclusions, we show examples of electron pitch angle distributions observed by LANL GEO and also take the derived magnetic field directions as the real ones so as to test the performance of empirical field models along the GEO orbits, with results suggesting dependence on solar cycles as well as satellite locations. This study demonstrates the validity and value of the method that infers local magnetic field directions from particle spin-resolved distributions.

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

    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.

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

    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.

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

    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.

  7. FIRST RESULTS ON THE DIRECTION STATISTICS OF PAIRS OF EPICENTERS OF NEIGHBOR EARTHQUAKES ON KAMCHATKA

    A. A. Gusev

    2016-01-01

    Full Text Available Small earthquakes, often treated as “background seismicity”, are not distributed in space-time in a random manner. Often, space-time clustering is studied, that manifests itself as aftershock sequences and swarms. These phenomena can be described as a deviation (increase of probability of short interevent distances and times as compared to the reference “pure random” or Poisson case; this tendency manifests itself in statistics of distances between epicenters. In the present work, we study the statistics of directions for vectors connecting pairs of epicenters of such small earthquakes which are close in space-time. Components of such pairs will be called “neighbors”, and the mentioned vectors will be called “link vectors”. A study of this kind is of interest from a number of viewpoints, such as: discovering new properties of statistical structure of observed fields of epicenters; establishing interactions between earthquake sources of small earthquakes, revealing geometrical properties of the pattern of active faults of a low rank. We will show that directions of link vectors clearly deviate from isotropy, and have instead non-uniform, often spiked, distribution of directions.Pairs of neighbors are extracted from the catalogue of small (ML=3.5–5.0 shallow earthquakes of the Kamchatka subduction zone. То define neighbors, bounds are set on the distance (10–60 km and relative delay (0.5 day between members of a pair. Before pair extraction, the work catalog was decimated to reduce space-time event density within dense clusters. With the catalog of pairs at hand, we constructed distributions of azimuths of link vectors (rose diagrams of directions. In Fig. 3 one can see example histograms and corresponding rose diagrams for two 10-year periods (see Table 1 for definitions and labels of the periods; processing was done using two variants of maximum delay: 0.5 and 5 days. Angles (modified azimuths, n in all histograms and rose

  8. Evaluation of the Correlation Coefficient of Polyethylene Glycol Treated and Direct Prolactin Results and Comparability with Different Assay System Results.

    Pal, Shyamali

    2017-12-01

    The presence of Macro prolactin is a significant cause of elevated prolactin resulting in misdiagnosis in all automated systems. Poly ethylene glycol (PEG) pretreatment is the preventive process but such process includes the probability of loss of a fraction of bioactive prolactin. Surprisingly, PEG treated EQAS & IQAS samples in Cobas e 411 are found out to be correlating with direct results of at least 3 immunoassay systems and treated and untreated Cobas e 411 results are comparable by a correlation coefficient. Comparison of EQAS, IQAS and patient samples were done to find out the trueness of such correlation factor. Study with patient's results have established the correlation coefficient is valid for very small concentration of prolactin also. EQAS, IQAS and 150 patient samples were treated with PEG and prolactin results of treated and untreated samples obtained from Roche Cobas e 411. 25 patient's results (treated) were compared with direct results in Advia Centaur, Architect I & Access2 systems. Correlation coefficient was obtained from trend line of the treated and untreated results. Two tailed p-value obtained from regression coefficient(r) and sample size. The correlation coefficient is in the range (0.761-0.771). Reverse correlation range is (1.289-1.301). r value of two sets of calculated results were 0.995. Two tailed p- value is zero approving dismissal of null hypothesis. The z-score of EQAS does not always assure authenticity of resultsPEG precipitation is correlated by the factor 0.761 even in very small concentrationsAbbreviationsGFCgel filtration chromatographyPEGpolyethylene glycolEQASexternal quality assurance systemM-PRLmacro prolactinPRLprolactinECLIAelectro-chemiluminescence immunoassayCLIAclinical laboratory improvement amendmentsIQASinternal quality assurance systemrregression coefficient.

  9. Web Platform vs In-Person Genetic Counselor for Return of Carrier Results From Exome Sequencing: A Randomized Clinical Trial.

    Biesecker, Barbara B; Lewis, Katie L; Umstead, Kendall L; Johnston, Jennifer J; Turbitt, Erin; Fishler, Kristen P; Patton, John H; Miller, Ilana M; Heidlebaugh, Alexis R; Biesecker, Leslie G

    2018-03-01

    A critical bottleneck in clinical genomics is the mismatch between large volumes of results and the availability of knowledgeable professionals to return them. To test whether a web-based platform is noninferior to a genetic counselor for educating patients about their carrier results from exome sequencing. A randomized noninferiority trial conducted in a longitudinal sequencing cohort at the National Institutes of Health from February 5, 2014, to December 16, 2016, was used to compare the web-based platform with a genetic counselor. Among the 571 eligible participants, 1 to 7 heterozygous variants were identified in genes that cause a phenotype that is recessively inherited. Surveys were administered after cohort enrollment, immediately following trial education, and 1 month and 6 months later to primarily healthy postreproductive participants who expressed interest in learning their carrier results. Both intention-to-treat and per-protocol analyses were applied. A web-based platform that integrated education on carrier results with personal test results was designed to directly parallel disclosure education by a genetic counselor. The sessions took a mean (SD) time of 21 (10.6), and 27 (9.3) minutes, respectively. The primary outcomes and noninferiority margins (δNI) were knowledge (0 to 8, δNI = -1), test-specific distress (0 to 30, δNI = +1), and decisional conflict (15 to 75, δNI = +6). After 462 participants (80.9%) provided consent and were randomized, all but 3 participants (n = 459) completed surveys following education and counseling; 398 (86.1%) completed 1-month surveys and 392 (84.8%) completed 6-month surveys. Participants were predominantly well-educated, non-Hispanic white, married parents; mean (SD) age was 63 (63.1) years and 246 (53.6%) were men. The web platform was noninferior to the genetic counselor on outcomes assessed at 1 and 6 months: knowledge (mean group difference, -0.18; lower limit of 97.5% CI, -0.63;

  10. Direct cerebral and cardiac 17O-MRI at 3 Tesla: initial results at natural abundance.

    Borowiak, Robert; Groebner, Jens; Haas, Martin; Hennig, Jürgen; Bock, Michael

    2014-02-01

    To establish direct (17)O-magnetic resonance imaging (MRI) for metabolic imaging at a clinical field strength of 3 T. An experimental setup including a surface coil and transmit/receive switch was constructed. Natural abundance in vivo brain images of a volunteer were acquired with a radial three-dimensional (3D) sequence in the visual cortex and in the heart with electrocardiogram (ECG)-gating. In the brain, a signal-to-noise ratio of 36 was found at a nominal resolution of (5.6 mm)(3), and a transverse relaxation time of T(2)* = (1.9 ± 0.2) ms was obtained. In the heart (17)O images were acquired with a temporal resolution of 200 ms. Cerebral and cardiac (17)O-MRI at natural abundance is feasible at 3 T.

  11. Subset of Kappa and Lambda Germline Sequences Result in Light Chains with a Higher Molecular Mass Phenotype.

    Barnidge, David R; Lundström, Susanna L; Zhang, Bo; Dasari, Surendra; Murray, David L; Zubarev, Roman A

    2015-12-04

    In our previous work, we showed that electrospray ionization of intact polyclonal kappa and lambda light chains isolated from normal serum generates two distinct, Gaussian-shaped, molecular mass distributions representing the light-chain repertoire. During the analysis of a large (>100) patient sample set, we noticed a low-intensity molecular mass distribution with a mean of approximately 24 250 Da, roughly 800 Da higher than the mean of the typical kappa molecular-mass distribution mean of 23 450 Da. We also observed distinct clones in this region that did not appear to contain any typical post-translational modifications that would account for such a large mass shift. To determine the origin of the high molecular mass clones, we performed de novo bottom-up mass spectrometry on a purified IgM monoclonal light chain that had a calculated molecular mass of 24 275.03 Da. The entire sequence of the monoclonal light chain was determined using multienzyme digestion and de novo sequence-alignment software and was found to belong to the germline allele IGKV2-30. The alignment of kappa germline sequences revealed ten IGKV2 and one IGKV4 sequences that contained additional amino acids in their CDR1 region, creating the high-molecular-mass phenotype. We also performed an alignment of lambda germline sequences, which showed additional amino acids in the CDR2 region, and the FR3 region of functional germline sequences that result in a high-molecular-mass phenotype. The work presented here illustrates the ability of mass spectrometry to provide information on the diversity of light-chain molecular mass phenotypes in circulation, which reflects the germline sequences selected by the immunoglobulin-secreting B-cell population.

  12. Use of the LUS in sequence allele designations to facilitate probabilistic genotyping of NGS-based STR typing results.

    Just, Rebecca S; Irwin, Jodi A

    2018-05-01

    Some of the expected advantages of next generation sequencing (NGS) for short tandem repeat (STR) typing include enhanced mixture detection and genotype resolution via sequence variation among non-homologous alleles of the same length. However, at the same time that NGS methods for forensic DNA typing have advanced in recent years, many caseworking laboratories have implemented or are transitioning to probabilistic genotyping to assist the interpretation of complex autosomal STR typing results. Current probabilistic software programs are designed for length-based data, and were not intended to accommodate sequence strings as the product input. Yet to leverage the benefits of NGS for enhanced genotyping and mixture deconvolution, the sequence variation among same-length products must be utilized in some form. Here, we propose use of the longest uninterrupted stretch (LUS) in allele designations as a simple method to represent sequence variation within the STR repeat regions and facilitate - in the nearterm - probabilistic interpretation of NGS-based typing results. An examination of published population data indicated that a reference LUS region is straightforward to define for most autosomal STR loci, and that using repeat unit plus LUS length as the allele designator can represent greater than 80% of the alleles detected by sequencing. A proof of concept study performed using a freely available probabilistic software demonstrated that the LUS length can be used in allele designations when a program does not require alleles to be integers, and that utilizing sequence information improves interpretation of both single-source and mixed contributor STR typing results as compared to using repeat unit information alone. The LUS concept for allele designation maintains the repeat-based allele nomenclature that will permit backward compatibility to extant STR databases, and the LUS lengths themselves will be concordant regardless of the NGS assay or analysis tools

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

    Pupko Tal

    2008-10-01

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

  14. Diagnostic accuracy of unenhanced, contrast-enhanced perfusion and angiographic MRI sequences for pulmonary embolism diagnosis: results of independent sequence readings

    Revel, Marie Pierre [Hopital Europeen Georges Pompidou, APHP, Departments of Radiology, Paris (France); Universite Paris Descartes Sorbonne Paris Cite, Paris (France); Hotel-Dieu, Service de Radiologie, Paris (France); Sanchez, Olivier; Meyer, Guy [Hopital Europeen Georges Pompidou, APHP, Respiratory and intensive care and, Paris (France); Universite Paris Descartes Sorbonne Paris Cite, Paris (France); INSERM Unite 765, Paris (France); Lefort, Catherine; Couchon, Sophie; Hernigou, Anne; Frija, Guy [Hopital Europeen Georges Pompidou, APHP, Departments of Radiology, Paris (France); Niarra, Ralph [Hopital Europeen Georges Pompidou, APHP, Clinical Epidemiology, Paris (France); Universite Paris Descartes Sorbonne Paris Cite, Paris (France); Chatellier, Gilles [Hopital Europeen Georges Pompidou, APHP, Clinical Epidemiology, Paris (France); Universite Paris Descartes Sorbonne Paris Cite, Paris (France); INSERM CIC-EC E4, Paris (France)

    2013-09-15

    To independently evaluate unenhanced, contrast-enhanced perfusion and angiographic MR sequences for pulmonary embolism (PE) diagnosis. Prospective investigation, including 274 patients who underwent perfusion, unenhanced 2D steady-state-free-precession (SSFP) and contrast-enhanced 3D angiographic MR sequences on a 1.5-T unit, in addition to CTA (CT angiography). Two independent readers evaluated each sequence independently in random order. Sensitivity, specificity, predictive values and inter-reader agreement were calculated for each sequence, excluding sequences judged inconclusive. Sensitivity was also calculated according to PE location. Contrast-enhanced angiographic sequences showed the highest sensitivity (82.9 and 89.7 %, reader 1 and reader 2, respectively), specificity (98.5 and 100 %) and agreement (kappa value 0.77). Unenhanced angiographic sequences, although less sensitive overall (68.7 and 76.4 %), were sensitive for the detection of proximal PE (92.7 and 100 %) and showed high specificity (96.1 and 99.1 %) and good agreement (kappa value 0.62). Perfusion sequences showed lower sensitivity (75.0 and 79.3 %), specificity (84.8 and 89.7 %) and agreement (kappa value 0.51), and a negative predictive value of 84.8 % at best. Compared with contrast-enhanced angiographic sequences, unenhanced sequences demonstrate lower sensitivity, except for proximal PE, but high specificity and agreement. The negative predictive value of perfusion sequences was insufficient to safely rule out PE. (orig.)

  15. The Hellenic Seismological Network Of Crete (HSNC): Validation and results of the 2013 aftershock sequences

    Chatzopoulos, Georgios; Papadopoulos, Ilias; Vallianatos, Filippos

    2015-04-01

    The number and quality of seismological networks in Europe has increased in the past decades. Nevertheless, the need for localized networks monitoring areas of great seismic and scientific interest is constant. Hellenic Seismological Network of Crete (HSNC) covers this need for the vicinity of the South Aegean Sea and Crete Island. In the present work with the use of Z-map software (www.seismo.ethz.ch) the spatial variability of Magnitude of Completeness (Mc) is calculated from HSNC's manual analysis catalogue of events for the period 2011 until today, proving the good coverage of HSNC in the areas. Furthermore the 2013, South Aegean seismicity where two large shallow earthquakes occurred in the vicinity of Crete Island, is discussed. The first event takes place on 15th June 2013 in the front of the Hellenic Arc, south from central Crete, while the second one on 12th October, 2013 on the western part of Crete. The two main shocks and their aftershock sequences have been relocated with the use of hypoinverse earthquake location software and an appropriate crust model. The HSNC identified more than 500 and 300 aftershocks respectively followed after the main events. The detailed construction of aftershocks catalogue permits the applicability of modern theories based on complexity sciences as described recently in the frame of non extensive statistical physics. In addition site effects in the stations locations are presented using event and noise recordings. This work was implemented through the project IMPACT-ARC in the framework of action "ARCHIMEDES III-Support of Research Teams at TEI of Crete" (MIS380353) of the Operational Program "Education and Lifelong Learning" and is co-financed by the European Union (European Social Fund) and Greek national funds References A. Tzanis and F. Vallianatos, "Distributed power-law seismicity changes and crustal deformation in the EW Hellenic Arc", Natural Hazards and Earth Systems Sciences, 3, 179-195, 2003 F. Vallianatos, G

  16. Acute unilateral foot drop as a result of direct blunt trauma to the ...

    This is a case report of an acute unilateral foot drop which occurred during a professional mixed martial arts (MMA) contest, specifically as a result of direct blunt trauma to the left peroneal nerve, without an accompanying fracture of the fibula. Keywords: foot extensor weakness, gait abnormality, contact sports, mixed martial ...

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

    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.

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

    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.

  19. Tailored graph ensembles as proxies or null models for real networks II: results on directed graphs

    Roberts, E S; Coolen, A C C; Schlitt, T

    2011-01-01

    We generate new mathematical tools with which to quantify the macroscopic topological structure of large directed networks. This is achieved via a statistical mechanical analysis of constrained maximum entropy ensembles of directed random graphs with prescribed joint distributions for in- and out-degrees and prescribed degree-degree correlation functions. We calculate exact and explicit formulae for the leading orders in the system size of the Shannon entropies and complexities of these ensembles, and for information-theoretic distances. The results are applied to data on gene regulation networks.

  20. Preliminary results on an innovative plasmonic device for macromolecules analysis and sequencing

    Francardi, Marco; Candeloro, Patrizio; Malara, Natalia Maria; Gentile, Francesco T.; Coluccio, Maria Laura; Perozziello, Gerardo; Gaggero, Aleesandro; De Angelis, Francesco De; Cherubini, Enrico; Di Fabrizio, Enzo M.

    2013-01-01

    In this work we present the fabrication and theoretical simulation for a new device constituted by a on Substrate Plasmonic Antenna (SPA) combined with a bio-functionalized Atomic Force Microscopy (AFM) cantilever. This device could represent a new strategy to sequence and analyze a single protein or DNA. The idea is to use an SPA composed of an innovative "wedding cake"shaped grating (WCG), in order to excite a Surface Plasmon Polariton (SPP) mode, and a 30-tilted Plasmonic Antenna (PA), able to compress adiabatically the SPP until the tip. The Plasmonic device is placed inside an electrical contact that could be used to unfold protein molecules or DNA. A bio-functionalized AFM tip can be used to fish a single biological element and for alignment with the SPA. Then the unfolded element could be scanned close to the PA and a Tip Enhanced Raman Signal (TERS) can be recorded from the biomolecule. The spatial resolution is limited by the size of the radius of curvature of the antenna, which in this work is about 15 nm, while the vertical scanning is controlled by the piezoelectric of the AFM set up. In this work we demonstrate the possibility to fabricate this innovative plasmonic device and we report FDTD simulations of the innovative WCG. The FDTD simulations show the generation of a plasmonic mode that, coupled with the antenna, give rise to an adiabatic compression which produce an increase of the electric field of about 40 times. © 2013 Elsevier B.V. All rights reserved.

  1. Preliminary results on an innovative plasmonic device for macromolecules analysis and sequencing

    Francardi, Marco

    2013-11-01

    In this work we present the fabrication and theoretical simulation for a new device constituted by a on Substrate Plasmonic Antenna (SPA) combined with a bio-functionalized Atomic Force Microscopy (AFM) cantilever. This device could represent a new strategy to sequence and analyze a single protein or DNA. The idea is to use an SPA composed of an innovative "wedding cake"shaped grating (WCG), in order to excite a Surface Plasmon Polariton (SPP) mode, and a 30-tilted Plasmonic Antenna (PA), able to compress adiabatically the SPP until the tip. The Plasmonic device is placed inside an electrical contact that could be used to unfold protein molecules or DNA. A bio-functionalized AFM tip can be used to fish a single biological element and for alignment with the SPA. Then the unfolded element could be scanned close to the PA and a Tip Enhanced Raman Signal (TERS) can be recorded from the biomolecule. The spatial resolution is limited by the size of the radius of curvature of the antenna, which in this work is about 15 nm, while the vertical scanning is controlled by the piezoelectric of the AFM set up. In this work we demonstrate the possibility to fabricate this innovative plasmonic device and we report FDTD simulations of the innovative WCG. The FDTD simulations show the generation of a plasmonic mode that, coupled with the antenna, give rise to an adiabatic compression which produce an increase of the electric field of about 40 times. © 2013 Elsevier B.V. All rights reserved.

  2. The Trojan Horse method for nuclear astrophysics: Recent results for direct reactions

    Tumino, A.; Gulino, M.; Spitaleri, C.; Cherubini, S.; Romano, S.; Cognata, M. La; Pizzone, R. G.; Rapisarda, G. G.; Lamia, L.

    2014-01-01

    The Trojan Horse method is a powerful indirect technique to determine the astrophysical factor for binary rearrangement processes A+x→b+B at astrophysical energies by measuring the cross section for the Trojan Horse (TH) reaction A+a→B+b+s in quasi free kinematics. The Trojan Horse Method has been successfully applied to many reactions of astrophysical interest, both direct and resonant. In this paper, we will focus on direct sub-processes. The theory of the THM for direct binary reactions will be shortly presented based on a few-body approach that takes into account the off-energy-shell effects and initial and final state interactions. Examples of recent results will be presented to demonstrate how THM works experimentally

  3. The Trojan Horse method for nuclear astrophysics: Recent results for direct reactions

    Tumino, A.; Gulino, M. [Laboratori Nazionali del Sud, Istituto Nazionale di Fisica Nucleare, Catania, Italy and Università degli Studi di Enna Kore, Enna (Italy); Spitaleri, C.; Cherubini, S.; Romano, S. [Laboratori Nazionali del Sud, Istituto Nazionale di Fisica Nucleare, Catania, Italy and Dipartimento di Fisica e Astronomia, Università di Catania, Catania (Italy); Cognata, M. La; Pizzone, R. G.; Rapisarda, G. G. [Laboratori Nazionali del Sud, Istituto Nazionale di Fisica Nucleare, Catania (Italy); Lamia, L. [Dipartimento di Fisica e Astronomia, Università di Catania, Catania (Italy)

    2014-05-09

    The Trojan Horse method is a powerful indirect technique to determine the astrophysical factor for binary rearrangement processes A+x→b+B at astrophysical energies by measuring the cross section for the Trojan Horse (TH) reaction A+a→B+b+s in quasi free kinematics. The Trojan Horse Method has been successfully applied to many reactions of astrophysical interest, both direct and resonant. In this paper, we will focus on direct sub-processes. The theory of the THM for direct binary reactions will be shortly presented based on a few-body approach that takes into account the off-energy-shell effects and initial and final state interactions. Examples of recent results will be presented to demonstrate how THM works experimentally.

  4. Temperature-modulated direct thermoelectric gas sensors: thermal modeling and results for fast hydrocarbon sensors

    Rettig, Frank; Moos, Ralf

    2009-01-01

    Direct thermoelectric gas sensors are a promising alternative to conductometric gas sensors. For accurate results, a temperature modulation technique in combination with a regression analysis is advantageous. However, the thermal time constant of screen-printed sensors is quite large. As a result, up to now the temperature modulation frequency (20 mHz) has been too low and the corresponding principle-related response time (50 s) has been too high for many applications. With a special design, respecting the physical properties of thermal waves and the use of signal processing similar to a lock-in-amplifier, it is possible to achieve response times of about 1 s. As a result, direct thermoelectric gas sensors with SnO 2 as a gas-sensitive material respond fast and are reproducible to the propane concentration in the ambient atmosphere. Due to the path-independent behavior of the thermovoltage and the temperature, the measured thermopower of two sensors is almost identical

  5. CBS Genome Atlas Database: a dynamic storage for bioinformatic results and sequence data

    Hallin, Peter Fischer; Ussery, David

    2004-01-01

    , these results counts to more than 220 pieces of information. The backbone of this solution consists of a program package written in Perl, which enables administrators to synchronize and update the database content. The MySQL database has been connected to the CBS web-server via PHP4, to present a dynamic web...... and frequent addition of new models are factors that require a dynamic database layout. Using basic tools like the GNU Make system, csh, Perl and MySQL, we have created a flexible database environment for storing and maintaining such results for a collection of complete microbial genomes. Currently...... content for users outside the center. This solution is tightly fitted to existing server infrastructure and the solutions proposed here can perhaps serve as a template for other research groups to solve database issues....

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

    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.

  7. Detection of lesions in multiple sclerosis by 2D FLAIR and single-slab 3D FLAIR sequences at 3.0 T: initial results

    Bink, Andrea; Gaa, Jochen; Lanfermann, Heinrich; Zanella, Friedhelm E.; Schmitt, Melanie; Mugler, John P.

    2006-01-01

    The aim of this study was to compare conventional 2D FLAIR and single-slab 3D FLAIR sequences in the detection of lesions in patients with multiple sclerosis. Eight patients with MS were examined at 3.0 T by using a 2D FLAIR sequence and a single-slab 3D FLAIR sequence. A comparison of lesion detectability was performed for the following regions: periventricular, nonperiventricular/juxtacortical and infratentorial. The contrast-to-noise ratios (CNRs) between lesions and brain tissue and CSF were calculated for each sequence. A total of 424 lesions were found using the 2D FLAIR sequence, while with the 3D FLAIR sequence 719 lesions were found. With the 2D FLAIR sequence, 41% fewer lesions were detected than with the 3D FLAIR sequence. Further, 40% fewer supratentorial and 62.5% fewer infratentorial lesions were found with the 2D FLAIR sequence. In images acquired with the 3D FLAIR sequence, the lesions had significantly higher CNRs than in images acquired with the 2D FLAIR sequence. These are the first results using a single-slab 3D FLAIR sequence at 3.0 T for detection of lesions in patients with MS. With the 3D FLAIR sequence significantly higher CNRs were achieved and significantly more lesions in patients with MS were detected. (orig.)

  8. INTERMEDIATE RESULTS AND LIMITS OF HARMONIZATION OF DIRECT TAXES IN THE EUROPEAN UNION

    Karina Ponomareva

    2017-01-01

    Full Text Available УДК 347.9The article is devoted to analysis of tax harmonization in the area of direct taxation in the European Union. Questions of positive and negative integration, common market and tax harmonization are analyzed.The author mentions the following benchmarks of the European tax integration: these are tax harmonization in the area of direct taxation, prohibition of discrimination and of unfair competition, leading role of fundamental freedoms in field of European integration.The direct effect of EU law is brought into light. The international treaty is a special source of law of Member States and it used in cases which can't be regulated by national legislation or by acts of integration law.Directives and regulations as sources of EU secondary law are described in the article. Their special features are also brought into light.International EU agreements and acts of cooperation in the area of taxation are also brought into light. The special role of soft law is also mentioned in the article.The special role of the European Court of Justice in forming of EU tax law is emphasized.The conclusion of the article is in the statement of importance of taxation in the forming of internal market in integration community.The expected results are important both from theoretical and practical points of view and include:working out the legal framework of direct taxation and finding out actual problems of integration tax law mentioning modern trends of cross-border taxation;recommendations of improving of harmonization mechanisms in the EAEU and improving of the Russian Tax Code.

  9. High-Alpha Research Vehicle Lateral-Directional Control Law Description, Analyses, and Simulation Results

    Davidson, John B.; Murphy, Patrick C.; Lallman, Frederick J.; Hoffler, Keith D.; Bacon, Barton J.

    1998-01-01

    This report contains a description of a lateral-directional control law designed for the NASA High-Alpha Research Vehicle (HARV). The HARV is a F/A-18 aircraft modified to include a research flight computer, spin chute, and thrust-vectoring in the pitch and yaw axes. Two separate design tools, CRAFT and Pseudo Controls, were integrated to synthesize the lateral-directional control law. This report contains a description of the lateral-directional control law, analyses, and nonlinear simulation (batch and piloted) results. Linear analysis results include closed-loop eigenvalues, stability margins, robustness to changes in various plant parameters, and servo-elastic frequency responses. Step time responses from nonlinear batch simulation are presented and compared to design guidelines. Piloted simulation task scenarios, task guidelines, and pilot subjective ratings for the various maneuvers are discussed. Linear analysis shows that the control law meets the stability margin guidelines and is robust to stability and control parameter changes. Nonlinear batch simulation analysis shows the control law exhibits good performance and meets most of the design guidelines over the entire range of angle-of-attack. This control law (designated NASA-1A) was flight tested during the Summer of 1994 at NASA Dryden Flight Research Center.

  10. Empowering genomic medicine by establishing critical sequencing result data flows: the eMERGE example.

    Aronson, Samuel; Babb, Lawrence; Ames, Darren; Gibbs, Richard A; Venner, Eric; Connelly, John J; Marsolo, Keith; Weng, Chunhua; Williams, Marc S; Hartzler, Andrea L; Liang, Wayne H; Ralston, James D; Devine, Emily Beth; Murphy, Shawn; Chute, Christopher G; Caraballo, Pedro J; Kullo, Iftikhar J; Freimuth, Robert R; Rasmussen, Luke V; Wehbe, Firas H; Peterson, Josh F; Robinson, Jamie R; Wiley, Ken; Overby Taylor, Casey

    2018-05-31

    The eMERGE Network is establishing methods for electronic transmittal of patient genetic test results from laboratories to healthcare providers across organizational boundaries. We surveyed the capabilities and needs of different network participants, established a common transfer format, and implemented transfer mechanisms based on this format. The interfaces we created are examples of the connectivity that must be instantiated before electronic genetic and genomic clinical decision support can be effectively built at the point of care. This work serves as a case example for both standards bodies and other organizations working to build the infrastructure required to provide better electronic clinical decision support for clinicians.

  11. Corrective results for the even-parity-quartet P states of lithium isoelectronic sequence

    Holoien, E.

    1982-01-01

    In order to secure a proper p-type behavior of the radial Slater orbitals r/sup n/exp(-etar/2) for the two p electrons near origin in the 1s2p2p configuration, the fixed n power must always be chosen greater than or equal to unity. Unfortunately, this restriction has not been applied to both p electrons in all 30 basic products of the 1967 trial wave function for the even-parity 4 p states, only correct for the one p electron in the case of 4p 0 states. According to this restriction only 14 basic products used are allowed. The remaining 16 basic products are not allowed and therefore have been omitted in the present investigation. This error has made the 1967 calculated total energies too low. Corrective results of the total energy using the allowed correlated 14-term wave function are given in this Communication. The present result for He - 1s2p 2 4 p indicates a position 148 meV in the continuum above the He 2 3 P threshold, in good agreement with recent theoretical calculations

  12. THE RESEARCH ACTIVITY OF THE UNIVERSITY TEACHERS: DIRECTIONS, RESULTS, AND PROSPECTS. SOCIOLOGICAL CONTENT

    I. A. Vasilyev

    2016-01-01

    Full Text Available The main purpose of an integrated monitoring research is the analysis of the main directions of research activity of faculty, staff and young scientists of the university.Methods. Scientific and theoretical analysis of publications on the researched topic are used as basic methods; sociological and diagnostic data collection methods; the method of statistical processing and classification of documentary and empirical data; the methods of content analysis and quantification of documentary and sociological information.Scientific novelty. The research is characterized by an integrated approach to the study of the problem: the basic provisions are analyzed; conclusions and recommendations of reports on research projects made by members of temporary research teams (or, university scientists and teaching staff. The classification (depending on the translation vectors results of dissertation works of graduate students, doctoral candidates is carried out in the course of the present study. Documentary information about the publication and presentation of scientific and pedagogical staff of the university is systematized; the report and information cards on the activities of innovative platforms are analyzed. The research team, with the direct participation of the author, after studying a few scientific publications on the subject, has developed an original method of complex research of the main directions of research activity of university scientists.Results. The presented research has allowed to note publication and innovative activity of the research and educational personnel, along with other its types, can act as the indicators characterizing the main directions of research activity both of higher education institution in general, and its concrete educational and scientific divisions. At the same, time the author emphasizes that efficiency of research process is caused not so much by quantitative as qualitative characteristics of concrete research

  13. Preliminary results from direct-to-facility vaccine deliveries in Kano, Nigeria.

    Aina, Muyi; Igbokwe, Uchenna; Jegede, Leke; Fagge, Rabiu; Thompson, Adam; Mahmoud, Nasir

    2017-04-19

    As part of its vaccine supply chain redesign efforts, Kano state now pushes vaccines directly from 6 state stores to primary health centers equipped with solar refrigerators. Our objective is to describe preliminary results from the first 20months of Kano's direct vaccine delivery operations. This is a retrospective review of Kano's direct vaccine delivery program. We analyzed trends in health facility vaccine stock levels, and examined the relationship between stock-out rates and each of cascade vaccine deliveries and timeliness of deliveries. Analysis of vaccination trends was based on administrative data from 27 sentinel health facilities. Costs for both the in-sourced and out-sourced approaches were estimated using a bottoms-up model-based approach. Overall stock adequacy increased from 54% in the first delivery cycle to 68% by cycle 33. Conversely, stock-out rates decreased from 41% to 10% over the same period. Similar trends were observed in the out-sourced and in-sourced programs. Stock-out rates rose incrementally with increasing number of cascade facilities, and delays in vaccine deliveries correlated strongly with stock-out rates. Recognizing that stock availability is one of many factors contributing to vaccinations, we nonetheless compared pre- and post- direct deliveries vaccinations in sentinel facilities, and found statistically significant upward trends for 4 out of 6 antigens. 1 antigen (measles) showed an upward trend that was not statistically significant. Hepatitis b vaccinations declined during the period. Overall, there appeared to be a one-year lag between commencement of direct deliveries and the increase in number of vaccinations. Weighted average cost per delivery is US$29.8 and cost per child immunized is US$0.7 per year. Direct vaccine delivery to health facilities in Kano, through a streamlined architecture, has resulted in decreased stock-outs and improved stock adequacy. Concurrent operation of insourced and outsourced programs has

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

    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.

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

    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.

  16. Cascade detection for the extraction of localized sequence features; specificity results for HIV-1 protease and structure-function results for the Schellman loop.

    Newell, Nicholas E

    2011-12-15

    The extraction of the set of features most relevant to function from classified biological sequence sets is still a challenging problem. A central issue is the determination of expected counts for higher order features so that artifact features may be screened. Cascade detection (CD), a new algorithm for the extraction of localized features from sequence sets, is introduced. CD is a natural extension of the proportional modeling techniques used in contingency table analysis into the domain of feature detection. The algorithm is successfully tested on synthetic data and then applied to feature detection problems from two different domains to demonstrate its broad utility. An analysis of HIV-1 protease specificity reveals patterns of strong first-order features that group hydrophobic residues by side chain geometry and exhibit substantial symmetry about the cleavage site. Higher order results suggest that favorable cooperativity is weak by comparison and broadly distributed, but indicate possible synergies between negative charge and hydrophobicity in the substrate. Structure-function results for the Schellman loop, a helix-capping motif in proteins, contain strong first-order features and also show statistically significant cooperativities that provide new insights into the design of the motif. These include a new 'hydrophobic staple' and multiple amphipathic and electrostatic pair features. CD should prove useful not only for sequence analysis, but also for the detection of multifactor synergies in cross-classified data from clinical studies or other sources. Windows XP/7 application and data files available at: https://sites.google.com/site/cascadedetect/home. nacnewell@comcast.net Supplementary information is available at Bioinformatics online.

  17. Geochemistry of the Bonin Fore-arc Volcanic Sequence: Results from IODP Expedition 352

    Godard, M.; Ryan, J. G.; Shervais, J. W.; Whattam, S. A.; Sakuyama, T.; Kirchenbaur, M.; Li, H.; Nelson, W. R.; Prytulak, J.; Pearce, J. A.; Reagan, M. K.

    2015-12-01

    The Izu-Bonin-Mariana intraoceanic arc system, in the western Pacific, results from ~52 My of subduction of the Pacific plate beneath the eastern margin of the Philippine Sea plate. Four sites were drilled south of the Bonin Islands during IODP Expedition 352 and 1.22 km of igneous basement was cored upslope to the west of the trough. These stratigraphically controlled igneous suites allow study of the earliest stages of arc development from seafloor spreading to convergence. We present the preliminary results of a detailed major and trace element (ICPMS) study on 128 igneous rocks drilled during Expedition 352. Mainly basalts and basaltic andesites were recovered at the two deeper water sites (U1440 and U1441) and boninites at the two westernmost sites (U1439 and U1442). Sites U1440 and U1441 basaltic suites are trace element depleted (e.g. Yb 4-6 x PM); they have fractionated REE patterns (LREE/HREE = 0.2-0.4 x C1-chondrites) compared to mid-ocean ridge basalts. They have compositions overlapping that of previously sampled Fore-Arc Basalts (FAB) series. They are characterized also by an increase in LILE contents relative to neighboring elements up-section (e.g. Rb/La ranging from <1 to 3-7 x PM at Site U1440) suggesting a progressive contamination of their source by fluids. This process in turn may have favored melting and efficient melt extraction from the source and thus its extreme depletion. Boninites are depleted in moderately incompatible elements with a decrease in their contents up-section (e.g. Yb = ~6.2 to 2.8 x C1-chondrite at Site U1439). These changes in trace element contents are associated with the development of a positive Zr-Hf anomaly relative to neighboring elements and a strong increase in LILE (e.g., Zr/Sm=~1 to 2.6 x PM and Rb/La=1-2 to 10-18). The progressive upward depletion of boninitic lavas could reveal the incorporation of harzburgitic residues from FAB generation into their mantle source.

  18. Prescreening whole exome sequencing results from patients with retinal degeneration for variants in genes associated with retinal degeneration

    Bryant L

    2017-12-01

    Full Text Available Laura Bryant,1 Olga Lozynska,1 Albert M Maguire,1–3 Tomas S Aleman,1–3 Jean Bennett1–3 1Center for Advanced Retinal and Ocular Therapeutics (CAROT, FM Kirby Center for Molecular Ophthalmology, Scheie Eye Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA; 2Department of Ophthalmology, The Children’s Hospital of Philadelphia, Philadelphia, PA, USA; 3Department of Ophthalmology, Scheie Eye Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA Background: Accurate clinical diagnosis and prognosis of retinal degeneration can be aided by the identification of the disease-causing genetic variant. It can confirm the clinical diagnosis as well as inform the clinician of the risk for potential involvement of other organs such as kidneys. It also aids in genetic counseling for affected individuals who want to have a child. Finally, knowledge of disease-causing variants informs laboratory investigators involved in translational research. With the advent of next-generation sequencing, identifying pathogenic mutations is becoming easier, especially the identification of novel pathogenic variants.Methods: We used whole exome sequencing on a cohort of 69 patients with various forms of retinal degeneration and in whom screens for previously identified disease-causing variants had been inconclusive. All potential pathogenic variants were verified by Sanger sequencing and, when possible, segregation analysis of immediate relatives. Potential variants were identified by using a semi-masked approach in which rare variants in candidate genes were identified without knowledge of the clinical diagnosis (beyond “retinal degeneration” or inheritance pattern. After the initial list of genes was prioritized, genetic diagnosis and inheritance pattern were taken into account.Results: We identified the likely pathogenic variants in 64% of the subjects. Seven percent had a single

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

    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

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

    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.

  1. Direct Stenting in Patients with Acute Lower Limb Arterial Occlusions: Immediate and Long-Term Results

    Galanakis, Nikolaos [University of Crete Medical School, Interventional Radiology Unit, Department of Medical Imaging, University Hospital Heraklion (Greece); Kontopodis, Nikolaos [University of Crete Medical School, Vascular Surgery Unit, Department of Cardiothoracic and Vascular Surgery, University Hospital Heraklion (Greece); Peteinarakis, Ioannis; Kehagias, Elias [University of Crete Medical School, Interventional Radiology Unit, Department of Medical Imaging, University Hospital Heraklion (Greece); Ioannou, Christos V. [University of Crete Medical School, Vascular Surgery Unit, Department of Cardiothoracic and Vascular Surgery, University Hospital Heraklion (Greece); Tsetis, Dimitrios, E-mail: tsetis@med.uoc.gr [University of Crete Medical School, Interventional Radiology Unit, Department of Medical Imaging, University Hospital Heraklion (Greece)

    2017-02-15

    PurposeThe purpose of this study is to accentuate the efficacy of direct stenting (stent placement without predilatation of the lesion) in patients with acute lower limb arterial ischemia (ALLI).Materials and MethodsBetween January 2010 and September 2015, 16 patients (11 men and 5 women) underwent direct stenting of acute arterial occlusions. All patients had contraindication for surgical revascularization or catheter-directed thrombolysis. According to SVS/ISCVS Classification, six patients had IIa and ten patients IIb ALLI. The occlusions were located in CIA, EIA, SFA, or popliteal artery. Mean follow-up time with clinical examination and color Duplex ultrasonography was 37.6 months (range 1–72). We analyzed the technical and clinical outcomes of the procedures, as well the complications and patency rates.ResultsTechnical success was achieved in all patients (16/16) and there was significant clinical improvement in 15 patients. There was neither distal embolization nor procedure-related complications. During the 6 years of follow-up, four patients died due to non-procedure-related causes and there were two minor and one major amputations. The primary patency rates and the amputation-free survival rates were 93.7 and 87% at 1 year, 75.2 and 71.2% at 3 years, and 75.2 and 62.3%, respectively, at 6 years.ConclusionsDirect stenting may be a valuable alternative procedure for acute arterial occlusions in selected cases with high technical success and significant clinical improvement.Level of EvidenceLevel 4, Case Series.

  2. Direct Stenting in Patients with Acute Lower Limb Arterial Occlusions: Immediate and Long-Term Results

    Galanakis, Nikolaos; Kontopodis, Nikolaos; Peteinarakis, Ioannis; Kehagias, Elias; Ioannou, Christos V.; Tsetis, Dimitrios

    2017-01-01

    PurposeThe purpose of this study is to accentuate the efficacy of direct stenting (stent placement without predilatation of the lesion) in patients with acute lower limb arterial ischemia (ALLI).Materials and MethodsBetween January 2010 and September 2015, 16 patients (11 men and 5 women) underwent direct stenting of acute arterial occlusions. All patients had contraindication for surgical revascularization or catheter-directed thrombolysis. According to SVS/ISCVS Classification, six patients had IIa and ten patients IIb ALLI. The occlusions were located in CIA, EIA, SFA, or popliteal artery. Mean follow-up time with clinical examination and color Duplex ultrasonography was 37.6 months (range 1–72). We analyzed the technical and clinical outcomes of the procedures, as well the complications and patency rates.ResultsTechnical success was achieved in all patients (16/16) and there was significant clinical improvement in 15 patients. There was neither distal embolization nor procedure-related complications. During the 6 years of follow-up, four patients died due to non-procedure-related causes and there were two minor and one major amputations. The primary patency rates and the amputation-free survival rates were 93.7 and 87% at 1 year, 75.2 and 71.2% at 3 years, and 75.2 and 62.3%, respectively, at 6 years.ConclusionsDirect stenting may be a valuable alternative procedure for acute arterial occlusions in selected cases with high technical success and significant clinical improvement.Level of EvidenceLevel 4, Case Series.

  3. Some additional results on the directional relationships between forces and accelerations in special relativity

    Gonzalez-Diaz, P.F.

    1979-01-01

    Some directional relationships between forces and accelerations in special relativity have been studied by considering the most general case of a body having x, y and z components of velocity, which is acted upon by a force with nonzero components. The behaviour of asub(y)/asub(x) and asub(y)/asub(z) vs. velocity for different force component ratios is studied in the general situation in which vsub(x) is unequal to vsub(y) is unequal to vsub(z). It is shown that one or two, suddenly varying, negative acceleration components can result for the body at sufficiently high velocities, and an explanation is given. (author)

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

    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

  5. Assimilation of wind speed and direction observations: results from real observation experiments

    Feng Gao

    2015-06-01

    Full Text Available The assimilation of wind observations in the form of speed and direction (asm_sd by the Weather Research and Forecasting Model Data Assimilation System (WRFDA was performed using real data and employing a series of cycling assimilation experiments for a 2-week period, as a follow-up for an idealised post hoc assimilation experiment. The satellite-derived Atmospheric Motion Vectors (AMV and surface dataset in Meteorological Assimilation Data Ingest System (MADIS were assimilated. This new method takes into account the observation errors of both wind speed (spd and direction (dir, and WRFDA background quality control (BKG-QC influences the choice of wind observations, due to data conversions between (u,v and (spd, dir. The impacts of BKG-QC, as well as the new method, on the wind analysis were analysed separately. Because the dir observational errors produced by different platforms are not known or tuned well in WRFDA, a practical method, which uses similar assimilation weights in comparative trials, was employed to estimate the spd and dir observation errors. The asm_sd produces positive impacts on analyses and short-range forecasts of spd and dir with smaller root-mean-square errors than the u,v-based system. The bias of spd analysis decreases by 54.8%. These improvements result partly from BKG-QC screening of spd and dir observations in a direct way, but mainly from the independent impact of spd (dir data assimilation on spd (dir analysis, which is the primary distinction from the standard WRFDA method. The potential impacts of asm_sd on precipitation forecasts were evaluated. Results demonstrate that the asm_sd is able to indirectly improve the precipitation forecasts by improving the prediction accuracies of key wind-related factors leading to precipitation (e.g. warm moist advection and frontogenesis.

  6. Gratitude, protective buffering, and cognitive dissonance: How families respond to pediatric whole exome sequencing in the absence of actionable results.

    Werner-Lin, Allison; Zaspel, Lori; Carlson, Mae; Mueller, Rebecca; Walser, Sarah A; Desai, Ria; Bernhardt, Barbara A

    2018-03-01

    Clinical genome and exome sequencing (CGES) may identify variants leading to targeted management of existing conditions. Yet, CGES often fails to identify pathogenic diagnostic variants and introduces uncertainties by detecting variants of uncertain significance (VUS) and secondary findings. This study investigated how families understand findings and adjust their perspectives on CGES. As part of NIH's Clinical Sequencing Exploratory Research Consortium, children were recruited from clinics at the Children's Hospital of Pennsylvania (CHOP) and offered exome sequencing. Primary pathogenic and possibly pathogenic, and some secondary findings were returned. Investigators digitally recorded results disclosure sessions and conducted 3-month follow up interviews with 10 adolescents and a parent. An interdisciplinary team coded all transcripts. Participants were initially disappointed with findings, yet reactions evolved within disclosure sessions and at 3-month interviews toward acceptance and satisfaction. Families erroneously expected, and prepared extensively, to learn about risk for common conditions. During disclosure sessions, parents and adolescents varied in how they monitored and responded to each others reactions. Several misinterpreted, or overestimated, the utility of findings to attribute meaning and achieve closure for the CGES experience. Participants perceived testing as an opportunity to improve disease management despite results that did not introduce new treatments or diagnoses. Future research may examine whether families experience cognitive dissonance regarding discrepancies between expectations and findings, and how protective buffering minimizes the burden of disappointment on loved ones. As CGES is increasingly integrated into clinical care providers must contend with tempering family expectations and interpretations of findings while managing complex medical care. © 2018 Wiley Periodicals, Inc.

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

    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.

  8. Direct Measurement of Tree Height Provides Different Results on the Assessment of LiDAR Accuracy

    Emanuele Sibona

    2016-12-01

    Full Text Available In this study, airborne laser scanning-based and traditional field-based survey methods for tree heights estimation are assessed by using one hundred felled trees as a reference dataset. Comparisons between remote sensing and field-based methods were applied to four circular permanent plots located in the western Italian Alps and established within the Alpine Space project NewFor. Remote sensing (Airborne Laser Scanning, ALS, traditional field-based (indirect measurement, IND, and direct measurement of felled trees (DIR methods were compared by using summary statistics, linear regression models, and variation partitioning. Our results show that tree height estimates by Airborne Laser Scanning (ALS approximated to real heights (DIR of felled trees. Considering the species separately, Larix decidua was the species that showed the smaller mean absolute difference (0.95 m between remote sensing (ALS and direct field (DIR data, followed by Picea abies and Pinus sylvestris (1.13 m and 1.04 m, respectively. Our results cannot be generalized to ALS surveys with low pulses density (<5/m2 and with view angles far from zero (nadir. We observed that the tree heights estimation by laser scanner is closer to actual tree heights (DIR than traditional field-based survey, and this was particularly valid for tall trees with conical shape crowns.

  9. Non-Maxwellian electron distributions resulting from direct laser acceleration in near-critical plasmas

    T. Toncian

    2016-01-01

    Full Text Available The irradiation of few-nm-thick targets by a finite-contrast high-intensity short-pulse laser results in a strong pre-expansion of these targets at the arrival time of the main pulse. The targets decompress to near and lower than critical densities with plasmas extending over few micrometers, i.e. multiple wavelengths. The interaction of the main pulse with such a highly localized but inhomogeneous target leads to the generation of a short channel and further self-focusing of the laser beam. Experiments at the Glass Hybrid OPCPA Scaled Test-bed (GHOST laser system at University of Texas, Austin using such targets measured non-Maxwellian, peaked electron distribution with large bunch charge and high electron density in the laser propagation direction. These results are reproduced in 2D PIC simulations using the EPOCH code, identifying direct laser acceleration (DLA [1] as the responsible mechanism. This is the first time that DLA has been observed to produce peaked spectra as opposed to broad, Maxwellian spectra observed in earlier experiments [2]. This high-density electrons have potential applications as injector beams for a further wakefield acceleration stage as well as for pump-probe applications.

  10. Performance limits of direct cryogenically cooled silicon monochromators - experimental results at the APS

    Lee, W.-K.; Fernandez, P.; Mills, D.M.

    2000-01-01

    The successful use of cryogenically cooled silicon monochromators at third-generation synchrotron facilities is well documented. At the Advanced Photon Source (APS) it has been shown that, at 100 mA operation with the standard APS undulator A, the cryogenically cooled silicon monochromator performs very well with minimal (<2 arcsec) or no observable thermal distortions. However, to date there has not been any systematic experimental study on the performance limits of this approach. This paper presents experimental results on the performance limits of these directly cooled crystals. The results show that if the beam is limited to the size of the radiation central cone then, at the APS, the crystal will still perform well at twice the present 100 mA single 2.4 m-long 3.3 cm-period undulator heat load. However, the performance would degrade rapidly if a much larger incident white-beam size is utilized

  11. Global interpretation of direct Dark Matter searches after CDMS-II results

    Kopp, Joachim; Schwetz, Thomas; Zupan, Jure

    2010-01-01

    We perform a global fit to data from Dark Matter (DM) direct detection experiments, including the recent CDMS-II results. We discuss possible interpretations of the DAMA annual modulation signal in terms of spin-independent and spin-dependent DM-nucleus interactions, both for elastic and inelastic scattering. We find that for the spin-dependent inelastic scattering off protons a good fit to all data is obtained. We present a simple toy model realizing such a scenario. In all the remaining cases the DAMA allowed regions are disfavored by other experiments or suffer from severe fine tuning of DM parameters with respect to the galactic escape velocity. Finally, we also entertain the possibility that the two events observed in CDMS-II are an actual signal of elastic DM scattering, and we compare the resulting CDMS-II allowed regions to the exclusion limits from other experiments

  12. Experimental Results for Direction of Arrival Estimation with a Single Acoustic Vector Sensor in Shallow Water

    Alper Bereketli

    2015-01-01

    Full Text Available We study the performances of several computationally efficient and simple techniques for estimating direction of arrival (DOA of an underwater acoustic source using a single acoustic vector sensor (AVS in shallow water. Underwater AVS is a compact device, which consists of one hydrophone and three accelerometers in a packaged form, measuring scalar pressure and three-dimensional acceleration simultaneously at a single position. A very controlled experimental setup is prepared to test how well-known techniques, namely, arctan-based, intensity-based, time domain beamforming, and frequency domain beamforming methods, perform in estimating DOA of a source in different circumstances. Experimental results reveal that for almost all cases beamforming techniques perform best. Moreover, arctan-based method, which is the simplest of all, provides satisfactory results for practical purposes.

  13. Macrosegregation Resulting from Directional Solidification Through an Abrupt Change in Cross-Sections

    Lauer, M.; Poirier, D. R.; Ghods, M.; Tewari, S. N.; Grugel, R. N.

    2017-01-01

    Simulations of the directional solidification of two hypoeutectic alloys (Al-7Si alloy and Al-19Cu) and resulting macrosegregation patterns are presented. The casting geometries include abrupt changes in cross-section from a larger width of 9.5 mm to a narrower 3.2 mm width then through an expansion back to a width of 9.5 mm. The alloys were chosen as model alloys because they have similar solidification shrinkages, but the effect of Cu on changing the density of the liquid alloy is about an order of magnitude greater than that of Si. The simulations compare well with experimental castings that were directionally solidified in a graphite mold in a Bridgman furnace. In addition to the simulations of the directional solidification in graphite molds, some simulations were effected for solidification in an alumina mold. This study showed that the mold must be included in numerical simulations of directional solidification because of its effect on the temperature field and solidification. For the model alloys used for the study, the simulations clearly show the interaction of the convection field with the solidifying alloys to produce a macrosegregation pattern known as "steepling" in sections with a uniform width. Details of the complex convection- and segregation-patterns at both the contraction and expansion of the cross-sectional area are revealed by the computer simulations. The convection and solidification through the expansions suggest a possible mechanism for the formation of stray grains. The computer simulations and the experimental castings have been part of on-going ground-based research with the goal of providing necessary background for eventual experiments aboard the ISS. For casting practitioners, the results of the simulations demonstrate that computer simulations should be applied to reveal interactions between alloy solidification properties, solidification conditions, and mold geometries on macrosegregation. The simulations also presents the

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

    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

  15. Tunneling splitting in double-proton transfer: direct diagonalization results for porphycene.

    Smedarchina, Zorka; Siebrand, Willem; Fernández-Ramos, Antonio

    2014-11-07

    Zero-point and excited level splittings due to double-proton tunneling are calculated for porphycene and the results are compared with experiment. The calculation makes use of a multidimensional imaginary-mode Hamiltonian, diagonalized directly by an effective reduction of its dimensionality. Porphycene has a complex potential energy surface with nine stationary configurations that allow a variety of tunneling paths, many of which include classically accessible regions. A symmetry-based approach is used to show that the zero-point level, although located above the cis minimum, corresponds to concerted tunneling along a direct trans - trans path; a corresponding cis - cis path is predicted at higher energy. This supports the conclusion of a previous paper [Z. Smedarchina, W. Siebrand, and A. Fernández-Ramos, J. Chem. Phys. 127, 174513 (2007)] based on the instanton approach to a model Hamiltonian of correlated double-proton transfer. A multidimensional tunneling Hamiltonian is then generated, based on a double-minimum potential along the coordinate of concerted proton motion, which is newly evaluated at the RI-CC2/cc-pVTZ level of theory. To make it suitable for diagonalization, its dimensionality is reduced by treating fast weakly coupled modes in the adiabatic approximation. This results in a coordinate-dependent mass of tunneling, which is included in a unique Hermitian form into the kinetic energy operator. The reduced Hamiltonian contains three symmetric and one antisymmetric mode coupled to the tunneling mode and is diagonalized by a modified Jacobi-Davidson algorithm implemented in the Jadamilu software for sparse matrices. The results are in satisfactory agreement with the observed splitting of the zero-point level and several vibrational fundamentals after a partial reassignment, imposed by recently derived selection rules. They also agree well with instanton calculations based on the same Hamiltonian.

  16. "We don't know her history, her background": adoptive parents' perspectives on whole genome sequencing results.

    Crouch, Julia; Yu, Joon-Ho; Shankar, Aditi G; Tabor, Holly K

    2015-02-01

    Exome sequencing and whole genome sequencing (ES/WGS) can provide parents with a wide range of genetic information about their children, and adoptive parents may have unique issues to consider regarding possible access to this information. The few papers published on adoption and genetics have focused on targeted genetic testing of children in the pre-adoption context. There are no data on adoptive parents' perspectives about pediatric ES/WGS, including their preferences about different kinds of results, and the potential benefits and risks of receiving results. To explore these issues, we conducted four exploratory focus groups with adoptive parents (N = 26). The majority lacked information about their children's biological family health history and ancestry, and many viewed WGS results as a way to fill in these gaps in knowledge. Some expressed concerns about protecting their children's future privacy and autonomy, but at the same time stated that WGS results could possibly help them be proactive about their children's health. A few parents expressed concerns about the risks of WGS in a pre-adoption context, specifically about decreasing a child's chance of adoption. These results suggest that issues surrounding genetic information in the post-adoption and ES/WGS contexts need to be considered, as well as concerns about risks in the pre-adoption context. A critical challenge for ES/WGS in the context of adoption will be balancing the right to know different kinds of genetic information with the right not to know. Specific guidance for geneticists and genetic counselors may be needed to maximize benefits of WGS while minimizing harms and prohibiting misuse of the information in the adoption process.

  17. Protein-Level Integration Strategy of Multiengine MS Spectra Search Results for Higher Confidence and Sequence Coverage.

    Zhao, Panpan; Zhong, Jiayong; Liu, Wanting; Zhao, Jing; Zhang, Gong

    2017-12-01

    Multiple search engines based on various models have been developed to search MS/MS spectra against a reference database, providing different results for the same data set. How to integrate these results efficiently with minimal compromise on false discoveries is an open question due to the lack of an independent, reliable, and highly sensitive standard. We took the advantage of the translating mRNA sequencing (RNC-seq) result as a standard to evaluate the integration strategies of the protein identifications from various search engines. We used seven mainstream search engines (Andromeda, Mascot, OMSSA, X!Tandem, pFind, InsPecT, and ProVerB) to search the same label-free MS data sets of human cell lines Hep3B, MHCCLM3, and MHCC97H from the Chinese C-HPP Consortium for Chromosomes 1, 8, and 20. As expected, the union of seven engines resulted in a boosted false identification, whereas the intersection of seven engines remarkably decreased the identification power. We found that identifications of at least two out of seven engines resulted in maximizing the protein identification power while minimizing the ratio of suspicious/translation-supported identifications (STR), as monitored by our STR index, based on RNC-Seq. Furthermore, this strategy also significantly improves the peptides coverage of the protein amino acid sequence. In summary, we demonstrated a simple strategy to significantly improve the performance for shotgun mass spectrometry by protein-level integrating multiple search engines, maximizing the utilization of the current MS spectra without additional experimental work.

  18. Comparison of direct deposition and root uptake results after the Fukushima Daiichi Nuclear Power Plant accident

    Tagami, Keiko; Uchida, Shigeo

    2012-01-01

    Field horsetail(Equisetum arvense) is a kind of fern, and the fertile shoots are eaten as vegetables in Japan in the spring. Since fern species tend to concentrate radiocaesium from soil, concentrations and distribution patterns of radiocaesium in the fertile shoots are of interest. In this study, distribution and food processing results were compared using samples collected in 2011(n=1) and 2012(n=3); the sample collected in 2011 received direct deposition from the Fukushima Daiichi Nuclear Power Plant accident while those collected in 2012 included radiocaesium mainly taken up from soil. About 200-300 shoots were collected at each sampling time. The 137 Cs concentration in samples collected in 2012 decreased by 100-200 times compared to that in 2011. The radiocaesium distribution patterns in strobili, leaves and stems of 2012 samples were almost the same as those of 2011; however, the patterns were different from those of potassium. The radiocaesium removal percentage by food processing (washing + boiling for 2.5min) was 70% in 2011, while that for 2012 samples was 32-72%; the effect of direct deposition and root uptake was not clear. (author)

  19. Clinical results and functional outcomes after direct intralaminar screw repair of spondylolysis.

    Menga, Emmanuel N; Kebaish, Khaled M; Jain, Amit; Carrino, John A; Sponseller, Paul D

    2014-01-01

    Prospective analysis. Our objective was to analyze clinical and functional results of patients with spondylolysis treated via direct intralaminar screw fixation and autograft, a minimally invasive and motion-preserving surgery. Spondylolysis is usually treated nonoperatively; multiple surgical techniques are available when nonoperative measures fail. No studies evaluate the clinical and functional outcomes and their correlation with pars defect size and disc morphology on magnetic resonance imaging. We reviewed patients with spondylolysis treated with intralaminar screw fixation and bone grafting from 2000 through 2010. Of the 31 patients (mean age, 16 yr; range, 10-37 yr), 25 (81%) were competitive athletes. Preoperative computed tomographic scans were used to measure the pars defect size, and preoperative magnetic resonance images were graded using Pfirrmann classification for correlation with postoperative outcomes. Student t test was used for analysis (significance, P spondylolysis repair for persistent pain starting 18 months after intralaminar screw fixation, 2 patients sustained unilateral intralaminar screw fractures at L5, and 1 patient required irrigation and debridement for a superficial postoperative infection. There was no correlation among preoperative magnetic resonance imaging disc morphology, defect size on computed tomography, patient age, and clinical outcomes. Direct repair of spondylolysis with intralaminar screws offers a low profile, reliable treatment with good functional outcome and a low complication rate in active patients. 4.

  20. Displaying results of direct detection dark matter experiments free of astrophysical uncertainties

    Rauch, Ludwig [Max Planck Institut fuer Kernphysik, Heidelberg (Germany); Collaboration: Collaboration XENON 100

    2015-07-01

    A number of experiments try to measure WIMP interactions by using different detector technologies and target elements. Hence, energy thresholds and sensitivities to light or heavy WIMP masses differ. However, due to large systematic uncertainties in the parameters defining the dark matter halo, a comparison of detectors is demanding. By mapping experimental results from the traditional cross section vs. dark matter mass parameter-space into a dark matter halo independent phase space, direct comparisons between experiments can be made. This is possible due to the monotonicity of the velocity integral which enables to combine all astrophysical assumptions into one parameter common to all experiments. In this talk the motivation as well as the mapping method are explained based on the XENON100 data.

  1. Direct-to-Consumer Genetic Testing: User Motivations, Decision Making, and Perceived Utility of Results.

    Roberts, J Scott; Gornick, Michele C; Carere, Deanna Alexis; Uhlmann, Wendy R; Ruffin, Mack T; Green, Robert C

    2017-01-01

    To describe the interests, decision making, and responses of consumers of direct-to-consumer personal genomic testing (DTC-PGT) services. Prior to 2013 regulatory restrictions on DTC-PGT services, 1,648 consumers from 2 leading companies completed Web surveys before and after receiving test results. Prior to testing, DTC-PGT consumers were as interested in ancestry (74% very interested) and trait information (72%) as they were in disease risks (72%). Among disease risks, heart disease (68% very interested), breast cancer (67%), and Alzheimer disease (66%) were of greatest interest prior to testing. Interest in disease risks was associated with female gender and poorer self-reported health (p decisions. © 2017 S. Karger AG, Basel.

  2. Some additional results on the directional relationships between forces and accelerations in special relativity

    Gonzales-Diaz, P.F.

    1979-01-01

    Some directional relationships between forces and accelerations in special relativity have been studied by considering the most general case of a body having x, y and z components of velocity, which is acted upon by a force with nonzero components. The behaviour of a sub(y)/ a sub(x) and a sub(y)/ a sub(z) vs. velocity for different force component ratios is studied in the general situation in which vsub(x) different from Vsub(y)different from vsub(z). It is shown that one or two, suddently varying, negative acceleration components can result for the body at sufficiently high velocities, and an explanation is given

  3. Environmental costs of a river watershed within the European water framework directive: Results from physical hydronomics

    Martinez, A.; Uche, J.; Valero, A.; Valero-Delgado, A.

    2010-01-01

    Physical hydronomics (PH) is the specific application of thermodynamics that physically characterizes the governance of water bodies, i.e., the Water Framework Directive (WFD) for European Union citizens. In this paper, calculation procedures for the exergy analysis of river basins are developed within the WFD guidelines and a case study is developed. Therefore, it serves as an example for the feasible application of PH in the environmental cost assessment of water bodies, accordingly to the principle of recovery of the costs related to water services in accordance with the polluter pays principle, one of the milestones of the WFD. The Foix River watershed, a small river located at the Inland Basins of Catalonia (IBC), has been analyzed. Main results, difficulties, and constraints encountered are shown in the paper. Following WFD's quantity and quality objectives previously defined, water costs are calculated and the equivalence between the exergy loss due to water users and the exergy variation along the river are also analyzed.

  4. Experimental results of a direct air-cooled ammonia–lithium nitrate absorption refrigeration system

    Llamas-Guillén, S.U.; Cuevas, R.; Best, R.; Gómez, V.H.

    2014-01-01

    Absorption thermal cooling systems driven by renewable energy are a viable option in order to reduce fossil fuel consumption and the associated emissions. This work shows the results of an air cooled absorption cooling prototype working with an ammonia–lithium nitrate mixture at high ambient temperatures. An absorption refrigeration system was designed and built. The prototype is a one stage ammonia–lithium nitrate air cooled chiller. The experimental system was instrumented to evaluate each component. This paper shows the operation conditions in the experimental unit as well as some of the heat loads encountered at different operating conditions. The system was operated successfully at ambient temperatures in the range of 25–35 °C. A series of test showed that even at ambient temperatures it can be operated at evaporator temperatures below 10 °C producing chilled water for air conditioning applications such as radiative cooling panels. The system proved to stabilize very quickly and no risk of crystallization was encountered so the first results are promising in order to continue with the development of a more advanced prototype. - Highlights: •Experimental results of a direct air-cooled ammonia–lithium nitrate system. •The prototype is a one stage ammonia–lithium nitrate air cooled chiller. •The absorption system was operated successfully at ambient temperatures. •Cooling loads of 4.5 kW were reached in the chilled water side

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

    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

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

    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.

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

    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

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

    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...

  9. Study liquid length penetration results obtained with a direct acting piezo electric injector

    Payri, Raul; Gimeno, Jaime; Bardi, Michele; Plazas, Alejandro H.

    2013-01-01

    Highlights: ► A direct acting injector capable of controlling needle lift has been used to determine liquid phase penetration. ► The influence of injection pressure, chamber density and chamber temperature have been measured. ► When needle lift is reduced the stabilized liquid length is shortened. ► The relationship between needle lift and liquid length makes needle lift as a new way to control the injection event. - Abstract: A state of the art prototype common rail injector featuring direct control of the needle by means of a piezo stack (direct acting) has been tested. Liquid phase penetration of the sprays in diesel engine-like conditions has been studied via imaging technique in a novel continuous flow test chamber that allows an accurate control on a wide range of thermodynamic conditions (up to 1000 K and 15 MPa). This state of the art injector fitted with a 7-hole nozzle, allows a fully flexible control on the nozzle needle movement, enabling various fuel injection rate typologies. The temporal evolution of the seven sprays has been studied recording movies of the injection event in evaporative conditions via Mie scattering imaging technique and using a high speed camera. The results showed a strong influence of needle position on the stabilized liquid length while the effect of the injection pressure is negligible: the decrease of the needle lift causes a pressure drop in the needle seat and thus a reduction in the effective pressure upstream of the orifices (in the nozzle sac). According to known literature the stabilized liquid-length depends mainly on effective diameter, spray cone-angle and fuel/air properties and does not depend on fuel velocity at the orifice outlet. Therefore, due to small change in the spray cone-angle, higher injection pressures give slightly lower liquid length. However, partial needle lifts has an opposite effect: when needle is partially lifted a dramatic increase of the spray cone-angle and a consequent reduction of

  10. First results from the NEWS-G direct dark matter search experiment at the LSM

    Arnaud, Q.; Asner, D.; Bard, J.-P.; Brossard, A.; Cai, B.; Chapellier, M.; Clark, M.; Corcoran, E. C.; Dandl, T.; Dastgheibi-Fard, A.; Dering, K.; Di Stefano, P.; Durnford, D.; Gerbier, G.; Giomataris, I.; Gorel, P.; Gros, M.; Guillaudin, O.; Hoppe, E. W.; Kamaha, A.; Katsioulas, I.; Kelly, D. G.; Martin, R. D.; McDonald, J.; Muraz, J.-F.; Mols, J.-P.; Navick, X.-F.; Papaevangelou, T.; Piquemal, F.; Roth, S.; Santos, D.; Savvidis, I.; Ulrich, A.; Vazquez de Sola Fernandez, F.; Zampaolo, M.

    2018-01-01

    New Experiments With Spheres-Gas (NEWS-G) is a direct dark matter detection experiment using Spherical Proportional Counters (SPCs) with light noble gases to search for low-mass Weakly Interacting Massive Particles (WIMPs). We report the results from the first physics run taken at the Laboratoire Souterrain de Modane (LSM) with SEDINE, a 60 cm diameter prototype SPC operated with a mixture of Ne + CH4 (0.7%) at 3.1 bars for a total exposure of 9.6 kg · days. New constraints are set on the spin-independent WIMP-nucleon scattering cross-section in the sub-GeV/c2 mass region. We exclude cross-sections above 4.4 ×10-37cm2 at 90% confidence level (C.L.) for a 0.5 GeV/c2 WIMP. The competitive results obtained with SEDINE are promising for the next phase of the NEWS-G experiment: a 140 cm diameter SPC to be installed at SNOLAB by summer 2018.

  11. Sequence assembly

    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....

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

    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.

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

    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.

  14. Reporting results from whole-genome and whole-exome sequencing in clinical practice: a proposal for Canada?

    Zawati, Ma'n H; Parry, David; Thorogood, Adrian; Nguyen, Minh Thu; Boycott, Kym M; Rosenblatt, David; Knoppers, Bartha Maria

    2014-01-01

    This article proposes recommendations for the use of whole-genome and whole-exome (WGS/WES) sequencing in clinical practice, endorsed by the board of directors of the Canadian College of Medical Geneticists. The publication of statements and recommendations by several international and national organisations on clinical WGS/WES has prompted a need for Canadian-specific guidance. A multi-disciplinary group consisting of lawyers, ethicists, genetic researchers, and clinical geneticists was assembled to review existing guidelines on WGS/WES and identify provisions relevant to the Canadian context. Definitions were provided to orient the recommendations and to minimize confusion with other recommendations. Recommendations include the following: WGS/WES should be used in a judicious and cost-efficient manner; WGS/WES should be used to answer a clinical question; and physicians need to explain to adult patients the nature of the results that could arise, so as to allow them to make informed choices over whether to take the test and which results they wish to receive. Recommendations are also provided for WGS/WES in the pediatric context, and for when results implicate patients' family members. These recommendations are only a proposal to be developed into comprehensive Canadian-based guidelines. They aim to promote discussion about the reporting of WGS/WES results, and to encourage the ethical implementation of these new technologies in the clinical setting.

  15. Three-year results after directional atherectomy of calcified stenotic lesions of the superficial femoral artery.

    Minko, P; Buecker, A; Jaeger, S; Katoh, M

    2014-10-01

    To investigate the 3-year outcome of patients with peripheral arterial disease (PAD) and heavily calcified stenotic lesions of the superficial femoral artery after directional atherectomy. Fifty-three patients (mean age 67 ± 10 years; 18 females, 35 males, TASC B and C, mean lesion length 7.9 ± 3.5 cm) with PAD (Rutherford 2-6) were enrolled into this prospective monocentric study. In total, 59 calcified lesions of the superficial femoral artery were treated with the Silverhawk atherectomy device (Covidien, Plymouth, MN, USA). Patients were followed-up for 36 months with a 6-month interval to perform clinical re-evaluation, including measurement of maximum walking distance and ankle-brachial index (ABI) as well as duplex-sonography. The primary success rate of the procedure was 92 %. In five cases (8 %), additional balloon-PTA and/or stent-PTA was necessary. Procedure-related embolization occurred in seven cases (12 %), which were all successfully treated by aspiration. The primary patency rate after 3 years was 55 %. Median Rutherford score decreased significantly from 5 to 0 after 36 months (p atherectomy was successfully applied to decrease the plaque burden. Results after 3 years showed a significant decrease of Rutherford score with persistent improvement of ABI and reasonable patency rate.

  16. Arctic transitions in the Land - Atmosphere System (ATLAS): Background, objectives, results, and future directions

    McGuire, A.D.; Sturm, M.; Chapin, F. S.

    2003-01-01

    This paper briefly reviews the background, objectives, and results of the Arctic Transitions in the Land-Atmosphere System (ATLAS) Project to date and provides thoughts on future directions. The key goal of the ATLAS Project is to improve understanding of controls over spatial and temporal variability of terrestrial processes in the Arctic that have potential consequences for the climate system, i.e., processes that affect the exchange of water and energy with the atmosphere, the exchange of radiatively active gases with the atmosphere, and the delivery of freshwater to the Arctic Ocean. Three important conclusions have emerged from research associated with the ATLAS Project. First, associated with the observation that the Alaskan Arctic has warmed significantly in the last 30 years, permafrost is warming, shrubs are expanding, and there has been a temporary release of carbon dioxide from tundra soils. Second, the winter is a more important period of biological activity than previously appreciated. Biotic processes, including shrub expansion and decomposition, affect snow structure and accumulation and affect the annual carbon budget of tundra ecosystems. Third, observed vegetation changes can have a significant positive feedback to regional warming. These vegetation effects are, however, less strong than those exerted by land-ocean heating contrasts and the topographic constraints on air mass movements. The papers of this special section provide additional insights related to these conclusions and to the overall goal of ATLAS.

  17. BIPM direct on-site Josephson voltage standard comparisons: 20 years of results

    Solve, Stephane; Stock, Michael

    2012-01-01

    The discovery of the Josephson effect has for the first time given national metrology institutes (NMIs) the possibility of maintaining voltage references which are stable in time. In addition, the introduction in 1990 of a conventional value for the Josephson constant, K J-90 , has greatly improved world-wide consistency among representations of the volt. For 20 years, the Bureau International des Poids et Mesures (BIPM) has conducted an ongoing, direct, on-site key comparison of Josephson voltage standards among NMIs under the denominations BIPM.EM-K10.a (1 V) and BIPM.EM-K10.b (10 V) in the framework of the mutual recognition arrangement (CIPM MRA). The results of 41 comparisons illustrate the consistency among primary voltage standards and have demonstrated that a relative total uncertainty of a few parts in 10 10 is achievable if a few precautions are taken with regard to the measurement set-up. Of particular importance are the grounding, efficient filters and high insulation resistance of the measurement leads, and clean microwave distribution along the propagation line to the Josephson array. This paper reviews the comparison scheme and technical issues that need to be taken into account to achieve a relative uncertainty at the level of a few parts in 10 10 or even a few parts in 10 11 in the best cases. (paper)

  18. Test results of pongamia pinnata methyl esters with direct injection diesel engine

    Bannikov, MG.; Chattha, J.A.; Khan, A.F.

    2011-01-01

    Pongamia Pinnata oil is considered as a potential source of biodiesel production in Pakistan. When selecting source for commercial production of biodiesel several criteria are used. One of them is that biodiesel or biodiesel/diesel fuel blends must provide satisfactory performance and emissions of the diesel engine without or with a little engine modification. In this research performance and emissions characteristics of a direct injection diesel engine running on Pongamia Pinnata methyl esters were discussed. Discussion was supported by an analysis of combustion characteristics derived from in-cylinder pressure data. Engine running on a neat biodiesel showed higher brake specific fuel consumption and lower brake fuel conversion efficiency at all loads, whereas emissions were improved except of carbon monoxide emission at high loads. Decrease in brake efficiency and reduction of nitrogen oxides emissions were attributed solely to the change in the rate of heat release. Deposits on fuel infector nozzle were observed when engine was running on the neat biodiesel. Based on test results conclusion was made that Pongamia biodiesel/diesel fuel blends can effectively be used as a diesel oil substitute. (author)

  19. Experiences of disability consumer-directed care users in Australia: results from a longitudinal qualitative study.

    Ottmann, Goetz; Laragy, Carmel; Haddon, Michelle

    2009-09-01

    The rapidly growing body of literature suggests that Consumer-directed Care (CDC) has the potential to empower consumers and improve the flexibility and quality of care. However, reports highlighting quality and risk concerns associated with CDC focusing on a longer time frame have been few. This paper presents the findings from a qualitative longitudinal evaluation of an Australian CDC programme. Focusing on the period between 2003 and 2008, it reports on the experiences of 12 families caring for a dependent family member. It is based on two external evaluations completed 6 and 36 months after enrollment, and one internal evaluation completed 48 months after enrollment. The findings were triangulated with internal memos, reports and minutes of meetings, as well as with the theoretical literature. The study demonstrates that CDC harbours considerable benefits for people with disabilities and their carers. However, the study also suggests that, over time, carers may experience an increased sense of isolation and lack of support as a result of their involvement in the CDC programme. The paper argues that the development of safeguards addressing these weaknesses is crucial for the sustainability of CDC programmes in contexts where risk cannot be simply transferred onto consumers.

  20. Experimental results of direct containment heating by high-pressure melt ejection into the Surtsey vessel: The DCH-3 and DCH-4 tests

    Allen, M.D.; Pilch, M.; Brockmann, J.E.; Tarbell, W.W.; Nichols, R.T.; Sweet, D.W.

    1991-08-01

    Two experiments, DCH-3 and DCH-4, were performed at the Surtsey test facility to investigate phenomena associated with a high-pressure melt ejection (HPME) reactor accident sequence resulting in direct containment heating (DCH). These experiments were performed using the same experimental apparatus with identical initial conditions, except that the Surtsey test vessel contained air in DCH-3 and argon in DCH-4. Inerting the vessel with argon eliminated chemical reactions between metallic debris and oxygen. Thus, a comparison of the pressure response in DCH-3 and DCH-4 gave an indication of the DCH contribution due to metal/oxygen reactions. 44 refs., 110 figs., 43 tabs

  1. Experimental results of direct containment heating by high-pressure melt ejection into the Surtsey vessel: The DCH-3 and DCH-4 tests

    Allen, M.D.; Pilch, M.; Brockmann, J.E.; Tarbell, W.W. (Sandia National Labs., Albuquerque, NM (United States)); Nichols, R.T. (Ktech Corp., Albuquerque, NM (United States)); Sweet, D.W. (AEA Technology, Winfrith (United Kingdom))

    1991-08-01

    Two experiments, DCH-3 and DCH-4, were performed at the Surtsey test facility to investigate phenomena associated with a high-pressure melt ejection (HPME) reactor accident sequence resulting in direct containment heating (DCH). These experiments were performed using the same experimental apparatus with identical initial conditions, except that the Surtsey test vessel contained air in DCH-3 and argon in DCH-4. Inerting the vessel with argon eliminated chemical reactions between metallic debris and oxygen. Thus, a comparison of the pressure response in DCH-3 and DCH-4 gave an indication of the DCH contribution due to metal/oxygen reactions. 44 refs., 110 figs., 43 tabs.

  2. 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

    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.

  3. 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.

    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.

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

    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

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

    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.

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

    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.

  7. Revealing the sequence and resulting cellular morphology of receptor-ligand interactions during Plasmodium falciparum invasion of erythrocytes.

    Greta E Weiss

    2015-02-01

    Full Text Available During blood stage Plasmodium falciparum infection, merozoites invade uninfected erythrocytes via a complex, multistep process involving a series of distinct receptor-ligand binding events. Understanding each element in this process increases the potential to block the parasite's life cycle via drugs or vaccines. To investigate specific receptor-ligand interactions, they were systematically blocked using a combination of genetic deletion, enzymatic receptor cleavage and inhibition of binding via antibodies, peptides and small molecules, and the resulting temporal changes in invasion and morphological effects on erythrocytes were filmed using live cell imaging. Analysis of the videos have shown receptor-ligand interactions occur in the following sequence with the following cellular morphologies; 1 an early heparin-blockable interaction which weakly deforms the erythrocyte, 2 EBA and PfRh ligands which strongly deform the erythrocyte, a process dependant on the merozoite's actin-myosin motor, 3 a PfRh5-basigin binding step which results in a pore or opening between parasite and host through which it appears small molecules and possibly invasion components can flow and 4 an AMA1-RON2 interaction that mediates tight junction formation, which acts as an anchor point for internalization. In addition to enhancing general knowledge of apicomplexan biology, this work provides a rational basis to combine sequentially acting merozoite vaccine candidates in a single multi-receptor-blocking vaccine.

  8. [Advance Directives in Family Practices: Results of a Survey of GP Patients on their Care Situation].

    Schnakenberg, Rieke; Just, Johannes; Thiessen, Vitali; Puth, Marie-Therese; Bleckwenn, Markus; Weckbecker, Klaus

    2017-07-26

    Background Advance directives (AD) are an important tool for documentation of patients' wishes and are therefore recommended to the elderly as well as patients with chronic diseases. However, there is no standardized procedure in Germany and no guideline for counseling patients who wish to write an AD with or without health care proxy. The aim of this study was to evaluate the care situation concerning the ADs and the role of the primary care physician in drafting the document Method We conducted semi-structured interviews with patients in primary care in North Rhine-Westphalia using a cross-sectional study design. Result Most of the 154 patients who were interviewed (average age: 58 years; 52% female) suffered from chronic diseases (79%), and about one-third (32%) already had an AD. Fear of "loss of autonomy" was the main reason for preparing an AD. Patients without AD were generally not opposed to the concept and named procrastination (43%) as the main reason for not having prepared one. The chance for preparing an AD increased by the factor 1.08 per life-year (Odds ratio (OR): 1.08; CI: 1.04-1.11). Patients with AD mostly got advice via the internet (22%), their primary care physicians (12%) and relatives (12%). Most patients were satisfied with their AD. Conclusion The majority of primary care patients do not make use of ADs. The primary care physicians play an important role in counseling and should motivate patients to complete ADs. Here, the establishment of quality standards would be desirable in the future. © Georg Thieme Verlag KG Stuttgart · New York.

  9. Phytostabilization of mine tailings using compost-assisted direct planting: Translating greenhouse results to the field.

    Gil-Loaiza, Juliana; White, Scott A; Root, Robert A; Solís-Dominguez, Fernando A; Hammond, Corin M; Chorover, Jon; Maier, Raina M

    2016-09-15

    Standard practice in reclamation of mine tailings is the emplacement of a 15 to 90cm soil/gravel/rock cap which is then hydro-seeded. In this study we investigate compost-assisted direct planting phytostabilization technology as an alternative to standard cap and plant practices. In phytostabilization the goal is to establish a vegetative cap using native plants that stabilize metals in the root zone with little to no shoot accumulation. The study site is a barren 62-hectare tailings pile characterized by extremely acidic pH as well as lead, arsenic, and zinc each exceeding 2000mgkg(-1). The study objective is to evaluate whether successful greenhouse phytostabilization results are scalable to the field. In May 2010, a 0.27ha study area was established on the Iron King Mine and Humboldt Smelter Superfund (IKMHSS) site with six irrigated treatments; tailings amended with 10, 15, or 20% (w/w) compost seeded with a mix of native plants (buffalo grass, arizona fescue, quailbush, mountain mahogany, mesquite, and catclaw acacia) and controls including composted (15 and 20%) unseeded treatments and an uncomposted unseeded treatment. Canopy cover ranging from 21 to 61% developed after 41 months in the compost-amended planted treatments, a canopy cover similar to that found in the surrounding region. No plants grew on unamended tailings. Neutrophilic heterotrophic bacterial counts were 1.5 to 4 orders of magnitude higher after 41months in planted versus unamended control plots. Shoot tissue accumulation of various metal(loids) was at or below Domestic Animal Toxicity Limits, with some plant specific exceptions in treatments receiving less compost. Parameters including % canopy cover, neutrophilic heterotrophic bacteria counts, and shoot uptake of metal(loids) are promising criteria to use in evaluating reclamation success. In summary, compost amendment and seeding, guided by preliminary greenhouse studies, allowed plant establishment and sustained growth over 4years

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

    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.

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

    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

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

    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.

  13. Palaeoenvironment and geoconservation of mammoths from the Nosak loess-palaeosol sequence (Drmno, northeastern Serbia): Initial results and perspectives

    Markovic, Slobodan B.; Korac, Miomir; Mrdic, Nemanja

    2014-01-01

    A Quaternary site at Drmno (comprising of Middle and Late Pleistocene loessepalaeosol sequences) near Kostolac, northeast Serbia, attracted attention from the general public and scientists, when several steppe mammoth and other mammal skeletons from Middle Pleistocene fluvial deposits were discov...

  14. EDELWEISS-II, direct Dark Matter search experiment: first data analysis and results

    Scorza, Silvia

    2009-01-01

    relies in the measurement of nuclear recoils that produce measurable effects in the crystal such ionization and heat. My PhD thesis is organized as follows. The first chapter aims to provide an introduction to the theoretical framework and the scientific motivation for the following work. The nature of DM has been one of the most challenging topics in contemporary physics since the first evidences of its existence had been found in the 1930's. Cosmologists and astrophysicists on one side, together with particle theorists on the other have put a lot of effort into this field: I will briefly account for their achievements and for the experimental strategies which can be set in this scenario. Since this thesis work was carried out within the EDELWEISS-II direct dark matter experiment, I will focus the next chapter on this topic, describing the main features. The second chapter is related to the set-up of the EDELWEISS-II, the current stage of the EDELWEISS experiment necessary after a first phase that achieved the best upper limit on the WIMP elastic scattering on nucleon as a function of WIMP mass in 2004. The set-up was conceived to reduce radioactive background observed in the first experiment phase. Thus, describing the starting point for this second stage, I will present detectors involved in, with a peculiar regard to the Ge-NTD type, the same implied in EDELWEISS-I, on which I have focused my thesis work. In the third chapter the performed Ge-NTD analysis chain is presented. Starting with the signal processing of the recorded data, I will enter in the essential analysis steps from calibration signals passing through measurements of thresholds and resolutions in order to predict nuclear and electronic recoil band and definition of fiducial zone to conclude determining a selection for likely WIMP candidate. These suggestions are applied in the fourth chapter, which presents the analysis and the results of the 8. cool down that takes places from November 2007 to March

  15. Description and pilot results from a novel method for evaluating return of incidental findings from next-generation sequencing technologies.

    Goddard, Katrina A B; Whitlock, Evelyn P; Berg, Jonathan S; Williams, Marc S; Webber, Elizabeth M; Webster, Jennifer A; Lin, Jennifer S; Schrader, Kasmintan A; Campos-Outcalt, Doug; Offit, Kenneth; Feigelson, Heather Spencer; Hollombe, Celine

    2013-09-01

    The aim of this study was to develop, operationalize, and pilot test a transparent, reproducible, and evidence-informed method to determine when to report incidental findings from next-generation sequencing technologies. Using evidence-based principles, we proposed a three-stage process. Stage I "rules out" incidental findings below a minimal threshold of evidence and is evaluated using inter-rater agreement and comparison with an expert-based approach. Stage II documents criteria for clinical actionability using a standardized approach to allow experts to consistently consider and recommend whether results should be routinely reported (stage III). We used expert opinion to determine the face validity of stages II and III using three case studies. We evaluated the time and effort for stages I and II. For stage I, we assessed 99 conditions and found high inter-rater agreement (89%), and strong agreement with a separate expert-based method. Case studies for familial adenomatous polyposis, hereditary hemochromatosis, and α1-antitrypsin deficiency were all recommended for routine reporting as incidental findings. The method requires definition of clinically actionable incidental findings and provide documentation and pilot testing of a feasible method that is scalable to the whole genome.

  16. Recent results from the first polar direct drive plastic capsule implosions on NIF

    Schmitt, Mark J.

    2012-10-01

    Polar direct drive (PDD) offers a simplified platform for conducting strongly driven implosions on NIF to investigate mix, hydro-burn and ignition-relevant physics. Its successful use necessitates a firm understanding and predictive capability of its implosion characteristics including hydro performance, symmetry and yield. To assess this capability, the first two PDD implosions of deuterium filled CH capsules were recently conducted at NIF. The P2 Legendre mode symmetry seen in these implosions agreed with pre-shot predictions even though the 700kJ drive energy produced intensities that far exceeded thresholds for both Raman and Brillouin stimulated scattering. These shots were also the first to employ image backlighting driven by two laser quads. Preliminary results indicate that the yield from the uncoated 2.25 mm diameter, 42 μm thick, CH shells was reduced by about a factor of two owing to as-shot laser drive asymmetries. Similarly, a small (sim50 μm) centroid offset between the upper and lower shell hemispheres seen in the first shot appears to be indicative of the laser quad energies. Overall, the implosion trajectories agreed with pre-shot predictions of bangtime. The second shot incorporated an 80 ?m wide,10 ?m deep depression encircling the equator of the capsule. This engineered feature was imposed to test our capability to predict the effect of high-mode features on yield and mix. A predicted yield reduction factor of 3 was not observed.[4pt] In collaboration with P. A. Bradley, J. A. Cobble, P. Hakel, S. C. Hsu, N. S. Krasheninnikova, G. A. Kyrala, G. R. Magelssen, T. J. Murphy, K. A. Obrey, R. C. Shah, I. L. Tregillis and F. J. Wysocki of Los Alamos National Laboratory; M. Marinak, R. Wallace, T. Parham, M. Cowan, S. Glenn, R. Benedetti and the NIF Operations Team of Lawrence Livermore National Laboratory; R. S. Craxton and P. W. McKenty of the Univ. Rochester; P. Fitzsimmons and A. Nikroo of General Atomics; H. Rinderknecht, M. Rosenberg, and M. G

  17. Characterization of the Darwin direct implicit particle-in-cell method and resulting guidelines for operation

    Gibbons, M.R.; Hewett, D.W.

    1997-01-01

    We investigate the linear dispersion and other properties of the Darwin Direct Implicit Particle-in-cell (DADIPIC) method in order to deduce guidelines for its use in the simulation of long time-scale, kinetic phenomena in plasmas. The Darwin part of this algorithm eliminates the Courant constraint for light propagation across a grid cell in a time step and divides the field solution into several elliptic equations. The direct implicit method is only applied to the electrostatic field relieving the need to resolve plasma oscillations. Linear theory and simulations verifying the theory are used to generate the desired guidelines as well as show the utility of DADIPIC for a wide range of low frequency, electromagnetic phenomena. We find that separation of the fields has made the task of predicting algorithm behavior easier and produced a robust method without restrictive constraints. 20 refs., 11 figs., 3 tabs

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

    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.

  19. The Research Results of the Individual Competences Influence on Direct Sales

    Barbara A. Sypniewska

    2009-10-01

    Full Text Available The article presents the influence of individual competences on the effects of sales consultants efforts working at few well-known cosmetic companies specializing in direct sales multi-level marketing. The research proves dependence between individual competences and the level of effects. The competences profile derived from the analyses, characteristic for each study group, stresses the benefits and practical implications of this research.

  20. About the constructive and functional particularities of spark ignition engines with gasoline direct injection: experimental results

    Niculae, M.; Ivan, F.; Neacsu, D.

    2017-08-01

    The paper aims to analyze and compare the environmental performances between a gasoline direct engine and a multi-point injection engine. There are analyzed the stages of emission formation during the New European Driving Cycle. The paper points out the dynamic, economic and environmental performances of spark ignition engines equipped with a GDI systems. Reason why, we believe the widespread implementation of this technology is today an immediate need.

  1. Community-directed interventions for priority health problems in Africa: results of a multicountry study.

    2010-07-01

    To determine the extent to which the community-directed approach used in onchocerciasis control in Africa could effectively and efficiently provide integrated delivery of other health interventions. A three-year experimental study was undertaken in 35 health districts from 2005 to 2007 in seven research sites in Cameroon, Nigeria and Uganda. Four trial districts and one comparison district were randomly selected in each site. All districts had established ivermectin treatment programmes, and in the trial districts four other established interventions - vitamin A supplementation, use of insecticide-treated nets, home management of malaria and short-course, directly-observed treatment for tuberculosis patients - were progressively incorporated into a community-directed intervention (CDI) process. At the end of each of the three study years, we performed quantitative evaluations of intervention coverage and provider costs, as well as qualitative assessments of the CDI process. With the CDI strategy, significantly higher coverage was achieved than with other delivery approaches for all interventions except for short-course, directly-observed treatment. The coverage of malaria interventions more than doubled. The district-level costs of delivering all five interventions were lower in the CDI districts, but no cost difference was found at the first-line health facility level. Process evaluation showed that: (i) participatory processes were important; (ii) recurrent problems with the supply of intervention materials were a major constraint to implementation; (iii) the communities and community implementers were deeply committed to the CDI process; (iv) community implementers were more motivated by intangible incentives than by external financial incentives. The CDI strategy, which builds upon the core principles of primary health care, is an effective and efficient model for integrated delivery of appropriate health interventions at the community level in Africa.

  2. Androgen radioimmunoassay in the ram: results of direct plasma testosterone and dehydroepiandrosterone measurement and physiological evaluation

    Garnier, D.-H.; Cotta, Y.; Terqui, M.

    1978-01-01

    Different radioimmunoassays of testosterone (T) dehydroepiandrosterone (DHA) and 5 α-dihydrotestosterone (5 α-DHT) were investigated for ram plasma. Specificity of the antisera, lack of noticeable binding in plasma, very low levels of other androgens allow direct plasma RIA for DHA and T by the double antibody technique. The levels obtained by this simplified method are in agreement with those found after extraction alone, after extraction and celite chromatography and after quantification with a completely different technique such as gas chromatography. The within assay variabilities for T and DHA were 4.7 p. 100 and 4.6 p. 100 respectively but vary with the level of steroid in plasma. The inter assay variabilities of T were 9.5 p. 100 and 3.2 p. 100 for 1.5 and 11.6 ng/ml of plasma respectively. The antiserum for 5 α-DHT have a specificity such that, even after celite chromatography some androgens (5 β-DHT) may interfere. However determinations of 5 α/5 β-DHT amounts are possible. The physiological validations of direct plasma T and DHA RIA were studied in various conditions. The DHA plasma variations are similar to those of T in Ram from birth to puberty, but the levels are lower. DHA plasma levels show a seasonal variation as does testosterone. Variations within 24 hrs of these two androgens were in synchrony. The direct plasma T and DHA assays are useful and inexpensive tools to characterize ram testicular function

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

    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.

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

    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.

  5. Recent results on fusion and direct reactions with weakly bound stable nuclei

    Shrivastava, A.

    2011-01-01

    Recent measurements of fusion and direct reactions in case of weakly bound stable nuclei at extreme sub-barrier energies using a sensitive off beam technique are presented. First section deals with deep sub-barrier fusion cross-section measurement for 67 Li + 198 Pt followed by the study of fragment capture reaction of 7 Li + 198 Pt. Deviation in the slope of the fusion excitation function, as observed in case of medium heavy systems, is absent in the present asymmetric systems at these low energies. This study shows the absence of fusion hindrance, suggesting modifications in models that explain deep sub-barrier fusion data to incorporate weakly bound asymmetric systems

  6. Differing results of direct and indirect solid phase radioimmunoassay for HBsAg in acute hepatitis

    Strohm, W.D.; Legler, K.; Gerlich, W.; Stamm, B.; Zimmer, S.; Biotest-Serum-Institut G.m.b.H., Frankfurt am Main; Goettingen Univ.

    1978-01-01

    In 54 patients suffering from active viral hepatitis the indirect solid phase radioimmunoassay (ind-SPRIA) for HBsAg was positive in 9 cases the direct solid phase radioimmunoassay (d-SPRIA) being negative. In 2 further cases ind-SPRIA was positive during several weeks but d-SPRIA only once. AntiHBc could be detected in 9 of these patients. In 7 patients the usual decrease of the transaminase activity was followed by a second elavation with prolongation of the disease. The unknown factor detected by ind-SPRIA suggests a special of acute hepatitis. (orig.) [de

  7. Mineral Trioxide Aggregate (MTA direct pulp capping: 10 years clinical results

    Lucio Daniele

    2017-06-01

    After 10-years follow-up period, 6 out of 80 teeth required an endodontic treatment, we did not find an increase of pulp calcifications, root resorptions, endodontic lesions. All teeth still alive have responded positively to the cold-temperature test. The three lesions had disappeared at the last X-ray control. All four symptomatic teeth preserved their pulp vitality. The successful treatment rate was 92.5%. Direct pulp capping with MTA can be considered an effective treatment of exposure due to tooth decay and can be considered a valid treatment option for teeth with a diagnosis of not-severe reversible pulpitis.

  8. Differing results of direct and indirect solid phase radioimmunoassay for HBsAg in acute hepatitis

    Strohm, W D; Legler, K; Gerlich, W; Stamm, B; Zimmer, S [Frankfurt Univ. (Germany, F.R.). Abt. fuer Gastroenterologie; Biotest-Serum-Institut G.m.b.H., Frankfurt am Main (Germany, F.R.); Goettingen Univ. (Germany, F.R.). Hygiene-Institut)

    1978-09-01

    In 54 patients suffering from active viral hepatitis the indirect solid phase radioimmunoassay (ind-SPRIA) for HBsAg was positive in 9 cases the direct solid phase radioimmunoassay (d-SPRIA) being negative. In 2 further cases ind-SPRIA was positive during several weeks but d-SPRIA only once. AntiHBc could be detected in 9 of these patients. In 7 patients the usual decrease of the transaminase activity was followed by a second elavation with prolongation of the disease. The unknown factor detected by ind-SPRIA suggests a special of acute hepatitis.

  9. Phytostabilization of Mine Tailings Using Compost-Assisted Direct Planting: Translating Greenhouse Results to the Field

    Gil-Loaiza, Juliana; White, Scott A.; Root, Robert A.; Solís-Dominguez, Fernando A.; Hammond, Corin M.; Chorover, Jon; Maier, Raina M.

    2016-01-01

    Standard practice in reclamation of mine tailings is the emplacement of a 15 to 90 cm soil/gravel/rock cap which is then hydro-seeded. In this study we investigate compost-assisted direct planting phytostabilization technology as an alternative to standard cap and plant practices. In phytostabilization the goal is to establish a vegetative cap using native plants that stabilize metals in the root zone with little to no shoot accumulation. The study site is a barren 62-hectare tailings pile ch...

  10. Results of a directed graph and fault tree assessment of a MC and A system

    Gilman, F.M.; Lambert, H.E.; Lim, J.J.

    1978-01-01

    An assessment of the effectiveness of the Material Control and Accounting System (MC and A) in a hypothetical nuclear facility, the TEST BED is presented. The key in assessing the TEST BED is the generation of adversary event sets. The adversary event sets are generated and analyzed by a directed graph (digraph) and fault tree procedure. Although the TEST BED is a system hardened against SNM theft, the assessment of the TEST BED finds several major weaknesses, and also indicates possible modifications to correct these weaknesses

  11. Assessing the aerosol direct and first indirect effects using ACM/GCM simulation results

    Huang, H.; Gu, Y.; Xue, Y.; Lu, C. H.

    2016-12-01

    Atmospheric aerosols have been found to play an important role in global climate change but there are still large uncertainty in evaluating its role in the climate system. The aerosols generally affect global and regional climate through the scattering and the absorption of solar radiation (direct effect) and through their influences on cloud particle, number and sizes (first indirect effect). The indirect effect will further affects cloud water content, cloud top albedo and surface precipitations. In this study, we investigate the global climatic effect of aerosols using a coupled NCEP Global Forecast System (GFS) and a land surface model (SSiB2) The OPAC (Optical Properties of Aerosols and Clouds) database is used for aerosol effect. The OPAC data provides the optical properties (i.e., the extinction, scattering and absorption coefficient, single-scattering albedo, asymmetry factor and phase function) of ten types of aerosols under various relative humidity conditions for investigating the global direct and first indirect effects of dust aerosols. For indirect forcings due to liquid water, we follow the approach presented by Jiang et al (2011), in which a parameterization of cloud effective radius was calculated to describe its variance with convective strength and aerosol concentration. Since the oceans also play an important role on aerosol climatic effect, we also design a set of simulations using a coupled atmosphere/ocean model (CFS) to evaluate the sensitivity of aerosol effect with two-way atmosphere-ocean interactions.

  12. DCH-2: Results from the second experiment performed in the Surtsey Direct Heating Test Facility

    Tarbell, W.W.; Nichols, R.T.; Brockmann, J.E.; Ross, J.W.; Oliver, M.S.; Lucero, D.A.

    1988-01-01

    This test involved 80 kg of molten core debris simulant ejected under pressure into a 1:10 linear scale model of a reactor cavity. The apparatus was placed in the Surtsey Direct Heating Test Facility to allow direct measurement of the temperature and pressure rise of the contained atmosphere. The molten material was ejected from the cavity as a dense cloud of particles and gas. The dispersed debris caused a rapid pressurization of the 103-m 3 atmosphere. Peak pressures ranged from 0.22 to 0.31 MPa above the ambient level. Peak temperatures were from 759 0 C to 1335 0 C, with the highest values recorded near the top of the chamber. Much of the debris (∼70%) was found adhered to the top and sides of the steel chamber. The pattern of the retained material suggested that the debris field propagated around the chamber following the contour of the vessel. Aerosol measurements indicated that ∼1% to ∼6.6% of the ejected mass was in the size range less than 10μm aerodynamic diameter. 8 refs., 28 figs., 6 tabs

  13. Refining the Results of a Classical SELEX Experiment by Expanding the Sequence Data Set of an Aptamer Pool Selected for Protein A

    Regina Stoltenburg

    2018-02-01

    Full Text Available New, as yet undiscovered aptamers for Protein A were identified by applying next generation sequencing (NGS to a previously selected aptamer pool. This pool was obtained in a classical SELEX (Systematic Evolution of Ligands by EXponential enrichment experiment using the FluMag-SELEX procedure followed by cloning and Sanger sequencing. PA#2/8 was identified as the only Protein A-binding aptamer from the Sanger sequence pool, and was shown to be able to bind intact cells of Staphylococcus aureus. In this study, we show the extension of the SELEX results by re-sequencing of the same aptamer pool using a medium throughput NGS approach and data analysis. Both data pools were compared. They confirm the selection of a highly complex and heterogeneous oligonucleotide pool and show consistently a high content of orphans as well as a similar relative frequency of certain sequence groups. But in contrast to the Sanger data pool, the NGS pool was clearly dominated by one sequence group containing the known Protein A-binding aptamer PA#2/8 as the most frequent sequence in this group. In addition, we found two new sequence groups in the NGS pool represented by PA-C10 and PA-C8, respectively, which also have high specificity for Protein A. Comparative affinity studies reveal differences between the aptamers and confirm that PA#2/8 remains the most potent sequence within the selected aptamer pool reaching affinities in the low nanomolar range of KD = 20 ± 1 nM.

  14. Refining the Results of a Classical SELEX Experiment by Expanding the Sequence Data Set of an Aptamer Pool Selected for Protein A.

    Stoltenburg, Regina; Strehlitz, Beate

    2018-02-24

    New, as yet undiscovered aptamers for Protein A were identified by applying next generation sequencing (NGS) to a previously selected aptamer pool. This pool was obtained in a classical SELEX (Systematic Evolution of Ligands by EXponential enrichment) experiment using the FluMag-SELEX procedure followed by cloning and Sanger sequencing. PA#2/8 was identified as the only Protein A-binding aptamer from the Sanger sequence pool, and was shown to be able to bind intact cells of Staphylococcus aureus . In this study, we show the extension of the SELEX results by re-sequencing of the same aptamer pool using a medium throughput NGS approach and data analysis. Both data pools were compared. They confirm the selection of a highly complex and heterogeneous oligonucleotide pool and show consistently a high content of orphans as well as a similar relative frequency of certain sequence groups. But in contrast to the Sanger data pool, the NGS pool was clearly dominated by one sequence group containing the known Protein A-binding aptamer PA#2/8 as the most frequent sequence in this group. In addition, we found two new sequence groups in the NGS pool represented by PA-C10 and PA-C8, respectively, which also have high specificity for Protein A. Comparative affinity studies reveal differences between the aptamers and confirm that PA#2/8 remains the most potent sequence within the selected aptamer pool reaching affinities in the low nanomolar range of K D = 20 ± 1 nM.

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

    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.

  16. THE MIDDLE TO UPPER PALEOLITHIC SEQUENCE OF BURAN-KAYA III (CRIMEA, UKRAINE) : NEW STRATIGRAPHIC, PALEOENVIRONMENTAL, AND CHRONOLOGICAL RESULTS

    Pean, Stephane; Puaud, Simon; Crepin, Laurent; Prat, Sandrine; Quiles, Anita; van der Plicht, Johannes; Valladas, Helene; Stuart, Anthony J.; Drucker, Dorothee G.; Patou-Mathis, Marylene; Lanoe, Francois; Yanevich, Aleksandr; Hatté, C.; Jull, A.J.T.

    2013-01-01

    Buran-Kaya III is a rockshelter located in Crimea (Ukraine). It provides an exceptional stratigraphic sequence extending from the Middle Paleolithic to the Neolithic. Nine Paleolithic layers have been attributed to the Streletskaya or eastern Szeletian, Micoquian, Aurignacian, Gravettian, and

  17. Results of Investigations of Failures of Geothermal Direct Use Well Pumps

    Culver, G.

    1994-12-01

    Failures of 13 geothermal direct-use well pumps were investigated and information obtained about an additional 5 pumps that have been in service up to 23 years, but have not failed. Pumps with extra long lateral and variable-speed drives had the highest correlation with reduced time in service. There appears to be at least circumstantial evidence that recirculation may be a cause of reduced pump life. If recirculation is a cause of pump failures, pump specifiers will need to be more aware of minimum flow conditions as well as maximum flow conditions when specifying pumps. Over-sizing pumps and the tendency to specify pumps with high flow and low Net Positive Suction Head (NPSH) could lead to increased problems with recirculation.

  18. Test Results from a Direct Drive Gas Reactor Simulator Coupled to a Brayton Power Conversion Unit

    Hervol, David S.; Briggs, Maxwell H.; Owen, Albert K.; Bragg-Sitton, Shannon M.; Godfroy, Thomas J.

    2010-01-01

    Component level testing of power conversion units proposed for use in fission surface power systems has typically been done using relatively simple electric heaters for thermal input. These heaters do not adequately represent the geometry or response of proposed reactors. As testing of fission surface power systems transitions from the component level to the system level it becomes necessary to more accurately replicate these reactors using reactor simulators. The Direct Drive Gas-Brayton Power Conversion Unit test activity at the NASA Glenn Research Center integrates a reactor simulator with an existing Brayton test rig. The response of the reactor simulator to a change in Brayton shaft speed is shown as well as the response of the Brayton to an insertion of reactivity, corresponding to a drum reconfiguration. The lessons learned from these tests can be used to improve the design of future reactor simulators which can be used in system level fission surface power tests.

  19. Direct measurement of nuclear cross-section of astrophysical interest: Results and perspectives

    Cavanna, Francesca; Prati, Paolo

    2018-03-01

    Stellar evolution and nucleosynthesis are interconnected by a wide network of nuclear reactions: the study of such connection is usually known as nuclear astrophysics. The main task of this discipline is the determination of nuclear cross-section and hence of the reaction rate in different scenarios, i.e. from the synthesis of a few very light isotopes just after the Big Bang to the heavy element production in the violent explosive end of massive stars. The experimental determination of reaction cross-section at the astrophysical relevant energies is extremely difficult, sometime impossible, due to the Coulomb repulsion between the interacting nuclei which turns out in cross-section values down to the fbar level. To overcome these obstacles, several experimental approaches have been developed and the adopted techniques can be roughly divided into two categories, i.e. direct and indirect methods. In this review paper, the general problem of nuclear astrophysics is introduced and discussed from the point of view of experimental approach. We focus on direct methods and in particular on the features of low-background experiments performed at underground laboratory facilities. The present knowledge of reactions involved in the Big Bang and stellar hydrogen-burning scenarios is discussed as well as the ongoing projects aiming to investigate mainly the helium- and carbon-burning phases. Worldwide, a new generation of experiment in the MeV range is in the design phase or at the very first steps and decisive progresses are expected to come in the next years.

  20. The Complex Outgassing of Comets and the Resulting Coma, a Direct Simulation Monte-Carlo Approach

    Fougere, Nicolas

    During its journey, when a comet gets within a few astronomical units of the Sun, solar heating liberates gases and dust from its icy nucleus forming a rarefied cometary atmosphere, the so-called coma. This tenuous atmosphere can expand to distances up to millions of kilometers representing orders of magnitude larger than the nucleus size. Most of the practical cases of coma studies involve the consideration of rarefied gas flows under non-LTE conditions where the hydrodynamics approach is not valid. Then, the use of kinetic methods is required to properly study the physics of the cometary coma. The Direct Simulation Monte-Carlo (DSMC) method is the method of choice to solve the Boltzmann equation, giving the opportunity to study the cometary atmosphere from the inner coma where collisions dominate and is in thermodynamic equilibrium to the outer coma where densities are lower and free flow conditions are verified. While previous studies of the coma used direct sublimation from the nucleus for spherically symmetric 1D models, or 2D models with a day/night asymmetry, recent observations of comets showed the existence of local small source areas such as jets, and extended sources via sublimating icy grains, that must be included into cometary models for a realistic representation of the physics of the coma. In this work, we present, for the first time, 1D, 2D, and 3D models that can take into account the full effects of conditions with more complex sources of gas with jets and/or icy grains. Moreover, an innovative work in a full 3D description of the cometary coma using a kinetic method with a realistic nucleus and outgassing is demonstrated. While most of the physical models used in this study had already been developed, they are included in one self-consistent coma model for the first time. The inclusion of complex cometary outgassing processes represents the state-of-the-art of cometary coma modeling. This provides invaluable information about the coma by

  1. Static multiplicities in heterogeneous azeotropic distillation sequences

    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...

  2. Evaluation of discrepancies between thermoluminescent dosimeter and direct-reading dosimeter results

    Shaw, K.R.

    1993-07-01

    Currently at Oak Ridge National Laboratory (ORNL), the responses of thermoluminescent dosimeters (TLDs) and direct-reading dosimeters (DRDs) are not officially compared or the discrepancies investigated. However, both may soon be required due to the new US Department of Energy (DOE) Radiological Control Manual. In the past, unofficial comparisons of the two dosimeters have led to discrepancies of up to 200%. This work was conducted to determine the reasons behind such discrepancies. For tests conducted with the TLDs, the reported dose was most often lower than the delivered dose, while DRDs most often responded higher than the delivered dose. Trends were identified in personnel DRD readings, and ft was concluded that more training and more control of the DRDs could improve their response. TLD responses have already begun to be improved; a new background subtraction method was implemented in April 1993, and a new dose algorithm is being considered. It was concluded that the DOE Radiological Control Manual requirements are reasonable for identifying discrepancies between dosimeter types, and more stringent administrative limits might even be considered

  3. SeqReporter: automating next-generation sequencing result interpretation and reporting workflow in a clinical laboratory.

    Roy, Somak; Durso, Mary Beth; Wald, Abigail; Nikiforov, Yuri E; Nikiforova, Marina N

    2014-01-01

    A wide repertoire of bioinformatics applications exist for next-generation sequencing data analysis; however, certain requirements of the clinical molecular laboratory limit their use: i) comprehensive report generation, ii) compatibility with existing laboratory information systems and computer operating system, iii) knowledgebase development, iv) quality management, and v) data security. SeqReporter is a web-based application developed using ASP.NET framework version 4.0. The client-side was designed using HTML5, CSS3, and Javascript. The server-side processing (VB.NET) relied on interaction with a customized SQL server 2008 R2 database. Overall, 104 cases (1062 variant calls) were analyzed by SeqReporter. Each variant call was classified into one of five report levels: i) known clinical significance, ii) uncertain clinical significance, iii) pending pathologists' review, iv) synonymous and deep intronic, and v) platform and panel-specific sequence errors. SeqReporter correctly annotated and classified 99.9% (859 of 860) of sequence variants, including 68.7% synonymous single-nucleotide variants, 28.3% nonsynonymous single-nucleotide variants, 1.7% insertions, and 1.3% deletions. One variant of potential clinical significance was re-classified after pathologist review. Laboratory information system-compatible clinical reports were generated automatically. SeqReporter also facilitated quality management activities. SeqReporter is an example of a customized and well-designed informatics solution to optimize and automate the downstream analysis of clinical next-generation sequencing data. We propose it as a model that may envisage the development of a comprehensive clinical informatics solution. Copyright © 2014 American Society for Investigative Pathology and the Association for Molecular Pathology. Published by Elsevier Inc. All rights reserved.

  4. DPS - a rapid method for genome sequencing of DNA-containing bacteriophages directly from a single plaque

    Kot, Witold Piotr; Vogensen, Finn Kvist; Sørensen, Søren Johannes

    2014-01-01

    Bacteriophages (phages) coexist with bacteria in all environments and influence microbial diversity, evolution and industrial production processes. As a result of this major impact of phages on microbes, tools that allow rapid characterization of phages are needed. Today, one of the most powerful...

  5. Recent results on searches for direct production of dark matter with the CMS detector

    CERN. Geneva

    2015-01-01

    With observed galactic excesses, tighter constraints from underground experiments, and a precise measurement of the relic density, our understanding of dark matter has greatly improved. As one of the few sources which can potentially produce dark matter, the LHC has the capability of complementing existing measurements. Recently, work by both ATLAS and CMS has been undertaken to unify the presentation of dark matter results, allowing for a robust comparison with other detector experiments. In this new light, we present two new results from CMS: the search for dark matter in Z + MET final state (Z decaying to leptons) and the search for dark matter in the monojet and hadronically decaying vector boson final state. Results are presented for simplified models, EFT and in terms of Higgs to invisible decays.

  6. Are Positive Illusions about Academic Competence always Adaptive, under All Circumstances: New Results and Future Directions

    Butler, Ruth

    2011-01-01

    The papers in this special issue provide a comprehensive examination of the prevalence and implications of positive biases in perceived academic competence at different ages in different countries. Main results showed that marked positive biases were rare, were associated with performance goals, were more adaptive than negative biases, but were…

  7. Lower extremity revascularization using directional atherectomy: 12-month prospective results of the DEFINITIVE LE study.

    McKinsey, James F; Zeller, Thomas; Rocha-Singh, Krishna J; Jaff, Michael R; Garcia, Lawrence A

    2014-08-01

    The aim of this study was to assess the safety and effectiveness of directional atherectomy (DA) for endovascular treatment of peripheral arterial disease (PAD) in infrainguinal arteries in patients with claudication or critical limb ischemia. To date, no prospective, multicenter, independently-adjudicated study has evaluated the effectiveness and durability of DA in the treatment of PAD. Previous DA studies have not been prospectively powered to evaluate any differences in outcomes in patients with and without diabetes. DEFINITIVE LE (Determination of EFfectiveness of the SilverHawk(®) PerIpheral Plaque ExcisioN System (SIlverHawk Device) for the Treatment of Infrainguinal VEssels / Lower Extremities) prospectively enrolled subjects at 47 multinational centers with an infrainguinal lesion length up to 20 cm. Primary endpoints were defined as primary patency at 12 months for claudicants and freedom from major unplanned amputation for critical limb ischemia (CLI) subjects. A pre-specified statistical hypothesis evaluated noninferiority of primary patency in diabetic versus nondiabetic claudicants. Independent angiographic and sonographic core laboratories assessed outcomes, and events were adjudicated by a clinical events committee. A total of 800 subjects were enrolled. The 12-month primary patency was 78% (95% confidence interval: 74.0% to 80.6%) in claudicants, with a 77% rate in the diabetic subgroup versus 78% in the nondiabetic subgroup (noninferior, p < 0.001). The rate of freedom from major unplanned amputation of the target limb at 12 months in CLI subjects was 95% (95% confidence interval: 90.7% to 97.4%). Periprocedural adverse events included embolization (3.8%), perforation (5.3%), and abrupt closure (2.0%). The bail-out stent rate was 3.2%. The DEFINITIVE LE study demonstrated that DA is a safe and effective treatment modality at 12 months for a diverse patient population with either claudication or CLI. Furthermore, DA was shown to be noninferior for

  8. Results of the German alternative fuel cycle evaluation and further efforts geared toward demonstration of direct disposal

    Papp, R.; Closs, K.D.

    1986-01-01

    In a comparative study initiated by the German Federal Ministry for Research and Technology which was carried out by Karlsruhe Nuclear Research Center in the period from 1981 to 1985, direct disposal of spent fuel was contrasted to the traditional fuel cycle with reprocessing and recycle. The results of the study did not exhibit decisive advantages of direct disposal over fuel reprocessing. Due to this face and legal requirements of the German Atomic Energy Act, the cabinet concluded to continue to adhere to fuel reprocessing as the preferred version of ''Entsorgung''. But the door was left ajar for the direct disposal alternative that, under present atomic law, is permissible for fuel for which reprocessing is neither technically feasible nor economically justified. An ambitious program has been launched in the Federal Republic of Germany (FRG), geared to bring direct disposal to a point of technical maturity

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

    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

    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

    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. Magnitude, direction and location of the resultant dipole moment of the pig heart.

    Hodgkin, B C; Nelson, C V; Angelakos, E T

    1976-04-01

    Vectorcardiograms were obtained from 50 young domestic pigs using the Nelson lead system. Compensation for body size and shape is achieved and the resultant dipole moment magnitude reflects heart size. A strong relationship was found between heart size and maximum magnitude. Dipole moment magnitude increased as four pigs increased from five to ten weeks of age. The dipole moment during QRS is considered in light of known pig heart excitation pattern. Dipole locations during QRS, calculated by computer solution of the Gabor-Nelson equations, were in agreement with heart location and excitation data.

  13. First results from the LHC Schottky Monitor operated with Direct Diode Detection

    Gasior, M

    2012-01-01

    The LHC is equipped with a Schottky diagnostic system based on 4.8 GHz resonant pick-ups. Their signals are processed according to a three-stage down-mixing scheme, working well in most beam conditions. An important exception is the period of energy ramp of proton beams, when the noise floor of the observed beam spectrum increases dramatically and the Schottky sidebands disappear. To study beam spectra in such conditions the signals from the Schottky pick-ups were split and the second half of their power was processed with a copy of the LHC tune measurement electronics, modified for this application. The experimental set-up is based on simple diode detectors followed by signal processing in the kHz range and 24-bit audio ADCs. With such a test system LHC beam spectra were successfully observed. This contribution presents the used hardware and obtained results.

  14. Results of the astrometry and direct imaging testbed for exoplanet detection

    Bendek, Eduardo A.; Belikov, Ruslan; Pluzhnik, Eugene; Guyon, Olivier; Milster, Thomas; Johnson, Lee; Finan, Emily; Knight, Justin; Rodack, Alexander

    2017-09-01

    Measuring masses of long-period planets around F, G, and K stars is necessary to characterize exoplanets and assess their habitability. Imaging stellar astrometry offers a unique opportunity to solve radial velocity system inclination ambiguity and determine exoplanet masses. The main limiting factor in sparse-field astrometry, besides photon noise, is the non-systematic dynamic distortions that arise from perturbations in the optical train. Even space optics suffer from dynamic distortions in the optical system at the sub-μas level. To overcome this limitation we propose a diffractive pupil that uses an array of dots on the primary mirror creating polychromatic diffraction spikes in the focal plane, which are used to calibrate the distortions in the optical system. By combining this technology with a high-performance coronagraph, measurements of planetary systems orbits and masses can be obtained faster and more accurately than by applying traditional techniques separately. In this paper, we present the results of the combined astrometry and and highcontrast imaging experiments performed at NASA Ames Research Center as part of a Technology Development for Exoplanet Missions program. We demonstrated 2.38x10-5 λ/D astrometric accuracy per axis and 1.72x10-7 raw contrast from 1.6 to 4.5 λ/D. In addition, using a simple average subtraction post-processing we demonstrated no contamination of the coronagraph field down to 4.79x10-9 raw contrast.

  15. Status of disposal techniques for spent fuel in Germany: Results of demonstration tests for direct disposal

    Engelmann, H.J.; Filbert, W.

    1993-01-01

    According to the Atomic Energy Act (1985) the Federal Government is responsible for establishing facilities to indemnify and dispose radioactive waste. According to Art. 9b of the Atomic Energy Act (1986) the construction and operation of such a repository requires approval of a plan. According to safety criteria applicable for disposing radioactive waste in mines, construction and operation of repository mines require application of acknowledged rules of technology, laws, ordinances and other regulations to protect operating staff and population from radiation damages. Shaft hoisting equipment for the transportation of radioactive waste in a repository mine must satisfy normal operational tasks and meet special safety-requirements. Its failure may result in danger for persons, release of radioactive substances into the plant and environment. That means, shaft hoisting equipment must be designed to satisfy the necessary safety requirements and be state of the art of science and technology. The aim of these demonstration tests is verification of technical feasibility of a shaft hoisting equipment with a payload of 85 t, underground for drift disposal of POLLUX-casks, and essential machine and mine-technical systems and components. The demonstration also includes safe radiation protection during transport and disposal operations. Investigations assume that radioactive waste is transported in containers that satisfy transport requirements for dangerous goods and have a type-B-certificate

  16. Direct Imaging of Stellar Surfaces: Results from the Stellar Imager (SI) Vision Mission Study

    Carpenter, Kenneth; Schrijver, Carolus; Karovska, Margarita

    2006-01-01

    The Stellar Imager (SI) is a UV-Optical, Space-Based Interferometer designed to enable 0.1 milli-arcsecond (mas) spectral imaging of stellar surfaces and stellar interiors (via asteroseismology) and of the Universe in general. SI is identified as a "Flagship and Landmark Discovery Mission'' in the 2005 Sun Solar System Connection (SSSC) Roadmap and as a candidate for a "Pathways to Life Observatory'' in the Exploration of the Universe Division (EUD) Roadmap (May, 2005). The ultra-sharp images of the Stellar Imager will revolutionize our view of many dynamic astrophysical processes: The 0.1 mas resolution of this deep-space telescope will transform point sources into extended sources, and snapshots into evolving views. SI's science focuses on the role of magnetism in the Universe, particularly on magnetic activity on the surfaces of stars like the Sun. SI's prime goal is to enable long-term forecasting of solar activity and the space weather that it drives in support of the Living With a Star program in the Exploration Era. SI will also revolutionize our understanding of the formation of planetary systems, of the habitability and climatology of distant planets, and of many magneto-hydrodynamically controlled processes in the Universe. In this paper we will discuss the results of the SI Vision Mission Study, elaborating on the science goals of the SI Mission and a mission architecture that could meet those goals.

  17. Comparative analysis of sequences from PT 2013

    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...

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

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

    2008-01-01

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

  19. Directional anisotropy in thermal infrared measurements over Toulouse city centre during the CAPITOUL measurement campaigns: first results

    Lagouarde, J.-P.; Irvine, M.

    2008-12-01

    The measurements of surface temperature are prone to important directional anisotropy related to the structure of the canopy and the radiative and energy exchanges inside of it. Directional effects must be taken into account for a number of practical applications such as the correction of large swath satellite data, the assimilation of thermal infrared (TIR) measurements in surface models, the design of future spatial missions… For urban canopies, experimental measurements of TIR directional anisotropy previously performed during summer days over Marseille in the framework of the ESCOMPTE campaign (2001) revealed significant angular surface temperature variations with noticeable hot spot effects whose intensity was related to the canopy structure. The CAPITOUL project ( http://medias.cnrs.fr/capitoul/ ) provided the opportunity to extend these results to other seasons and to nighttime conditions. The experimental setup is based on the use of 2 airborne TIR cameras with different lenses, inclination and resolution, and installed aboard a small aircraft. The flight protocol allowed the retrieval of directional anisotropy in all azimutal directions and in a range of zenith viewing angles between nadir and 62°. Measurements were performed during several intensive operation periods (IOP) in summer (2004 july), autumn (2004 September and October) and winter (2005 February). Only the first results of the 2004 autumn and 2005 winter IOPs are presented in this paper. The results obtained in daytime conditions confirm the systematic hot spot effects observed in previous experiments over cities. The variations found seem to be particularly important in winter when sun elevation is low: for instance they range between -4 and 10 K between oblique and nadir viewing in February. During nighttime conditions, angular variations are much lower (always less than 2 K between nadir and 60° zenithal viewing angle), whichever the azimutal viewing direction.

  20. 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

    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.

  1. A validation of direct grey Dancoff factors results for cylindrical cells in cluster geometry by the Monte Carlo method

    Rodrigues, Leticia Jenisch; Bogado, Sergio; Vilhena, Marco T.

    2008-01-01

    The WIMS code is a well known and one of the most used codes to handle nuclear core physics calculations. Recently, the PIJM module of the WIMS code was modified in order to allow the calculation of Grey Dancoff factors, for partially absorbing materials, using the alternative definition in terms of escape and collision probabilities. Grey Dancoff factors for the Canadian CANDU-37 and CANFLEX assemblies were calculated with PIJM at five symmetrically distinct fuel pin positions. The results, obtained via Direct Method, i.e., by direct calculation of escape and collision probabilities, were satisfactory when compared with the ones of literature. On the other hand, the PIJMC module was developed to calculate escape and collision probabilities using Monte Carlo method. Modifications in this module were performed to determine Black Dancoff factors, considering perfectly absorbing fuel rods. In this work, we proceed further in the task of validating the Direct Method by the Monte Carlo approach. To this end, the PIJMC routine is modified to compute Grey Dancoff factors using the cited alternative definition. Results are reported for the mentioned CANDU-37 and CANFLEX assemblies obtained with PIJMC, at the same fuel pin positions as with PIJM. A good agreement is observed between the results from the Monte Carlo and Direct methods

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

    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

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

    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.

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

    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.

  5. Results of a Direct Search Using Synchrotron Radiation for the Low-Energy (229)Th Nuclear Isomeric Transition.

    Jeet, Justin; Schneider, Christian; Sullivan, Scott T; Rellergert, Wade G; Mirzadeh, Saed; Cassanho, A; Jenssen, H P; Tkalya, Eugene V; Hudson, Eric R

    2015-06-26

    We report the results of a direct search for the (229)Th (I(π)=3/2(+)←5/2(+)) nuclear isomeric transition, performed by exposing (229)Th-doped LiSrAlF(6) crystals to tunable vacuum-ultraviolet synchrotron radiation and observing any resulting fluorescence. We also use existing nuclear physics data to establish a range of possible transition strengths for the isomeric transition. We find no evidence for the thorium nuclear transition between 7.3 eV and 8.8 eV with transition lifetime (1-2) s≲τ≲(2000-5600)  s. This measurement excludes roughly half of the favored transition search area and can be used to direct future searches.

  6. Application of High-Throughput Next-Generation Sequencing for HLA Typing on Buccal Extracted DNA: Results from over 10,000 Donor Recruitment Samples.

    Yuxin Yin

    Full Text Available Unambiguous HLA typing is important in hematopoietic stem cell transplantation (HSCT, HLA disease association studies, and solid organ transplantation. However, current molecular typing methods only interrogate the antigen recognition site (ARS of HLA genes, resulting in many cis-trans ambiguities that require additional typing methods to resolve. Here we report high-resolution HLA typing of 10,063 National Marrow Donor Program (NMDP registry donors using long-range PCR by next generation sequencing (NGS approach on buccal swab DNA.Multiplex long-range PCR primers amplified the full-length of HLA class I genes (A, B, C from promotor to 3' UTR. Class II genes (DRB1, DQB1 were amplified from exon 2 through part of exon 4. PCR amplicons were pooled and sheared using Covaris fragmentation. Library preparation was performed using the Illumina TruSeq Nano kit on the Beckman FX automated platform. Each sample was tagged with a unique barcode, followed by 2×250 bp paired-end sequencing on the Illumina MiSeq. HLA typing was assigned using Omixon Twin software that combines two independent computational algorithms to ensure high confidence in allele calling. Consensus sequence and typing results were reported in Histoimmunogenetics Markup Language (HML format. All homozygous alleles were confirmed by Luminex SSO typing and exon novelties were confirmed by Sanger sequencing.Using this automated workflow, over 10,063 NMDP registry donors were successfully typed under high-resolution by NGS. Despite known challenges of nucleic acid degradation and low DNA concentration commonly associated with buccal-based specimens, 97.8% of samples were successfully amplified using long-range PCR. Among these, 98.2% were successfully reported by NGS, with an accuracy rate of 99.84% in an independent blind Quality Control audit performed by the NDMP. In this study, NGS-HLA typing identified 23 null alleles (0.023%, 92 rare alleles (0.091% and 42 exon novelties (0.042%.Long

  7. Application of High-Throughput Next-Generation Sequencing for HLA Typing on Buccal Extracted DNA: Results from over 10,000 Donor Recruitment Samples.

    Yin, Yuxin; Lan, James H; Nguyen, David; Valenzuela, Nicole; Takemura, Ping; Bolon, Yung-Tsi; Springer, Brianna; Saito, Katsuyuki; Zheng, Ying; Hague, Tim; Pasztor, Agnes; Horvath, Gyorgy; Rigo, Krisztina; Reed, Elaine F; Zhang, Qiuheng

    2016-01-01

    Unambiguous HLA typing is important in hematopoietic stem cell transplantation (HSCT), HLA disease association studies, and solid organ transplantation. However, current molecular typing methods only interrogate the antigen recognition site (ARS) of HLA genes, resulting in many cis-trans ambiguities that require additional typing methods to resolve. Here we report high-resolution HLA typing of 10,063 National Marrow Donor Program (NMDP) registry donors using long-range PCR by next generation sequencing (NGS) approach on buccal swab DNA. Multiplex long-range PCR primers amplified the full-length of HLA class I genes (A, B, C) from promotor to 3' UTR. Class II genes (DRB1, DQB1) were amplified from exon 2 through part of exon 4. PCR amplicons were pooled and sheared using Covaris fragmentation. Library preparation was performed using the Illumina TruSeq Nano kit on the Beckman FX automated platform. Each sample was tagged with a unique barcode, followed by 2×250 bp paired-end sequencing on the Illumina MiSeq. HLA typing was assigned using Omixon Twin software that combines two independent computational algorithms to ensure high confidence in allele calling. Consensus sequence and typing results were reported in Histoimmunogenetics Markup Language (HML) format. All homozygous alleles were confirmed by Luminex SSO typing and exon novelties were confirmed by Sanger sequencing. Using this automated workflow, over 10,063 NMDP registry donors were successfully typed under high-resolution by NGS. Despite known challenges of nucleic acid degradation and low DNA concentration commonly associated with buccal-based specimens, 97.8% of samples were successfully amplified using long-range PCR. Among these, 98.2% were successfully reported by NGS, with an accuracy rate of 99.84% in an independent blind Quality Control audit performed by the NDMP. In this study, NGS-HLA typing identified 23 null alleles (0.023%), 92 rare alleles (0.091%) and 42 exon novelties (0.042%). Long

  8. Multi-virulence-locus sequence typing of Staphylococcus lugdunensis generates results consistent with a clonal population structure and is reliable for epidemiological typing.

    Didi, Jennifer; Lemée, Ludovic; Gibert, Laure; Pons, Jean-Louis; Pestel-Caron, Martine

    2014-10-01

    Staphylococcus lugdunensis is an emergent virulent coagulase-negative staphylococcus responsible for severe infections similar to those caused by Staphylococcus aureus. To understand its potentially pathogenic capacity and have further detailed knowledge of the molecular traits of this organism, 93 isolates from various geographic origins were analyzed by multi-virulence-locus sequence typing (MVLST), targeting seven known or putative virulence-associated loci (atlLR2, atlLR3, hlb, isdJ, SLUG_09050, SLUG_16930, and vwbl). The polymorphisms of the putative virulence-associated loci were moderate and comparable to those of the housekeeping genes analyzed by multilocus sequence typing (MLST). However, the MVLST scheme generated 43 virulence types (VTs) compared to 20 sequence types (STs) based on MLST, indicating that MVLST was significantly more discriminating (Simpson's index [D], 0.943). No hypervirulent lineage or cluster specific to carriage strains was defined. The results of multilocus sequence analysis of known and putative virulence-associated loci are consistent with a clonal population structure for S. lugdunensis, suggesting a coevolution of these genes with housekeeping genes. Indeed, the nonsynonymous to synonymous evolutionary substitutions (dN/dS) ratio, the Tajima's D test, and Single-likelihood ancestor counting (SLAC) analysis suggest that all virulence-associated loci were under negative selection, even atlLR2 (AtlL protein) and SLUG_16930 (FbpA homologue), for which the dN/dS ratios were higher. In addition, this analysis of virulence-associated loci allowed us to propose a trilocus sequence typing scheme based on the intragenic regions of atlLR3, isdJ, and SLUG_16930, which is more discriminant than MLST for studying short-term epidemiology and further characterizing the lineages of the rare but highly pathogenic S. lugdunensis. Copyright © 2014, American Society for Microbiology. All Rights Reserved.

  9. Antimicrobial susceptibility determined by the E test, Löwenstein-Jensen proportion, and DNA sequencing methods among Mycobacterium tuberculosis isolates discrepancies, preliminary results

    Maria Inês Moura Freixo

    2004-02-01

    Full Text Available Mycobacterium tuberculosis strains resistant to streptomycin (SM, isoniazid (INH, and/or rifampin (RIF as determined by the conventional Löwenstein-Jensen proportion method (LJPM were compared with the E test, a minimum inhibitory concentration susceptibility method. Discrepant isolates were further evaluated by BACTEC and by DNA sequence analyses for mutations in genes most often associated with resistance to these drugs (rpsL, katG, inhA, and rpoB. Preliminary discordant E test results were seen in 75% of isolates resistant to SM and in 11% to INH. Discordance improved for these two drugs (63% for SM and none for INH when isolates were re-tested but worsened for RIF (30%. Despite good agreement between phenotypic results and sequencing analyses, wild type profiles were detected on resistant strains mainly for SM and INH. It should be aware that susceptible isolates according to molecular methods might contain other mechanisms of resistance. Although reproducibility of the LJPM susceptibility method has been established, variable E test results for some M. tuberculosis isolates poses questions regarding its reproducibility particularly the impact of E test performance which may vary among laboratories despite adherence to recommended protocols. Further studies must be done to enlarge the evaluated samples and looked possible mutations outside of the hot spot sequenced gene among discrepant strains.

  10. Photocatalytic hydrogen production under direct solar light in a CPC based solar reactor: Reactor design and preliminary results

    Jing Dengwei; Liu Huan; Zhang Xianghui; Zhao Liang; Guo Liejin

    2009-01-01

    In despite of so many types of solar reactors designed for solar detoxification purposes, few attempts have been made for photocatalytic hydrogen production, which in our option, is one of the most promising approaches for solar to chemical energy conversion. Addressing both the similarity and dissimilarity for these two processes and by fully considering the special requirements for the latter reaction, a Compound Parabolic Concentrator (CPC) based photocatalytic hydrogen production solar reactor has been designed for the first time. The design and optimization of this CPC based solar reactor has been discussed in detail. Preliminary results demonstrated that efficient photocatalytic hydrogen production under direct solar light can be accomplished by coupling tubular reactors with CPC concentrators. It is anticipated that this first demonstration of concentrator-based solar photocatalytic hydrogen production would draw attention for further studies in this promising direction.

  11. Biaxial direct tensile tests in a large range of strain rates. Results on a ferritic nuclear steel

    Albertini, C.; Labibes, K.; Montagnani, M.; Pizzinato, E.V.; Solomos, G.; Viaccoz, B. [Commission of the European Communities, Ispra (Italy). Joint Research Centre

    2000-09-01

    Constitutive equations are usually calibrated only trough the experimental results obtained by means of unixial tests because of the lack of adequate biaxial experimental data especially at high strain rate conditions. These data are however important for the validation of analytical models and also for the predictions of mechanical behaviour of real structures subjected to multiaxial loading by numerical simulations. In this paper some developments are shown concerning biaxial cruciform specimens and different experimental machines allowing biaxial tests in a large range of strain rates. This experimental campaign has also allowed study of the influence of changing the strain paths. Diagrams of equivalent stress versus straining direction and also equivalent plastic fracture strain versus straining direction are shown. (orig.)

  12. Changes in Storm Flow as a Result of Direct Seed Farming Practices on the Columbia Plateau Semiarid Croplands

    Williams, J. D.

    2004-12-01

    -time precipitation patterns for the Columbia Plateau. Four runoff events were recorded from October 2002 through September 2003; the stage recorder failed in the conventionally tilled drainage during two of the events. During the events in which the runoff was recorded, the conventionally tilled drainage yielded 19.39 m3 and 20.83 m3; for those same events the 10.0 ha direct seed drainage yielded 0 m3 and 7.24 m3. Total recorded runoff for the year from the conventionally tilled drainage was 40.21 m3, and 40.96 m3 from the 10.0 ha direct seeded drainage. Total annual erosion from the conventionally tilled drainage was 127.05 kg/ha and 8.18 kg/ha from the direct seeded drainage. No runoff or erosion were recorded from the direct seeded 25.0, 18.1 drainages, or the 1.6 ha hillslope. From October 2003 through September 2004, one runoff event was missed and eight events were recorded from the conventionally tilled drainage, yielding 149.89-m3 runoff, and 286.71-kg/ha soil loss. The direct seeded drainages and hillslope produced no runoff or erosion. Under the climatic conditions during these two winters, the direct seed practices used in this study effectively controlled, runoff and erosion compared to a conventionally farmed drainage, at scales both larger than and smaller than the conventionally drained area. These results demonstrate the immediate soil and water conservation effectiveness of the direct seed technology. They also portend changes in the downstream processes as channels adjust to reduced stormflow volume and energy, and a reduced sediment supply.

  13. Question-answer sequences in survey interviews

    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

  14. Multimodal sequence learning.

    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.

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

    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.

  16. Treatment of Angio-Seal-Related Femoral Artery Occlusion Using Directional Atherectomy-Primary Results and Midterm Follow-Up.

    Babaev, Anvar; Gokhale, Rohit; Zavlunova, Susanna; Attubato, Michael

    2016-11-01

    We describe a novel approach for the endovascular treatment of femoral artery occlusion as a result of Angio-Seal closure device deployment. Angio-Seal is the most commonly used vascular closure device following percutaneous coronary and peripheral catheterizations worldwide. A rare complication of Angio-Seal deployment is an occlusion of the femoral artery leading to limb ischemia requiring revascularization. Given its unique ability to cut both atherosclerotic plaque and the Angio-Seal anchor with a collagen plug at operator-directed planes, TurboHawk/HawkOne atherectomy device can be a fast and effective approach to treat Angio-Seal-associated femoral artery occlusions. We studied 13 consecutive patients who developed Angio-Seal-associated femoral artery occlusions that occurred from 3 hours to several weeks after catheterization. These patients were successfully treated with TurboHawk/HawkOne directional atherectomy followed by balloon angioplasty with no complications. During a mean follow-up period of 20.4 ± 17.3 months, 12 patients remained claudication free with no evidence of obstructive arterial disease of the treated segment on imaging studies. One patient developed restenosis that was treated with repeat atherectomy and balloon angioplasty following which he was asymptomatic at follow-up. The use of directional atherectomy followed by balloon angioplasty is a quick, safe, and effective endovascular approach to treating Angio-Seal-associated femoral artery occlusions. It is associated with an excellent success rate, no complications, and good midterm outcomes.

  17. Post-test probability for neonatal hyperbilirubinemia based on umbilical cord blood bilirubin, direct antiglobulin test, and ABO compatibility results.

    Peeters, Bart; Geerts, Inge; Van Mullem, Mia; Micalessi, Isabel; Saegeman, Veroniek; Moerman, Jan

    2016-05-01

    Many hospitals opt for early postnatal discharge of newborns with a potential risk of readmission for neonatal hyperbilirubinemia. Assays/algorithms with the possibility to improve prediction of significant neonatal hyperbilirubinemia are needed to optimize screening protocols and safe discharge of neonates. This study investigated the predictive value of umbilical cord blood (UCB) testing for significant hyperbilirubinemia. Neonatal UCB bilirubin, UCB direct antiglobulin test (DAT), and blood group were determined, as well as the maternal blood group and the red blood cell antibody status. Moreover, in newborns with clinically apparent jaundice after visual assessment, plasma total bilirubin (TB) was measured. Clinical factors positively associated with UCB bilirubin were ABO incompatibility, positive DAT, presence of maternal red cell antibodies, alarming visual assessment and significant hyperbilirubinemia in the first 6 days of life. UCB bilirubin performed clinically well with an area under the receiver-operating characteristic curve (AUC) of 0.82 (95 % CI 0.80-0.84). The combined UCB bilirubin, DAT, and blood group analysis outperformed results of these parameters considered separately to detect significant hyperbilirubinemia and correlated exponentially with hyperbilirubinemia post-test probability. Post-test probabilities for neonatal hyperbilirubinemia can be calculated using exponential functions defined by UCB bilirubin, DAT, and ABO compatibility results. • The diagnostic value of the triad umbilical cord blood bilirubin measurement, direct antiglobulin testing and blood group analysis for neonatal hyperbilirubinemia remains unclear in literature. • Currently no guideline recommends screening for hyperbilirubinemia using umbilical cord blood. What is New: • Post-test probability for hyperbilirubinemia correlated exponentially with umbilical cord blood bilirubin in different risk groups defined by direct antiglobulin test and ABO blood group

  18. Human antibody responses to Schistosoma mansoni: does antigen directed, isotype restriction result in the production of blocking antibodies?

    David W. Dunne

    1987-01-01

    Full Text Available After treatment young Kenyan schoolchildren are highly susceptible to reinfection with Schistosoma mansoni. Older children and adults are resistant to reinfection. There is no evidence that this age related resistance is due to a slow development of protective immunological mechanisms, rather, it appears that young children are susceptible because of the presence of blocking antibodies which decline with age, thus allowing the expression of protective responses. Correlations between antibody responses to different stages of the parasite life-cycle suggest that, in young children, antigen directed, isotype restriction of the response against cross-reactive polysaccharide egg antigens results in an ineffectual, or even blocking antibody response to the schistosomulum.

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

    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...

  20. Putting instruction sequences into effect

    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

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

    De Rosa, Felice

    2006-01-01

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

  2. results

    Salabura Piotr

    2017-01-01

    Full Text Available HADES experiment at GSI is the only high precision experiment probing nuclear matter in the beam energy range of a few AGeV. Pion, proton and ion beams are used to study rare dielectron and strangeness probes to diagnose properties of strongly interacting matter in this energy regime. Selected results from p + A and A + A collisions are presented and discussed.

  3. Direct results of recent multidisciplinary ethno-genetic research of the Serbs and the Serbian population (in Aleksandrovac district

    Todorović Ivica

    2014-01-01

    Full Text Available The paper presents immediate results of a multidisciplinary research into ethno genesis, that is, the origin of the Serbs and the Serbian population, based on genetic indicators. The most direct results of the carried out survey are 85 haplotypes with 17 DYS markers/locuses of the respondents from Aleksandrovac district, a representative area as it is in the very centre of Serbian, Kosovo-Resava linguistic and cultural zone. Unlike previous texts that the authors have written on this subject, this paper, for the first time, presents actual results which correlate ethnological facts - starting from older up to latest records on origin - with genetic results obtained owing to the cooperation of the SASA Institute of Ethnography and the Laboratory for DNA analysis of the National forensic centre at the Ministry of Interior, Republic of Serbia. In this way, new findings, which could have been summoned only by parallel use of ethnological and genetic information (and which are given in the paper as clear proofs of necessity and effectiveness of the applied methodological approach, are being obtained and presented. Among other things, the given results of the preliminary survey (compared with the latest relevant surveys by other authors and institutions indicate the dominance of 12a and R1a haplogroups, decisive in the ethnogenesis of the Slavs, which matches common Serbian perception of the Serbs as of a nation of the Slav language and origin.

  4. Factors that affect implementation of a nurse staffing directive: results from a qualitative multi-case evaluation.

    Robinson, Claire H; Annis, Ann M; Forman, Jane; Krein, Sarah L; Yankey, Nicholas; Duffy, Sonia A; Taylor, Beth; Sales, Anne E

    2016-08-01

    To assess implementation of the Veterans Health Administration staffing methodology directive. In 2010 the Veterans Health Administration promulgated a staffing methodology directive for inpatient nursing units to address staffing and budget forecasting. A qualitative multi-case evaluation approach assessed staffing methodology implementation. Semi-structured telephone interviews were conducted from March - June 2014 with Nurse Executives and their teams at 21 facilities. Interviews focused on the budgeting process, implementation experiences, use of data, leadership support, and training. An implementation score was created for each facility using a 4-point rating scale. The scores were used to select three facilities (low, medium and high implementation) for more detailed case studies. After analysing interview summaries, the evaluation team developed a four domain scoring structure: (1) integration of staffing methodology into budget development; (2) implementation of the Directive elements; (3) engagement of leadership and staff; and (4) use of data to support the staffing methodology process. The high implementation facility had leadership understanding and endorsement of staffing methodology, confidence in and ability to work with data, and integration of staffing methodology results into the budgeting process. The low implementation facility reported poor leadership engagement and little understanding of data sources and interpretation. Implementation varies widely across facilities. Implementing staffing methodology in facilities with complex and changing staffing needs requires substantial commitment at all organizational levels especially for facilities that have traditionally relied on historical levels to budget for staffing. Published 2016. This article is a U.S. Government work and is in the public domain in the USA.

  5. Reexamining results of Iwatoyama tumulus by means of directive antenna; Shikosei antenna wo mochiita Iwatoyama kofun no saijikken

    Okamoto, K [Osaka Institute of Technology, Osaka (Japan); Kobayashi, Y [Kyoto University, Kyoto (Japan); Yoda, M [Shiga Prefecture Board of Education, Shiga (Japan)

    1996-05-01

    Investigation was conducted into the Iwatoyama tumulus located at Oaza Yoshida, Yame City, Fukuoka Prefecture, in January 1995, when a directional antenna was used. For the verification of the reliability of the result, another investigation was conducted in the same way. As in the previous effort, a traverse line of 18.8m was provided, and a sub-traverse line of the same length was provided 1m south of the traverse line. Reflection amplitude obtained during this investigation was smaller than that in the previous investigation, which was attributed to it that the contrast in dielectric constants between the rock constituting the main body in the cave and the cavity inside is high in winter and low in summer. In the second investigation, probably because the sub-traverse line was nearer to the southern end of the stone chamber, it became possible to evaluate the area of the stone chamber in the east-west direction, which confirms the conclusion of the first investigation that `it has to be inferred that the tumulus has its stone chamber ceiling at the depth of approximately 3.7m at a spot approximately 9.5-15.0m distant from the survey base for the round foot of the Iwatoyama tumulus and that therefore there exists a cave-type stone chamber with its ceiling 2.5-3.0m high.` 3 refs., 6 figs.

  6. Quantitative risk trends deriving from PSA-based event analyses. Analysis of results from U.S.NRC's accident sequence precursor program

    Watanabe, Norio

    2004-01-01

    The United States Nuclear Regulatory Commission (U.S.NRC) has been carrying out the Accident Sequence Precursor (ASP) Program to identify and categorize precursors to potential severe core damage accident sequences using the probabilistic safety assessment (PSA) technique. The ASP Program has identified a lot of risk significant events as precursors that occurred at U.S. nuclear power plants. Although the results from the ASP Program include valuable information that could be useful for obtaining and characterizing risk significant insights and for monitoring risk trends in nuclear power industry, there are only a few attempts to determine and develop the trends using the ASP results. The present study examines and discusses quantitative risk trends for the industry level, using two indicators, that is, the occurrence frequency of precursors and the annual core damage probability, deriving from the results of the ASP analysis. It is shown that the core damage risk at U.S. nuclear power plants has been lowered and the likelihood of risk significant events has been remarkably decreasing. As well, the present study demonstrates that two risk indicators used here can provide quantitative information useful for examining and monitoring the risk trends and/or risk characteristics in nuclear power industry. (author)

  7. One-Year Outcomes Following Directional Atherectomy of Infrapopliteal Artery Lesions: Subgroup Results of the Prospective, Multicenter DEFINITIVE LE Trial.

    Rastan, Aljoscha; McKinsey, James F; Garcia, Lawrence A; Rocha-Singh, Krishna J; Jaff, Michael R; Noory, Elias; Zeller, Thomas

    2015-12-01

    To report a subgroup analysis of the prospective, multicenter, single-arm DEFINITIVE LE trial to assess the effectiveness of directional atherectomy for the treatment of infrapopliteal artery lesions at 1 year. In the DEFINITIVE LE trial, follow-up assessments occurred up to 1 year postprocedure. Of the 800 patients enrolled, 145 subjects with 189 infrapopliteal lesions met the criteria for this analysis. Seventy (48.3%) and 75 (51.7%) patients were suffering critical limb ischemia (CLI) and intermittent claudication, respectively; 68.3% (99/145) had diabetes. The mean lesion length was 58±44 mm (all lesions); 20.2% were occluded. The primary endpoint for patients with claudication was duplex ultrasound-derived primary patency, while for subjects with CLI it was freedom from major amputation of the target limb at 1 year. Endpoints and adverse events were independently assessed. Procedure success (≤30% residual stenosis) was achieved in 84% of treated lesions. The 1-year primary patency rate was 84% (claudicants 89.6% and CLI patients 78%, p=0.11), and the freedom from major amputation rate was 97.1% (claudicants 100% and CLI 93.8%, p=0.03). In both claudication and CLI patients, significant improvements in Rutherford category and objective measures of walking distance and quality of life were seen at 1 year in comparison to baseline. This study demonstrates that directional atherectomy in infrapopliteal arteries results in promising technical and clinical results at 1 year for claudicant as well as CLI patients. © The Author(s) 2015.

  8. NUCLEAR HEATING IN LIF DOSEMETERS IN A FUSION NEUTRON FIELD, TRIAL OF DIRECT COMPARISON OF EXPERIMENTAL AND SIMULATED RESULTS.

    Pohorecki, Wladyslaw; Obryk, Barbara

    2017-09-29

    The results of nuclear heating measured by means of thermoluminescent dosemeters (TLD-LiF) in a Cu block irradiated by 14 MeV neutrons are presented. The integral Cu experiment relevant for verification of copper nuclear data at neutron energies characteristic for fusion facilities was performed in the ENEA FNG Laboratory at Frascati. Five types of TLDs were used: highly photon sensitive LiF:Mg,Cu,P (MCP-N), 7LiF:Mg,Cu,P (MCP-7) and standard, lower sensitivity LiF:Mg,Ti (MTS-N), 7LiF:Mg,Ti (MTS-7) and 6LiF:Mg,Ti (MTS-6). Calibration of the detectors was performed with gamma rays in terms of air-kerma (10 mGy of 137Cs air-kerma). Nuclear heating in the Cu block was also calculated with the use of MCNP transport code Nuclear heating in Cu and air in TLD's positions was calculated as well. The nuclear heating contribution from all simulated by MCNP6 code particles including protons, deuterons, alphas tritons and heavier ions produced by the neutron interactions were calculated. A trial of the direct comparison between experimental results and results of simulation was performed. © The Author 2017. Published by Oxford University Press. All rights reserved. For Permissions, please email: journals.permissions@oup.com.

  9. 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.

    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.

  10. De novo generation of helper virus-satellite chimera RNAs results in disease attenuation and satellite sequence acquisition in a host-dependent manner.

    Pyle, J D; Scholthof, Karen-Beth G

    2018-01-15

    Panicum mosaic virus (PMV) is a helper RNA virus for satellite RNAs (satRNAs) and a satellite virus (SPMV). Here, we describe modifications that occur at the 3'-end of a satRNA of PMV, satS. Co-infections of PMV+satS result in attenuation of the disease symptoms induced by PMV alone in Brachypodium distachyon and proso millet. The 375 nt satS acquires ~100-200 nts from the 3'-end of PMV during infection and is associated with decreased abundance of the PMV RNA and capsid protein in millet. PMV-satS chimera RNAs were isolated from native infections of St. Augustinegrass and switchgrass. Phylogenetic analyses revealed that the chimeric RNAs clustered according to the host species from which they were isolated. Additionally, the chimera satRNAs acquired non-viral "linker" sequences in a host-specific manner. These results highlight the dynamic regulation of viral pathogenicity by satellites, and the selective host-dependent, sequence-based pressures for driving satRNA generation and genome compositions. Copyright © 2017 Elsevier Inc. All rights reserved.

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

    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.

  12. Use of test results from the percolation leaching test (TS3) in the framework of the Construction Products Directive

    Van Zomeren, A.; Dijkstra, J.J. [ECN Environment and Energy Engineering, Petten (Netherlands); Mesman, M.; Spijker, J. [National Institute for Public Health and the Environment RIVM, Bilthoven (Netherlands); Eikelboom, R. [Ministry of Infrastructure and Environment IenM, Den Haag (Netherlands)

    2013-10-15

    The enforcement of the European Construction Products Directive (and the more actual Construction Products Regulation) has led to the development of European harmonised standards for assessment of the emission of 'dangerous substances' from construction materials. According to Basic Working Requirement (BWR) number 3, the emissions from construction products to soil and groundwater should not have an unacceptable impact on the environmental quality over the life cycle of the product. In this paper the technical needs and boundary conditions of leaching tests to obtain meaningful and reliable test results are explained. Although this paper will not go into detail on 'impact assessment' and the resulting development of regulatory criteria, we will show that the technical needs and boundary conditions of a test are to some extent dependent on what type of information is needed by regulators for environmental impact assessment. This short paper focuses on explaining the principles of testing leaching behaviour of aggregates, and briefly explains the leaching of size reduced and non-size reduced particles. It provides information for the actual discussions on size reduction before leaching tests.

  13. Cytomegalovirus sequence variability, amplicon length, and DNase-sensitive non-encapsidated genomes are obstacles to standardization and commutability of plasma viral load results.

    Naegele, Klaudia; Lautenschlager, Irmeli; Gosert, Rainer; Loginov, Raisa; Bir, Katia; Helanterä, Ilkka; Schaub, Stefan; Khanna, Nina; Hirsch, Hans H

    2018-04-22

    Cytomegalovirus (CMV) management post-transplantation relies on quantification in blood, but inter-laboratory and inter-assay variability impairs commutability. An international multicenter study demonstrated that variability is mitigated by standardizing plasma volumes, automating DNA extraction and amplification, and calibration to the 1st-CMV-WHO-International-Standard as in the FDA-approved Roche-CAP/CTM-CMV. However, Roche-CAP/CTM-CMV showed under-quantification and false-negative results in a quality assurance program (UK-NEQAS-2014). To evaluate factors contributing to quantification variability of CMV viral load and to develop optimized CMV-UL54-QNAT. The UL54 target of the UK-NEQAS-2014 variant was sequenced and compared to 329 available CMV GenBank sequences. Four Basel-CMV-UL54-QNAT assays of 361 bp, 254 bp, 151 bp, and 95 bp amplicons were developed that only differed in reverse primer positions. The assays were validated using plasmid dilutions, UK-NEQAS-2014 sample, as well as 107 frozen and 69 prospectively collected plasma samples from transplant patients submitted for CMV QNAT, with and without DNase-digestion prior to nucleic acid extraction. Eight of 43 mutations were identified as relevant in the UK-NEQAS-2014 target. All Basel-CMV-UL54 QNATs quantified the UK-NEQAS-2014 but revealed 10-fold increasing CMV loads as amplicon size decreased. The inverse correlation of amplicon size and viral loads was confirmed using 1st-WHO-International-Standard and patient samples. DNase pre-treatment reduced plasma CMV loads by >90% indicating the presence of unprotected CMV genomic DNA. Sequence variability, amplicon length, and non-encapsidated genomes obstruct standardization and commutability of CMV loads needed to develop thresholds for clinical research and management. Besides regular sequence surveys, matrix and extraction standardization, we propose developing reference calibrators using 100 bp amplicons. Copyright © 2018 Elsevier B.V. All

  14. RNAi-directed downregulation of vacuolar H(+ -ATPase subunit a results in enhanced stomatal aperture and density in rice.

    Huiying Zhang

    Full Text Available Stomatal movement plays a key role in plant development and response to drought and salt stress by regulating gas exchange and water loss. A number of genes have been demonstrated to be involved in the regulation of this process. Using inverse genetics approach, we characterized the function of a rice (Oryza sativa L. vacuolar H(+-ATPase subunit A (OsVHA-A gene in stomatal conductance regulation and physiological response to salt and osmotic stress. OsVHA-A was constitutively expressed in different rice tissues, and the fusion protein of GFP-OsVHA-A was exclusively targeted to tonoplast when transiently expressed in the onion epidermal cells. Heterologous expression of OsVHA-A was able to rescue the yeast mutant vma1Δ (lacking subunit A activity phenotype, suggesting that it partially restores the activity of V-ATPase. Meanwhile, RNAi-directed knockdown of OsVHA-A led to a reduction of vacuolar H(+-ATPase activity and an enhancement of plasma membrane H(+-ATPase activity, thereby increasing the concentrations of extracellular H(+ and intracellular K(+ and Na(+ under stress conditions. Knockdown of OsVHA-A also resulted in the upregulation of PAM3 (plasma membrane H(+-ATPase 3 and downregulation of CAM1 (calmodulin 1, CAM3 (calmodulin 3 and YDA1 (YODA, a MAPKK gene. Altered level of the ion concentration and the gene expression by knockdown of OsVHA-A probably resulted in expanded aperture of stomatal pores and increased stomatal density. In addition, OsVHA-A RNAi plants displayed significant growth inhibition under salt and osmotic stress conditions. Taken together, our results suggest that OsVHA-A takes part in regulating stomatal density and opening via interfering with pH value and ionic equilibrium in guard cells and thereby affects the growth of rice plants.

  15. [Transcranial direct current stimulation (tDCS) for depression: Results of nearly a decade of clinical research].

    Palm, U; Ayache, S S; Padberg, F; Lefaucheur, J-P

    2016-02-01

    Since 2006 transcranial direct current stimulation (tDCS) has been investigated in the treatment of depression. In this review, we discuss the implications and clinical perspectives that tDCS may have as a therapeutic tool in depression from the results reported in this domain. A comprehensive literature review has found nearly thirty articles - all in English - on this topic, corresponding to clinical studies, placebo-controlled or not, case reports and reviews. Several meta-analyses showed that the antidepressant effects of active tDCS are significant against placebo, but variable, mainly due to the heterogeneity of the patients included in the studies, for example regarding the resistance to antidepressant treatment. Specific recommendations for the use of tDCS in treating depression may not yet be available, but some elements of good practice can be highlighted. Of particular note is that anodal tDCS of the left prefrontal cortex at 2mA for 20 minutes per day has a potential therapeutic value without risk of significant side effects: tDCS offers safe conditions for clinical use in the treatment of depression. Copyright © 2015 L’Encéphale, Paris. Published by Elsevier Masson SAS. All rights reserved.

  16. [Endovascular treatment of acute iliofemoral deep venous thrombosis - our results with catheter-directed thrombolysis and AngioJet].

    Berencsi, Anikó; Dósa, Edit; Nemes, Balázs; Hüttl, Kálmán; Legeza, Péter; Oláh, Zoltán; Kristóf, Vera; Acsády, György; Sótonyi, Péter

    2017-03-01

    Most of the patients with iliofemoral thrombosis treated with anticoagulants only are affected with postthrombotic syndrome (PTS) that worsens the patients' quality of life. In the acute phase of proximal deep venous thrombosis (DVT) catheter-directed (CDT) and pharmacomechanical thrombolysis may be a reasonable alternative therapeutic method. Our aim was to summarize our results using these methods. Since 2009 twenty-four patients with iliofemoral DVT were treated with these endovascular procedures and with stenting at our Institution. The median age of the patients was 35.83 ± 15.9 years, the female: male ratio was approximately 2:1. The mean time between the onset of the symptoms and the procedures was eleven days. CDT alone was performed in 8 patients, thrombus aspiration in addition to CDT using AngioJet device in 16 patients; in 19 cases the procedure was completed with venous stenting. During the follow-up we performed US examinations and estimated the severity of PTS by Villalta-scale. The total recanalization-rate was more than 50%, which even improved during the follow-up. The total lysis time and the amount of used recombinant tissue plasminogen activator decreased significantly by applying the AngioJet. We did not find any severe PTS among our patients during the follow-up visits. Our data suggests that these methods can be used efficiently and safely in the treatment of acute iliofemoral DVT.

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

    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

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

    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...

  19. Refining the Results of a Classical SELEX Experiment by Expanding the Sequence Data Set of an Aptamer Pool Selected for Protein A

    Regina Stoltenburg; Beate Strehlitz

    2018-01-01

    New, as yet undiscovered aptamers for Protein A were identified by applying next generation sequencing (NGS) to a previously selected aptamer pool. This pool was obtained in a classical SELEX (Systematic Evolution of Ligands by EXponential enrichment) experiment using the FluMag-SELEX procedure followed by cloning and Sanger sequencing. PA#2/8 was identified as the only Protein A-binding aptamer from the Sanger sequence pool, and was shown to be able to bind intact cells of Staphylococcus aur...

  20. 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.

    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.

  1. Self-reported responsiveness to direct-to-consumer drug advertising and medication use: results of a national survey

    Somes Grant W

    2011-09-01

    Full Text Available Abstract Background Direct-to-consumer (DTC marketing of pharmaceuticals is controversial, yet effective. Little is known relating patterns of medication use to patient responsiveness to DTC. Methods We conducted a secondary analysis of data collected in national telephone survey on knowledge of and attitudes toward DTC advertisements. The survey of 1081 U.S. adults (response rate = 65% was conducted by the Food and Drug Administration (FDA. Responsiveness to DTC was defined as an affirmative response to the item: "Has an advertisement for a prescription drug ever caused you to ask a doctor about a medical condition or illness of your own that you had not talked to a doctor about before?" Patients reported number of prescription and over-the-counter (OTC medicines taken as well as demographic and personal health information. Results Of 771 respondents who met study criteria, 195 (25% were responsive to DTC. Only 7% respondents taking no prescription were responsive, whereas 45% of respondents taking 5 or more prescription medications were responsive. This trend remained significant (p trend .0009 even when controlling for age, gender, race, educational attainment, income, self-reported health status, and whether respondents "liked" DTC advertising. There was no relationship between the number of OTC medications taken and the propensity to discuss health-related problems in response to DTC advertisements (p = .4. Conclusion There is a strong cross-sectional relationship between the number of prescription, but not OTC, drugs used and responsiveness to DTC advertising. Although this relationship could be explained by physician compliance with patient requests for medications, it is also plausible that DTC advertisements have a particular appeal to patients prone to taking multiple medications. Outpatients motivated to discuss medical conditions based on their exposure to DTC advertising may require a careful medication history to evaluate for

  2. Self-reported responsiveness to direct-to-consumer drug advertising and medication use: results of a national survey.

    Dieringer, Nicholas J; Kukkamma, Lisa; Somes, Grant W; Shorr, Ronald I

    2011-09-23

    ABSTRACT: BACKGROUND: Direct-to-consumer (DTC) marketing of pharmaceuticals is controversial, yet effective. Little is known relating patterns of medication use to patient responsiveness to DTC. METHODS: We conducted a secondary analysis of data collected in national telephone survey on knowledge of and attitudes toward DTC advertisements. The survey of 1081 U.S. adults (response rate = 65%) was conducted by the Food and Drug Administration (FDA). Responsiveness to DTC was defined as an affirmative response to the item: "Has an advertisement for a prescription drug ever caused you to ask a doctor about a medical condition or illness of your own that you had not talked to a doctor about before?" Patients reported number of prescription and over-the-counter (OTC) medicines taken as well as demographic and personal health information. RESULTS: Of 771 respondents who met study criteria, 195 (25%) were responsive to DTC. Only 7% respondents taking no prescription were responsive, whereas 45% of respondents taking 5 or more prescription medications were responsive. This trend remained significant (p trend .0009) even when controlling for age, gender, race, educational attainment, income, self-reported health status, and whether respondents "liked" DTC advertising. There was no relationship between the number of OTC medications taken and the propensity to discuss health-related problems in response to DTC advertisements (p = .4). CONCLUSION: There is a strong cross-sectional relationship between the number of prescription, but not OTC, drugs used and responsiveness to DTC advertising. Although this relationship could be explained by physician compliance with patient requests for medications, it is also plausible that DTC advertisements have a particular appeal to patients prone to taking multiple medications. Outpatients motivated to discuss medical conditions based on their exposure to DTC advertising may require a careful medication history to evaluate for therapeutic

  3. 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.)

    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...

  4. Rapid Diagnostics of Onboard Sequences

    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

  5. Do the results of respirable dust samples obtained from direct-on-filter X-ray diffraction, direct-on-filter infrared and indirect infrared (KBr pellet) methods correlate?

    Pretorius, C

    2010-11-01

    Full Text Available The objective of this study was to determine whether a correlation exists between the quartz results obtained from direct-on-filter X-ray Diffraction analysis, direct-on-filter Fourier-Transform Infrared analysis and indirect analysis (Potassium...

  6. Effects of gut-directed hypnotherapy on IBS in different clinical settings-results from two randomized, controlled trials.

    Lindfors, Perjohan; Unge, Peter; Arvidsson, Patrik; Nyhlin, Henry; Björnsson, Einar; Abrahamsson, Hasse; Simrén, Magnus

    2012-02-01

    Gut-directed hypnotherapy has been found to be effective in irritable bowel syndrome (IBS). However, randomized, controlled studies are rare and few have been performed outside highly specialized research centers. The objective of this study was to study the effect of gut-directed hypnotherapy in IBS in different clinical settings outside the traditional research units. The study population included IBS patients refractory to standard management. In study 1, patients were randomized to receive gut-directed hypnotherapy (12 sessions, 1 h/week) in psychology private practices or supportive therapy, whereas patients were randomized to receive gut-directed hypnotherapy in a small county hospital or to serve as waiting list controls in study 2. Gastrointestinal symptom severity and quality of life were evaluated at baseline, at 3 months follow-up and after 1 year. We randomized 138 IBS patients refractory to standard management, 90 in study 1 and 48 in study 2. In both the studies, IBS-related symptoms were improved at 3 months in the gut-directed hypnotherapy groups (Phypnotherapy group than in the control group (Phypnotherapy is an effective treatment alternative for patients with refractory IBS, but the effectiveness is lower when the therapy is given outside the highly specialized research centers.

  7. Estimation of Source Term Behaviors in SBO Sequence in a Typical 1000MWth PWR and Comparison with Other Source Term Results

    Kim, Tae Woon; Han, Seok Jung; Ahn, Kwang Il; Fynan, Douglas; Jung, Yong Hoon [KAERI, Daejeon (Korea, Republic of)

    2016-05-15

    Since the Three Mile Island (TMI) (1979), Chernobyl (1986), Fukushima Daiichi (2011) accidents, the assessment of radiological source term effects on the environment has been a key concern of nuclear safety. In the Fukushima Daiichi accident, the long-term SBO (station blackout) accident occurs. Using the worst case assumptions like in Fukushima accident on the accident sequences and on the availability of safety systems, the thermal hydraulic behaviors, core relocation and environmental source terms behaviors are estimated for long-term SBO accident for OPR-1000 reactor. MELCOR code version 1.8.6 is used in this analysis. Source term results estimated in this study is compared with other previous studies and estimated results in Fukushima accidents in UNSCEAR-2013 report. This study estimated that 11 % of iodine can be released to environment and 2% of cesium can be released to environment. UNSCEAR-2013 report estimated that 2 - 8 % of iodine have been released to environment and 1 - 3 % of cesium have been released to the environment. They have similar results in the aspect of release fractions of iodine and cesium to environment.

  8. [Some aspects of pharmacotherapy of tinnitus. Compound therapy with Xylocaine and directive counseling--long-term results].

    Rogowski, Marek; Sieśkiewicz, Andrzej; Rózańska-Kudelska, Małgorzata; Walenczak, Izabela

    2004-01-01

    29 out of 49 patients, who were treated in 1996-1998 with Xylocaine and directive counselling for their tinitus, were reevaluated. Non of the patients used any other pharmacological treatment of the tinnitus or underwent full tinnitus retraining therapy (TRT) since 10-days treatment with Xylocaine had been completed. Initially 65.3% of patients declared improvement in their tinnitus. After over 5 years of observation success rate decreased to only 41.3%. Since the positive effect of 10-days treatment with Xylocaine and directive counselling was not stable we concluded that tinnitus patients should receive full TRT.

  9. An international effort towards developing standards for best practices in analysis, interpretation and reporting of clinical genome sequencing results in the CLARITY Challenge

    Brownstein, Catherine A; Beggs, Alan H; Homer, Nils

    2014-01-01

    and reporting. The CLARITY Challenge was designed to spur convergence in methods for diagnosing genetic disease starting from clinical case history and genome sequencing data. DNA samples were obtained from three families with heritable genetic disorders and genomic sequence data were donated by sequencing......Background : There is tremendous potential for genome sequencing to improve clinical diagnosis and care once it becomes routinely accessible, but this will require formalizing research methods into clinical best practices in the areas of sequence data generation, analysis, interpretation......, demonstrating a need for consistent fine-tuning of the generally accepted methods. There was greater diversity of the final clinical report content and in the patient consenting process, demonstrating that these areas require additional exploration and standardization. Conclusions : The CLARITY Challenge...

  10. Improving temporal bone dissection using self-directed virtual reality simulation: results of a randomized blinded control trial.

    Zhao, Yi Chen; Kennedy, Gregor; Yukawa, Kumiko; Pyman, Brian; O'Leary, Stephen

    2011-03-01

    A significant benefit of virtual reality (VR) simulation is the ability to provide self-direct learning for trainees. This study aims to determine whether there are any differences in performance of cadaver temporal bone dissections between novices who received traditional teaching methods and those who received unsupervised self-directed learning in a VR temporal bone simulator. Randomized blinded control trial. Royal Victorian Eye and Ear Hospital. Twenty novice trainees. After receiving an hour lecture, participants were randomized into 2 groups to receive an additional 2 hours of training via traditional teaching methods or self-directed learning using a VR simulator with automated guidance. The simulation environment presented participants with structured training tasks, which were accompanied by real-time computer-generated feedback as well as real operative videos and photos. After the training, trainees were asked to perform a cortical mastoidectomy on a cadaveric temporal bone. The dissection was videotaped and assessed by 3 otologists blinded to participants' teaching group. The overall performance scores of the simulator-based training group were significantly higher than those of the traditional training group (67% vs 29%; P < .001), with an intraclass correlation coefficient of 0.93, indicating excellent interrater reliability. Using other assessments of performance, such as injury size, the VR simulator-based training group also performed better than the traditional group. This study indicates that self-directed learning on VR simulators can be used to improve performance on cadaver dissection in novice trainees compared with traditional teaching methods alone.

  11. Self-directed learning can outperform direct instruction in the course of a modern German medical curriculum - results of a mixed methods trial.

    Peine, Arne; Kabino, Klaus; Spreckelsen, Cord

    2016-06-03

    Modernised medical curricula in Germany (so called "reformed study programs") rely increasingly on alternative self-instructed learning forms such as e-learning and curriculum-guided self-study. However, there is a lack of evidence that these methods can outperform conventional teaching methods such as lectures and seminars. This study was conducted in order to compare extant traditional teaching methods with new instruction forms in terms of learning effect and student satisfaction. In a randomised trial, 244 students of medicine in their third academic year were assigned to one of four study branches representing self-instructed learning forms (e-learning and curriculum-based self-study) and instructed learning forms (lectures and seminars). All groups participated in their respective learning module with standardised materials and instructions. Learning effect was measured with pre-test and post-test multiple-choice questionnaires. Student satisfaction and learning style were examined via self-assessment. Of 244 initial participants, 223 completed the respective module and were included in the study. In the pre-test, the groups showed relatively homogenous scores. All students showed notable improvements compared with the pre-test results. Participants in the non-self-instructed learning groups reached scores of 14.71 (seminar) and 14.37 (lecture), while the groups of self-instructed learners reached higher scores with 17.23 (e-learning) and 15.81 (self-study). All groups improved significantly (p learning group, whose self-assessment improved by 2.36. The study shows that students in modern study curricula learn better through modern self-instructed methods than through conventional methods. These methods should be used more, as they also show good levels of student acceptance and higher scores in personal self-assessment of knowledge.

  12. 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

    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

  13. 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

    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.

  14. Experimental Results for Minimum-Time Trajectory Tracking of a Direct-Drive Three-Link Planar Arm

    DRIESSEN,BRIAN; PARKER,GORDON G.

    1999-09-01

    This work is an experimental investigation of the ability of a real three-link direct-drive arm to track model-based minimum-time trajectories that have been found off-line. Sufficiently large velocity gains in the computed torque control law were not achievable with the velocity sensors described herein. This indicates the critical importance of the velocity sensing when attempting to track trajectories that push the envelope of the system's torque capabilities.

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

    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...

  16. Impact of Sequencing Radiation Therapy and Chemotherapy on Long-Term Local Toxicity for Early Breast Cancer: Results of a Randomized Study at 15-Year Follow-Up

    Pinnarò, Paola; Giordano, Carolina; Farneti, Alessia [Department of Radiation Oncology, Regina Elena National Cancer Institute, Rome (Italy); Strigari, Lidia; Landoni, Valeria [Department of Physics, Regina Elena National Cancer Institute, Rome (Italy); Marucci, Laura; Petrongari, Maria Grazia [Department of Radiation Oncology, Regina Elena National Cancer Institute, Rome (Italy); Sanguineti, Giuseppe, E-mail: sanguineti@ifo.it [Department of Radiation Oncology, Regina Elena National Cancer Institute, Rome (Italy)

    2016-07-15

    Purpose: To compare long-term late local toxicity after either concomitant or sequential chemoradiation therapy after breast-conserving surgery. Methods and Materials: From 1997 to 2002, women aged 18 to 75 years who underwent breast-conserving surgery and axillary dissection for early breast cancer and in whom CMF (cyclophosphamide, methotrexate, and 5-fluorouracil) chemotherapy was planned were randomized between concomitant and sequential radiation therapy. Radiation therapy was delivered to the whole breast through tangential fields to 50 Gy in 20 fractions over a period of 4 weeks, followed by an electron boost. Surviving patients were tentatively contacted and examined between March and September 2014. Patients in whom progressive disease had developed or who had undergone further breast surgery were excluded. Local toxicity (fibrosis, telangiectasia, and breast atrophy or retraction) was scored blindly to the treatment received. A logistic regression was run to investigate the effect of treatment sequence after correction for several patient-, treatment-, and tumor-related covariates on selected endpoints. The median time to cross-sectional analysis was 15.7 years (range, 12.0-17.8 years). Results: Of 206 patients randomized, 154 (74.8%) were potentially eligible. Of these, 43 (27.9%) refused participation and 4 (2.6%) had been lost to follow-up, and for 5 (3.2%), we could not restore planning data; thus, the final number of analyzed patients was 102. No grade 4 toxicity had been observed, whereas the number of grade 3 toxicity events was low (<8%) for each item, allowing pooling of grade 2 and 3 events for further analysis. Treatment sequence (concomitant vs sequential) was an independent predictor of grade 2 or 3 fibrosis according to both the National Cancer Institute Common Terminology Criteria for Adverse Events (odds ratio [OR], 4.05; 95% confidence interval [CI], 1.34-12.2; P=.013) and the SOMA (Subjective, Objective, Management and Analytic

  17. Impact of Sequencing Radiation Therapy and Chemotherapy on Long-Term Local Toxicity for Early Breast Cancer: Results of a Randomized Study at 15-Year Follow-Up

    Pinnarò, Paola; Giordano, Carolina; Farneti, Alessia; Strigari, Lidia; Landoni, Valeria; Marucci, Laura; Petrongari, Maria Grazia; Sanguineti, Giuseppe

    2016-01-01

    Purpose: To compare long-term late local toxicity after either concomitant or sequential chemoradiation therapy after breast-conserving surgery. Methods and Materials: From 1997 to 2002, women aged 18 to 75 years who underwent breast-conserving surgery and axillary dissection for early breast cancer and in whom CMF (cyclophosphamide, methotrexate, and 5-fluorouracil) chemotherapy was planned were randomized between concomitant and sequential radiation therapy. Radiation therapy was delivered to the whole breast through tangential fields to 50 Gy in 20 fractions over a period of 4 weeks, followed by an electron boost. Surviving patients were tentatively contacted and examined between March and September 2014. Patients in whom progressive disease had developed or who had undergone further breast surgery were excluded. Local toxicity (fibrosis, telangiectasia, and breast atrophy or retraction) was scored blindly to the treatment received. A logistic regression was run to investigate the effect of treatment sequence after correction for several patient-, treatment-, and tumor-related covariates on selected endpoints. The median time to cross-sectional analysis was 15.7 years (range, 12.0-17.8 years). Results: Of 206 patients randomized, 154 (74.8%) were potentially eligible. Of these, 43 (27.9%) refused participation and 4 (2.6%) had been lost to follow-up, and for 5 (3.2%), we could not restore planning data; thus, the final number of analyzed patients was 102. No grade 4 toxicity had been observed, whereas the number of grade 3 toxicity events was low (<8%) for each item, allowing pooling of grade 2 and 3 events for further analysis. Treatment sequence (concomitant vs sequential) was an independent predictor of grade 2 or 3 fibrosis according to both the National Cancer Institute Common Terminology Criteria for Adverse Events (odds ratio [OR], 4.05; 95% confidence interval [CI], 1.34-12.2; P=.013) and the SOMA (Subjective, Objective, Management and Analytic

  18. Next-generation sequencing indicates false-positive MRD results and better predicts prognosis after SCT in patients with childhood ALL.

    Kotrova, M; van der Velden, V H J; van Dongen, J J M; Formankova, R; Sedlacek, P; Brüggemann, M; Zuna, J; Stary, J; Trka, J; Fronkova, E

    2017-07-01

    Minimal residual disease (MRD) monitoring via quantitative PCR (qPCR) detection of Ag receptor gene rearrangements has been the most sensitive method for predicting prognosis and making post-transplant treatment decisions for patients with ALL. Despite the broad clinical usefulness and standardization of this method, we and others have repeatedly reported the possibility of false-positive MRD results caused by massive B-lymphocyte regeneration after stem cell transplantation (SCT). Next-generation sequencing (NGS) enables precise and sensitive detection of multiple Ag receptor rearrangements, thus providing a more specific readout compared to qPCR. We investigated two cohorts of children with ALL who underwent SCT (30 patients and 228 samples). The first cohort consisted of 17 patients who remained in long-term CR after SCT despite having low MRD positivity (SCT monitoring using qPCR. Only one of 27 qPCR-positive samples was confirmed to be positive by NGS. Conversely, 10 of 15 samples with low qPCR-detected MRD positivity from 13 patients who subsequently relapsed were also confirmed to be positive by NGS (P=0.002). These data show that NGS has a better specificity in post-SCT ALL management and indicate that treatment interventions aimed at reverting impending relapse should not be based on qPCR only.

  19. 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.

    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.

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

    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)

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

    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.

  2. Mixed Sequence Reader: A Program for Analyzing DNA Sequences with Heterozygous Base Calling

    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

  3. Test results on direct containment heating by high-pressure melt ejection into the Surtsey vessel: The TDS test series

    Allen, M.D.; Blanchat, T.K.; Pilch, M.M.

    1994-08-01

    The Technology Development and Scoping (TDS) test series was conducted to test and develop instrumentation and procedures for performing steam-driven, high-pressure melt ejection (HPME) experiments at the Surtsey Test Facility to investigate direct containment heating (DCH). Seven experiments, designated TDS-1 through TDS-7, were performed in this test series. These experiments were conducted using similar initial conditions; the primary variable was the initial pressure in the Surtsey vessel. All experiments in this test series were performed with a steam driving gas pressure of ≅ 4 MPa, 80 kg of lumina/iron/chromium thermite melt simulant, an initial hole diameter of 4.8 cm (which ablated to a final hole diameter of ≅ 6 cm), and a 1/10th linear scale model of the Surry reactor cavity. The Surtsey vessel was purged with argon ( 2 ) to limit the recombination of hydrogen and oxygen, and gas grab samples were taken to measure the amount of hydrogen produced

  4. Sequencing of chemotherapy (CT) and radiotherapy (RT) following conservative surgery (CS) for patients with early-stage breast cancer: results of a randomized trial

    Recht, A; Come, SE; Silver, B; Gelman, RS; Hayes, DF; Shulman, LN; Henderson, IC; Harris, JR

    1995-07-01

    .03). Overall outcome and patterns of failure were analyzed by intent-to-treat; all enrolled pts were included. Median FU in surviving pts was 58 mo (range, 10-124 mo). Results: 5-yr actuarial failure rates (i.e., failure at any site) and overall survival (OS) rates were not statistically different between the arms, but the 5-yr actuarial total risk of developing distant metastases (DM) (i.e, at any time during observation) was significantly greater in the RT-first arm. The first sites of failure in the RT-first and CT-first arms were: local failure (LF) with or without simultaneous DM or regional nodal failure (RNF) - 9 vs. 14; RNF without other failure - 0 vs. 2; and DM (with or without simultaneous RNF) - 36 vs. 18. Of note, 1 LF in the RT-first arm was among the 2 pts who refused their assigned sequence. Because of differing lengths of potential observation for each pt, the 5-yr crude failure rates were used to assess the difference in patterns of failure. The difference was of borderline significance. The proportions of pts receiving at least 85% of the planned drug doses were lower in the RT-first arm than the CT-first arm for cyclophosphamide (46% v. 64%, p-bar=0.006), doxorubicin (43% vs. 64%, p-bar=0.002), and d.15 methotrexate (22% vs. 46%, p-bar=0.0002). There were no differences between the arms in the d.1 methotrexate or 5FU doses. Conclusions: The overall risk of distant failure was higher in the RT-first arm in this study. This may reflect both the longer interval to initiating CT and the lower drug doses given in pts first receiving RT. The risk of local failure was higher in the CT-first arm, consistent with prior studies suggesting that the SRI has an impact on the effectiveness of RT. Further study is needed of other factors that may affect these results. Alternative ways of combining RT and CT which do not sacrifice their effectiveness while minimizing treatment toxicity should be explored.

  5. Sequencing of chemotherapy (CT) and radiotherapy (RT) following conservative surgery (CS) for patients with early-stage breast cancer: results of a randomized trial

    Recht, A; Come, SE; Silver, B; Gelman, RS; Hayes, DF; Shulman, LN; Henderson, IC; Harris, JR

    1995-01-01

    .03). Overall outcome and patterns of failure were analyzed by intent-to-treat; all enrolled pts were included. Median FU in surviving pts was 58 mo (range, 10-124 mo). Results: 5-yr actuarial failure rates (i.e., failure at any site) and overall survival (OS) rates were not statistically different between the arms, but the 5-yr actuarial total risk of developing distant metastases (DM) (i.e, at any time during observation) was significantly greater in the RT-first arm. The first sites of failure in the RT-first and CT-first arms were: local failure (LF) with or without simultaneous DM or regional nodal failure (RNF) - 9 vs. 14; RNF without other failure - 0 vs. 2; and DM (with or without simultaneous RNF) - 36 vs. 18. Of note, 1 LF in the RT-first arm was among the 2 pts who refused their assigned sequence. Because of differing lengths of potential observation for each pt, the 5-yr crude failure rates were used to assess the difference in patterns of failure. The difference was of borderline significance. The proportions of pts receiving at least 85% of the planned drug doses were lower in the RT-first arm than the CT-first arm for cyclophosphamide (46% v. 64%, p-bar=0.006), doxorubicin (43% vs. 64%, p-bar=0.002), and d.15 methotrexate (22% vs. 46%, p-bar=0.0002). There were no differences between the arms in the d.1 methotrexate or 5FU doses. Conclusions: The overall risk of distant failure was higher in the RT-first arm in this study. This may reflect both the longer interval to initiating CT and the lower drug doses given in pts first receiving RT. The risk of local failure was higher in the CT-first arm, consistent with prior studies suggesting that the SRI has an impact on the effectiveness of RT. Further study is needed of other factors that may affect these results. Alternative ways of combining RT and CT which do not sacrifice their effectiveness while minimizing treatment toxicity should be explored

  6. A direct sensitivity approach to predict hourly ozone resulting from compliance with the National Ambient Air Quality Standard.

    Simon, Heather; Baker, Kirk R; Akhtar, Farhan; Napelenok, Sergey L; Possiel, Norm; Wells, Benjamin; Timin, Brian

    2013-03-05

    In setting primary ambient air quality standards, the EPA's responsibility under the law is to establish standards that protect public health. As part of the current review of the ozone National Ambient Air Quality Standard (NAAQS), the US EPA evaluated the health exposure and risks associated with ambient ozone pollution using a statistical approach to adjust recent air quality to simulate just meeting the current standard level, without specifying emission control strategies. One drawback of this purely statistical concentration rollback approach is that it does not take into account spatial and temporal heterogeneity of ozone response to emissions changes. The application of the higher-order decoupled direct method (HDDM) in the community multiscale air quality (CMAQ) model is discussed here to provide an example of a methodology that could incorporate this variability into the risk assessment analyses. Because this approach includes a full representation of the chemical production and physical transport of ozone in the atmosphere, it does not require assumed background concentrations, which have been applied to constrain estimates from past statistical techniques. The CMAQ-HDDM adjustment approach is extended to measured ozone concentrations by determining typical sensitivities at each monitor location and hour of the day based on a linear relationship between first-order sensitivities and hourly ozone values. This approach is demonstrated by modeling ozone responses for monitor locations in Detroit and Charlotte to domain-wide reductions in anthropogenic NOx and VOCs emissions. As seen in previous studies, ozone response calculated using HDDM compared well to brute-force emissions changes up to approximately a 50% reduction in emissions. A new stepwise approach is developed here to apply this method to emissions reductions beyond 50% allowing for the simulation of more stringent reductions in ozone concentrations. Compared to previous rollback methods, this

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

    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.

  8. A 3D T1-weighted gradient-echo sequence for routine use in 3D radiosurgical treatment planning of brain metastases: first clinical results

    Hawighorst, H.; Schad, L.R.; Gademann, G.; Knopp, M.V.; Wenz, F.; Kaick, G. van

    1995-01-01

    The authors report on a 3D sequence for MRI of the brain and its application in radiosurgical treatment planning of 35 brain metastases. The measuring sequence, called magnetization - prepared rapid gradient echo (MPRAGE), was compared with 2D T1-weighted spin-echo (SE) sequences following intravenous contrast-medium application in 19 patients with brain metastases. The average diameter of all lesions was similar in both sequences, with 16.8 and 17.0 mm for SE and MPRAGE, respectively. Target point definition was equal in 29 metastases, and in 6 cases superior on MPRAGE, due to better gray-white matter contrast and increased contrast enhancement. In cases of bleeding metastases there was improved depiction of internal structures in 3D MRI. Postprocessing of 3D MPRAGE data created multiplanar reconstruction along any chosen plane with isotropic spatial resolution, which helped to improve radiosurgical isodose distribution in 4 cases when compared to 2D SE. However, sensitivity of 3D MPRAGE to detect small lesions (< 3 mm) was decreased in one patient with more than 50 metastases. We conclude that 3D gradient-echo (GE) imaging might be of great value for radiosurgical treatment planning, but does not replace 2D SE with its current parameters. (orig.)

  9. Direct anthelmintic effects of a purified chicory extract against free-living stages of Cooperia oncophora: preliminary results

    Pena-Espinoza, Miguel Angel; Williams, A.; Enemark, Heidi L.

    2013-01-01

    with methanol as the extraction medium. The resulting extract was dried and fractionated using solid-phase extraction (SPE) cartridges to enhance isolation of secondary metabolites such as sesquiterpene lactones. The obtained elutate was dried, dissolved in 100 % DMSO and serially diluted to obtain...

  10. Augmentation of spelling therapy with transcranial direct current stimulation in primary progressive aphasia: Preliminary results and challenges.

    Tsapkini, Kyrana; Frangakis, Constantine; Gomez, Yessenia; Davis, Cameron; Hillis, Argye E

    Primary progressive aphasia (PPA) is a neurodegenerative disease that primarily affects language functions and often begins in the fifth or sixth decade of life. The devastating effects on work and family life call for the investigation of treatment alternatives. In this article, we present new data indicating that neuromodulatory treatment, using transcranial direct current stimulation (tDCS) combined with a spelling intervention, shows some promise for maintaining or even improving language, at least temporarily, in PPA. The main aim of the present article is to determine whether tDCS plus spelling intervention is more effective than spelling intervention alone in treating written language in PPA. We also asked whether the effects of tDCS are sustained longer than the effects of spelling intervention alone. We present data from six PPA participants who underwent anodal tDCS or sham plus spelling intervention in a within-subject crossover design. Each stimulation condition lasted 3 weeks or a total of 15 sessions with a 2-month interval in between. Participants were evaluated on treatment tasks as well as on other language and cognitive tasks at 2-week and 2-month follow-up intervals after each stimulation condition. All participants showed improvement in spelling (with sham or tDCS). There was no difference in the treated items between the two conditions. There was, however, consistent and significant improvement for untrained items only in the tDCS plus spelling intervention condition. Furthermore, the improvement lasted longer in the tDCS plus spelling intervention condition compared to sham plus spelling intervention condition. Neuromodulation with tDCS offers promise as a means of augmenting language therapy to improve written language function at least temporarily in PPA. The consistent finding of generalisation of treatment benefits to untreated items and the superior sustainability of treatment effects with tDCS justifies further investigations. However

  11. Finite element analysis of pedestrian lower limb fractures by direct force: the result of being run over or impact?

    Li, Zhengdong; Zou, Donghua; Liu, Ningguo; Zhong, Liangwei; Shao, Yu; Wan, Lei; Huang, Ping; Chen, Yijiu

    2013-06-10

    The elucidation and prediction of the biomechanics of lower limb fractures could serve as a useful tool in forensic practices. Finite element (FE) analysis could potentially help in the understanding of the fracture mechanisms of lower limb fractures frequently caused by car-pedestrian accidents. Our aim was (1) to develop and validate a FE model of the human lower limb, (2) to assess the biomechanics of specific injuries concerning run-over and impact loading conditions, and (3) to reconstruct one real car-pedestrian collision case using the model created in this study. We developed a novel lower limb FE model and simulated three different loading scenarios. The geometry of the model was reconstructed using Mimics 13.0 based on computed tomography (CT) scans from an actual traffic accident. The material properties were based upon a synthesis of data found in published literature. The FE model validation and injury reconstruction were conducted using the LS-DYNA code. The FE model was validated by a comparison of the simulation results of three-point bending, overall lateral impact tests and published postmortem human surrogate (PMHS) results. Simulated loading scenarios of running-over the thigh with a wheel, the impact on the upper leg, and impact on the lower thigh were conducted with velocities of 10 m/s, 20 m/s, and 40 m/s, respectively. We compared the injuries resulting from one actual case with the simulated results in order to explore the possible fracture bio-mechanism. The peak fracture forces, maximum bending moments, and energy lost ratio exhibited no significant differences between the FE simulations and the literature data. Under simulated run-over conditions, the segmental fracture pattern was formed and the femur fracture patterns and mechanisms were consistent with the actual injury features of the case. Our study demonstrated that this simulation method could potentially be effective in identifying forensic cases and exploring of the injury

  12. Results and status of the Edelweiss Wimp search experiment; Experience Edelweiss de recherche directe de Wimps: resultats et perspectives

    Benoit, A.; Berge, L.; Blumer, J.; Broniatowski, A.; Censier, B.; Chabert, L.; Chambon, B.; Chapellier, M.; Chardin, G.; Charvin, P.; Jesus, M. de; Drain, D.; Di Stefano, P.; Dumoulin, L.; Eitel, K.; Fesquet, M.; Firucci, S.; Gascon, J.; Gerbier, G.; Gerlic, E.; Goldbach, C.; Goyot, M.; Gros, M.; Habermahl, F.; Horn, M.; Hadjout, J.P.; Herve, S.; Juillard, A.; Kikuchi, C.; Lesquen, A. de; Luca, M.; Mallet, J.; Marnieros, S.; Martineau, O.; Mosca, L.; Navick, X.F.; Nollez, G.; Pari, P.; Riccio, C.; Sanglard, V.; Stern, M.; Vagneron, L.; Villard, V

    2005-07-01

    In the Edelweiss experiment, nuclear recoils induced by elastic collisions with WIMPs (weakly interacting massive particle) from the galactic halo are identified in low-temperature Ge detectors where the ratio of the heat and ionization signals provide an event-by-event discrimination of nuclear recoils from the dominant background coming from {gamma}-rays interactions. The Edelweiss experiment is located in the Modane underground facility in order to cut the muon flux drastically. We present here the results obtained during the first part of the experiment named Edelweiss-I that ended in the beginning of 2004. Since october 2002, 3 optimized 320 grams detectors have been simultaneously operated at a regulated temperature of 0.017 K and about 50 kg*day were added to the previous published data. These data are still under analysis but preliminary results concerning the upper limit at 90% CL (confidence level) confirm the limit already published in 2002. The first run of Edelweiss-II is due to begin during summer 2005, we are expecting to gain 2 orders of magnitude in terms of detector sensitivity and reach 0.002 events/day*kg. (A.C.)

  13. Genome Sequencing

    Sato, Shusei; Andersen, Stig Uggerhøj

    2014-01-01

    The current Lotus japonicus reference genome sequence is based on a hybrid assembly of Sanger TAC/BAC, Sanger shotgun and Illumina shotgun sequencing data generated from the Miyakojima-MG20 accession. It covers nearly all expressed L. japonicus genes and has been annotated mainly based on transcr......The current Lotus japonicus reference genome sequence is based on a hybrid assembly of Sanger TAC/BAC, Sanger shotgun and Illumina shotgun sequencing data generated from the Miyakojima-MG20 accession. It covers nearly all expressed L. japonicus genes and has been annotated mainly based...

  14. Alternate Directed Anthropogenic Shifts in Genotype Result in Different Ecological Outcomes in Coho Salmon Oncorhynchus kisutch Fry.

    Rosalind A Leggatt

    Full Text Available Domesticated and growth hormone (GH transgenic salmon provide an interesting model to compare effects of selected versus engineered phenotypic change on relative fitness in an ecological context. Phenotype in domestication is altered via polygenic selection of traits over multiple generations, whereas in transgenesis is altered by a single locus in one generation. These established and emerging technologies both result in elevated growth rates in culture, and are associated with similar secondary effects such as increased foraging, decreased predator avoidance, and similar endocrine and gene expression profiles. As such, there is concern regarding ecological consequences should fish that have been genetically altered escape to natural ecosystems. To determine if the type of genetic change influences fitness components associated with ecological success outside of the culture environments they were produced for, we examined growth and survival of domesticated, transgenic, and wild-type coho salmon fry under different environmental conditions. In simple conditions (i.e. culture with unlimited food, transgenic fish had the greatest growth, while in naturalized stream tanks (limited natural food, with or without predators domesticated fish had greatest growth and survival of the three fish groups. As such, the largest growth in culture conditions may not translate to the greatest ecological effects in natural conditions, and shifts in phenotype over multiple rather than one loci may result in greater success in a wider range of conditions. These differences may arise from very different historical opportunities of transgenic and domesticated strains to select for multiple growth pathways or counter-select against negative secondary changes arising from elevated capacity for growth, with domesticated fish potentially obtaining or retaining adaptive responses to multiple environmental conditions not yet acquired in recently generated transgenic

  15. Compressing DNA sequence databases with coil

    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 growth of cobalt aluminum double hydroxides on graphene nanosheets and the capacitive properties of the resulting composites

    Kim, Yuna; Kim, Seok

    2015-01-01

    We synthesized graphene nanosheets (GNs)/cobalt aluminum (CoAl) double hydroxide composites through a layer-by-layer deposition process while varying the concentration of the graphene precursor used. The CoAl layered double hydroxide particles were uniformly distributed on the surfaces of the graphene layers and effectively prevented the agglomeration of the GNs, resulting in a higher reactive surface area and easier ion transport. We employed X-ray diffraction analysis, energy-dispersive X-ray spectroscopy, field-emission scanning electron microscopy, and field-emission transmission electron microscopy to investigate the microstructures and morphologies of the composites. In addition, cyclic voltammetry, electrochemical impedance spectroscopy, and galvanostatic charge/discharge measurements were performed to analyze the electrochemical behaviors of the composites. The as-prepared composites showed desirable electrochemical characteristics, including high specific capacitances, low resistances, and high cycling stabilities. In particular, the composite formed by optimizing the GNs/CoAl ratio (the electrolyte used was a 6 M aqueous KOH solution) exhibited the maximum specific capacitance, which was 974 F g −1

  17. Analysis of tracer tests with multirate diffusion models: recent results and future directions within the WIPP project

    McKenna, S.A.; Meigs, L.C.; Altman, S.J.; Haggerty, R.

    1998-01-01

    A series of single-well injection-withdrawal (SWIW) and two-well convergent-flow (TWCF) tracer tests were conducted in the Culebra dolomite at the WIPP site in late 1995 and early 1996. Modeling analyses over the past year have focused on reproducing the observed mass-recovery curves and understanding the basis physical processes controlling tracer transport in SWIW and TWCF tests. To date, specific modeling efforts have focused on five SWIW tests and one TWCF pathway at each of two different locations. An inverse parameter-estimation procedure was implemented to model the SWIW and TWCF tests with both traditional and multirate double-porosity formulations. The traditional model assumes a single diffusion rate while the multirate model uses a first-order approximation to model a continuous distribution of diffusion coefficients. Conceptually, the multirate model represents variable matrix block sizes within the Culebra as observed in geologic investigations and also variability in diffusion rates within the matrix blocks as observed with X-ray imaging in the laboratory. Single-rate double-porosity models cannot provide an adequate match to the SWIW data. Multirate double-porosity models provide excellent fits to all five SWIW mass-recovery curves. Models of the TWCF tests show that, at one location, the tracer test can be modeled with both single-rate and multirate double-porosity models. At the other location, only the multi-rate double-porosity model is capable of explaining the test results

  18. Serum 3,3'-L-diiodothyronine, a direct radioimmunoassay in human serum: method and clinical results

    Burger, A.; Sakoloff, C.

    1977-01-01

    A specific radioimmunoassay for 3,3'-diiodothyronine (T 2 ) is described which is capable of detecting as little as 1.3 ng/dl. The antiserum recognizes mainly T 2 ; biliary conjugates of T 2 bind slightly to the antibody. The intraassay and interassay coefficients of variation were, respectively, 5.7% and 13.1%. T 2 was detected in the serum of hypothyroid patients treated with triiodothyronine (T 3 ) and in euthyroid subjects treated with reverse triiodothyronine (rT 3 ). These results suggest that both T 3 and rT 3 are deiodinated to T 2 . Serum concentrations of T 2 in normal subjects decreased with age. Between 20 and 40 years the mean concentration was 4.3 +- 2.0 ng/dl (2 SD), between 41 and 60 years it varied from 1.9 to 5.8 ng/dl (3.8 +- 0.3 ng/dl, SE) and in elderly subjects have 60 years concentrations varied from unmeasurable to 4 ng/dl (2.9 +- 0.4 ng/dl, SE). Low serum T 2 concentrations were found in anorexia nervosa (2.5 +- 0.3 ng/dl, SE). In hypothyroidism the serum concentrations were low or unmeasurable. As most of the hypothyroid subjects were elderly their serum T 2 concentrations overlapped with the low values found in the elderly euthyroid subjects. In classical hyperthyroidism serum T 2 concentrations were greatly increased (3.3 to 31 ng/dl (11.8 +- 2.7 ng/dl, SE) but in ''T 3 toxicosis'' the concentrations were only modestly increased

  19. SU-F-SPS-03: Direct Measurement of Organ Doses Resulting From Head and Cervical Spine Trauma CT Protocols

    Carranza, C; Lipnharski, I; Quails, N; Correa, N; Rill, L; Arreola, M [University of Florida, Gainesville, FL (United States)

    2016-06-15

    Purpose: This retrospective study analyzes the exposure history of emergency department (ED) patients undergoing head and cervical spine trauma computed tomography (CT) studies. This study investigated dose levels received by trauma patients and addressed any potential concerns regarding radiation dose issues. Methods: Under proper IRB approval, a cohort of 300 trauma cases of head and cervical spine trauma CT scans received in the ED was studied. The radiological image viewing software of the hospital was used to view patient images and image data. The following parameters were extracted: the imaging history of patients, the reported dose metrics from the scanner including the volumetric CT Dose Index (CTDIvol) and Dose Length Product (DLP). A postmortem subject was scanned using the same scan techniques utilized in a standard clinical head and cervical spine trauma CT protocol with 120 kVp and 280 mAs. The CTDIvol was recorded for the subject and the organ doses were measured using optically stimulated luminescent (OSL) dosimeters. Typical organ doses to the brain, thyroid, lens, salivary glands, and skin, based on the cadaver studies, were then calculated and reported for the cohort. Results: The CTDIvol reported by the CT scanner was 25.5 mGy for the postmortem subject. The average CTDIvol from the patient cohort was 34.1 mGy. From these metrics, typical average organ doses in mGy were found to be: Brain (44.57), Thyroid (33.40), Lens (82.45), Salivary Glands (61.29), Skin (47.50). The imaging history of the cohort showed that on average trauma patients received 26.1 scans over a lifetime. Conclusion: The average number of scans received on average by trauma ED patients shows that radiation doses in trauma patients may be a concern. Available dose tracking software would be helpful to track doses in trauma ED patients, highlighting the importance of minimizing unnecessary scans and keeping doses ALARA.

  20. Early results from an angiosome-directed open surgical technique for venous arterialization in patients with critical lower limb ischemia

    Kim Houlind

    2013-12-01

    Full Text Available Background: Patients with critical lower limb ischemia without patent pedal arteries cannot be treated by the conventional arterial reconstruction. Venous arterialization has been suggested to improve limb salvage in this subgroup of patients but has not gained wide acceptance. We report our early experience after implementing deep and superficial venous arterialization of the lower limb. Materials and methods: Ten patients with critical ischemia and without crural or pedal arteries available for conventional bypass surgery or angioplasty were treated with distal venous arterialization. Inflow was from the most distal unobstructed segment. Run-off was the dorsal pedal venous arch (n=5, the dorsal pedal venous arch and a concomitant vein of the posterior tibial artery (n=3, or the dorsal pedal venous arch and a concomitant vein of the common plantar artery (n=2 depending on the location of the ischemic lesion. Venous valves were destroyed using antegrade valvulotomes, guide wires, knob needles, or retrograde valvulotomes via an extra incision. Results: Seven of the operated limbs were amputated after 23 (1–256 days (median [range]. The main reasons for amputation were lack of healing of either the original wound, of incisional wounds on the foot, or persisting pain at rest. In three cases, the bypass was open at the time of amputation. Two patients experienced complete wound healing after 231 and 342 days, respectively. By the end of follow-up, the last patient was ambulating with slow wound healing but without pain 309 days after surgery. Conclusion: Venous arterialization may be used as a treatment of otherwise unsalveable limbs. The success rate is, however, limited. Technical optimization of the technique is warranted.

  1. Analysis of Tracer Tests with Multirate Diffusion Models: Recent Results and Future Directions within the WIPP Project

    ALTMAN, SUSAN J.; HAGGERTY, ROY; MCKENNA, SEAN A.; MEIGS, LUCY C.

    1999-01-01

    A series of single-well injection-withdrawal (SWIW) and two-well convergent-flow (TWCF) tracer tests were conducted in the Culebra dolomite at the WIPP site in late 1995 and early 1996. Modeling analyses over the past year have focused on reproducing the observed mass-recovery curves and understanding the basic physical processes controlling tracer transport in SWIW and TWCF tests. To date, specific modeling efforts have focused on five SWIW tests and one TWCF pathway at each of two different locations (H-11 and H-19 hydropads). An inverse parameter-estimation procedure was implemented to model the SWIW and TWCF tests with both traditional and multirate double-porosity formulations. The traditional model assumes a single diffusion rate while the multirate model uses a first-order approximation to model a continuous distribution of diffusion coefficients. Conceptually, the multirate model represents variable matrix block sizes within the Culebra as observed in geologic investigations and also variability in diffusion rates within the matrix blocks as observed with X-ray imaging in the laboratory. Single-rate double-porosity models cannot provide an adequate match to the SWIW data. Multirate double-porosity models provide excellent fits to all five SWIW mass-recovery curves. Models of the TWCF tests show that, at one location, the tracer test can be modeled with both single-rate and multirate double-porosity models. At the other location, only the multi-rate double-porosity model is capable of explaining the test results

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

    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...

  3. Genetic homogeneity in longtail tuna Thunnus tonggol (Bleeker, 1851) from the northwest coast of India inferred from direct sequencing analysis of the mitochondrial DNA D-loop region

    Kunal, S.P.; GirishKumar; Menezes, M.R.; Meena, R.M.

    of population differentiation showed no significant genetic differentiation between the two sampling localities (~HST = 0.005, P = 0.200) Results were further corroborated by a non-significant nearest-neighbour statistic (Snn = 0.489, P = 0...

  4. Cost that is Directly Incurred as a Result of Operating the Train Service on the 1520 mm Rail with Primarily Freight Transportation

    Hudenko, J; Ribakova, N; Počs, R

    2016-01-01

    Under the Directive 2012/34/EU (21 November 2012) "the charges for … [rail] infrastructure … shall be set at the cost that is directly incurred as a result of operating the train service". This charging rule is new for Baltic States’ railways, where due to the favorable geographic position a full cost application without detalization was possible. Although, a big number of relevant studies on the issue was made in EU, all of them covered only 1435mm railways with primarily passenger transport...

  5. Direct CP violation results in $K^{\\pm} \\rightarrow 3\\pi^{\\pm}$ decays from NA48/2 experiment at CERN

    Biino, Cristina

    2006-01-01

    After firmly establishing direct CP Violation in two pions decays of neutral kaons, the NA48 experiment, during the 2003 run at CERN-SPS, has collected more than 1.6 billion of charged kaon decays into three charged pions, using a unique double beam technique which allows a high level of control on systematic effects. The measurement of the direct CP violation Dalitz plot linear slope asymmetry parameter A$_{g}$ is reported. This result corresponds to more than an order of magnitude improvement in precision with respect to previous experiments and is limited by the statistics of the data sample.

  6. Changes in state of stress on the southern san andreas fault resulting from the california earthquake sequence of april to june 1992.

    Jaumé, S C; Sykes, L R

    1992-11-20

    The April to June 1992 Landers earthquake sequence in southern California modified the state of stress along nearby segments of the San Andreas fault, causing a 50-kilometer segment of the fault to move significantly closer to failure where it passes through a compressional bend near San Gorgonio Pass. The decrease in compressive normal stress may also have reduced fluid pressures along that fault segment. As pressures are reequilibrated by diffusion, that fault segment should move closer to failure with time. That fault segment and another to the southeast probably have not ruptured in a great earthquake in about 300 years.

  7. Direct and self-reported measures of physical activity and sedentary behaviours by weight status in school-aged children: results from ISCOLE-Kenya.

    Muthuri, Stella K; Wachira, Lucy-Joy M; Onywera, Vincent O; Tremblay, Mark S

    2015-01-01

    Previous work has shown little association between self-report and directly measured physical activity. The objective of this study was to investigate the relationships between self-reported and directly assessed measures of physical activity and sedentary time by weight status in Kenyan children. Direct assessment of body weight, physical activity and sedentary time of 563 children was collected through anthropometry and accelerometry, while self-reported assessment was achieved by administering a questionnaire. Under/healthy weight children had significantly higher directly measured mean daily minutes of moderate-to-vigorous physical activity (MVPA) compared to overweight/obese children (39 vs 20 minutes); had lower mean weekend-day minutes of sedentary time (346 vs 365 minutes); had a higher proportion who met accepted physical activity guidelines (15.3% vs 2.6%); and a higher number reported using active transportation to/from school (49.2% vs 32.4%). Self-reported time spent outside before and after school and active transport to/from school were significantly associated with mean weekday minutes of MVPA (r-value range = 0.12-0.36), but only for the under/healthy weight children. The results of this study found a number of differences in the accumulation of MVPA and sedentary time by weight status and weak-to-moderate correlations between self-report and direct measures of weekday and weekend-day physical activity among the under/healthy weight children.

  8. Characterization of fungi in office dust: Comparing results of microbial secondary metabolites, fungal internal transcribed spacer region sequencing, viable culture and other microbial indices.

    Park, J-H; Sulyok, M; Lemons, A R; Green, B J; Cox-Ganser, J M

    2018-05-04

    Recent developments in molecular and chemical methods have enabled the analysis of fungal DNA and secondary metabolites, often produced during fungal growth, in environmental samples. We compared 3 fungal analytical methods by analysing floor dust samples collected from an office building for fungi using viable culture, internal transcribed spacer (ITS) sequencing and secondary metabolites using liquid chromatography-tandem mass spectrometry. Of the 32 metabolites identified, 29 had a potential link to fungi with levels ranging from 0.04 (minimum for alternariol monomethylether) to 5700 ng/g (maximum for neoechinulin A). The number of fungal metabolites quantified per sample ranged from 8 to 16 (average = 13/sample). We identified 216 fungal operational taxonomic units (OTUs) with the number per sample ranging from 6 to 29 (average = 18/sample). We identified 37 fungal species using culture, and the number per sample ranged from 2 to 13 (average = 8/sample). Agreement in identification between ITS sequencing and culturing was weak (kappa = -0.12 to 0.27). The number of cultured fungal species poorly correlated with OTUs, which did not correlate with the number of metabolites. These suggest that using multiple measurement methods may provide an improved understanding of fungal exposures in indoor environments and that secondary metabolites may be considered as an additional source of exposure. © 2018 John Wiley & Sons A/S. Published by John Wiley & Sons Ltd.

  9. Acid-fast Smear and Histopathology Results Provide Guidance for the Appropriate Use of Broad-Range Polymerase Chain Reaction and Sequencing for Mycobacteria.

    Miller, Kennon; Harrington, Susan M; Procop, Gary W

    2015-08-01

    New molecular diagnostic tests are attractive because of the potential they hold for improving diagnostics in microbiology. The value of these tests, which is often assumed, should be investigated to determine the best use of these potentially powerful tools. To investigate the usefulness of broad-range polymerase chain reaction (PCR), followed by sequencing, in mycobacterial infections. We reviewed the test performance of acid-fast bacilli (AFB) PCR and traditional diagnostic methods (histopathology, AFB smear, and culture). We assessed the diagnostic effect and cost of the unrestricted ordering of broad-range PCR for the detection and identification of mycobacteria in clinical specimens. The AFB PCR was less sensitive than culture and histopathology and was less specific than culture, AFB smear, and histopathology. During 18 months, $93 063 was spent on 183 patient specimens for broad-range PCR and DNA sequencing for mycobacteria to confirm one culture-proven Mycobacterium tuberculosis infection that was also known to be positive by AFB smear and histopathology. In this cohort, there was a false-negative AFB PCR for M tuberculosis and a false-positive AFB PCR for Mycobacterium lentiflavum . Testing of AFB smear-negative specimens from patients without an inflammatory response supportive of a mycobacterial infection is costly and has not been proven to improve patient care. Traditional diagnostics (histopathology, AFB smear, and culture) should remain the primary methods for the detection of mycobacteria in clinical specimens.

  10. 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

    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

  11. Site directed recombination

    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.

  12. Risk and direct protective factors for youth violence: results from the Centers for Disease Control and Prevention's Multisite Violence Prevention Project.

    Henry, David B; Tolan, Patrick H; Gorman-Smith, Deborah; Schoeny, Michael E

    2012-08-01

    This study was conducted as part of a multisite effort to examine risk and direct protective factors for youth violence. The goal was to identify those factors in the lives of young people that increase or decrease the risk of violence. These analyses fill an important gap in the literature, as few studies have examined risk and direct protective factors for youth violence across multiple studies. Data on 4432 middle-school youth, from the CDC Multisite Violence Prevention Project were used. Evaluations were made of effects of variables coded as risk and direct protective factors in the fall of 6th grade on violence measured in spring of 7th and 8th grades. Factors tested included depression, delinquency, alcohol and drug involvement, involvement in family activities, academic achievement, attitudes toward school, truancy, and peer deviance. Most variables were coded with two sets of dummy variables indicating risk and protective directions of effects. Results showed that higher teacher-rated study skills were associated with lower subsequent violence across genders and ethnic groups. Affiliation with deviant peers was significantly associated with increased subsequent violence among youth reporting their race/ethnicity as white or other, marginally associated with increased violence among African-American youth, and unrelated among Latino youth. This study identified some factors than should be areas of interest for effective prevention programs. Some ethnic differences also should be considered in planning of prevention. The CDC Multisite Violence Prevention Project completed enrollment prior to July 2005. Copyright © 2012. Published by Elsevier Inc.

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

    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.

  14. Culture and Next-generation sequencing-based drug susceptibility testing unveil high levels of drug-resistant-TB in Djibouti: results from the first national survey.

    Tagliani, Elisa; Hassan, Mohamed Osman; Waberi, Yacine; De Filippo, Maria Rosaria; Falzon, Dennis; Dean, Anna; Zignol, Matteo; Supply, Philip; Abdoulkader, Mohamed Ali; Hassangue, Hawa; Cirillo, Daniela Maria

    2017-12-15

    Djibouti is a small country in the Horn of Africa with a high TB incidence (378/100,000 in 2015). Multidrug-resistant TB (MDR-TB) and resistance to second-line agents have been previously identified in the country but the extent of the problem has yet to be quantified. A national survey was conducted to estimate the proportion of MDR-TB among a representative sample of TB patients. Sputum was tested using XpertMTB/RIF and samples positive for MTB and resistant to rifampicin underwent first line phenotypic susceptibility testing. The TB supranational reference laboratory in Milan, Italy, undertook external quality assurance, genotypic testing based on whole genome and targeted-deep sequencing and phylogenetic studies. 301 new and 66 previously treated TB cases were enrolled. MDR-TB was detected in 34 patients: 4.7% of new and 31% of previously treated cases. Resistance to pyrazinamide, aminoglycosides and capreomycin was detected in 68%, 18% and 29% of MDR-TB strains respectively, while resistance to fluoroquinolones was not detected. Cluster analysis identified transmission of MDR-TB as a critical factor fostering drug resistance in the country. Levels of MDR-TB in Djibouti are among the highest on the African continent. High prevalence of resistance to pyrazinamide and second-line injectable agents have important implications for treatment regimens.

  15. Internal event analysis for Laguna Verde Unit 1 Nuclear Power Plant. Accident sequence quantification and results; Analisis de eventos internos para la Unidad 1 de la Central Nucleoelectrica de Laguna Verde. Cuantificacion de secuencias de accidente y resultados

    Huerta B, A; Aguilar T, O; Nunez C, A; Lopez M, R [Comision Nacional de Seguridad Nuclear y Salvaguardias, 03000 Mexico D.F. (Mexico)

    1994-07-01

    The Level 1 results of Laguna Verde Nuclear Power Plant PRA are presented in the {sup I}nternal Event Analysis for Laguna Verde Unit 1 Nuclear Power Plant, CNSNS-TR 004, in five volumes. The reports are organized as follows: CNSNS-TR 004 Volume 1: Introduction and Methodology. CNSNS-TR4 Volume 2: Initiating Event and Accident Sequences. CNSNS-TR 004 Volume 3: System Analysis. CNSNS-TR 004 Volume 4: Accident Sequence Quantification and Results. CNSNS-TR 005 Volume 5: Appendices A, B and C. This volume presents the development of the dependent failure analysis, the treatment of the support system dependencies, the identification of the shared-components dependencies, and the treatment of the common cause failure. It is also presented the identification of the main human actions considered along with the possible recovery actions included. The development of the data base and the assumptions and limitations in the data base are also described in this volume. The accident sequences quantification process and the resolution of the core vulnerable sequences are presented. In this volume, the source and treatment of uncertainties associated with failure rates, component unavailabilities, initiating event frequencies, and human error probabilities are also presented. Finally, the main results and conclusions for the Internal Event Analysis for Laguna Verde Nuclear Power Plant are presented. The total core damage frequency calculated is 9.03x 10-5 per year for internal events. The most dominant accident sequences found are the transients involving the loss of offsite power, the station blackout accidents, and the anticipated transients without SCRAM (ATWS). (Author)

  16. Genomic sequencing in clinical trials

    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...

  17. Biosensors for DNA sequence detection

    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.

  18. Sequence swapping does not result in conformation swapping for the beta4/beta5 and beta8/beta9 beta-hairpin turns in human acidic fibroblast growth factor.

    Kim, Jaewon; Lee, Jihun; Brych, Stephen R; Logan, Timothy M; Blaber, Michael

    2005-02-01

    The beta-turn is the most common type of nonrepetitive structure in globular proteins, comprising ~25% of all residues; however, a detailed understanding of effects of specific residues upon beta-turn stability and conformation is lacking. Human acidic fibroblast growth factor (FGF-1) is a member of the beta-trefoil superfold and contains a total of five beta-hairpin structures (antiparallel beta-sheets connected by a reverse turn). beta-Turns related by the characteristic threefold structural symmetry of this superfold exhibit different primary structures, and in some cases, different secondary structures. As such, they represent a useful system with which to study the role that turn sequences play in determining structure, stability, and folding of the protein. Two turns related by the threefold structural symmetry, the beta4/beta5 and beta8/beta9 turns, were subjected to both sequence-swapping and poly-glycine substitution mutations, and the effects upon stability, folding, and structure were investigated. In the wild-type protein these turns are of identical length, but exhibit different conformations. These conformations were observed to be retained during sequence-swapping and glycine substitution mutagenesis. The results indicate that the beta-turn structure at these positions is not determined by the turn sequence. Structural analysis suggests that residues flanking the turn are a primary structural determinant of the conformation within the turn.

  19. Effective Endovascular Treatment of Calcified Femoropopliteal Disease With Directional Atherectomy and Distal Embolic Protection: Final Results of the DEFINITIVE Ca++ Trial

    Roberts, David; Niazi, Khusrow; Miller, William; Krishnan, Prakash; Gammon, Roger; Schreiber, Theodore; Shammas, Nicolas W; Clair, Daniel

    2014-01-01

    Objectives The purpose of the DEFINITIVE Ca++ study was to evaluate the safety and effectiveness of directional atherectomy and distal embolic protection, used together to treat moderate to severely calcified femoropopliteal lesions. Background Despite advances in endovascular treatment modalities, treatment of calcified lesions remains a challenge. Methods A total of 133 subjects with 168 moderate to severely calcified lesions were enrolled. Lesions were treated with directional atherectomy devices, coupled with distal embolic protection. Results The 30-day freedom from MAE rate was 93.1%. Per angiographic core laboratory assessment, the primary effectiveness endpoint (≤50% residual diameter stenosis) was achieved in 92.0% (lower confidence bound of 87.6%) of lesions. By core lab analysis, these results did not achieve the success criteria (90%) for the primary effectiveness objective. Per site assessment, the objective was met with the endpoint being achieved in 97.0% (lower confidence bound 93.8%). A mean residual diameter stenosis of 33.3% was achieved with the directional atherectomy device. This was further decreased to 24.1% with the use of adjunctive therapy. The proportion of asymptomatic subjects [Rutherford Clinical Category (RCC) = 0] increased from 0% at baseline to 52.3% at the 30-day follow-up visit. In total, 88.5% of subjects experienced an improvement of one or more Rutherford categories. Conclusions The results of the DEFINITIVE Ca++ study demonstrate that the SilverHawk™ and TurboHawk™ atherectomy devices are safe and effective in the endovascular treatment of moderate to severely calcified lesions in the superficial femoral and/or popliteal arteries when used with the SpiderFX™ distal embolic protection device. © 2014 Wiley Periodicals, Inc. PMID:24402764

  20. The direct and indirect effects of lurasidone monotherapy on functional improvement among patients with bipolar depression: results from a randomized placebo-controlled trial.

    Rajagopalan, Krithika; Bacci, Elizabeth Dansie; Wyrwich, Kathleen W; Pikalov, Andrei; Loebel, Antony

    2016-12-01

    Bipolar depression is characterized by depressive symptoms and impairment in many areas of functioning, including work, family, and social life. The objective of this study was to assess the independent, direct effect of lurasidone treatment on functioning improvement, and examine the indirect effect of lurasidone treatment on functioning improvement, mediated through improvements in depression symptoms. Data from a 6-week placebo-controlled trial assessing the effect of lurasidone monotherapy versus placebo in patients with bipolar depression was used. Patient functioning was measured using the Sheehan disability scale (SDS). Descriptive statistics were used to assess the effect of lurasidone on improvement on the SDS total and domain scores (work/school, social, and family life), as well as number of days lost and unproductive due to symptoms. Path analyses evaluated the total effect (β1), as well as the indirect effect (β2×β3) and direct effect (β4) of lurasidone treatment on SDS total score change, using standardized beta path coefficients and baseline scores as covariates. The direct effect of treatment on SDS total score change and indirect effects accounting for mediation through depression improvement were examined for statistical significance and magnitude using MPlus. In this 6-week trial (N = 485), change scores from baseline to 6-weeks were significantly larger for both lurasidone treatment dosage groups versus placebo on the SDS total and all three SDS domain scores (p accounting for depression improvement. Results demonstrated statistically significant improvement in functioning among patients on lurasidone monotherapy compared to placebo. Improvement in functioning among patients on lurasidone was largely mediated through a reduction in depression symptoms, but lurasidone also had a medium and statistically significant independent direct effect in improving functioning.

  1. Effective endovascular treatment of calcified femoropopliteal disease with directional atherectomy and distal embolic protection: final results of the DEFINITIVE Ca⁺⁺ trial.

    Roberts, David; Niazi, Khusrow; Miller, William; Krishnan, Prakash; Gammon, Roger; Schreiber, Theodore; Shammas, Nicolas W; Clair, Daniel

    2014-08-01

    The purpose of the DEFINITIVE Ca(++) study was to evaluate the safety and effectiveness of directional atherectomy and distal embolic protection, used together to treat moderate to severely calcified femoropopliteal lesions. Despite advances in endovascular treatment modalities, treatment of calcified lesions remains a challenge. A total of 133 subjects with 168 moderate to severely calcified lesions were enrolled. Lesions were treated with directional atherectomy devices, coupled with distal embolic protection. The 30-day freedom from MAE rate was 93.1%. Per angiographic core laboratory assessment, the primary effectiveness endpoint (≤50% residual diameter stenosis) was achieved in 92.0% (lower confidence bound of 87.6%) of lesions. By core lab analysis, these results did not achieve the success criteria (90%) for the primary effectiveness objective. Per site assessment, the objective was met with the endpoint being achieved in 97.0% (lower confidence bound 93.8%). A mean residual diameter stenosis of 33.3% was achieved with the directional atherectomy device. This was further decreased to 24.1% with the use of adjunctive therapy. The proportion of asymptomatic subjects [Rutherford Clinical Category (RCC) = 0] increased from 0% at baseline to 52.3% at the 30-day follow-up visit. In total, 88.5% of subjects experienced an improvement of one or more Rutherford categories. The results of the DEFINITIVE Ca++ study demonstrate that the SilverHawk and TurboHawk atherectomy devices are safe and effective in the endovascular treatment of moderate to severely calcified lesions in the superficial femoral and/or popliteal arteries when used with the SpiderFX distal embolic protection device. © 2014 The Authors. Catheterization and Cardiovascular Interventions. Published by Wiley Periodicals, Inc.

  2. Thyroid doses in Belarus resulting from the Chernobyl accident: comparison of the estimates based on direct thyroid measurements and on measurements of 131I in milk

    Shinkarev, Sergey; Gavrilin, Yury; Khrouch, Valery; Savkin, Mikhail; Bouville, Andre; Luckyanov, Nicholas

    2008-01-01

    A substantial increase of childhood cancer cases observed in Belarus, Ukraine and Russia after the Chernobyl accident has been associated with thyroid exposure to radio iodines following the accident. A large number of direct thyroid measurements (i.e. measurement of the exposure rate near the thyroid of the subject)were conducted in Belarus during a few weeks after the accident. Individual thyroid doses based on results of the direct thyroid measurements were estimated for about 126,000 Belarusian residents and settlement-average thyroid doses for adults were calculated for 426 contaminated settlements in Gomel and Mogilev Oblasts. Another set of settlement-average thyroid doses for adults was estimated based on results of activity measurements in milk samples for 28 settlements (with not less than 2 spectrometric measurements) and 155 settlements (with not less than 5 total beta-activity measurements) in Gomel and Mogilev Oblasts. Concentrations of 131 I in milk were derived from these measurements. In the estimation of this set of thyroid doses, it was assumed that adults consumed 0.5 L d -1 of milk locally produced. The two sets of dose estimates were compared for 47 settlements, for which simultaneously were available a dose estimate based on thyroid measurements and a dose estimate based either on spectrometric or radiometric milk data. The settlement average thyroid doses based on milk activity measurements were higher than those based on direct thyroid measurements by a factor of 1.8 for total beta-activity measurements (30 settlements were compared) and by a factor of 2.4 for spectrometric measurements (17 settlements). This systematic difference can be explained by overestimation of the milk consumption rate used in the calculation of the milk-based thyroid doses and/or by application of individual countermeasures by people. (author)

  3. Algorithm for counting large directed loops

    Bianconi, Ginestra [Abdus Salam International Center for Theoretical Physics, Strada Costiera 11, 34014 Trieste (Italy); Gulbahce, Natali [Theoretical Division and Center for Nonlinear Studies, Los Alamos National Laboratory, NM 87545 (United States)

    2008-06-06

    We derive a Belief-Propagation algorithm for counting large loops in a directed network. We evaluate the distribution of the number of small loops in a directed random network with given degree sequence. We apply the algorithm to a few characteristic directed networks of various network sizes and loop structures and compare the algorithm with exhaustive counting results when possible. The algorithm is adequate in estimating loop counts for large directed networks and can be used to compare the loop structure of directed networks and their randomized counterparts.

  4. Experimental data suggesting that inflammation mediated rat liver mitochondrial dysfunction results from secondary hypoxia rather than from direct effects of inflammatory mediators

    Adelheid eWeidinger

    2013-06-01

    Full Text Available Systemic inflammatory response (SIR comprises direct effects of inflammatory mediators (IM and indirect effects, such as secondary circulatory failure which results in tissue hypoxia (HOX. These two key components, SIR and HOX, cause multiple organ failure (MOF. Since HOX and IM occur and interact simultaneously in vivo, it is difficult to clarify their individual pathological impact. To eliminate this interaction, precision cut liver slices (PCLS were used in this study aiming to dissect the effects of HOX and IM on mitochondrial function, integrity of cellular membrane and the expression of genes associated with inflammation. HOX was induced by incubating PCLS or rat liver mitochondria at pO2<1% followed by reoxygenation (HOX/ROX model. Inflammatory injury was stimulated by incubating PCLS with IM (IM model. We found upregulation of inducible nitric oxide synthase (iNOS expression only in the IM model, while heme oxygenase 1 (HO-1 expression was upregulated only in the HOX/ROX model. Elevated expression of interleukin 6 (IL-6 was found in both models reflecting converging pathways regulating the expression of this gene. Both models caused damage to hepatocytes resulting in the release of alanine aminotransferase (ALT. The leakage of aspartate aminotransferase (AST was observed only during the hypoxic phase in the HOX/ROX model. The reoxygenation phase of HOX, but not IM, drastically impaired mitochondrial electron supply via complex I and II. Additional experiments performed with isolated mitochondria showed that free iron, released during HOX, is likely a key prerequisite of mitochondrial dysfunction induced during the reoxygenation phase. Our data suggests that mitochondrial dysfunction, previously observed in in vivo SIR-models is the result of secondary circulatory failure inducing HOX rather than the result of a direct interaction of IM with liver cells.

  5. Aspects of coverage in medical DNA sequencing

    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.

  6. Body fluid identification using a targeted mRNA massively parallel sequencing approach - results of a EUROFORGEN/EDNAP collaborative exercise

    Ingold, S; Dørum, G; Hanson, E

    2018-01-01

    to specified protocols. The provided primer pools for the Illumina MiSeq/FGx and the Ion Torrent PGM/S5 platforms included 33 and 29 body fluid specific targets, respectively, to identify blood, saliva, semen, vaginal secretion, menstrual blood and skin. The results demonstrated moderate to high count values...

  7. Region segmentation along image sequence

    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

  8. Mapping sequences by parts

    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.

  9. Report on 1981 result of Sunshine Project. Research on direct liquefaction reactor of coal; 1981 nendo sekitan no chokusetsu ekika hannoki no kenkyu seika hokokusho

    NONE

    1981-07-01

    This paper explains the results of research on direct liquefaction reaction of coal in fiscal 1981. The direct liquefaction is a reaction of three phases, gas-liquid-solid, under high temperature and high pressure. A tube type was employed in order to increase volume efficiency of the reactor, the continuous phase disperse number was decreased in order to bring it close to plug flow, and the paste Re number was increased to some extent in order to prevent sedimentation of coal particles. Hydrogen was supplied from the tube halfway for the purpose of supplementing the lowering of hydrogen partial pressure with the progress of reaction. A gas-liquid separator was installed so that increase in gas quantity was controlled in the rear stage of the reactor. As for catalysts, iron ore-sulfur system was examined which was promising as a disposable catalyst in place of the conventional iron system. Effect of catalytic addition was clearly recognizable in comparison with non-catalytic, with an exothermic peak observed comparable to the coal hydrogenation reaction of 350-420 degree C. Its catalytic effect was also presumable from the high pressure differential thermal analysis curve. The catalytic mechanism in the case where sulfur is added to hematite and limonite is similar to that of Fe{sub 2}O{sub 3} - sulfur catalyst, with the center of activity supposed to be Fe{sub 1-x}S. The catalytic effect is largely dependent on the particle size. (NEDO)

  10. Estimation of shortwave direct aerosol radiative forcing at four locations on the Indo-Gangetic plains: Model results and ground measurement

    Bibi, Humera; Alam, Khan; Bibi, Samina

    2017-08-01

    This study provides observational results of aerosol optical and radiative characteristics over four locations in IGP. Spectral variation of Aerosol Optical Depth (AOD), Single Scattering Albedo (SSA) and Asymmetry Parameter (AP) were analysed using AErosol RObotic NETwork (AERONET) data. The analysis revealed that coarse particles were dominant in summer and pre-monsoon, while fine particles were more pronounced in winter and post-monsoon. Furthermore, the spatio-temporal variations of Shortwave Direct Aerosol Radiative Forcing (SDARF) and Shortwave Direct Aerosol Radiative Forcing Efficiency (SDARFE) at the Top Of Atmosphere (TOA), SURface (SUR) and within ATMosphere (ATM) were calculated using SBDART model. The atmospheric Heating Rate (HR) associated with SDARFATM were also computed. It was observed that the monthly averaged SDARFTOA and SDARFSUR were found to be negative leading to positive SDARFATM during all the months over all sites. The increments in net atmospheric forcing lead to maximum HR in November-December and May. The seasonal analysis of SDARF revealed that SDARFTOA and SDARFSUR were negative during all seasons. The SW atmospheric absorption translates to highest atmospheric HR during summer over Karachi and during pre-monsoon over Lahore, Jaipur and Kanpur. Like SDARF, the monthly and seasonal variations of SDARFETOA and SDARFESUR were found to be negative, resulting in positive atmospheric forcing. Additionally, to compare the model estimated forcing against AERONET derived forcing, the regression analysis of AERONET-SBDART forcing were carried out. It was observed that SDARF at SUR and TOA showed relatively higher correlation over Lahore, moderate over Jaipur and Kanpur and lower over Karachi. Finally, the analysis of National Oceanic and Atmospheric Administration Hybrid Single Particle Lagrangian Integrated Trajectory (HYSPLIT) model revealed that air masses were arriving from multiple source locations.

  11. Behavioural changes, sharing behaviour and psychological responses after receiving direct-to-consumer genetic test results: a systematic review and meta-analysis.

    Stewart, Kelly F J; Wesselius, Anke; Schreurs, Maartje A C; Schols, Annemie M W J; Zeegers, Maurice P

    2018-01-01

    It has been hypothesised that direct-to-consumer genetic tests (DTC-GTs) could stimulate health behaviour change. However, genetic testing may also lead to anxiety and distress or unnecessarily burden the health care system. The aim is to review and meta-analyse the effects of DTC-GT on (1) behaviour change, (2) psychological response and (3) medical consumption. A systematic literature search was performed in three databases, using "direct-to-consumer genetic testing" as a key search term. Random effects meta-analyses were performed when at least two comparable outcomes were available. After selection, 19 articles were included involving 11 unique studies. Seven studies involved actual consumers who paid the retail price, whereas four included participants who received free genetic testing as part of a research trial (non-actual consumers). In meta-analysis, 23% had a positive lifestyle change. More specifically, improved dietary and exercise practices were both reported by 12%, whereas 19% quit smoking. Seven percent of participants had subsequent preventive checks. Thirty-three percent shared their results with any health care professional and 50% with family and/or friends. Sub-analyses show that behaviour change was more prevalent among non-actual consumers, whereas sharing was more prevalent among actual consumers. Results on psychological responses showed that anxiety, distress and worry were low or absent and that the effect faded with time. DTC-GT has potential to be effective as a health intervention, but the right audience needs to be addressed with tailored follow-up. Research is needed to identify consumers who do and do not change behaviour or experience adverse psychological responses.

  12. Car sequencing is NP-hard: a short proof

    B Estellon; F Gardi

    2013-01-01

    In this note, a new proof is given that the car sequencing (CS) problem is NP-hard. Established from the Hamiltonian Path problem, the reduction is direct while closing some gaps remaining in the previous NP-hardness results. Since CS is studied in many operational research courses, this result and its proof are particularly interesting for teaching purposes.

  13. Digital PCR provides sensitive and absolute calibration for high throughput sequencing

    Fan H Christina

    2009-03-01

    Full Text Available Abstract Background Next-generation DNA sequencing on the 454, Solexa, and SOLiD platforms requires absolute calibration of the number of molecules to be sequenced. This requirement has two unfavorable consequences. First, large amounts of sample-typically micrograms-are needed for library preparation, thereby limiting the scope of samples which can be sequenced. For many applications, including metagenomics and the sequencing of ancient, forensic, and clinical samples, the quantity of input DNA can be critically limiting. Second, each library requires a titration sequencing run, thereby increasing the cost and lowering the throughput of sequencing. Results We demonstrate the use of digital PCR to accurately quantify 454 and Solexa sequencing libraries, enabling the preparation of sequencing libraries from nanogram quantities of input material while eliminating costly and time-consuming titration runs of the sequencer. We successfully sequenced low-nanogram scale bacterial and mammalian DNA samples on the 454 FLX and Solexa DNA sequencing platforms. This study is the first to definitively demonstrate the successful sequencing of picogram quantities of input DNA on the 454 platform, reducing the sample requirement more than 1000-fold without pre-amplification and the associated bias and reduction in library depth. Conclusion The digital PCR assay allows absolute quantification of sequencing libraries, eliminates uncertainties associated with the construction and application of standard curves to PCR-based quantification, and with a coefficient of variation close to 10%, is sufficiently precise to enable direct sequencing without titration runs.

  14. Serial Versus Direct Dilation of Small Diameter Stents Results in a More Predictable and Complete Intentional Transcatheter Stent Fracture: A PICES Bench Testing Study.

    Crystal, Matthew A; Morgan, Gareth J; Danon, Saar; Gray, Robert G; Gruenstein, Daniel H; Gordon, Brent M; Goldstein, Bryan H

    2018-01-01

    Balloon-expandable stents, implanted in infants and children with congenital heart disease (CHD), often require redilation to match somatic growth. Small diameter stents may eventually require longitudinal surgical transection to prevent iatrogenic vascular stenosis. Intentional transcatheter stent fracture (TSF) is an emerging alternative approach to stent transection, but little is known about the optimal stent substrate and best protocol to improve the likelihood of successful TSF. Bench testing was performed with a stent dilation protocol. After recording baseline characteristics, stents were serially or directly dilated using ultra-high-pressure balloons (UHPB) until fracture occurred or further stent dilation was not possible. Stent characteristics recorded were as follows: cell design, metallurgy, mechanism, and uniformity of fracture. Stents tested included bare-metal coronary stents, premounted small diameter stents, and ePTFE-covered small diameter premounted stents. Ninety-four stents representing 9 distinct models were maximally dilated, with 80 (85%) demonstrating evidence of fracture. Comprehensive fracture details were recorded in 64 stents: linear and complete in 34/64 stents (53.1%), linear and incomplete in 9/64 stents (14.1%), transverse/complex and complete in 6/64 stents (9.4%), and transverse/complex and incomplete in 15/64 stents (23.4%). Stent fracture was not accomplished in some stent models secondary to significant shortening, i.e., "napkin-ring" formation. Serial dilation resulted in evidence of fracture in 62/67 (92.5%) stents compared with 18/27 (66.7%) stents in the direct dilation group (p = 0.003). Intentional TSF is feasible in an ex vivo model. Serial dilation more reliably expanded the stent and allowed for ultimate stent fracture, whereas direct large diameter dilation of stents was more likely to generate a "napkin-ring" configuration, which may be more resistant to fracture. In vivo animal and human testing is necessary to

  15. PN Sequence Preestimator Scheme for DS-SS Signal Acquisition Using Block Sequence Estimation

    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.

  16. Next-generation sequencing library preparation method for identification of RNA viruses on the Ion Torrent Sequencing Platform.

    Chen, Guiqian; Qiu, Yuan; Zhuang, Qingye; Wang, Suchun; Wang, Tong; Chen, Jiming; Wang, Kaicheng

    2018-05-09

    Next generation sequencing (NGS) is a powerful tool for the characterization, discovery, and molecular identification of RNA viruses. There were multiple NGS library preparation methods published for strand-specific RNA-seq, but some methods are not suitable for identifying and characterizing RNA viruses. In this study, we report a NGS library preparation method to identify RNA viruses using the Ion Torrent PGM platform. The NGS sequencing adapters were directly inserted into the sequencing library through reverse transcription and polymerase chain reaction, without fragmentation and ligation of nucleic acids. The results show that this method is simple to perform, able to identify multiple species of RNA viruses in clinical samples.

  17. HIDDEN SEQUENCES IN RESULTS OF TESTS IDENTIFYING

    Sviatoslav Yutskevych

    2013-10-01

    Full Text Available Normal 0 false false false MicrosoftInternetExplorer4 Describes a method and a general algorithm for the experimental data series corresponding to a given recurrence relation search program. Search-analytical model different from the existing search models is offered /* Style Definitions */ table.MsoNormalTable {mso-style-name:"Обычная таблица"; mso-tstyle-rowband-size:0; mso-tstyle-colband-size:0; mso-style-noshow:yes; mso-style-parent:""; mso-padding-alt:0cm 5.4pt 0cm 5.4pt; mso-para-margin:0cm; mso-para-margin-bottom:.0001pt; mso-pagination:widow-orphan; font-size:10.0pt; font-family:"Times New Roman"; mso-ansi-language:#0400; mso-fareast-language:#0400; mso-bidi-language:#0400;}

  18. Transcriptome sequencing of the Microarray Quality Control (MAQC RNA reference samples using next generation sequencing

    Thierry-Mieg Danielle

    2009-06-01

    Full Text Available Abstract Background Transcriptome sequencing using next-generation sequencing platforms will soon be competing with DNA microarray technologies for global gene expression analysis. As a preliminary evaluation of these promising technologies, we performed deep sequencing of cDNA synthesized from the Microarray Quality Control (MAQC reference RNA samples using Roche's 454 Genome Sequencer FLX. Results We generated more that 3.6 million sequence reads of average length 250 bp for the MAQC A and B samples and introduced a data analysis pipeline for translating cDNA read counts into gene expression levels. Using BLAST, 90% of the reads mapped to the human genome and 64% of the reads mapped to the RefSeq database of well annotated genes with e-values ≤ 10-20. We measured gene expression levels in the A and B samples by counting the numbers of reads that mapped to individual RefSeq genes in multiple sequencing runs to evaluate the MAQC quality metrics for reproducibility, sensitivity, specificity, and accuracy and compared the results with DNA microarrays and Quantitative RT-PCR (QRTPCR from the MAQC studies. In addition, 88% of the reads were successfully aligned directly to the human genome using the AceView alignment programs with an average 90% sequence similarity to identify 137,899 unique exon junctions, including 22,193 new exon junctions not yet contained in the RefSeq database. Conclusion Using the MAQC metrics for evaluating the performance of gene expression platforms, the ExpressSeq results for gene expression levels showed excellent reproducibility, sensitivity, and specificity that improved systematically with increasing shotgun sequencing depth, and quantitative accuracy that was comparable to DNA microarrays and QRTPCR. In addition, a careful mapping of the reads to the genome using the AceView alignment programs shed new light on the complexity of the human transcriptome including the discovery of thousands of new splice variants.

  19. A Commercially Available Portion-Controlled Diet Program Is More Effective for Weight Loss than a Self-Directed Diet: Results from a Randomized Clinical Trial

    Chad M. Cook

    2017-11-01

    Full Text Available ObjectiveTo examine changes in weight and related outcomes in response to a commercial weight loss program compared to a self-directed diet in adults with overweight or obesity.DesignParticipants were randomly assigned [stratified by body mass index (BMI and age] to a commercial weight loss program (n = 38 or to a self-directed Dietary Approaches to Stop Hypertension (DASH diet (n = 40 for a 16-week period. Daily energy intake goals were 1,500 kcal/d for men and 1,200 kcal/d for women, except for the first week of the commercial program (1,000 kcal/d. This study was registered at http://ClinicalTrials.gov (NCT03017443.ParticipantsPrimarily Caucasian (71% women (n = 61 and men (n = 17 from the greater metropolitan area of the city of Chicago, IL, USA. with a mean baseline BMI of 34.4 kg/m2, body weight of 95.7 kg, and age of 50.4 years.ResultsData = mean (95% CI. At week 16, the commercial program group lost significantly more body weight [−5.9 (−7.5, −4.3 kg vs. −1.8 (−2.9, −0.8 kg; or −6.4 vs. −1.8% of initial body weight, respectively], fat mass [−4.4 (−5.7, −3.1 kg vs. −1.2 (−2.1, −0.4 kg] and total body circumference (chest + waist + hip + upper arm + thigh [−16.9 (−21.5, −12.3 cm vs. −5.8 (−9.0, −2.6 cm] (p < 0.01 for all. Additionally, more participants in the commercial program group lost a clinically meaningful amount of weight, defined as ≥5% of initial body weight, at week 16 (58% vs. 13%, p < 0.001.ConclusionThe commercial program resulted in greater weight loss and improvements in body composition/anthropometric parameters compared to a self-directed DASH diet over a 16-week period. Some important limitations were that no objective measurements of dietary intake or physical activity were collected to potentially ascertain the independent or combined effects of these components on weight loss (or lack thereof. Additionally, future

  20. Next-generation sequencing

    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...

  1. Substance use disorders and self- and other-directed violence among adults: Results from the National Survey on Drug Use And Health.

    Harford, Thomas C; Yi, Hsiao-Ye; Chen, Chiung M; Grant, Bridget F

    2018-01-01

    Previous studies have identified a violence typology of self- and other-directed violence. This study examines the extent to which substance use disorders (SUDs) as defined by the Diagnostic and Statistical Manual of Mental Disorders, Fourth Edition (DSM-IV), independent of serious psychological distress, major depressive episodes, assault arrest, and criminal justice involvement, are associated with these violence categories. Data were obtained from the National Survey on Drug Use and Health (NSDUH) pooled across survey years 2008-2015, with a combined sample of 314,881 adult respondents. According to self-report data on suicide attempt (self-directed) and attacking someone with the intent for serious injury (other-directed), violence was categorized in four categories: none, self-directed only, other-directed only, and combined self-/other-directed. Multinomial logistic regression was used to estimate the adjusted odds ratios associated with the risk factors for different forms of violence. Nicotine dependence and the number of DSM-IV SUDs criteria (except the criterion of legal problems) for alcohol, marijuana, and pain reliever use disorders are significantly associated with the self-/other-directed violence categories. Cross-sectional data do not allow assessment of directionality of important factors. The identification of the combined self- and other-directed violence among adults in the general population extends studies in the adolescent population, and significant correlation between self- and other-directed violence provides additional support for clinical studies that established this association. Findings expand the associated risk factors identified in previous studies for the adult population. Prevention and treatment programs need to address both forms of violence and suicidality. Copyright © 2017 Elsevier B.V. All rights reserved.

  2. Accuracy of Colposcopically Directed Biopsy: Results from an Online Quality Assurance Programme for Colposcopy in a Population-Based Cervical Screening Setting in Italy

    Sideri, Mario; Garutti, Paola; Costa, Silvano; Cristiani, Paolo; Sassoli de Bianchi, Priscilla; Naldoni, Carlo

    2015-01-01

    Purpose. To report the accuracy of colposcopically directed biopsy in an internet-based colposcopy quality assurance programme in northern Italy. Methods. A web application was made accessible on the website of the regional Administration. Fifty-nine colposcopists out of the registered 65 logged in, viewed a posted set of 50 digital colpophotographs, classified them for colposcopic impression and need for biopsy, and indicated the most appropriate site for biopsy with a left-button mouse click on the image. Results. Total biopsy failure rate, comprising both nonbiopsy and incorrect selection of biopsy site, was 0.20 in CIN1, 0.11 in CIN2, 0.09 in CIN3, and 0.02 in carcinoma. Errors in the selection of biopsy site were stable between 0.08 and 0.09 in the three grades of CIN while decreasing to 0.01 in carcinoma. In multivariate analysis, the risk of incorrect selection of biopsy site was 1.97 for CIN2, 2.52 for CIN3, and 0.29 for carcinoma versus CIN1. Conclusions. Although total biopsy failure rate decreased regularly with increasing severity of histological diagnosis, the rate of incorrect selection of biopsy site was stable up to CIN3. In multivariate analysis, CIN2 and CIN3 had an independently increased risk of incorrect selection of biopsy site. PMID:26180805

  3. Long-term results of positron emission tomography-directed management of the neck in node-positive head and neck cancer after organ preservation therapy.

    Sjövall, Johanna; Chua, Benjamin; Pryor, David; Burmeister, Elizabeth; Foote, Matthew C; Panizza, Benedict; Burmeister, Bryan H; Porceddu, Sandro V

    2015-03-01

    The current study presents the long-term results from a study designed to evaluate a restaging positron emission tomography (PET) directed policy whereby neck dissections were omitted in all node positive head and neck squamous cell carcinoma (N+HNSCC) patients with PET-negative lymph nodes after definitive radiotherapy (RT), with or without chemotherapy. A post-therapy nodal response assessment with PET and computed tomography (CT) was performed in patients who achieved a complete response at the primary site after definitive radiotherapy. Patients with PET-negative lymph nodes were observed regardless of residual CT abnormalities. One hundred and twelve patients, the majority of whom (83 patients, 74%) had oropharyngeal primaries, were treated on protocol. Median follow-up was 62months. Negative and positive predictive values for the restaging PET was 97.1% and 77.8% respectively, with only one patient who was PET-negative after treatment experiencing an isolated nodal relapse. PET-guided management of the neck following organ preservation therapy effectively spares neck dissections in patients with N+HNSCC without compromising isolated nodal control or overall survival. Crown Copyright © 2014. Published by Elsevier Ltd. All rights reserved.

  4. Thermal Aging Study of a Dow Corning SE 1700 Porous Structure Made by Direct Ink Writing: 1-Year Results and Long-Term Predictions

    Small, Ward [Lawrence Livermore National Lab. (LLNL), Livermore, CA (United States); Pearson, Mark A. [Lawrence Livermore National Lab. (LLNL), Livermore, CA (United States); Maiti, Amitesh [Lawrence Livermore National Lab. (LLNL), Livermore, CA (United States); Metz, Thomas R. [Lawrence Livermore National Lab. (LLNL), Livermore, CA (United States); Duoss, Eric B. [Lawrence Livermore National Lab. (LLNL), Livermore, CA (United States); Wilson, Thomas S. [Lawrence Livermore National Lab. (LLNL), Livermore, CA (United States)

    2015-11-13

    Dow Corning SE 1700 (reinforced polydimethylsiloxane) porous structures were made by direct ink writing (DIW). The specimens (~50% porosity) were subjected to various compressive strains (15, 30, 45%) and temperatures (room temperature, 35, 50, 70°C) in a nitrogen atmosphere (active purge) for 1 year. Compression set and load retention of the aged specimens were measured periodically during the study. Compression set increased with strain and temperature. After 1 year, specimens aged at room temperature, 35, and 50°C showed ~10% compression set (relative to the applied compressive deflection), while those aged at 70°C showed 20-40%. Due to the increasing compression set, load retention decreased with temperature, ranging from ~90% at room temperature to ~60-80% at 70°C. Long-term compression set and load retention at room temperature were predicted by applying time-temperature superposition (TTS). The predictions show compression set relative to the compressive deflection will be ~10-15% with ~70-90% load retention after 50 years at 15-45% strain, suggesting the material will continue to be mechanically functional. Comparison of the results to previously acquired data for cellular (M97*, M9760, M9763) and RTV (S5370) silicone foams suggests that the SE 1700 DIW porous specimens are on par with, or outperform, the legacy foams.

  5. Mis-specified cells die by an active gene-directed process, and inhibition of this death results in cell fate transformation in Drosophila

    Werz, Christian; Lee, Tom V.; Lee, Peter L.; Lackey, Melinda; Bolduc, Clare; Stein, David S.; Bergmann, Andreas

    2009-01-01

    Summary Incorrectly specified or mis-specified cells often undergo cell death or are transformed to adopt a different cell fate during development. The underlying cause for this distinction is largely unknown. In many developmental mutants in Drosophila, large numbers of mis-specified cells die synchronously, providing a convenient model for analysis of this phenomenon. The maternal mutant bicoid is particularly useful model with which to address this issue because its mutant phenotype is a combination of both transformation of tissue (acron to telson) and cell death in the presumptive head and thorax regions. We show that a subset of these mis-specified cells die through an active gene-directed process involving transcriptional upregulation of the cell death inducer hid. Upregulation of hid also occurs in oskar mutants and other segmentation mutants. In hid bicoid double mutants, mis-specified cells in the presumptive head and thorax survive and continue to develop, but they are transformed to adopt a different cell fate. We provide evidence that the terminal torso signaling pathway protects the mis-specified telson tissue in bicoid mutants from hid-induced cell death, whereas mis-specified cells in the head and thorax die, presumably because equivalent survival signals are lacking. These data support a model whereby mis-specification can be tolerated if a survival pathway is provided, resulting in cellular transformation. PMID:16280349

  6. SNAD: sequence name annotation-based designer

    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.

  7. Concomitant Use of Transcranial Direct Current Stimulation and Computer-Assisted Training for the Rehabilitation of Attention in Traumatic Brain Injured Patients: Behavioral and Neuroimaging Results.

    Sacco, Katiuscia; Galetto, Valentina; Dimitri, Danilo; Geda, Elisabetta; Perotti, Francesca; Zettin, Marina; Geminiani, Giuliano C

    2016-01-01

    Divided attention (DA), the ability to distribute cognitive resources among two or more simultaneous tasks, may be severely compromised after traumatic brain injury (TBI), resulting in problems with numerous activities involved with daily living. So far, no research has investigated whether the use of non-invasive brain stimulation associated with neuropsychological rehabilitation might contribute to the recovery of such cognitive function. The main purpose of this study was to assess the effectiveness of 10 transcranial direct current stimulation (tDCS) sessions combined with computer-assisted training; it also intended to explore the neural modifications induced by the treatment. Thirty-two patients with severe TBI participated in the study: 16 were part of the experimental group, and 16 part of the control group. The treatment included 20' of tDCS, administered twice a day for 5 days. The electrodes were placed on the dorso-lateral prefrontal cortex. Their location varied across patients and it depended on each participant's specific area of damage. The control group received sham tDCS. After each tDCS session, the patient received computer-assisted cognitive training on DA for 40'. The results showed that the experimental group significantly improved in DA performance between pre- and post-treatment, showing faster reaction times (RTs), and fewer omissions. No improvement was detected between the baseline assessment (i.e., 1 month before treatment) and the pre-training assessment, or within the control group. Functional magnetic resonance imaging (fMRI) data, obtained on the experimental group during a DA task, showed post-treatment lower cerebral activations in the right superior temporal gyrus (BA 42), right and left middle frontal gyrus (BA 6), right postcentral gyrus (BA 3) and left inferior frontal gyrus (BA 9). We interpreted such neural changes as normalization of previously abnormal hyperactivations.

  8. Exposure to second-hand smoke and direct healthcare costs in children – results from two German birth cohorts, GINIplus and LISAplus

    Batscheider Ariane

    2012-10-01

    Full Text Available Abstract Background Although the negative health consequences of the exposure to second hand tobacco smoke during childhood are already known, evidence on the economic consequences is still rare. The aim of this study was to estimate excess healthcare costs of exposure to tobacco smoke in German children. Methods The study is based on data from two birth cohort studies of 3,518 children aged 9-11 years with information on healthcare utilisation and tobacco smoke exposure: the GINIplus study (German Infant Study On The Influence Of Nutrition Intervention Plus Environmental And Genetic Influences On Allergy Development and the LISAplus study (Influence of Life-Style Factors On The Development Of The Immune System And Allergies In East And West Germany Plus The Influence Of Traffic Emissions And Genetics. Direct medical costs were estimated using a bottom-up approach (base year 2007. We investigated the impact of tobacco smoke exposure in different environments on the main components of direct healthcare costs using descriptive analysis and a multivariate two-step regression analysis. Results Descriptive analysis showed that average annual medical costs (physician visits, physical therapy and hospital treatment were considerably higher for children exposed to second-hand tobacco smoke at home (indoors or on patio/balcony compared with those who were not exposed. Regression analysis confirmed these descriptive trends: the odds of positive costs and the amount of total costs are significantly elevated for children exposed to tobacco smoke at home after adjusting for confounding variables. Combining the two steps of the regression model shows smoking attributable total costs per child exposed at home of €87 [10–165] (patio/balcony and €144 [6–305] (indoors compared to those with no exposure. Children not exposed at home but in other places showed only a small, but not significant, difference in total costs compared to those with no exposure

  9. Sequencing genes in silico using single nucleotide polymorphisms

    Zhang Xinyi

    2012-01-01

    Full Text Available Abstract Background The advent of high throughput sequencing technology has enabled the 1000 Genomes Project Pilot 3 to generate complete sequence data for more than 906 genes and 8,140 exons representing 697 subjects. The 1000 Genomes database provides a critical opportunity for further interpreting disease associations with single nucleotide polymorphisms (SNPs discovered from genetic association studies. Currently, direct sequencing of candidate genes or regions on a large number of subjects remains both cost- and time-prohibitive. Results To accelerate the translation from discovery to functional studies, we propose an in silico gene sequencing method (ISS, which predicts phased sequences of intragenic regions, using SNPs. The key underlying idea of our method is to infer diploid sequences (a pair of phased sequences/alleles at every functional locus utilizing the deep sequencing data from the 1000 Genomes Project and SNP data from the HapMap Project, and to build prediction models using flanking SNPs. Using this method, we have developed a database of prediction models for 611 known genes. Sequence prediction accuracy for these genes is 96.26% on average (ranges 79%-100%. This database of prediction models can be enhanced and scaled up to include new genes as the 1000 Genomes Project sequences additional genes on additional individuals. Applying our predictive model for the KCNJ11 gene to the Wellcome Trust Case Control Consortium (WTCCC Type 2 diabetes cohort, we demonstrate how the prediction of phased sequences inferred from GWAS SNP genotype data can be used to facilitate interpretation and identify a probable functional mechanism such as protein changes. Conclusions Prior to the general availability of routine sequencing of all subjects, the ISS method proposed here provides a time- and cost-effective approach to broadening the characterization of disease associated SNPs and regions, and facilitating the prioritization of candidate

  10. Energy and direction distribution of neutrons in workplace fields: Implication of the results from the EVIDOS project for the set-up of simulated workplace fields

    Luszik-Bhadra, M.; Lacoste, V.; Reginatto, M.; Zimbal, A.

    2007-01-01

    Workplace neutron spectra from nuclear facilities obtained within the European project EVIDOS are compared with those of the simulated workplace fields CANEL and SIGMA and fields set-up with radionuclide sources at the PTB. Contributions of neutrons to ambient dose equivalent and personal dose equivalent are given in three energy intervals (for thermal, intermediate and fast neutrons) together with the corresponding direction distribution, characterised by three different types of distributions (isotropic, weakly directed and directed). The comparison shows that none of the simulated workplace fields investigated here can model all the characteristics of the fields observed at power reactors. (authors)

  11. Phylogenomics of Phrynosomatid Lizards: Conflicting Signals from Sequence Capture versus Restriction Site Associated DNA Sequencing

    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

  12. One hundred and thirteen attempts at directional coronary atherectomy: the early and combined experience of two European centres using quantitative angiography to assess their results

    V.A.W.M. Umans (Victor); E. Haine; J. Renkin; P.J. de Feyter (Pim); W. Wijns (William); P.W.J.C. Serruys (Patrick)

    1992-01-01

    textabstractDirectional coronary atherectomy has been introduced as an alternative to conventional balloon angioplasty when treating coronary artery stenoses with complex lesion morphology. To determine the immediate efficacy of coronary atherectomy in patients with such lesions, the first 113

  13. Relationship of endometrial thickness detected by transvaginal sonography with the results of endometrial biopsy & hysteroscopic directed biopsy in post menopausal bleeding

    Vahid Dastjerdi M

    2008-05-01

    Full Text Available Background: Post-menopausal hemorrhage is one of the most common complains in gynecologic clinics. More than 60% of these cases have abnormal findings in diagnostic work ups. There is contraversy about the best diagnostic method for evaluating post-menopausal hemorrhage. The aim of this study was to evaluate the results of Trans-Vaginal Ultrasonography and compare its result to ones derived from direct endometrial biopsy and Hysteroscopy findings.Methods: In a cross-sectional study, menopausal women who attended the outpatient clinic of Arash Hospital, Tehran University of medical Sciences, from April 2005 to March 2006 with the complain of hemorrhage were evaluated. In all of these patients, after getting informed consent, Trans-Vaginal Ultrasonography, Dilatation and Curettage and Hysteroscopy were performed.Results: The total number of 90 women was recruited to the study with the age range of 41-80 years. The mean age of participants was 53.84 ± 6 years and 4.3 ± 5.1 years had passed from their menopause. The mean thickness of endometrium, measured by Trans Vaginal ultrasonography was 6.25 ± 3.7 millimeter. In the biopsy derived specimens, the most finding pathological presentation was atrophy (48.9% and the Proliferative endometrium had the second prevalence (36.7%. Atrophy (44.4% and Proliferative endometrium (33.3% were the most prevalent finding in Hysteroscopy. There was a significant difference in endometrial thickness between groups of different pathological findings. A significant difference in endometrial thickness was also seen between groups with different Hysteroscopic finding. By grouping the data according to endometrial thickness, it became evident that endometrial thickness can predict the outcome of endometrial biopsy and Hysteroscopic finding efficiently. We used ROC curves to find the best grouping threshold for endometrial thickness to achieve the best sensitivity and specificity.Conclusion: Measuring the endometrial

  14. 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.

    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.

  15. Droplet heat transfer and chemical reactions during direct containment heating

    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

  16. Does migratory distance affect fuelling in a medium-distance passerine migrant?: results from direct and step-wise simulated magnetic displacements

    Mihaela Ilieva

    2016-03-01

    Full Text Available In birds, fat accumulation before and during migration has been shown to be endogenously controlled and tuned by, among other factors, the Earth's magnetic field. However, our knowledge about the influence of the geomagnetic field on the fuelling in migrating birds is still limited to just a few nocturnally migrating passerine species. In order to study if variations of the magnetic field can also influence the fuelling of both day- and night-migrating passerines, we caught first-year dunnocks (Prunella modularis and subjected them to three magnetic field conditions simulated by a system of magnetic coils: (1 local geomagnetic field of southern Sweden, (2 magnetic field corresponding to the centre of the expected wintering area, and (3 magnetic field met at the northern limit of the species' breeding distribution. We did not find a difference in mass increase between the birds kept in a local magnetic field and a field resembling their wintering area, irrespectively of the mode of magnetic displacement, i.e. direct or step-wise. However, the dunnocks magnetically displaced north showed a lower rate of fuelling in comparison to the control group, probably due to elevated activity. Compared with previous studies, our results suggest that the fuelling response to magnetic displacements during the migration period is specific to the eco-physiological situation. Future studies need to address if there is an effect of magnetic field manipulation on the level of migratory activity in dunnocks and how widespread the influence of local geomagnetic field parameters is on fuelling decisions in different bird species, which have different migratory strategies, distances and migration history.

  17. Cranial neuronavigation with direct integration of 11C methionine positron emission tomography (PET) data - results of a pilot study in 32 surgical cases

    Braun, V.; Dempf, S.; Richter, H.P.; Weller, R.; Reske, S.-N.; Schanchenmayr, W.

    2002-01-01

    MRI detects small intracranial lesions, but has difficulties in differentiating between tumor, gliosis and edema. 11 C methionine-PET may help to overcome this problem. For its appropriate intra-operative use, it must be integrated into neuronavigation. We present the results of our pilot study with this method. 32 patients with 34 intracranial lesions detected by MRI underwent additional 11 C methionine-PET, because the pathophysiological behavior or the tumor delineation was unclear. All lesions were treated surgically. In 25 patients PET data could be integrated directly into cranial neuronavigation. 11 C methionine uptake was observed in 27/34 lesions, 26 of them were tumors: 14 malignant and 7 benign gliomas, 3 gliomas without further histological typing, one Ewing sarcoma and one non-Hodgkin lymphoma. Only one 11 C methionine positive lesion was non-tumorous: it was staged as post-irradiation necrosis in a patient operated on for a malignant glioma. 3/7 11 C-methionine negative lesions were classified as gliosis (n = 2) and M. Whipple (n = 1), but 4/7 were tumors: 2 astrocytomas WHO o II, 1 DNT and one astrocytoma WHO o III. The sensitivity of 11 C methionine-PET was 87 %, the specificity 75 %, the positive predictive value 96 % and the negative predictive value 43 %. In all tumorous cases with positive tracer uptake the borderline area of the tumor was better defined by C methionine-PET than by MRI. Interpretation: A positive 11 C methionine-PET is highly suspicious of a tumor, a negative one does not exclude it. 11 C methionine-PET seems to be more sensitive than MRI for differentiating between tumor and edema or gliosis. Simultaneous integration MRI and 11 C methionine-PET into cranial neuronavigation can facilitate cross total tumor removal in glioma surgery. (author)

  18. Carvedilol for prevention of restenosis after directional coronary atherectomy : final results of the European carvedilol atherectomy restenosis (EUROCARE) trial : Final Results of the European Carvedilol Atherectomy Restenosis (EUROCARE) Trial

    J. Puel (Jacques); E.W.J. Montauban van Swijndregt (Eline); H.D. Glogar (Helmut); R. Seabra-Gomes (Ricardo); J. Goicolea (Javier); U. Hauf-Zachariou; R. Simon (Rudiger); P. Coste (Pierre); W.R. Rutsch (Wolfgang); A. Betriu; H.A. Katus (Hugo); W. Wijns (William); R. Melkert (Rein); J.J.R.M. Bonnier (Hans); B. Hofling; P.W.J.C. Serruys (Patrick); D.P. Foley (David)

    2000-01-01

    textabstractBACKGROUND: In addition to its known properties as a competitive, nonselective beta and alpha-1 receptor blocker, carvedilol directly inhibits vascular myocyte migration and proliferation and exerts antioxidant effects that are considerably greater than those of vitamin

  19. Science in bullet points: How to compile scientific results to underpin guidelines for CO2 storage for the German transposition of the European CCS Directive

    Streibel, Martin

    2015-04-01

    In 2012 the German Parliament passed the transposition of the EC Directive 2009/31/EC the "Carbon Dioxide Storage Law" (KSpG). The law focuses on the demonstration of the CO2 storage technology and mainly regulates the storage part of the Carbon Capture and Storage (CCS) chain. As the law has a conceptual character, appendix 1 provides a description of criteria for the characterisation and assessment of a potential CO2 storage site starting with field data ending with requirements for dynamic modelling of the storage complex. Appendix 2 describes the expected monitoring system during all relevant phases of a life cycle of a CO2 storage site. The criteria given in the appendices are of general nature, which reflects on one hand that the CO2 storage technology is still being developed and on the other hand that site specific aspects needs to be considered. In 2004 the Federal Ministry of Education and Research of Germany launched the programme GEOTECHNOLOGIEN with one key aspect being the development of technologies for a sustainable storage of carbon dioxide in geological formations. Within this research field more than 30 projects in three phases have been funded until the end of 2014. In order to benefit from the gathered knowledge and use the experiences for the policy/law making process the umbrella project AUGE has been launched in October 2012 with a life time of three years. The aim of the project is to review and compile all results of projects funded during the three phases to underpin the appendices of the KSpG. In the first part of the paper the most important findings of the project with regard to the overall risk of a geological CO2 storage and the procedure of compiling the guidance document will be discussed. Milestones of this project were • the compilation of the results of national, European and international projects; • interviews with stakeholders; • a workshops to define state of the art for certain involved technologies and existing gaps

  20. Formatt: Correcting protein multiple structural alignments by incorporating sequence alignment

    Daniels Noah M

    2012-10-01

    Full Text Available Abstract Background The quality of multiple protein structure alignments are usually computed and assessed based on geometric functions of the coordinates of the backbone atoms from the protein chains. These purely geometric methods do not utilize directly protein sequence similarity, and in fact, determining the proper way to incorporate sequence similarity measures into the construction and assessment of protein multiple structure alignments has proved surprisingly difficult. Results We present Formatt, a multiple structure alignment based on the Matt purely geometric multiple structure alignment program, that also takes into account sequence similarity when constructing alignments. We show that Formatt outperforms Matt and other popular structure alignment programs on the popular HOMSTRAD benchmark. For the SABMark twilight zone benchmark set that captures more remote homology, Formatt and Matt outperform other programs; depending on choice of embedded sequence aligner, Formatt produces either better sequence and structural alignments with a smaller core size than Matt, or similarly sized alignments with better sequence similarity, for a small cost in average RMSD. Conclusions Considering sequence information as well as purely geometric information seems to improve quality of multiple structure alignments, though defining what constitutes the best alignment when sequence and structural measures would suggest different alignments remains a difficult open question.

  1. Teaching Task Sequencing via Verbal Mediation.

    Rusch, Frank R.; And Others

    1987-01-01

    Verbal sequence training was used to teach a moderately mentally retarded woman to sequence job-related tasks. Learning to say the tasks in the proper sequence resulted in the employee performing her tasks in that sequence, and the employee was capable of mediating her own work behavior when scheduled changes occurred. (Author/JDD)

  2. Quantum-Sequencing: Fast electronic single DNA molecule sequencing

    Casamada Ribot, Josep; Chatterjee, Anushree; Nagpal, Prashant

    2014-03-01

    A major goal of third-generation sequencing technologies is to develop a fast, reliable, enzyme-free, high-throughput and cost-effective, single-molecule sequencing method. Here, we present the first demonstration of unique ``electronic fingerprint'' of all nucleotides (A, G, T, C), with single-molecule DNA sequencing, using Quantum-tunneling Sequencing (Q-Seq) at room temperature. We show that the electronic state of the nucleobases shift depending on the pH, with most distinct states identified at acidic pH. We also demonstrate identification of single nucleotide modifications (methylation here). Using these unique electronic fingerprints (or tunneling data), we report a partial sequence of beta lactamase (bla) gene, which encodes resistance to beta-lactam antibiotics, with over 95% success rate. These results highlight the potential of Q-Seq as a robust technique for next-generation sequencing.

  3. Ab initio study of charge transfer between lithium and aromatic hydrocarbons. Can the results be directly transferred to the lithium-graphene interaction?

    Sadlej-Sosnowska, N

    2014-08-28

    We have used electronic density calculations to study neutral complexes of Li with aromatic hydrocarbons. The charge transferred between a Li atom and benzene, coronene, circumcoronene, and circumcircumcoronene has been studied by ab initio methods (at the HF and MP2 level). Toward this aim, the method of integrating electron density in two cuboid fragments of space was applied. One of the fragments was constructed so that it enclosed the bulk of the electron density of lithium; the second, the bulk of the electron density of hydrocarbon. It was found that for each complex two conformations were identified: the most stable with a greater vertical Li-hydrocarbon distance, on the order of 2.5 Å, and another of higher energy with a corresponding distance less than 2 Å. In all cases the transfer of a fractional number, 0.1-0.3 electrons, between Li and hydrocarbon was found; however, the direction of the transfer was not the same in all complexes investigated. The structures of complexes of the first configuration could be represented as Li(σ-)···AH(σ+), whereas the opposite direction of charge transfer was found for complexes of the second configuration, with higher energy. The directions of the dipole moments in the complexes supported these conclusions because they directly measure the redistribution of electron density in a complex with respect to substrates.

  4. Evaluation of capture ELISA for detection of antineutrophil cytoplasmic antibodies directed against proteinase 3 in Wegener's granulomatosis : first results from a multicentre study

    Csernok, E; Holle, J; Hellmich, B; Willem, J; Tervaert, C; Kallenberg, CGM; Limburg, PC; Niles, J; Pan, GL; Specks, U; Westman, K; Wieslander, J; Gross, WL

    Objective: To evaluate the performance characteristics of direct and capture ELISA for the detection of PR3-ANCA in Wegener's granulomatosis (WG) in international ANCA reference laboratories. Methods: Serum samples were derived from patients with histological and clinical diagnosis of WG (n = 60),

  5. ABS: Sequence alignment by scanning

    Bonny, Mohamed Talal

    2011-08-01

    Sequence alignment is an essential tool in almost any computational biology research. It processes large database sequences and considered to be high consumers of computation time. Heuristic algorithms are used to get approximate but fast results. We introduce fast alignment algorithm, called Alignment By Scanning (ABS), to provide an approximate alignment of two DNA sequences. We compare our algorithm with the well-known alignment algorithms, the FASTA (which is heuristic) and the \\'Needleman-Wunsch\\' (which is optimal). The proposed algorithm achieves up to 76% enhancement in alignment score when it is compared with the FASTA Algorithm. The evaluations are conducted using different lengths of DNA sequences. © 2011 IEEE.

  6. ABS: Sequence alignment by scanning

    Bonny, Mohamed Talal; Salama, Khaled N.

    2011-01-01

    Sequence alignment is an essential tool in almost any computational biology research. It processes large database sequences and considered to be high consumers of computation time. Heuristic algorithms are used to get approximate but fast results. We introduce fast alignment algorithm, called Alignment By Scanning (ABS), to provide an approximate alignment of two DNA sequences. We compare our algorithm with the well-known alignment algorithms, the FASTA (which is heuristic) and the 'Needleman-Wunsch' (which is optimal). The proposed algorithm achieves up to 76% enhancement in alignment score when it is compared with the FASTA Algorithm. The evaluations are conducted using different lengths of DNA sequences. © 2011 IEEE.

  7. Rapid Polymer Sequencer

    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.

  8. Hormonal therapy followed by chemotherapy or the reverse sequence as first-line treatment of hormone-responsive, human epidermal growth factor receptor-2 negative metastatic breast cancer patients: results of an observational study.

    Bighin, Claudia; Dozin, Beatrice; Poggio, Francesca; Ceppi, Marcello; Bruzzi, Paolo; D'Alonzo, Alessia; Levaggi, Alessia; Giraudi, Sara; Lambertini, Matteo; Miglietta, Loredana; Vaglica, Marina; Fontana, Vincenzo; Iacono, Giuseppina; Pronzato, Paolo; Del Mastro, Lucia

    2017-07-04

    Introduction Although hormonal-therapy is the preferred first-line treatment for hormone-responsive, HER2 negative metastatic breast cancer, no data from clinical trials support the choice between hormonal-therapy and chemotherapy.Methods Patients were divided into two groups according to the treatment: chemotherapy or hormonal-therapy. Outcomes in terms of clinical benefit and median overall survival (OS) were retrospectively evaluated in the two groups. To calculate the time spent in chemotherapy with respect to OS in the two groups, the proportion of patients in chemotherapy relative to those present in either group was computed at every day from the start of therapy.Results From 1999 to 2013, 119 patients received first-line hormonal-therapy (HT-first group) and 100 first-line chemotherapy (CT-first group). Patients in the CT-first group were younger and with poorer prognostic factors as compared to those in HT-first group. Clinical benefit (77 vs 81%) and median OS (50.7 vs 51.1 months) were similar in the two groups. Time spent in chemotherapy was significantly longer during the first 3 years in CT-first group (54-34%) as compared to the HT-first group (11-18%). This difference decreased after the third year and overall was 28% in the CT-first group and 18% in the HT-first group.Conclusions The sequence first-line chemotherapy followed by hormonal-therapy, as compared with the opposite sequence, is associated with a longer time of OS spent in chemotherapy. However, despite the poorer prognostic factors, patients in the CT-first group had a superimposable OS than those in the HT-first group.

  9. 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).

    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.

  10. How Generalizable Are the Results From Trials of Direct Antiviral Agents to People Coinfected With HIV/HCV in the Real World?

    Saeed, Sahar; Strumpf, Erin C.; Walmsley, Sharon L.; Rollet-Kurhajec, Kathleen; Pick, Neora; Martel-Laferri?re, Valerie; Hull, Mark; Gill, M. John; Cox, Joseph; Cooper, Curtis; Klein, Marina B.

    2016-01-01

    Background. ?Direct-acting antivirals (DAAs) against hepatitis C virus (HCV) have been described as revolutionary. However, it remains uncertain how effective these drugs will be for individuals coinfected with human immunodeficiency virus (HIV)?HCV. Bridging this gap between efficacy and effectiveness requires a focus on the generalizability of clinical trials. Methods. ?Generalizability of DAA trials was assessed by applying the eligibility criteria from 5 efficacy trials: NCT01479868, PHOT...

  11. Innovation Incubator: LiquidCool Solutions Technical Evaluation. Laboratory Study and Demonstration Results of a Directed-Flow, Liquid Submerged Server for High-Efficiency Data Centers

    Kozubal, Eric J [National Renewable Energy Lab. (NREL), Golden, CO (United States)

    2017-12-12

    LiquidCool Solutions (LCS) has developed liquid submerged server (LSS) technology that changes the way computer electronics are cooled. The technology provides an option to cool electronics by the direct contact flow of dielectric fluid (coolant) into a sealed enclosure housing all the electronics of a single server. The intimate dielectric fluid contact with electronics improves the effectiveness of heat removal from the electronics.

  12. Understanding the direction of the relationship between white matter hyperintensities of vascular origin, sleep quality, and chronic kidney disease-Results from the Atahualpa Project.

    Del Brutto, Oscar H; Mera, Robertino M

    2018-02-01

    The burden of cerebral small vessel disease, sleep disorders, and chronic kidney disease is on the rise in remote rural settings. However, information on potential links between these conditions is limited. We aimed to assess the relationships between these conditions in community-dwelling older adults living in rural Ecuador. Atahualpa residents aged ≥60 years were offered a brain MRI. A venous blood sample was obtained for serum creatinine determination. Baseline interviews and procedures were directed to assess demographics, cardiovascular risk factors, and sleep quality. Using generalized structural equation modeling (GSEM), we assessed the associations between white matter hyperintensities (WMH) of vascular origin, sleep quality and kidney function, as well as the directions of the relationships between these variables. Of 423 candidates, 314 (74%) were enrolled. Moderate-to-severe WMH were noticed in 74 (24%) individuals, poor sleep quality in 101 (31%), and moderate-to-severe chronic kidney disease in 28 (9%). GSEM showed that the direction of the effect was from kidney function to WMH and from the latter to sleep quality. Of independent variables investigated, worse kidney function was associated with age, high glucose levels and male sex. WMH was associated with cholesterol blood levels, blood pressure, level of education and severe edentulism. Poor sleep quality was associated with poor physical activity. This population based study shows that chronic kidney disease is associated with increased severity of WMH, which, in turn, is associated with a poor sleep quality. Copyright © 2017 Elsevier B.V. All rights reserved.

  13. Universal sequence map (USM of arbitrary discrete sequences

    Almeida Jonas S

    2002-02-01

    Full Text Available Abstract Background For over a decade the idea of representing biological sequences in a continuous coordinate space has maintained its appeal but not been fully realized. The basic idea is that any sequence of symbols may define trajectories in the continuous space conserving all its statistical properties. Ideally, such a representation would allow scale independent sequence analysis – without the context of fixed memory length. A simple example would consist on being able to infer the homology between two sequences solely by comparing the coordinates of any two homologous units. Results We have successfully identified such an iterative function for bijective mappingψ of discrete sequences into objects of continuous state space that enable scale-independent sequence analysis. The technique, named Universal Sequence Mapping (USM, is applicable to sequences with an arbitrary length and arbitrary number of unique units and generates a representation where map distance estimates sequence similarity. The novel USM procedure is based on earlier work by these and other authors on the properties of Chaos Game Representation (CGR. The latter enables the representation of 4 unit type sequences (like DNA as an order free Markov Chain transition table. The properties of USM are illustrated with test data and can be verified for other data by using the accompanying web-based tool:http://bioinformatics.musc.edu/~jonas/usm/. Conclusions USM is shown to enable a statistical mechanics approach to sequence analysis. The scale independent representation frees sequence analysis from the need to assume a memory length in the investigation of syntactic rules.

  14. Laser mass spectrometry for DNA sequencing, disease diagnosis, and fingerprinting

    Winston Chen, C.H.; Taranenko, N.I.; Zhu, Y.F.; Chung, C.N.; Allman, S.L.

    1997-03-01

    Since laser mass spectrometry has the potential for achieving very fast DNA analysis, the authors recently applied it to DNA sequencing, DNA typing for fingerprinting, and DNA screening for disease diagnosis. Two different approaches for sequencing DNA have been successfully demonstrated. One is to sequence DNA with DNA ladders produced from Snager`s enzymatic method. The other is to do direct sequencing without DNA ladders. The need for quick DNA typing for identification purposes is critical for forensic application. The preliminary results indicate laser mass spectrometry can possibly be used for rapid DNA fingerprinting applications at a much lower cost than gel electrophoresis. Population screening for certain genetic disease can be a very efficient step to reducing medical costs through prevention. Since laser mass spectrometry can provide very fast DNA analysis, the authors applied laser mass spectrometry to disease diagnosis. Clinical samples with both base deletion and point mutation have been tested with complete success.

  15. Commercial Art: Scope and Sequence.

    Nashville - Davidson County Metropolitan Public Schools, TN.

    This scope and sequence guide, developed for a commercial art vocational education program, represents an initial step in the development of a systemwide articulated curriculum sequence for all vocational programs within the Metropolitan Nashville Public School System. It was developed as a result of needs expressed by teachers, parents, and the…

  16. Shotgun protein sequencing.

    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.

  17. Sequencing chess

    Atashpendar, Arshia; Schilling, Tanja; Voigtmann, Thomas

    2016-10-01

    We analyze the structure of the state space of chess by means of transition path sampling Monte Carlo simulations. Based on the typical number of moves required to transpose a given configuration of chess pieces into another, we conclude that the state space consists of several pockets between which transitions are rare. Skilled players explore an even smaller subset of positions that populate some of these pockets only very sparsely. These results suggest that the usual measures to estimate both the size of the state space and the size of the tree of legal moves are not unique indicators of the complexity of the game, but that considerations regarding the connectedness of states are equally important.

  18. Is sequence awareness mandatory for perceptual sequence learning: An assessment using a pure perceptual sequence learning design.

    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.

  19. Sequence Read Archive (SRA)

    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...

  20. 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.

    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.

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

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

    2007-02-21

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

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

    Sara Imari Walker

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

  3. Direct simulation Monte Carlo ray tracing model of light scattering by a class of real particles and comparison with PROGRA2 experimental results

    Mikrenska, M.; Koulev, P.; Renard, J.-B.; Hadamcik, E.; Worms, J.-C.

    2006-01-01

    The Direct Simulation Monte Carlo (DSMC) model is presented for three-dimensional single scattering of natural light by suspended, randomly oriented, optically homogeneous and isotropic, rounded and stochastically rough cubic particles. The modelled particles have large size parameter that allows geometric optics approximation to be used. The proposed computational model is simple and flexible. It is tested by comparison with known geometric optics solution for a perfect cube and Lorenz-Mie solution for a sphere, as extreme cases of the class of rounded cubes. Scattering and polarization properties of particles with various geometrical and optical characteristics are examined. The experimental study of real NaCl crystals with new Progra 2 instrument in microgravity conditions is conducted. The experimental and computed polarization and brightness phase curves are compared

  4. πN → πN and KN → KN low energy data and partial wave analyses recent results and new directions

    Kelly, R.L.

    1975-07-01

    This review deals with πN → πN and KN → KN physics below about 3 GeV/c. An attempt is made to convey the state of the art, and to point out what appear to be promising directions for future research. The situation as of about one year ago is summarized in the 1974 Review of Particle Properties and in London conference talks so more recent developments are considered. A comprehensive survey of πN → πN data between the Δ region and 3 GeV/c is given. Problems associated with spin-rotation experiments are discussed, and the current πN → πN partial wave analyses. I = 1 and I = 0 KN → KN analyses, respectively, are considered

  5. Store-directed price promotions and communications strategies improve healthier food supply and demand: impact results from a randomized controlled, Baltimore City store-intervention trial.

    Budd, Nadine; Jeffries, Jayne K; Jones-Smith, Jessica; Kharmats, Anna; McDermott, Ann Yelmokas; Gittelsohn, Joel

    2017-12-01

    Small food store interventions show promise to increase healthy food access in under-resourced areas. However, none have tested the impact of price discounts on healthy food supply and demand. We tested the impact of store-directed price discounts and communications strategies, separately and combined, on the stocking, sales and prices of healthier foods and on storeowner psychosocial factors. Factorial design randomized controlled trial. Twenty-four corner stores in low-income neighbourhoods of Baltimore City, MD, USA. Stores were randomized to pricing intervention, communications intervention, combined pricing and communications intervention, or control. Stores that received the pricing intervention were given a 10-30 % price discount by wholesalers on selected healthier food items during the 6-month trial. Communications stores received visual and interactive materials to promote healthy items, including signage, taste tests and refrigerators. All interventions showed significantly increased stock of promoted foods v. There was a significant treatment effect for daily unit sales of healthy snacks (β=6·4, 95 % CI 0·9, 11·9) and prices of healthy staple foods (β=-0·49, 95 % CI -0·90, -0·03) for the combined group v. control, but not for other intervention groups. There were no significant intervention effects on storeowner psychosocial factors. All interventions led to increased stock of healthier foods. The combined intervention was effective in increasing sales of healthier snacks, even though discounts on snacks were not passed to the consumer. Experimental research in small stores is needed to understand the mechanisms by which store-directed price promotions can increase healthy food supply and demand.

  6. How Well Do Customers of Direct-to-Consumer Personal Genomic Testing Services Comprehend Genetic Test Results? Findings from the Impact of Personal Genomics Study.

    Ostergren, Jenny E; Gornick, Michele C; Carere, Deanna Alexis; Kalia, Sarah S; Uhlmann, Wendy R; Ruffin, Mack T; Mountain, Joanna L; Green, Robert C; Roberts, J Scott

    2015-01-01

    To assess customer comprehension of health-related personal genomic testing (PGT) results. We presented sample reports of genetic results and examined responses to comprehension questions in 1,030 PGT customers (mean age: 46.7 years; 59.9% female; 79.0% college graduates; 14.9% non-White; 4.7% of Hispanic/Latino ethnicity). Sample reports presented a genetic risk for Alzheimer's disease and type 2 diabetes, carrier screening summary results for >30 conditions, results for phenylketonuria and cystic fibrosis, and drug response results for a statin drug. Logistic regression was used to identify correlates of participant comprehension. Participants exhibited high overall comprehension (mean score: 79.1% correct). The highest comprehension (range: 81.1-97.4% correct) was observed in the statin drug response and carrier screening summary results, and lower comprehension (range: 63.6-74.8% correct) on specific carrier screening results. Higher levels of numeracy, genetic knowledge, and education were significantly associated with greater comprehension. Older age (≥ 60 years) was associated with lower comprehension scores. Most customers accurately interpreted the health implications of PGT results; however, comprehension varied by demographic characteristics, numeracy and genetic knowledge, and types and format of the genetic information presented. Results suggest a need to tailor the presentation of PGT results by test type and customer characteristics. © 2015 S. Karger AG, Basel.

  7. Does Stress Result in You Exercising Less? Or Does Exercising Result in You Being Less Stressed? Or Is It Both? Testing the Bi-directional Stress-Exercise Association at the Group and Person (N of 1) Level.

    Burg, Matthew M; Schwartz, Joseph E; Kronish, Ian M; Diaz, Keith M; Alcantara, Carmela; Duer-Hefele, Joan; Davidson, Karina W

    2017-12-01

    Psychosocial stress contributes to heart disease in part by adversely affecting maintenance of health behaviors, while exercise can reduce stress. Assessing the bi-directional relationship between stress and exercise has been limited by lack of real-time data and theoretical and statistical models. This lack may hinder efforts to promote exercise maintenance. We test the bi-directional relationship between stress and exercise using real-time data for the average person and the variability-individual differences-in this relationship. An observational study was conducted within a single cohort randomized controlled experiment. Healthy young adults, (n = 79) who reported only intermittent exercise, completed 12 months of stress monitoring by ecological momentary assessment (at the beginning of, end of, and during the day) and continuous activity monitoring by Fitbit. A random coefficients linear mixed model was used to predict end-of-day stress from the occurrence/non-occurrence of exercise that day; a logistic mixed model was used to predict the occurrence/non-occurrence of exercise from ratings of anticipated stress. Separate regression analyses were also performed for each participant. Sensitivity analysis tested all models, restricted to the first 180 days of observation (prior to randomization). We found a significant average inverse (i.e., negative) effect of exercise on stress and of stress on exercise. There was significant between-person variability. Of N = 69, exercise was associated with a stress reduction for 15, a stress increase for 2, and no change for the remainder. We also found that an increase in anticipated stress reported the previous night or that morning was associated with a significant 20-22% decrease (OR = 0.78-0.80) in the odds of exercising that day. Of N = 69, this increase in stress reduced the likelihood of exercise for 17, increased the odds for 1, and had no effect for the remainder. We were unable to identify psychosocial

  8. Dog Y chromosomal DNA sequence: identification, sequencing and SNP discovery

    Kirkness Ewen

    2006-10-01

    Full Text Available Abstract Background Population genetic studies of dogs have so far mainly been based on analysis of mitochondrial DNA, describing only the history of female dogs. To get a picture of the male history, as well as a second independent marker, there is a need for studies of biallelic Y-chromosome polymorphisms. However, there are no biallelic polymorphisms reported, and only 3200 bp of non-repetitive dog Y-chromosome sequence deposited in GenBank, necessitating the identification of dog Y chromosome sequence and the search for polymorphisms therein. The genome has been only partially sequenced for one male dog, disallowing mapping of the sequence into specific chromosomes. However, by comparing the male genome sequence to the complete female dog genome sequence, candidate Y-chromosome sequence may be identified by exclusion. Results The male dog genome sequence was analysed by Blast search against the human genome to identify sequences with a best match to the human Y chromosome and to the female dog genome to identify those absent in the female genome. Candidate sequences were then tested for male specificity by PCR of five male and five female dogs. 32 sequences from the male genome, with a total length of 24 kbp, were identified as male specific, based on a match to the human Y chromosome, absence in the female dog genome and male specific PCR results. 14437 bp were then sequenced for 10 male dogs originating from Europe, Southwest Asia, Siberia, East Asia, Africa and America. Nine haplotypes were found, which were defined by 14 substitutions. The genetic distance between the haplotypes indicates that they originate from at least five wolf haplotypes. There was no obvious trend in the geographic distribution of the haplotypes. Conclusion We have identified 24159 bp of dog Y-chromosome sequence to be used for population genetic studies. We sequenced 14437 bp in a worldwide collection of dogs, identifying 14 SNPs for future SNP analyses, and

  9. Library Design-Facilitated High-Throughput Sequencing of Synthetic Peptide Libraries.

    Vinogradov, Alexander A; Gates, Zachary P; Zhang, Chi; Quartararo, Anthony J; Halloran, Kathryn H; Pentelute, Bradley L

    2017-11-13

    A methodology to achieve high-throughput de novo sequencing of synthetic peptide mixtures is reported. The approach leverages shotgun nanoliquid chromatography coupled with tandem mass spectrometry-based de novo sequencing of library mixtures (up to 2000 peptides) as well as automated data analysis protocols to filter away incorrect assignments, noise, and synthetic side-products. For increasing the confidence in the sequencing results, mass spectrometry-friendly library designs were developed that enabled unambiguous decoding of up to 600 peptide sequences per hour while maintaining greater than 85% sequence identification rates in most cases. The reliability of the reported decoding strategy was additionally confirmed by matching fragmentation spectra for select authentic peptides identified from library sequencing samples. The methods reported here are directly applicable to screening techniques that yield mixtures of active compounds, including particle sorting of one-bead one-compound libraries and affinity enrichment of synthetic library mixtures performed in solution.

  10. Directional Atherectomy Followed by a Paclitaxel-Coated Balloon to Inhibit Restenosis and Maintain Vessel Patency: Twelve-Month Results of the DEFINITIVE AR Study.

    Zeller, Thomas; Langhoff, Ralf; Rocha-Singh, Krishna J; Jaff, Michael R; Blessing, Erwin; Amann-Vesti, Beatrice; Krzanowski, Marek; Peeters, Patrick; Scheinert, Dierk; Torsello, Giovanni; Sixt, Sebastian; Tepe, Gunnar

    2017-09-01

    Studies assessing drug-coated balloons (DCB) for the treatment of femoropopliteal artery disease are encouraging. However, challenging lesions, such as severely calcified, remain difficult to treat with DCB alone. Vessel preparation with directional atherectomy (DA) potentially improves outcomes of DCB. DEFINITIVE AR study (Directional Atherectomy Followed by a Paclitaxel-Coated Balloon to Inhibit Restenosis and Maintain Vessel Patency-A Pilot Study of Anti-Restenosis Treatment) was a multicenter randomized trial designed to estimate the effect of DA before DCB to facilitate the development of future end point-driven randomized studies. One hundred two patients with claudication or rest pain were randomly assigned 1:1 to DA+DCB (n=48) or DCB alone (n=54), and 19 additional patients with severely calcified lesions were treated with DA+DCB. Mean lesion length was 11.2±4.0 cm for DA+DCB and 9.7±4.1 cm for DCB ( P =0.05). Predilation rate was 16.7% for DA+DCB versus 74.1% for DCB; postdilation rate was 6.3% for DA+DCB versus 33.3% for DCB. Technical success was superior for DA+DCB (89.6% versus 64.2%; P =0.004). Overall bail-out stenting rate was 3.7%, and rate of flow-limiting dissections was 19% for DCB and 2% for DA+DCB ( P =0.01). One-year primary outcome of angiographic percent diameter stenosis was 33.6±17.7% for DA+DCB versus 36.4±17.6% for DCB ( P =0.48), and clinically driven target lesion revascularization was 7.3% for DA+DCB and 8.0% for DCB ( P =0.90). Duplex ultrasound patency was 84.6% for DA+DCB, 81.3% for DCB ( P =0.78), and 68.8% for calcified lesions. Freedom from major adverse events at 1 year was 89.3% for DA+DCB and 90.0% for DCB ( P =0.86). DA+DCB treatment was effective and safe, but the study was not powered to show significant differences between the 2 methods of revascularization in 1-year follow-up. An adequately powered randomized trial is warranted. http://www.clinicaltrials.gov. Unique Identifier: NCT01366482. Copyright © 2017 The

  11. Multiparty Quantum Secret Sharing of Secure Direct Communication Using Teleportation

    Wang Jian; Zhang Quan; Tang Chaojing

    2007-01-01

    We present an (n,n) threshold quantum secret sharing scheme of secure direct communication using Greenberger-Horne-Zeilinger state and teleportation. After ensuring the security of the quantum channel, the sender encodes the secret message directly on a sequence of particle states and transmits it to the receivers by teleportation. The receivers can recover the secret message by combining their measurement results with the sender's result. If a perfect quantum channel is used, our scheme is completely secure because the transmitting particle sequence does not carry the secret message. We also show our scheme is secure for noise quantum channel.

  12. Randomized, sham-controlled trial based on transcranial direct current stimulation and wrist robot-assisted integrated treatment on subacute stroke patients: Intermediate results.

    Mazzoleni, Stefano; Tran, Vi Do; Iardella, Laura; Dario, Paolo; Posteraro, Federico

    2017-07-01

    The main goal of this study is to analyse the effects of combined transcranial direct current stimulation (tDCS) and wrist robot-assisted therapy in subacute stroke patients. Twenty-four patients were included in this study and randomly assigned to the experimental (EG) or control group (CG). All participants performed wrist robot-assisted training a) in conjunction with tDCS (real stimulation for patients in EG) or b) without tDCS (sham stimulation for patients in CG). Clinical scales and kinematic parameters recorded by the robot were used for the assessment. Clinical outcome measures show a significant decrease in motor impairment after the treatment in both groups. Kinematic data show several significant improvements after the integrated therapy in both groups. However, no significant differences in both clinical outcome measures and kinematic parameters was found between two groups. The potential advantages of combined tDCS and wrist robot-assisted therapy in subacute stroke patients are still unclear.

  13. Directly administered antiretroviral therapy for HIV-infected drug users does not have an impact on antiretroviral resistance: results from a randomized controlled trial.

    Maru, Duncan Smith-Rohrberg; Kozal, Michael J; Bruce, R Douglas; Springer, Sandra A; Altice, Frederick L

    2007-12-15

    Directly administered antiretroviral therapy (DAART) is an effective intervention that improves clinical outcomes among HIV-infected drug users. Its effects on antiretroviral drug resistance, however, are unknown. We conducted a community-based, prospective, randomized controlled trial of DAART compared with self-administered therapy (SAT). We performed a modified intention-to-treat analysis among 115 subjects who provided serum samples for HIV genotypic resistance testing at baseline and at follow-up. The main outcomes measures included total genotypic sensitivity score, future drug options, number of new drug resistance mutations (DRMs), and number of new major International AIDS Society (IAS) mutations. The adjusted probability of developing at least 1 new DRM did not differ between the 2 arms (SAT: 0.41 per person-year [PPY], DAART: 0.49 PPY; adjusted relative risk [RR] = 1.04; P = 0.90), nor did the number of new mutations (SAT: 0.76 PPY, DAART: 0.83 PPY; adjusted RR = 0.99; P = 0.99) or the probability of developing new major IAS new drug mutations (SAT: 0.30 PPY, DAART: 0.33 PPY; adjusted RR = 1.12; P = 0.78). On measures of GSS and FDO, the 2 arms also did not differ. In this trial, DAART provided on-treatment virologic benefit for HIV-infected drug users without affecting the rate of development of antiretroviral medication resistance.

  14. General directions and recently test modelling results of lithium capillary-pore systems as plasma facing components for tokamak-reactor

    Evtikhin, V.A.; Lyublinski, I.E.; Vertkov, A.V.; Azizov, E.A.; Mirnov, S.V.; Lazaret, V.B.; Safronov, V.M.

    2003-01-01

    Full text: At present the most promising principal solution of the divertor problem appears to be the use of liquid metals and primarily of lithium Capillary-Pore Systems (CPS) as of plasma facing material. A solid CPS filled with liquid lithium will have high resistance to surface and volume damage because of neutron radiation effects, melting, splashing and thermal stress induced cracking in steady state and during plasma transitions (disruptions, ELMs, VDEs, runaways) to provide the normal operation of divertor target plates and first wall protection elements. These materials would not be the sources of impurities inducing the raise of Z eff and they will not be collected as dust in the divertor area and in ducts. The key directions of experimental investigation of lithium CPS behaviour in first wall and divertor operation simulating conditions are considered. Experiments with lithium CPS in plasma disruption simulation conditions on the hydrogen plasma accelerator MK-200UG (∼10-15 MJ/m 2 , ∼50 μs) have been performed. Shielding lithium plasma layer formation and high stability of these systems have been shown. The new lithium limiter with a thermal regulation system tests on up graded T-11M tokamak (plasma current up to 100 kA, pulse length ∼0.3 s) have been performed. Sorption and desorption of plasma-forming gas, lithium emission into discharge, lithium erosion, limiter deposited power are investigated in this tests

  15. Development of Electronic Medical Record-Based "Rounds Report" Results in Improved Resident Efficiency, More Time for Direct Patient Care and Education, and Less Resident Duty Hour Violations.

    Ham, Phillip B; Anderton, Toby; Gallaher, Ryan; Hyrman, Mike; Simmerman, Erika; Ramanathan, Annamalai; Fallaw, David; Holsten, Steven; Howell, Charles Gordon

    2016-09-01

    Surgeons frequently report frustration and loss of efficiency with electronic medical record (EMR) systems. Together, surgery residents and a programmer at Augusta University created a rounds report (RR) summarizing 24 hours of vitals, intake/output, labs, and other values for each inpatient that were previously transcribed by hand. The objective of this study was to evaluate the RR's effect on surgery residents. Surgery residents were queried to assess the RR's impact. Outcome measures were time spent preparing for rounds, direct patient care time, educational activity time, rates of incorrect/incomplete data on rounds, and rate of duty hour violations. Hospital wide, 17,200 RRs were generated in the 1-month study. Twenty-three surgery residents participated. Time spent preparing for rounds decreased per floor patient (15.6 ± 3.0 vs 6.0 ± 1.2, P care unit patient (19.9 ± 2.9 vs 7.5 ± 1.2 P care increased from 45.1 ± 5.6 to 54.0 ± 5.7 per cent (P = 0.0044). Educational activity time increased from 35.2 ± 5.4 to 54.7 ± 7.1 minutes per resident per day (P = 0.0004). Reported duty hour violations decreased 58 per cent (P care at academic medical centers.

  16. A Manual Transportable Instrument Platform for Ground-Based Spectro-Directional Observations (ManTIS and the Resultant Hyperspectral Field Goniometer System

    Marcel Buchhorn

    2013-11-01

    Full Text Available This article presents and technically describes a new field spectro-goniometer system for the ground-based characterization of the surface reflectance anisotropy under natural illumination conditions developed at the Alfred Wegener Institute (AWI. The spectro-goniometer consists of a Manual Transportable Instrument platform for ground-based Spectro-directional observations (ManTIS, and a hyperspectral sensor system. The presented measurement strategy shows that the AWI ManTIS field spectro-goniometer can deliver high quality hemispherical conical reflectance factor (HCRF measurements with a pointing accuracy of ±6 cm within the constant observation center. The sampling of a ManTIS hemisphere (up to 30° viewing zenith, 360° viewing azimuth needs approx. 18 min. The developed data processing chain in combination with the software used for the semi-automatic control provides a reliable method to reduce temporal effects during the measurements. The presented visualization and analysis approaches of the HCRF data of an Arctic low growing vegetation showcase prove the high quality of spectro-goniometer measurements. The patented low-cost and lightweight ManTIS instrument platform can be customized for various research needs and is available for purchase.

  17. DNA Sequencing by Capillary Electrophoresis

    Karger, Barry L.; Guttman, Andras

    2009-01-01

    Sequencing of human and other genomes has been at the center of interest in the biomedical field over the past several decades and is now leading toward an era of personalized medicine. During this time, DNA sequencing methods have evolved from the labor intensive slab gel electrophoresis, through automated multicapillary electrophoresis systems using fluorophore labeling with multispectral imaging, to the “next generation” technologies of cyclic array, hybridization based, nanopore and single molecule sequencing. Deciphering the genetic blueprint and follow-up confirmatory sequencing of Homo sapiens and other genomes was only possible by the advent of modern sequencing technologies that was a result of step by step advances with a contribution of academics, medical personnel and instrument companies. While next generation sequencing is moving ahead at break-neck speed, the multicapillary electrophoretic systems played an essential role in the sequencing of the Human Genome, the foundation of the field of genomics. In this prospective, we wish to overview the role of capillary electrophoresis in DNA sequencing based in part of several of our articles in this journal. PMID:19517496

  18. [Complete genome sequencing and sequence analysis of BCG Tice].

    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.

  19. Sequence-dependent DNA deformability studied using molecular dynamics simulations.

    Fujii, Satoshi; Kono, Hidetoshi; Takenaka, Shigeori; Go, Nobuhiro; Sarai, Akinori

    2007-01-01

    Proteins recognize specific DNA sequences not only through direct contact between amino acids and bases, but also indirectly based on the sequence-dependent conformation and deformability of the DNA (indirect readout). We used molecular dynamics simulations to analyze the sequence-dependent DNA conformations of all 136 possible tetrameric sequences sandwiched between CGCG sequences. The deformability of dimeric steps obtained by the simulations is consistent with that by the crystal structures. The simulation results further showed that the conformation and deformability of the tetramers can highly depend on the flanking base pairs. The conformations of xATx tetramers show the most rigidity and are not affected by the flanking base pairs and the xYRx show by contrast the greatest flexibility and change their conformations depending on the base pairs at both ends, suggesting tetramers with the same central dimer can show different deformabilities. These results suggest that analysis of dimeric steps alone may overlook some conformational features of DNA and provide insight into the mechanism of indirect readout during protein-DNA recognition. Moreover, the sequence dependence of DNA conformation and deformability may be used to estimate the contribution of indirect readout to the specificity of protein-DNA recognition as well as nucleosome positioning and large-scale behavior of nucleic acids.

  20. Cognitive effects of transcranial direct current stimulation in depression: Results from the SELECT-TDCS trial and insights for further clinical trials.

    Brunoni, André Russowsky; Tortella, Gabriel; Benseñor, Isabela Martins; Lotufo, Paulo Andrade; Carvalho, André Ferrer; Fregni, Felipe

    2016-09-15

    Cognitive dysfunction treatment remains an unmet clinical need in major depressive disorder (MDD). Transcranial direct current stimulation (tDCS) may improve cognitive symptoms in MDD. Our aim was to investigate the cognitive effects of tDCS in the Sertraline vs. Electric Current Therapy for Treating Depression Clinical Study (SELECT-TDCS). We also explored whether tDCS could have mood-independent cognitive effects. One hundred twenty MDD patients aged from 18 to 65 years received 12 sessions of active/sham tDCS (2mA for 30min) and real/placebo 50mg/d sertraline over 6 weeks in a factorial trial. We analyzed whether changes in performance of neuropsychological tests (Trail Making, Digit Span, Stroop Task, Mini-Mental Status Exam and Montreal Cognitive Assessment) occurred over time, according to treatment group and depression improvement. Exploratory analyses were carried out to verify the influence of clinical and demographic variables on the outcomes. Cognitive improvement was showed in most tests used, although they occurred regardless of intervention type and depression improvement. Further exploratory analyses revealed that clinical response and education level could have mediated pro-cognitive tDCS effects on some of the tests used. The neuropsychological battery used might not have been sensitive to detect tDCS-induced effects on cognition. Lack of simultaneous cognitive training during application may have also limited its cognitive effects. We found no evidence of beneficial or deleterious cognitive effects of tDCS as a treatment for depression. We discussed clinical trial design considerations for further tDCS studies assessing cognitive effects, including sample and outcomes considerations. Copyright © 2016 Elsevier B.V. All rights reserved.

  1. Potential spillover educational effects of cancer-related direct-to-consumer advertising on cancer patients' increased information seeking behaviors: results from a cohort study.

    Tan, Andy S L

    2014-06-01

    Spillover effects of exposure to direct-to-consumer advertising (DTCA) of cancer treatments on patients' general inquiry about their treatments and managing their illness are not well understood. This study examines the effects of cancer patients' exposure to cancer-related DTCA on subsequent health information seeking behaviors from clinician and non-clinician sources (lay media and interpersonal contacts). Using a longitudinal survey design over 3 years, data was collected from cancer survivors diagnosed with colorectal, breast, or prostate cancer who were randomly sampled from the Pennsylvania Cancer Registry. Study outcome measures include patients' information engagement with their clinicians and information seeking from non-medical sources about cancer treatment and quality of life issues, measured in the second survey. The predictor variable is the frequency of exposure to cancer-related DTCA since diagnosis, measured at the round 1 survey. The analyses utilized lagged-weighted multivariate regressions and adjusted for round 1 levels of patient-clinician engagement, information seeking from nonmedical sources, and confounders. Exposure to cancer-related DTCA is associated with increased levels of subsequent patient-clinician information engagement (B = .023, 95% CI = .005-.040, p = .012), controlling for confounders. In comparison, exposure to DTCA is marginally significant in predicting health information seeking from non-clinician sources (B = .009, 95% CI = -.001-.018, p = .067). Cancer-related DTCA has potentially beneficial spillover effects on health information seeking behaviors among cancer patients. Exposure to DTCA predicts (a little) more patient engagement with their physicians.

  2. Potential Spillover Educational Effects Of Cancer-Related Direct-To-Consumer Advertising On Cancer Patients’ Increased Information Seeking Behaviors: Results From A Cohort Study

    Tan, Andy SL

    2014-01-01

    Spillover effects of exposure to direct-to-consumer advertising (DTCA) of cancer treatments on patients’ general inquiry about their treatments and managing their illness are not well understood. This study examines the effects of cancer patients’ exposure to cancer-related DTCA on subsequent health information seeking behaviors from clinician and non-clinician sources (lay media and interpersonal contacts). Using a longitudinal survey design over three years, data was collected from cancer survivors diagnosed with colorectal, breast, or prostate cancer who were randomly sampled from the Pennsylvania Cancer Registry. Study outcome measures include patients’ information engagement with their clinicians and information seeking from non-medical sources about cancer treatment and quality of life issues, measured in the second survey. The predictor variable is the frequency of exposure to cancer-related DTCA since diagnosis, measured at the round 1 survey. The analyses utilized lagged weighted multivariate regressions and adjusted for round 1 levels of patient-clinician engagement, information seeking from non-medical sources, and confounders. Exposure to cancer-related DTCA is associated with increased levels of subsequent patient-clinician information engagement (B=.023, 95%CI=.005 to .040, p=.012), controlling for confounders. In comparison, exposure to DTCA is marginally significant in predicting health information seeking from non-clinician sources (B=.009, 95%CI=−.001 to .018, p=.067). Cancer-related DTCA has potentially beneficial spillover effects on health information seeking behaviors among cancer patients. Exposure to DTCA predicts (a little) more patient engagement with their physicians. PMID:24254248

  3. Healthcare resource use, direct and indirect costs of hypoglycemia in type 1 and type 2 diabetes, and nationwide projections. Results of the HYPOS-1 study.

    Giorda, C B; Rossi, M C; Ozzello, O; Gentile, S; Aglialoro, A; Chiambretti, A; Baccetti, F; Gentile, F M; Romeo, F; Lucisano, G; Nicolucci, A

    2017-03-01

    To obtain an accurate picture of the total costs of hypoglycemia, including the indirect costs and comparing the differences between type 1 (T1DM) and type 2 diabetes mellitus (T2DM). HYPOS-1 was a multicenter, retrospective cohort study which analyzed the data of 2229 consecutive patients seen at 18 diabetes clinics. Data on healthcare resource use and indirect costs by diabetes type were collected via a questionnaire. The domains of inpatient admission and hospital stay, work days lost, and third-party assistance were also explored. Resource utilization was reported as estimated incidence rates (IRs) of hypoglycemic episodes per 100 person-years and estimated costs as IRs per person-years. For every 100 patients with T1DM, 9 emergency room (ER) visits and 6 emergency medical service calls for hypoglycemia were required per year; for every 100 patients with T2DM, 3 ER visits and 1 inpatient admission were required, with over 3 nights spent in hospital. Hypoglycemia led to 58 work days per 100 person-years lost by the patient or a family member in T1DM versus 19 in T2DM. The costs in T1DM totaled €90.99 per person-year and €62.04 in T2DM. Direct and indirect costs making up the total differed by type of diabetes (60% indirect costs in T1DM versus 43% in T2DM). The total cost associated with hypoglycemia in Italy is estimated to be €107 million per year. Indirect costs meaningfully contribute to the total costs associated with hypoglycemia. As compared with T1DM, T2DM requires fewer ER visits and incurs lower indirect costs but more frequent hospital use. Copyright © 2016 The Italian Society of Diabetology, the Italian Society for the Study of Atherosclerosis, the Italian Society of Human Nutrition, and the Department of Clinical Medicine and Surgery, Federico II University. Published by Elsevier B.V. All rights reserved.

  4. Image sequence analysis

    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 ...

  5. Next-generation sequencing offers new insights into DNA degradation

    Overballe-Petersen, Søren; Orlando, Ludovic Antoine Alexandre; Willerslev, Eske

    2012-01-01

    The processes underlying DNA degradation are central to various disciplines, including cancer research, forensics and archaeology. The sequencing of ancient DNA molecules on next-generation sequencing platforms provides direct measurements of cytosine deamination, depurination and fragmentation...... rates that previously were obtained only from extrapolations of results from in vitro kinetic experiments performed over short timescales. For example, recent next-generation sequencing of ancient DNA reveals purine bases as one of the main targets of postmortem hydrolytic damage, through base...... elimination and strand breakage. It also shows substantially increased rates of DNA base-loss at guanosine. In this review, we argue that the latter results from an electron resonance structure unique to guanosine rather than adenosine having an extra resonance structure over guanosine as previously suggested....

  6. Assessing representativeness of sampling methods for reaching men who have sex with men: a direct comparison of results obtained from convenience and probability samples.

    Schwarcz, Sandra; Spindler, Hilary; Scheer, Susan; Valleroy, Linda; Lansky, Amy

    2007-07-01

    Convenience samples are used to determine HIV-related behaviors among men who have sex with men (MSM) without measuring the extent to which the results are representative of the broader MSM population. We compared results from a cross-sectional survey of MSM recruited from gay bars between June and October 2001 to a random digit dial telephone survey conducted between June 2002 and January 2003. The men in the probability sample were older, better educated, and had higher incomes than men in the convenience sample, the convenience sample enrolled more employed men and men of color. Substance use around the time of sex was higher in the convenience sample but other sexual behaviors were similar. HIV testing was common among men in both samples. Periodic validation, through comparison of data collected by different sampling methods, may be useful when relying on survey data for program and policy development.

  7. RNA-Pareto: interactive analysis of Pareto-optimal RNA sequence-structure alignments.

    Schnattinger, Thomas; Schöning, Uwe; Marchfelder, Anita; Kestler, Hans A

    2013-12-01

    Incorporating secondary structure information into the alignment process improves the quality of RNA sequence alignments. Instead of using fixed weighting parameters, sequence and structure components can be treated as different objectives and optimized simultaneously. The result is not a single, but a Pareto-set of equally optimal solutions, which all represent different possible weighting parameters. We now provide the interactive graphical software tool RNA-Pareto, which allows a direct inspection of all feasible results to the pairwise RNA sequence-structure alignment problem and greatly facilitates the exploration of the optimal solution set.

  8. Association studies using family pools of outcrossing crops based on allele-frequency estimates from DNA sequencing

    Ashraf, Bilal; Jensen, Just; Asp, Torben

    2014-01-01

    effect from F2-family pools was verified and it was shown that the underestimation of the allele effect is correctly described. The optimal design for an association study when sequencing budget would be fixed is obtained using large sample size and lower sequence depth, and using higher SNP density......F2 families are frequently used in breeding of outcrossing species, for instance to obtain trait measurements on plots. We propose to perform association studies by obtaining a matching “family genotype” from sequencing a pooled sample of the family, and to directly use allele frequencies computed...... (resulting in higher LD with causative mutations) and lower sequencing depth. Therefore, association studies using genotyping by sequencing are optimal and use low sequencing depth per sample. The developed framework for association studies using allele frequencies from sequencing can be modified for other...

  9. Coseismic and Early Post-Seismic Slip Distributions of the 2012 Emilia (Northern Italy) Seismic Sequence: New Insights in the Faults Activation and Resulting Stress Changes on Adjacent Faults

    Cheloni, D.; Giuliani, R.; D'Agostino, N.; Mattone, M.; Bonano, M.; Fornaro, G.; Lanari, R.; Reale, D.

    2015-12-01

    The 2012 Emilia sequence (main shocks Mw 6.1 May 20 and Mw 5.9 May 29) ruptured two thrust segments of a ~E-W trending fault system of the buried Ferrara Arc, along a portion of the compressional system of the Apennines that had remained silent during past centuries. Here we use the rupture geometry constrained by the aftershocks and new geodetic data (levelling, InSAR and GPS measurements) to estimate an improved coseismic slip distribution of the two main events. In addition, we use post-seismic displacements, described and analyzed here for the first time, to infer a brand new post-seismic slip distribution of the May 29 event in terms of afterslip on the same coseismic plane. In particular, in this study we use a catalog of precisely relocated aftershocks to explore the different proposed geometries of the proposed thrust segments that have been published so far and estimate the coseismic and post-seismic slip distributions of the ruptured planes responsible for the two main seismic events from a joint inversion of the geodetic data.Joint inversion results revealed that the two earthquakes ruptured two distinct planar thrust faults, characterized by single main coseismic patches located around the centre of the rupture planes, in agreement with the seismological and geological information pointing out the Ferrara and the Mirandola thrust faults, as the causative structures of the May 20 and May 29 main shocks respectively.The preferred post-seismic slip distribution related to the 29 May event, yielded to a main patch of afterslip (equivalent to a Mw 5.6 event) located westward and up-dip of the main coseismic patch, suggesting that afterslip was triggered at the edges of the coseismic asperity. We then use these co- and post-seismic slip distribution models to calculate the stress changes on adjacent fault.

  10. Memory and learning with rapid audiovisual sequences

    Keller, Arielle S.; Sekuler, Robert

    2015-01-01

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

  11. Memory and learning with rapid audiovisual sequences.

    Keller, Arielle S; Sekuler, Robert

    2015-01-01

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

  12. 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.

    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.

  13. Concomitant use of transcranial Direct Current Stimulation and computer-assisted training for the rehabilitation of attention in traumatic brain injured patients: behavioral and neuroimaging results

    Katiuscia eSacco

    2016-03-01

    Full Text Available Divided attention, the ability to distribute cognitive resources among two or more simultaneous tasks, may be severely compromised after traumatic brain injury (TBI, resulting in problems with numerous activities involved with daily living. So far, no research has investigated whether the use of non-invasive brain stimulation associated with neuropsychological rehabilitation might contribute to the recovery of such cognitive function. The main purpose of this study was to assess the effectiveness of 10 tDCS sessions combined with computer-assisted training; it also intended to explore the neural modifications induced by the treatment. Thirty-two patients with severe TBI participated in the study: sixteen were part of the experimental group, and sixteen part of the control group. The treatment included 20’ of tDCS, administered twice a day for 5 days. The electrodes were placed on the dorso-lateral prefrontal cortex. Their location varied across patients and it depended on each participant’s specific area of damage. The control group received sham tDCS. After each tDCS session, the patient received computer-assisted cognitive training on divided attention for 40’. The results showed that the experimental group significantly improved in divided attention performance between pre- and post-treatment, showing faster reaction times, and fewer omissions. No improvement was detected between the baseline assessment (i.e., one month before treatment and the pre-training assessment, or within the control group. Functional magnetic resonance imaging data, obtained on the experimental group during a divided attention task, showed post-treatment lower cerebral activations in the right superior temporal gyrus (BA 42, right and left middle frontal gyrus (BA 6, right postcentral gyrus (BA 3 and left inferior frontal gyrus (BA 9. We interpreted such neural changes as normalization of previously abnormal hyperactivations.

  14. Direct spectral analysis of tea samples using 266 nm UV pulsed laser-induced breakdown spectroscopy and cross validation of LIBS results with ICP-MS.

    Gondal, M A; Habibullah, Y B; Baig, Umair; Oloore, L E

    2016-05-15

    Tea is one of the most common and popular beverages spanning vast array of cultures all over the world. The main nutritional benefits of drinking tea are its anti-oxidant properties, presumed protection against certain cancers, inhibition of inflammation and possible protective effects against diabetes. Laser induced breakdown spectrometer (LIBS) was assembled as a powerful tool for qualitative and quantitative analysis of various brands of tea samples using 266 nm pulsed UV laser. LIBS spectra for six brands of tea samples in the wavelength range of 200-900 nm was recorded and all elements present in our tea samples were identified. The major toxic elements detected in several brands of tea samples were bromine, chromium and minerals like iron, calcium, potassium and silicon. The spectral assignment was conducted prior to the determination of concentration of each element. For quantitative analysis, calibration curves were drawn for each element using standard samples prepared in known concentration in the tea matrix. The plasma parameters (electron temperature and electron density) were also determined prior to the tea samples spectroscopic analysis. The concentration of iron, chromium, potassium, bromine, copper, silicon and calcium detected in all tea samples was between 378-656, 96-124, 1421-6785, 99-1476, 17-36, 2-11 and 92-130 mg L(-1) respectively. The limits of detection estimated for Fe, Cr, K, Br, Cu, Si, Ca in tea samples were 22, 12, 14, 11, 6, 1 and 12 mg L(-1) respectively. To further confirm the accuracy of our LIBS results, we determined the concentration of each element present in tea samples by using standard analytical technique like ICP-MS. The concentrations detected with our LIBS system are in excellent agreement with ICP-MS results. The system assembled for spectral analysis in this work could be highly applicable for testing the quality and purity of food and also pharmaceuticals products. Copyright © 2016 Elsevier B.V. All rights reserved.

  15. Sequence periodicity in nucleosomal DNA and intrinsic curvature.

    Nair, T Murlidharan

    2010-05-17

    Most eukaryotic DNA contained in the nucleus is packaged by wrapping DNA around histone octamers. Histones are ubiquitous and bind most regions of chromosomal DNA. In order to achieve smooth wrapping of the DNA around the histone octamer, the DNA duplex should be able to deform and should possess intrinsic curvature. The deformability of DNA is a result of the non-parallelness of base pair stacks. The stacking interaction between base pairs is sequence dependent. The higher the stacking energy the more rigid the DNA helix, thus it is natural to expect that sequences that are involved in wrapping around the histone octamer should be unstacked and possess intrinsic curvature. Intrinsic curvature has been shown to be dictated by the periodic recurrence of certain dinucleotides. Several genome-wide studies directed towards mapping of nucleosome positions have revealed periodicity associated with certain stretches of sequences. In the current study, these sequences have been analyzed with a view to understand their sequence-dependent structures. Higher order DNA structures and the distribution of molecular bend loci associated with 146 base nucleosome core DNA sequence from C. elegans and chicken have been analyzed using the theoretical model for DNA curvature. The curvature dispersion calculated by cyclically permuting the sequences revealed that the molecular bend loci were delocalized throughout the nucleosome core region and had varying degrees of intrinsic curvature. The higher order structures associated with nucleosomes of C.elegans and chicken calculated from the sequences revealed heterogeneity with respect to the deviation of the DNA axis. The results points to the possibility of context dependent curvature of varying degrees to be associated with nucleosomal DNA.

  16. Nonparametric combinatorial sequence models.

    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.

  17. Blazar Sequence in Fermi Era Liang Chen

    Abstract. In this paper, we review the latest research results on the topic of blazar sequence. It seems that the blazar sequence is phenomenally ruled out, while the theoretical blazar sequence still holds. We point out that black hole mass is a dominated parameter accounting for high-power- high-synchrotron-peaked and ...

  18. Accident Sequence Precursor Analysis for SGTR by Using Dynamic PSA Approach

    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

  19. Climatic trends and anomalies in Europe 1675-1715. High resolution spatio-temporal reconstructions from direct meteorological observations and proxy data: Methods and results

    Frenzel, B.; Pfister, C.; Glaeser, B.

    1994-01-01

    This volume contains the proceedings of a conference held at the University of Bern in Switzerland on 2-4 September 1992 by a group of historical geographers, historians, palaeobotanists and meteorologists originating from fifteen European nations as well as from China and Japan. It was the first international symposium of this kind for which the participants had previously submitted various kinds of palaeoclimatic data - early instrumental series, documentary data, dendroclimatic data - in a standardized form to a common data base in order to have this evidence ready to include in a pan-European multi-proxy mapping scheme at the time of the meeting. A team of meteorological experts worked on interpreting some of these data in terms of rough monthly synoptic weather situations in order to test the suitability of the evidence for this purpose. This volume includes both the regional contributions of the individual partners presented at the Bern workshop, as well as the two hundred monthly synoptic weather maps which resulted from the common effort of the group of meteorologists at the Copenhagen meeting. (orig.)

  20. Performance assessment of the direct disposal in unsaturated tuff or spent nuclear fuel and high-level waste owned by USDOE: Volume 2, Methodology and results

    Rechard, R.P. [ed.

    1995-03-01

    This assessment studied the performance of high-level radioactive waste and spent nuclear fuel in a hypothetical repository in unsaturated tuff. The results of this 10-month study are intended to help guide the Office of Environment Management of the US Department of Energy (DOE) on how to prepare its wastes for eventual permanent disposal. The waste forms comprised spent fuel and high-level waste currently stored at the Idaho National Engineering Laboratory (INEL) and the Hanford reservations. About 700 metric tons heavy metal (MTHM) of the waste under study is stored at INEL, including graphite spent nuclear fuel, highly enriched uranium spent fuel, low enriched uranium spent fuel, and calcined high-level waste. About 2100 MTHM of weapons production fuel, currently stored on the Hanford reservation, was also included. The behavior of the waste was analyzed by waste form and also as a group of waste forms in the hypothetical tuff repository. When the waste forms were studied together, the repository was assumed also to contain about 9200 MTHM high-level waste in borosilicate glass from three DOE sites. The addition of the borosilicate glass, which has already been proposed as a final waste form, brought the total to about 12,000 MTHM.

  1. Performance assessment of the direct disposal in unsaturated tuff or spent nuclear fuel and high-level waste owned by USDOE: Volume 2, Methodology and results

    Rechard, R.P.

    1995-03-01

    This assessment studied the performance of high-level radioactive waste and spent nuclear fuel in a hypothetical repository in unsaturated tuff. The results of this 10-month study are intended to help guide the Office of Environment Management of the US Department of Energy (DOE) on how to prepare its wastes for eventual permanent disposal. The waste forms comprised spent fuel and high-level waste currently stored at the Idaho National Engineering Laboratory (INEL) and the Hanford reservations. About 700 metric tons heavy metal (MTHM) of the waste under study is stored at INEL, including graphite spent nuclear fuel, highly enriched uranium spent fuel, low enriched uranium spent fuel, and calcined high-level waste. About 2100 MTHM of weapons production fuel, currently stored on the Hanford reservation, was also included. The behavior of the waste was analyzed by waste form and also as a group of waste forms in the hypothetical tuff repository. When the waste forms were studied together, the repository was assumed also to contain about 9200 MTHM high-level waste in borosilicate glass from three DOE sites. The addition of the borosilicate glass, which has already been proposed as a final waste form, brought the total to about 12,000 MTHM

  2. First Results from the Dense Extragalactic GBT+ARGUS Survey (DEGAS): A Direct, Quantitative Test of the Role of Gas Density in Star Formation

    Kepley, Amanda; Bigiel, Frank; Bolatto, Alberto; Church, Sarah; Cleary, Kieran; Frayer, David; Gallagher, Molly; Gundersen, Joshua; Harris, Andrew; Hughes, Annie; Jimenez-Donaire, Maria Jesus; Kessler, Sarah; Lee, Cheoljong; Leroy, Adam; Li, Jialu; Donovan Meyer, Jennifer; Rosolowsky, Erik; Sandstrom, Karin; Schinnener, Eva; Schruba, Andreas; Sieth, Matt; Usero, Antonio

    2018-01-01

    Gas density plays a central role in all modern theories of star formation. A key test of these theories involves quantifying the resolved gas density distribution and its relationship to star formation within a wide range of galactic environments. Until recently, this experiment has been difficult to perform owing to the faint nature of key molecular gas tracers like HCN and HCO+, but the superior sensitivity of modern millimeter instruments like ALMA and the IRAM 30m make these types of experiments feasible. In particular, the sensitivity and resolution provided by large aperture of the GBT combined with fast mapping speeds made possible by its new 16-pixel, 3mm focal plane array (Argus) make the GBT an almost-ideal instrument for this type of study. The Dense Extragalactic GBT+Argus Survey (DEGAS) will leverage these capabilities to perform the largest, resolved survey of molecular gas tracers in nearby galaxies, ultimately mapping a suite of four molecular gas tracers in the inner 2’ by 2’ of 36 nearby galaxies. When complete in 2020, DEGAS will be the largest resolved survey of dense molecular gas tracers in nearby galaxies. This talk will present early results from the first observations for this Green Bank Telescope large survey and highlight some exciting future possibilities for this survey.

  3. Serum 3,3'-L-diiodothyronine, a direct radioimmunoassay in human serum: method and clinical results. [/sup 125/I tracer technique

    Burger, A.; Sakoloff, C.

    1977-09-01

    A specific radioimmunoassay for 3,3'-diiodothyronine (T/sub 2/) is described which is capable of detecting as little as 1.3 ng/dl. The antiserum recognizes mainly T/sub 2/; biliary conjugates of T/sub 2/ bind slightly to the antibody. The intraassay and interassay coefficients of variation were, respectively, 5.7% and 13.1%. T/sub 2/ was detected in the serum of hypothyroid patients treated with triiodothyronine (T/sub 3/) and in euthyroid subjects treated with reverse triiodothyronine (rT/sub 3/). These results suggest that both T/sub 3/ and rT/sub 3/ are deiodinated to T/sub 2/. Serum concentrations of T/sub 2/ in normal subjects decreased with age. Between 20 and 40 years the mean concentration was 4.3 +- 2.0 ng/dl (2 SD), between 41 and 60 years it varied from 1.9 to 5.8 ng/dl (3.8 +- 0.3 ng/dl, SE) and in elderly subjects have 60 years concentrations varied from unmeasurable to 4 ng/dl (2.9 +- 0.4 ng/dl, SE). Low serum T/sub 2/ concentrations were found in anorexia nervosa (2.5 +- 0.3 ng/dl, SE). In hypothyroidism the serum concentrations were low or unmeasurable. As most of the hypothyroid subjects were elderly their serum T/sub 2/ concentrations overlapped with the low values found in the elderly euthyroid subjects. In classical hyperthyroidism serum T/sub 2/ concentrations were greatly increased (3.3 to 31 ng/dl (11.8 +- 2.7 ng/dl, SE) but in ''T/sub 3/ toxicosis'' the concentrations were only modestly increased (2.4 to 8.8 ng/dl, 5.2 +- 0.8 ng/dl, SE).

  4. Leukocyte- and platelet-rich fibrin (L-PRF) for long-term delivery of growth factor in rotator cuff repair: review, preliminary results and future directions.

    Zumstein, Matthias A; Berger, Simon; Schober, Martin; Boileau, Pascal; Nyffeler, Richard W; Horn, Michael; Dahinden, Clemens A

    2012-06-01

    Surgical repair of the rotator cuff repair is one of the most common procedures in orthopedic surgery. Despite it being the focus of much research, the physiological tendon-bone insertion is not recreated following repair and there is an anatomic non-healing rate of up to 94%. During the healing phase, several growth factors are upregulated that induce cellular proliferation and matrix deposition. Subsequently, this provisional matrix is replaced by the definitive matrix. Leukocyte- and platelet-rich fibrin (L-PRF) contain growth factors and has a stable dense fibrin matrix. Therefore, use of LPRF in rotator cuff repair is theoretically attractive. The aim of the present study was to determine 1) the optimal protocol to achieve the highest leukocyte content; 2) whether L-PRF releases growth factors in a sustained manner over 28 days; 3) whether standard/gelatinous or dry/compressed matrix preparation methods result in higher growth factor concentrations. 1) The standard L-PRF centrifugation protocol with 400 x g showed the highest concentration of platelets and leukocytes. 2) The L-PRF clots cultured in medium showed a continuous slow release with an increase in the absolute release of growth factors TGF-β1, VEGF and MPO in the first 7 days, and for IGF1, PDGF-AB and platelet activity (PF4=CXCL4) in the first 8 hours, followed by a decrease to close to zero at 28 days. Significantly higher levels of growth factor were expressed relative to the control values of normal blood at each culture time point. 3) Except for MPO and the TGFβ-1, there was always a tendency towards higher release of growth factors (i.e., CXCL4, IGF-1, PDGF-AB, and VEGF) in the standard/gelatinous- compared to the dry/compressed group. L-PRF in its optimal standard/gelatinous-type matrix can store and deliver locally specific healing growth factors for up to 28 days and may be a useful adjunct in rotator cuff repair.

  5. Genome Sequence Databases (Overview): Sequencing and Assembly

    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. Topological disposition of the sequences -QRKIVE- and -KETYY in native (Na+ + K+)-ATPase

    Bayer, R.

    1990-01-01

    The dispositions with respect to the plane of the membrane of lysine-905 in the internal sequence -EQRKIVE- and of lysine-1012 in the carboxy-terminal sequence -RRPGGWVEKETYY of the α-polypeptide of sodium and potassium ion activated adenosinetriphosphatase have been determined. These lysines are found in peptides released from the intact α-polypeptide by the extracellular protease from Staphylococcus aureus strain V8 and by trypsin, respectively. Synthetic peptides containing terminal sequences of these were used to prepare polyclonal antibodies, which were then used to prepare immunoadsorbents directed against the respective peptides. Sealed, right-side-out membrane vesicles containing native (Na + + K + )-ATPase were labeled with pyridoxal phosphate and sodium [ 3 H]borohydride in the absence or presence of saponin. The labeled α-polypeptide was isolated from these vesicles and digested with appropriate proteases. The incorporation of radioactivity into the peptides binding to the immunoadsorbent directed against the sequence pyrERXIVE increased 3-fold int the presence of saponin as a result of the increased accessibility of this portion of the protein to the reagent when the vesicles were breached by saponin; hence, this sequence is located on the cytoplasmic face of the membrane. It was inferred that the carboxy-terminal sequence -KETYY is on the extracytoplasmic face since the incorporation of radioactivity into peptides binding to the immunoadsorbent directed against the sequence -ETYY did not change when the vesicles were breached with saponin

  7. Topological disposition of the sequences -QRKIVE- and -KETYY in native (Na sup + + K sup + )-ATPase

    Bayer, R. (Univ. of California, San Diego, La Jolla (USA))

    1990-03-06

    The dispositions with respect to the plane of the membrane of lysine-905 in the internal sequence -EQRKIVE- and of lysine-1012 in the carboxy-terminal sequence -RRPGGWVEKETYY of the {alpha}-polypeptide of sodium and potassium ion activated adenosinetriphosphatase have been determined. These lysines are found in peptides released from the intact {alpha}-polypeptide by the extracellular protease from Staphylococcus aureus strain V8 and by trypsin, respectively. Synthetic peptides containing terminal sequences of these were used to prepare polyclonal antibodies, which were then used to prepare immunoadsorbents directed against the respective peptides. Sealed, right-side-out membrane vesicles containing native (Na{sup +} + K{sup +})-ATPase were labeled with pyridoxal phosphate and sodium ({sup 3}H)borohydride in the absence or presence of saponin. The labeled {alpha}-polypeptide was isolated from these vesicles and digested with appropriate proteases. The incorporation of radioactivity into the peptides binding to the immunoadsorbent directed against the sequence pyrERXIVE increased 3-fold int the presence of saponin as a result of the increased accessibility of this portion of the protein to the reagent when the vesicles were breached by saponin; hence, this sequence is located on the cytoplasmic face of the membrane. It was inferred that the carboxy-terminal sequence -KETYY is on the extracytoplasmic face since the incorporation of radioactivity into peptides binding to the immunoadsorbent directed against the sequence -ETYY did not change when the vesicles were breached with saponin.

  8. The VirusBanker database uses a Java program to allow flexible searching through Bunyaviridae sequences

    Gibbs Mark J

    2008-02-01

    Full Text Available Abstract Background Viruses of the Bunyaviridae have segmented negative-stranded RNA genomes and several of them cause significant disease. Many partial sequences have been obtained from the segments so that GenBank searches give complex results. Sequence databases usually use HTML pages to mediate remote sorting, but this approach can be limiting and may discourage a user from exploring a database. Results The VirusBanker database contains Bunyaviridae sequences and alignments and is presented as two spreadsheets generated by a Java program that interacts with a MySQL database on a server. Sequences are displayed in rows and may be sorted using information that is displayed in columns and includes data relating to the segment, gene, protein, species, strain, sequence length, terminal sequence and date and country of isolation. Bunyaviridae sequences and alignments may be downloaded from the second spreadsheet with titles defined by the user from the columns, or viewed when passed directly to the sequence editor, Jalview. Conclusion VirusBanker allows large datasets of aligned nucleotide and protein sequences from the Bunyaviridae to be compiled and winnowed rapidly using criteria that are formulated heuristically.

  9. Integrated sequence analysis. Final report

    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

  10. Direct detection of hemophilia B F9 gene mutation using multiplex PCR and conformation sensitive gel electrophoresis

    Ki Young Yoo

    2010-03-01

    Full Text Available Purpose : The F9 gene is known to be the causative gene for hemophilia B, but unfortunately the detection rate for restriction fragment length polymorphism-based linkage analysis is only 55.6%. Direct DNA sequencing can detect 98% of mutations, but this alternative procedure is very costly. Here, we conducted multiplex polymerase chain reactions (PCRs and conformation sensitive gel electrophoresis (CSGE to perform a screened DNA sequencing for the F9 gene, and we compared the results with direct sequencing in terms of accuracy, cost, simplicity, and time consumption. Methods : A total of 27 unrelated hemophilia B patients were enrolled. Direct DNA sequencing was performed for 27 patients by a separate institute, and multiplex PCR-CSGE screened sequencing was done in our laboratory. Results of the direct DNA sequencing were used as a reference, to which the results of the multiplex PCR-CSGE screened sequencing were compared. For the patients whose mutation was not detected by the 2 methods, multiplex ligation-dependent probe amplification (MLPA was conducted. Results : With direct sequencing, the mutations could be identified from 26 patients (96.3%, whereas for multiplex PCR- CSGE screened sequencing, the mutations could be detected in 23 (85.2%. One patient’s mutation was identified by MLPA. A total of 21 different mutations were found among the 27 patients. Conclusion : Multiplex PCR-CSGE screened DNA sequencing detected 88.9% of mutations and reduced costs by 55.7% compared with direct DNA sequencing. However, it was more labor-intensive and time-consuming.

  11. Rapid DNA sequencing by horizontal ultrathin gel electrophoresis.

    Brumley, R L; Smith, L M

    1991-01-01

    A horizontal polyacrylamide gel electrophoresis apparatus has been developed that decreases the time required to separate the DNA fragments produced in enzymatic sequencing reactions. The configuration of this apparatus and the use of circulating coolant directly under the glass plates result in heat exchange that is approximately nine times more efficient than passive thermal transfer methods commonly used. Bubble-free gels as thin as 25 microns can be routinely cast on this device. The appl...

  12. Long sequence correlation coprocessor

    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.

  13. Roles of repetitive sequences

    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.

  14. Anomaly Detection in Sequences

    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...

  15. DNA sequencing conference, 2

    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.

  16. sequenceMiner algorithm

    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....

  17. Sequence analysis of Leukemia DNA

    Nacong, Nasria; Lusiyanti, Desy; Irawan, Muhammad. Isa

    2018-03-01

    Cancer is a very deadly disease, one of which is leukemia disease or better known as blood cancer. The cancer cell can be detected by taking DNA in laboratory test. This study focused on local alignment of leukemia and non leukemia data resulting from NCBI in the form of DNA sequences by using Smith-Waterman algorithm. SmithWaterman algorithm was invented by TF Smith and MS Waterman in 1981. These algorithms try to find as much as possible similarity of a pair of sequences, by giving a negative value to the unequal base pair (mismatch), and positive values on the same base pair (match). So that will obtain the maximum positive value as the end of the alignment, and the minimum value as the initial alignment. This study will use sequences of leukemia and 3 sequences of non leukemia.

  18. The Direct Results of Integrated Marketing

    Sevier, Robert A.

    2004-01-01

    Discussions among college and university administrators on improving marketing efforts often revolve around questions about whether the marketing function should be centralized or decentralized. An impetus of these discussions is the increased marketing sophistication of many boards. Many trustees are strongly urging their institutions to apply…

  19. NeSSM: a Next-generation Sequencing Simulator for Metagenomics.

    Ben Jia

    Full Text Available BACKGROUND: Metagenomics can reveal the vast majority of microbes that have been missed by traditional cultivation-based methods. Due to its extremely wide range of application areas, fast metagenome sequencing simulation systems with high fidelity are in great demand to facilitate the development and comparison of metagenomics analysis tools. RESULTS: We present here a customizable metagenome simulation system: NeSSM (Next-generation Sequencing Simulator for Metagenomics. Combining complete genomes currently available, a community composition table, and sequencing parameters, it can simulate metagenome sequencing better than existing systems. Sequencing error models based on the explicit distribution of errors at each base and sequencing coverage bias are incorporated in the simulation. In order to improve the fidelity of simulation, tools are provided by NeSSM to estimate the sequencing error models, sequencing coverage bias and the community composition directly from existing metagenome sequencing data. Currently, NeSSM supports single-end and pair-end sequencing for both 454 and Illumina platforms. In addition, a GPU (graphics processing units version of NeSSM is also developed to accelerate the simulation. By comparing the simulated sequencing data from NeSSM with experimental metagenome sequencing data, we have demonstrated that NeSSM performs better in many aspects than existing popular metagenome simulators, such as MetaSim, GemSIM and Grinder. The GPU version of NeSSM is more than one-order of magnitude faster than MetaSim. CONCLUSIONS: NeSSM is a fast simulation system for high-throughput metagenome sequencing. It can be helpful to develop tools and evaluate strategies for metagenomics analysis and it's freely available for academic users at http://cbb.sjtu.edu.cn/~ccwei/pub/software/NeSSM.php.

  20. Comparative performance of the BGISEQ-500 versus Illumina HiSeq2500 sequencing platforms for palaeogenomic sequencing

    Mak, Sarah Siu Tze Mak; Gopalakrishnan, Shyam Sunder; Carøe, Christian

    2017-01-01

    on degraded DNA, then directly compared the sequencing performance and data quality of the BGISEQ-500 to the Illumina HiSeq2500 platform, on DNA extracted from eight historic and ancient dog and wolf samples. Results: The data generated was largely comparable between sequencing platforms...... difference was also observed in the mitochondrial DNA percentages recovered (p = 0.018), although we believe this is likely a stochastic effect relating to the extremely low levels of mitochondria that were sequenced from three of the samples with overall very low levels of endogenous DNA. Conclusions......: Although we acknowledge our analyses were limited to animal material, our observations suggest that the BGISEQ-500 holds the potential to represent valid and potentially valuable alternative platform for palaeogenomic data generation, that is worthy of future exploration by those interested...

  1. Optimization of sequence alignment for simple sequence repeat regions

    Ogbonnaya Francis C

    2011-07-01

    Full Text Available Abstract Background Microsatellites, or simple sequence repeats (SSRs, are tandemly repeated DNA sequences, including tandem copies of specific sequences no longer than six bases, that are distributed in the genome. SSR has been used as a molecular marker because it is easy to detect and is used in a range of applications, including genetic diversity, genome mapping, and marker assisted selection. It is also very mutable because of slipping in the DNA polymerase during DNA replication. This unique mutation increases the insertion/deletion (INDELs mutation frequency to a high ratio - more than other types of molecular markers such as single nucleotide polymorphism (SNPs. SNPs are more frequent than INDELs. Therefore, all designed algorithms for sequence alignment fit the vast majority of the genomic sequence without considering microsatellite regions, as unique sequences that require special consideration. The old algorithm is limited in its application because there are many overlaps between different repeat units which result in false evolutionary relationships. Findings To overcome the limitation of the aligning algorithm when dealing with SSR loci, a new algorithm was developed using PERL script with a Tk graphical interface. This program is based on aligning sequences after determining the repeated units first, and the last SSR nucleotides positions. This results in a shifting process according to the inserted repeated unit type. When studying the phylogenic relations before and after applying the new algorithm, many differences in the trees were obtained by increasing the SSR length and complexity. However, less distance between different linage had been observed after applying the new algorithm. Conclusions The new algorithm produces better estimates for aligning SSR loci because it reflects more reliable evolutionary relations between different linages. It reduces overlapping during SSR alignment, which results in a more realistic

  2. A STUDY ON DETERMINING THE REFERENCE SPREADING SEQUENCES FOR A DS/CDMACOMMUNICATION SYSTEM

    Cebrail ÇİFTLİKLİ

    2002-02-01

    Full Text Available In a direct sequence/code division multiple access (DS/CDMA system, the role of the spreading sequences (codes is crucial since the multiple access interference (MAI is the main performance limitation. In this study, we propose an accurate criterion which enables the determination of the reference spreading codes which yield lower bit error rates (BER's in a given code set for a DS/CDMA system using despreading sequences weighted by stepping chip waveforms. The numerical results show that the spreading codes determined by the proposed criterion are the most suitable codes for using as references.

  3. Situation models and memory: the effects of temporal and causal information on recall sequence.

    Brownstein, Aaron L; Read, Stephen J

    2007-10-01

    Participants watched an episode of the television show Cheers on video and then reported free recall. Recall sequence followed the sequence of events in the story; if one concept was observed immediately after another, it was recalled immediately after it. We also made a causal network of the show's story and found that recall sequence followed causal links; effects were recalled immediately after their causes. Recall sequence was more likely to follow causal links than temporal sequence, and most likely to follow causal links that were temporally sequential. Results were similar at 10-minute and 1-week delayed recall. This is the most direct and detailed evidence reported on sequential effects in recall. The causal network also predicted probability of recall; concepts with more links and concepts on the main causal chain were most likely to be recalled. This extends the causal network model to more complex materials than previous research.

  4. Whole Exome Sequencing Reveals Genetic Predisposition in a Large Family with Retinitis Pigmentosa

    Juan Wu

    2014-01-01

    Full Text Available Next-generation sequencing has become more widely used to reveal genetic defect in monogenic disorders. Retinitis pigmentosa (RP, the leading cause of hereditary blindness worldwide, has been attributed to more than 67 disease-causing genes. Due to the extreme genetic heterogeneity, using general molecular screening alone is inadequate for identifying genetic predispositions in susceptible individuals. In order to identify underlying mutation rapidly, we utilized next-generation sequencing in a four-generation Chinese family with RP. Two affected patients and an unaffected sibling were subjected to whole exome sequencing. Through bioinformatics analysis and direct sequencing confirmation, we identified p.R135W transition in the rhodopsin gene. The mutation was subsequently confirmed to cosegregate with the disease in the family. In this study, our results suggest that whole exome sequencing is a robust method in diagnosing familial hereditary disease.

  5. Asynchronous, Decentralized DS-CDMA Using Feedback-Controlled Spreading Sequences for Time-Dispersive Channels

    Miyatake, Teruhiko; Chiba, Kazuki; Hamamura, Masanori; Tachikawa, Shin'ichi

    We propose a novel asynchronous direct-sequence codedivision multiple access (DS-CDMA) using feedback-controlled spreading sequences (FCSSs) (FCSS/DS-CDMA). At the receiver of FCSS/DS-CDMA, the code-orthogonalizing filter (COF) pr