WorldWideScience

Sample records for direct sequencing application

  1. Direct, rapid RNA sequence analysis

    International Nuclear Information System (INIS)

    Peattie, D.A.

    1987-01-01

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

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

    African Journals Online (AJOL)

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

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

    Directory of Open Access Journals (Sweden)

    Preissler Steffen

    2011-09-01

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

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

    Science.gov (United States)

    Tan, M K

    1991-08-01

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

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

    Science.gov (United States)

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

    2005-08-01

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

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

    Science.gov (United States)

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

    2017-01-20

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

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

    International Nuclear Information System (INIS)

    Rhodes, C.K.

    1993-01-01

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

  8. Generalized locally Toeplitz sequences theory and applications

    CERN Document Server

    Garoni, Carlo

    2017-01-01

    Based on their research experience, the authors propose a reference textbook in two volumes on the theory of generalized locally Toeplitz sequences and their applications. This first volume focuses on the univariate version of the theory and the related applications in the unidimensional setting, while the second volume, which addresses the multivariate case, is mainly devoted to concrete PDE applications. This book systematically develops the theory of generalized locally Toeplitz (GLT) sequences and presents some of its main applications, with a particular focus on the numerical discretization of differential equations (DEs). It is the first book to address the relatively new field of GLT sequences, which occur in numerous scientific applications and are especially dominant in the context of DE discretizations. Written for applied mathematicians, engineers, physicists, and scientists who (perhaps unknowingly) encounter GLT sequences in their research, it is also of interest to those working in the fields of...

  9. Direct application of geothermal energy

    Energy Technology Data Exchange (ETDEWEB)

    Reistad, G.M.

    1980-01-01

    An overall treatment of direct geothermal applications is presented with an emphasis on the above-ground engineering. The types of geothermal resources and their general extent in the US are described. The potential market that may be served with geothermal energy is considered briefly. The evaluation considerations, special design aspects, and application approaches for geothermal energy use in each of the applications are considered. The present applications in the US are summarized and a bibliography of recent studies and applications is provided. (MHR)

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

    Directory of Open Access Journals (Sweden)

    Marta Brozynska

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

  11. Geothermal Direct Heat Application Potential

    Energy Technology Data Exchange (ETDEWEB)

    Lienau, Paul J

    1989-01-01

    The geothermal direct-use industry growth trends, potential, needs, and how they can be met, are addressed. Recent investigations about the current status of the industry and the identification of institutional and technical needs provide the basis on which this paper is presented. Initial drilling risk is the major obstacle to direct-use development. The applications presented include space and district heating projects, heat pumps (heating and cooling), industrial processes, resorts and pools, aquaculture and agriculture.

  12. Neural Networks and Their Applications in Noise - Information Storage and Retrieval Systems, and in the Rejection of Narrow-Band Interference in Direct Sequence Spread Spectrum Receivers.

    Science.gov (United States)

    Bijjani, Richard

    1990-01-01

    The introduction of neural network models has created new algorithms and application opportunities in parallel signal processing. Here, an M-ary extension of the Hopfield model is presented and is shown to have a substantially higher error correction capability, when compared to the Hopfield model. A digital image processing experiment is successfully conducted to illustrate the new model, and a holographic implementation is proposed. The use of neural networks and of linear combination filters are investigated in connection with the problem of user identification in code division multiple access systems. A multi-layer back-propagation perceptron model is then presented as a means of detecting a wideband signal in the presence of narrowband jammers and additive white Gaussian noise. The performance of the neural network is compared to that of the estimation type filter that uses a least mean squared adaptive filter, in terms of the interference rejection capability, the bit error rate and the overall robustness of the system. The nonlinear neural network filter is found to offer a faster convergence rate and an overall better performance over the LMS Widrow-Hoff filter.

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

    NARCIS (Netherlands)

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

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

  14. Constructing and sampling directed graphs with given degree sequences

    International Nuclear Information System (INIS)

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

    2012-01-01

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

  15. Clinical applications of sequencing take center stage

    OpenAIRE

    Glusman, Gustavo

    2013-01-01

    A report on the Advances in Genome Biology and Technology (AGBT) meeting, Marco Island, Florida, USA, February 20-23, 2013. This year's Advances in Genome Biology and Technology (AGBT) meeting reflected the current state of 'next generation' sequencing (NGS) technologies: significantly reduced competition and innovation, and a strong focus on standardization and application. Announcements of technological breakthroughs - a hallmark of previous AGBT meetings - were markedly absent, but existin...

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

    Directory of Open Access Journals (Sweden)

    Gevorg Grigoryan

    2006-06-01

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

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

    Science.gov (United States)

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

    2017-09-01

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

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

    Science.gov (United States)

    Che, Di; Yuan, Feng; Shieh, William

    2017-04-17

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

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

    Science.gov (United States)

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

    2017-05-01

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

  20. Application status and vistas of sequence stratigraphy to the exploration of sandstone-hosted uranium deposits

    International Nuclear Information System (INIS)

    Guo Qingyin; Chen Zuyi; Yu Jinshui; Han Shuqin

    2008-01-01

    Sequence stratigraphy is a newly developed subject based on seismostratigraphy, and has been widely applied in the exploration of hydrocarbon and other sedimentogenic mineral deposits and great achievements have been obtained. However, the application of sequence stratigraphy to the exploration of sandstone-hosted uranium deposits is just at the beginning. In this paper, some primary research achievements of sequence stratigraphy to the exploration of sandstone-hosted uranium deposits are summarized, and problems and their reasons of the application of sequence stratigraphy are discussed. Further more, according to characteristics of sandstone-hosted uranium deposits and the development of sequence stratigraphy, the application vistas of sequence stratigraphy to the exploration of sandstone-hosted uranium deposits are estimated. Finally, application directions are proposed, and some specific suggestions are given. (authors)

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

    Science.gov (United States)

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

    1999-01-01

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

  2. CATEGORIZATION OF EVENT SEQUENCES FOR LICENSE APPLICATION

    Energy Technology Data Exchange (ETDEWEB)

    G.E. Ragan; P. Mecheret; D. Dexheimer

    2005-04-14

    The purposes of this analysis are: (1) Categorize (as Category 1, Category 2, or Beyond Category 2) internal event sequences that may occur before permanent closure of the repository at Yucca Mountain. (2) Categorize external event sequences that may occur before permanent closure of the repository at Yucca Mountain. This includes examining DBGM-1 seismic classifications and upgrading to DBGM-2, if appropriate, to ensure Beyond Category 2 categorization. (3) State the design and operational requirements that are invoked to make the categorization assignments valid. (4) Indicate the amount of material put at risk by Category 1 and Category 2 event sequences. (5) Estimate frequencies of Category 1 event sequences at the maximum capacity and receipt rate of the repository. (6) Distinguish occurrences associated with normal operations from event sequences. It is beyond the scope of the analysis to propose design requirements that may be required to control radiological exposure associated with normal operations. (7) Provide a convenient compilation of the results of the analysis in tabular form. The results of this analysis are used as inputs to the consequence analyses in an iterative design process that is depicted in Figure 1. Categorization of event sequences for permanent retrieval of waste from the repository is beyond the scope of this analysis. Cleanup activities that take place after an event sequence and other responses to abnormal events are also beyond the scope of the analysis.

  3. CATEGORIZATION OF EVENT SEQUENCES FOR LICENSE APPLICATION

    International Nuclear Information System (INIS)

    G.E. Ragan; P. Mecheret; D. Dexheimer

    2005-01-01

    The purposes of this analysis are: (1) Categorize (as Category 1, Category 2, or Beyond Category 2) internal event sequences that may occur before permanent closure of the repository at Yucca Mountain. (2) Categorize external event sequences that may occur before permanent closure of the repository at Yucca Mountain. This includes examining DBGM-1 seismic classifications and upgrading to DBGM-2, if appropriate, to ensure Beyond Category 2 categorization. (3) State the design and operational requirements that are invoked to make the categorization assignments valid. (4) Indicate the amount of material put at risk by Category 1 and Category 2 event sequences. (5) Estimate frequencies of Category 1 event sequences at the maximum capacity and receipt rate of the repository. (6) Distinguish occurrences associated with normal operations from event sequences. It is beyond the scope of the analysis to propose design requirements that may be required to control radiological exposure associated with normal operations. (7) Provide a convenient compilation of the results of the analysis in tabular form. The results of this analysis are used as inputs to the consequence analyses in an iterative design process that is depicted in Figure 1. Categorization of event sequences for permanent retrieval of waste from the repository is beyond the scope of this analysis. Cleanup activities that take place after an event sequence and other responses to abnormal events are also beyond the scope of the analysis

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

    Science.gov (United States)

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

    2018-01-08

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

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

    Science.gov (United States)

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

    2017-12-01

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

  6. A Directed Signature Scheme and its Applications

    OpenAIRE

    Lal, Sunder; Kumar, Manoj

    2004-01-01

    This paper presents a directed signature scheme with the property that the signature can be verified only with the help of signer or signature receiver. We also propose its applications to share verification of signatures and to threshold cryptosystems.

  7. Applications of High Throughput Nucleotide Sequencing

    DEFF Research Database (Denmark)

    Waage, Johannes Eichler

    equally large demands in data handling, analysis and interpretation, perhaps defining the modern challenge of the computational biologist of the post-genomic era. The first part of this thesis consists of a general introduction to the history, common terms and challenges of next generation sequencing......-sequencing, a study of the effects on alternative RNA splicing of KO of the nonsense mediated RNA decay system in Mus, using digital gene expression and a custom-built exon-exon junction mapping pipeline is presented (article I). Evolved from this work, a Bioconductor package, spliceR, for classifying alternative...

  8. Applications of Genomic Sequencing in Pediatric CNS Tumors.

    Science.gov (United States)

    Bavle, Abhishek A; Lin, Frank Y; Parsons, D Williams

    2016-05-01

    Recent advances in genome-scale sequencing methods have resulted in a significant increase in our understanding of the biology of human cancers. When applied to pediatric central nervous system (CNS) tumors, these remarkable technological breakthroughs have facilitated the molecular characterization of multiple tumor types, provided new insights into the genetic basis of these cancers, and prompted innovative strategies that are changing the management paradigm in pediatric neuro-oncology. Genomic tests have begun to affect medical decision making in a number of ways, from delineating histopathologically similar tumor types into distinct molecular subgroups that correlate with clinical characteristics, to guiding the addition of novel therapeutic agents for patients with high-risk or poor-prognosis tumors, or alternatively, reducing treatment intensity for those with a favorable prognosis. Genomic sequencing has also had a significant impact on translational research strategies in pediatric CNS tumors, resulting in wide-ranging applications that have the potential to direct the rational preclinical screening of novel therapeutic agents, shed light on tumor heterogeneity and evolution, and highlight differences (or similarities) between pediatric and adult CNS tumors. Finally, in addition to allowing the identification of somatic (tumor-specific) mutations, the analysis of patient-matched constitutional (germline) DNA has facilitated the detection of pathogenic germline alterations in cancer genes in patients with CNS tumors, with critical implications for genetic counseling and tumor surveillance strategies for children with familial predisposition syndromes. As our understanding of the molecular landscape of pediatric CNS tumors continues to advance, innovative applications of genomic sequencing hold significant promise for further improving the care of children with these cancers.

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

    DEFF Research Database (Denmark)

    Nielsen, Peter E.

    2008-01-01

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

  10. Enrichment of target sequences for next-generation sequencing applications in research and diagnostics.

    Science.gov (United States)

    Altmüller, Janine; Budde, Birgit S; Nürnberg, Peter

    2014-02-01

    Abstract Targeted re-sequencing such as gene panel sequencing (GPS) has become very popular in medical genetics, both for research projects and in diagnostic settings. The technical principles of the different enrichment methods have been reviewed several times before; however, new enrichment products are constantly entering the market, and researchers are often puzzled about the requirement to take decisions about long-term commitments, both for the enrichment product and the sequencing technology. This review summarizes important considerations for the experimental design and provides helpful recommendations in choosing the best sequencing strategy for various research projects and diagnostic applications.

  11. Applications of Next-Generation Sequencing Technologies to Diagnostic Virology

    Directory of Open Access Journals (Sweden)

    Giorgio Palù

    2011-11-01

    Full Text Available Novel DNA sequencing techniques, referred to as “next-generation” sequencing (NGS, provide high speed and throughput that can produce an enormous volume of sequences with many possible applications in research and diagnostic settings. In this article, we provide an overview of the many applications of NGS in diagnostic virology. NGS techniques have been used for high-throughput whole viral genome sequencing, such as sequencing of new influenza viruses, for detection of viral genome variability and evolution within the host, such as investigation of human immunodeficiency virus and human hepatitis C virus quasispecies, and monitoring of low-abundance antiviral drug-resistance mutations. NGS techniques have been applied to metagenomics-based strategies for the detection of unexpected disease-associated viruses and for the discovery of novel human viruses, including cancer-related viruses. Finally, the human virome in healthy and disease conditions has been described by NGS-based metagenomics.

  12. FASH: A web application for nucleotides sequence search

    Directory of Open Access Journals (Sweden)

    Chew Paul

    2008-05-01

    Full Text Available Abstract FASH (Fourier Alignment Sequence Heuristics is a web application, based on the Fast Fourier Transform, for finding remote homologs within a long nucleic acid sequence. Given a query sequence and a long text-sequence (e.g, the human genome, FASH detects subsequences within the text that are remotely-similar to the query. FASH offers an alternative approach to Blast/Fasta for querying long RNA/DNA sequences. FASH differs from these other approaches in that it does not depend on the existence of contiguous seed-sequences in its initial detection phase. The FASH web server is user friendly and very easy to operate. Availability FASH can be accessed at https://fash.bgu.ac.il:8443/fash/default.jsp (secured website

  13. Application of Next-generation Sequencing in Clinical Molecular Diagnostics

    Directory of Open Access Journals (Sweden)

    Morteza Seifi

    2017-05-01

    Full Text Available ABSTRACT Next-generation sequencing (NGS is the catch all terms that used to explain several different modern sequencing technologies which let us to sequence nucleic acids much more rapidly and cheaply than the formerly used Sanger sequencing, and as such have revolutionized the study of molecular biology and genomics with excellent resolution and accuracy. Over the past years, many academic companies and institutions have continued technological advances to expand NGS applications from research to the clinic. In this review, the performance and technical features of current NGS platforms were described. Furthermore, advances in the applying of NGS technologies towards the progress of clinical molecular diagnostics were emphasized. General advantages and disadvantages of each sequencing system are summarized and compared to guide the selection of NGS platforms for specific research aims.

  14. Application of high-throughput DNA sequencing in phytopathology.

    Science.gov (United States)

    Studholme, David J; Glover, Rachel H; Boonham, Neil

    2011-01-01

    The new sequencing technologies are already making a big impact in academic research on medically important microbes and may soon revolutionize diagnostics, epidemiology, and infection control. Plant pathology also stands to gain from exploiting these opportunities. This manuscript reviews some applications of these high-throughput sequencing methods that are relevant to phytopathology, with emphasis on the associated computational and bioinformatics challenges and their solutions. Second-generation sequencing technologies have recently been exploited in genomics of both prokaryotic and eukaryotic plant pathogens. They are also proving to be useful in diagnostics, especially with respect to viruses. Copyright © 2011 by Annual Reviews. All rights reserved.

  15. [Sequencing technology in gene diagnosis and its application].

    Science.gov (United States)

    Yibin, Guo

    2014-11-01

    The study of gene mutation is one of the hot topics in the field of life science nowadays, and the related detection methods and diagnostic technology have been developed rapidly. Sequencing technology plays an indispensable role in the definite diagnosis and classification of genetic diseases. In this review, we summarize the research progress in sequencing technology, evaluate the advantages and disadvantages of 1(st) ~3(rd) generation of sequencing technology, and describe its application in gene diagnosis. Also we made forecasts and prospects on its development trend.

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

    OpenAIRE

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

    2016-01-01

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

  17. Nonlinear dynamics new directions models and applications

    CERN Document Server

    Ugalde, Edgardo

    2015-01-01

    This book, along with its companion volume, Nonlinear Dynamics New Directions: Theoretical Aspects, covers topics ranging from fractal analysis to very specific applications of the theory of dynamical systems to biology. This second volume contains mostly new applications of the theory of dynamical systems to both engineering and biology. The first volume is devoted to fundamental aspects and includes a number of important new contributions as well as some review articles that emphasize new development prospects. The topics addressed in the two volumes include a rigorous treatment of fluctuations in dynamical systems, topics in fractal analysis, studies of the transient dynamics in biological networks, synchronization in lasers, and control of chaotic systems, among others. This book also: ·         Develops applications of nonlinear dynamics on a diversity of topics such as patterns of synchrony in neuronal networks, laser synchronization, control of chaotic systems, and the study of transient dynam...

  18. Directional interstitial brachytherapy from simulation to application

    Science.gov (United States)

    Lin, Liyong

    design optimization and construction of the first prototype directional source. Potential clinical applications and potential benefits of directional sources have been shown for prostate and breast tumors.

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

    Science.gov (United States)

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

    2016-12-01

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

  20. The development and application of a Mycoplasma gallisepticum sequence database.

    Science.gov (United States)

    Armour, Natalie K; Laibinis, Victoria A; Collett, Stephen R; Ferguson-Noel, Naola

    2013-01-01

    Molecular analysis was conducted on 36 Mycoplasma gallisepticum DNA extracts from tracheal swab samples of commercial poultry in seven South African provinces between 2009 and 2012. Twelve unique M. gallisepticum genotypes were identified by polymerase chain reaction and sequence analysis of the 16S-23S rRNA intergenic spacer region (IGSR), M. gallisepticum cytadhesin 2 (mgc2), MGA_0319 and gapA genetic regions. The DNA sequences of these genotypes were distinct from those of M. gallisepticum isolates in a database composed of sequences from other countries, vaccine and reference strains. The most prevalent genotype (SA-WT#7) was detected in samples from commercial broilers, broiler breeders and layers in five provinces. South African M. gallisepticum sequences were more similar to those of the live vaccines commercially available in South Africa, but were distinct from that of F strain vaccine, which is not registered for use in South Africa. The IGSR, mgc2 or MGA_0319 sequences of three South African genotypes were identical to those of the ts-11 vaccine strain, necessitating a combination of mgc2 and IGSR targeted sequencing to differentiate South African wild-type genotypes from ts-11 vaccine. To identify and differentiate all 12 wild-types, mgc2, IGSR and MGA_0319 sequencing was required. Sequencing of gapA was least effective at strain differentiation. This research serves as a model for the development of an M. gallisepticum sequence database, and illustrates its application to characterize M. gallisepticum genotypes, select diagnostic tests and better understand the epidemiology of M. gallisepticum.

  1. GuiTope: an application for mapping random-sequence peptides to protein sequences.

    Science.gov (United States)

    Halperin, Rebecca F; Stafford, Phillip; Emery, Jack S; Navalkar, Krupa Arun; Johnston, Stephen Albert

    2012-01-03

    Random-sequence peptide libraries are a commonly used tool to identify novel ligands for binding antibodies, other proteins, and small molecules. It is often of interest to compare the selected peptide sequences to the natural protein binding partners to infer the exact binding site or the importance of particular residues. The ability to search a set of sequences for similarity to a set of peptides may sometimes enable the prediction of an antibody epitope or a novel binding partner. We have developed a software application designed specifically for this task. GuiTope provides a graphical user interface for aligning peptide sequences to protein sequences. All alignment parameters are accessible to the user including the ability to specify the amino acid frequency in the peptide library; these frequencies often differ significantly from those assumed by popular alignment programs. It also includes a novel feature to align di-peptide inversions, which we have found improves the accuracy of antibody epitope prediction from peptide microarray data and shows utility in analyzing phage display datasets. Finally, GuiTope can randomly select peptides from a given library to estimate a null distribution of scores and calculate statistical significance. GuiTope provides a convenient method for comparing selected peptide sequences to protein sequences, including flexible alignment parameters, novel alignment features, ability to search a database, and statistical significance of results. The software is available as an executable (for PC) at http://www.immunosignature.com/software and ongoing updates and source code will be available at sourceforge.net.

  2. GuiTope: an application for mapping random-sequence peptides to protein sequences

    Directory of Open Access Journals (Sweden)

    Halperin Rebecca F

    2012-01-01

    Full Text Available Abstract Background Random-sequence peptide libraries are a commonly used tool to identify novel ligands for binding antibodies, other proteins, and small molecules. It is often of interest to compare the selected peptide sequences to the natural protein binding partners to infer the exact binding site or the importance of particular residues. The ability to search a set of sequences for similarity to a set of peptides may sometimes enable the prediction of an antibody epitope or a novel binding partner. We have developed a software application designed specifically for this task. Results GuiTope provides a graphical user interface for aligning peptide sequences to protein sequences. All alignment parameters are accessible to the user including the ability to specify the amino acid frequency in the peptide library; these frequencies often differ significantly from those assumed by popular alignment programs. It also includes a novel feature to align di-peptide inversions, which we have found improves the accuracy of antibody epitope prediction from peptide microarray data and shows utility in analyzing phage display datasets. Finally, GuiTope can randomly select peptides from a given library to estimate a null distribution of scores and calculate statistical significance. Conclusions GuiTope provides a convenient method for comparing selected peptide sequences to protein sequences, including flexible alignment parameters, novel alignment features, ability to search a database, and statistical significance of results. The software is available as an executable (for PC at http://www.immunosignature.com/software and ongoing updates and source code will be available at sourceforge.net.

  3. Efficient alignment of pyrosequencing reads for re-sequencing applications

    Directory of Open Access Journals (Sweden)

    Russo Luis MS

    2011-05-01

    Full Text Available Abstract Background Over the past few years, new massively parallel DNA sequencing technologies have emerged. These platforms generate massive amounts of data per run, greatly reducing the cost of DNA sequencing. However, these techniques also raise important computational difficulties mostly due to the huge volume of data produced, but also because of some of their specific characteristics such as read length and sequencing errors. Among the most critical problems is that of efficiently and accurately mapping reads to a reference genome in the context of re-sequencing projects. Results We present an efficient method for the local alignment of pyrosequencing reads produced by the GS FLX (454 system against a reference sequence. Our approach explores the characteristics of the data in these re-sequencing applications and uses state of the art indexing techniques combined with a flexible seed-based approach, leading to a fast and accurate algorithm which needs very little user parameterization. An evaluation performed using real and simulated data shows that our proposed method outperforms a number of mainstream tools on the quantity and quality of successful alignments, as well as on the execution time. Conclusions The proposed methodology was implemented in a software tool called TAPyR--Tool for the Alignment of Pyrosequencing Reads--which is publicly available from http://www.tapyr.net.

  4. Peanut (Arachis hypogaea Expressed Sequence Tag Project: Progress and Application

    Directory of Open Access Journals (Sweden)

    Suping Feng

    2012-01-01

    Full Text Available Many plant ESTs have been sequenced as an alternative to whole genome sequences, including peanut because of the genome size and complexity. The US peanut research community had the historic 2004 Atlanta Genomics Workshop and named the EST project as a main priority. As of August 2011, the peanut research community had deposited 252,832 ESTs in the public NCBI EST database, and this resource has been providing the community valuable tools and core foundations for various genome-scale experiments before the whole genome sequencing project. These EST resources have been used for marker development, gene cloning, microarray gene expression and genetic map construction. Certainly, the peanut EST sequence resources have been shown to have a wide range of applications and accomplished its essential role at the time of need. Then the EST project contributes to the second historic event, the Peanut Genome Project 2010 Inaugural Meeting also held in Atlanta where it was decided to sequence the entire peanut genome. After the completion of peanut whole genome sequencing, ESTs or transcriptome will continue to play an important role to fill in knowledge gaps, to identify particular genes and to explore gene function.

  5. Controlling the bond scission sequence of oxygenates for energy applications

    Science.gov (United States)

    Stottlemyer, Alan L.

    The so called "Holy Grail" of heterogeneous catalysis is a fundamental understanding of catalyzed chemical transformations which span multidimensional scales of both length and time, enabling rational catalyst design. Such an undertaking is realizable only with an atomic level understanding of bond formation and destruction with respect to intrinsic properties of the metal catalyst. In this study, we investigate the bond scission sequence of small oxygenates (methanol, ethanol, ethylene glycol) on bimetallic transition metal catalysts and transition metal carbide catalysts. Oxygenates are of interest both as hydrogen carriers for reforming to H2 and CO and as fuels in direct alcohol fuel cells (DAFC). To address the so-called "materials gap" and "pressure gap" this work adopted three parallel research approaches: (1) ultra high vacuum (UHV) studies including temperature programmed desorption (TPD) and high-resolution electron energy loss spectroscopy (HREELS) on polycrystalline surfaces; (2) DFT studies including thermodynamic and kinetic calculations; (3) electrochemical studies including cyclic voltammetry (CV) and chronoamperometry (CA). Recent studies have suggested that tungsten monocarbide (WC) may behave similarly to Pt for the electrooxidation of oxygenates. TPD was used to quantify the activity and selectivity of oxygenate decomposition for WC and Pt-modifiedWC (Pt/WC) as compared to Pt. While decomposition activity was generally higher on WC than on Pt, scission of the C-O bond resulted in alkane/alkene formation on WC, an undesired product for DAFC. When Pt was added to WC by physical vapor deposition C-O bond scission was limited, suggesting that Pt synergistically modifies WC to improve the selectivity toward C-H bond scission to produce H2 and CO. Additionally, TPD confirmed WC and Pt/WC to be more CO tolerant than Pt. HREELS results verified that surface intermediates were different on Pt/WC as compared to Pt or WC and evidence of aldehyde

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

    DEFF Research Database (Denmark)

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

    2004-01-01

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

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

    OpenAIRE

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

    2017-01-01

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

  8. DNAApp: a mobile application for sequencing data analysis.

    Science.gov (United States)

    Nguyen, Phi-Vu; Verma, Chandra Shekhar; Gan, Samuel Ken-En

    2014-11-15

    There have been numerous applications developed for decoding and visualization of ab1 DNA sequencing files for Windows and MAC platforms, yet none exists for the increasingly popular smartphone operating systems. The ability to decode sequencing files cannot easily be carried out using browser accessed Web tools. To overcome this hurdle, we have developed a new native app called DNAApp that can decode and display ab1 sequencing file on Android and iOS. In addition to in-built analysis tools such as reverse complementation, protein translation and searching for specific sequences, we have incorporated convenient functions that would facilitate the harnessing of online Web tools for a full range of analysis. Given the high usage of Android/iOS tablets and smartphones, such bioinformatics apps would raise productivity and facilitate the high demand for analyzing sequencing data in biomedical research. The Android version of DNAApp is available in Google Play Store as 'DNAApp', and the iOS version is available in the App Store. More details on the app can be found at www.facebook.com/APDLab; www.bii.a-star.edu.sg/research/trd/apd.php The DNAApp user guide is available at http://tinyurl.com/DNAAppuser, and a video tutorial is available on Google Play Store and App Store, as well as on the Facebook page. samuelg@bii.a-star.edu.sg. © The Author 2014. Published by Oxford University Press.

  9. DNAApp: a mobile application for sequencing data analysis

    Science.gov (United States)

    Nguyen, Phi-Vu; Verma, Chandra Shekhar; Gan, Samuel Ken-En

    2014-01-01

    Summary: There have been numerous applications developed for decoding and visualization of ab1 DNA sequencing files for Windows and MAC platforms, yet none exists for the increasingly popular smartphone operating systems. The ability to decode sequencing files cannot easily be carried out using browser accessed Web tools. To overcome this hurdle, we have developed a new native app called DNAApp that can decode and display ab1 sequencing file on Android and iOS. In addition to in-built analysis tools such as reverse complementation, protein translation and searching for specific sequences, we have incorporated convenient functions that would facilitate the harnessing of online Web tools for a full range of analysis. Given the high usage of Android/iOS tablets and smartphones, such bioinformatics apps would raise productivity and facilitate the high demand for analyzing sequencing data in biomedical research. Availability and implementation: The Android version of DNAApp is available in Google Play Store as ‘DNAApp’, and the iOS version is available in the App Store. More details on the app can be found at www.facebook.com/APDLab; www.bii.a-star.edu.sg/research/trd/apd.php The DNAApp user guide is available at http://tinyurl.com/DNAAppuser, and a video tutorial is available on Google Play Store and App Store, as well as on the Facebook page. Contact: samuelg@bii.a-star.edu.sg PMID:25095882

  10. VoSeq: a voucher and DNA sequence web application.

    Directory of Open Access Journals (Sweden)

    Carlos Peña

    Full Text Available There is an ever growing number of molecular phylogenetic studies published, due to, in part, the advent of new techniques that allow cheap and quick DNA sequencing. Hence, the demand for relational databases with which to manage and annotate the amassing DNA sequences, genes, voucher specimens and associated biological data is increasing. In addition, a user-friendly interface is necessary for easy integration and management of the data stored in the database back-end. Available databases allow management of a wide variety of biological data. However, most database systems are not specifically constructed with the aim of being an organizational tool for researchers working in phylogenetic inference. We here report a new software facilitating easy management of voucher and sequence data, consisting of a relational database as back-end for a graphic user interface accessed via a web browser. The application, VoSeq, includes tools for creating molecular datasets of DNA or amino acid sequences ready to be used in commonly used phylogenetic software such as RAxML, TNT, MrBayes and PAUP, as well as for creating tables ready for publishing. It also has inbuilt BLAST capabilities against all DNA sequences stored in VoSeq as well as sequences in NCBI GenBank. By using mash-ups and calls to web services, VoSeq allows easy integration with public services such as Yahoo! Maps, Flickr, Encyclopedia of Life (EOL and GBIF (by generating data-dumps that can be processed with GBIF's Integrated Publishing Toolkit.

  11. Next generation sequencing and its applications in forensic genetics.

    Science.gov (United States)

    Børsting, Claus; Morling, Niels

    2015-09-01

    It has been almost a decade since the first next generation sequencing (NGS) technologies emerged and quickly changed the way genetic research is conducted. Today, full genomes are mapped and published almost weekly and with ever increasing speed and decreasing costs. NGS methods and platforms have matured during the last 10 years, and the quality of the sequences has reached a level where NGS is used in clinical diagnostics of humans. Forensic genetic laboratories have also explored NGS technologies and especially in the last year, there has been a small explosion in the number of scientific articles and presentations at conferences with forensic aspects of NGS. These contributions have demonstrated that NGS offers new possibilities for forensic genetic case work. More information may be obtained from unique samples in a single experiment by analyzing combinations of markers (STRs, SNPs, insertion/deletions, mRNA) that cannot be analyzed simultaneously with the standard PCR-CE methods used today. The true variation in core forensic STR loci has been uncovered, and previously unknown STR alleles have been discovered. The detailed sequence information may aid mixture interpretation and will increase the statistical weight of the evidence. In this review, we will give an introduction to NGS and single-molecule sequencing, and we will discuss the possible applications of NGS in forensic genetics. Copyright © 2015 Elsevier Ireland Ltd. All rights reserved.

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

    KAUST Repository

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

    2018-01-01

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

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

    KAUST Repository

    Teng, Haotian

    2018-04-10

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

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

    DEFF Research Database (Denmark)

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

    2018-01-01

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

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

    Directory of Open Access Journals (Sweden)

    Sandeep J Joseph

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

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

    DEFF Research Database (Denmark)

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

    2014-01-01

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

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

    Science.gov (United States)

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

    2007-02-01

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

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

    Science.gov (United States)

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

    2007-02-01

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

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

    Science.gov (United States)

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

    2017-05-26

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

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

    Science.gov (United States)

    Wimmer, Katharina; Wernstedt, Annekatrin

    2014-01-01

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

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

    DEFF Research Database (Denmark)

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

    2017-01-01

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

  2. An investigation of application of the golden ratio and Fibonacci sequence in fashion design and pattern making

    Science.gov (United States)

    Kazlacheva, Z. I.

    2017-10-01

    The Golden ratio and Fibonacci sequence are used as proportions in design as symbols of beauty and harmony. That symbolism is a result of the strong connections in their mathematical nature. The Golden section is a number, introduced with Greek letter φ, which is found by dividing a line into two parts as the longer part divided by the smaller part is equal as the whole length of longer and smaller parts divided by the longer part. Fibonacci sequence is a series of numbers where every number is equal to the two numbers before it. An investigation of application of proportions based on the Golden ratio and Fibonacci sequence in the fashion design and pattern making of ladies’ clothing is the main aim of the paper. Based on the study it may be concluded that in fashion design and pattern making the Golden ratio and Fibonacci sequence can be used in creation of beautiful and harmonic forms directly or with the help of geometrical figures as: In directly use the Golden and Fibonacci numbers proportions can be in one and the same or different directions. In the application with the help of geometrical shapes the Golden and Fibonacci figures combine proportioning and form creation. The Golden and Fibonacci shapes can be used directly as forms or as frames of forms creation of elements and pieces. Its application can be in different directions and location according the bodice. The Golden section and Fibonacci sequence can combine proportions with other principles of design as symmetry, rhythm, etc.

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

    International Nuclear Information System (INIS)

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

    2008-01-01

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

  4. Directions for Web and E-Commerce Applications Security

    OpenAIRE

    Thuraisingham, Bhavani; Clifton, Chris; Gupta, Amar; Bertino, Elisa; Ferrari, Elena

    2003-01-01

    This paper provides directions for web and e-commerce applications security. In particular, access control policies, workflow security, XML security and federated database security issues pertaining to the web and ecommerce applications are discussed.

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

    Science.gov (United States)

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

    2015-01-01

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

  6. Application of the Seveso Directive in France

    International Nuclear Information System (INIS)

    Pineau, J.-P.

    1999-01-01

    First, the paper presents a brief summary of the French actual regulation on installations registered for the protection of the environment and covered by the Seveso I Directive. Then the paper discusses research and development needs for a sound implementation of the Directive, and for the new requirements on safety reports established by the Seveso II Directive. Further, it discusses issues connected with coverage of hazardous activities, learning from accidents, technical and organisational measures (safety management systems and emergency response) and human factors. The conclusions stress the need for networking and dissemination of accident investigations, development of safety management systems, and research on cognitive ergonomics and psychology related to the decision making and interventions of the operator. (Copyright (c) 1999 Elsevier Science B.V., Amsterdam. All rights reserved.)

  7. Virtual Reality: Emerging Applications and Future Directions

    Science.gov (United States)

    Ludlow, Barbara L.

    2015-01-01

    Virtual reality is an emerging technology that has resulted in rapid expansion in the development of virtual immersive environments for use as educational simulations in schools, colleges and universities. This article presents an overview of virtual reality, describes a number of applications currently being used by special educators for…

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

    Directory of Open Access Journals (Sweden)

    Nguyen Xuan Quyen

    2013-01-01

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

  9. Directly driven generators for wind power applications

    Energy Technology Data Exchange (ETDEWEB)

    Lampola, P [Helsinki Univ. of Technology, Espoo (Finland). Lab. of Electromechanics

    1996-12-31

    The article deals with an analysis of directly driven, low-speed wind generators. The generators studied were a permanent-magnet synchronous machine and an asynchronous machine. The machines were compared with a typical generator of a wind power plant. The electromagnetic optimization of the machines was done by the finite element method. The rated power of the generators was 500 kW and the rotational speed was 40 rpm. (author)

  10. Directly driven generators for wind power applications

    Energy Technology Data Exchange (ETDEWEB)

    Lampola, P. [Helsinki Univ. of Technology, Espoo (Finland). Lab. of Electromechanics

    1995-12-31

    The article deals with an analysis of directly driven, low-speed wind generators. The generators studied were a permanent-magnet synchronous machine and an asynchronous machine. The machines were compared with a typical generator of a wind power plant. The electromagnetic optimization of the machines was done by the finite element method. The rated power of the generators was 500 kW and the rotational speed was 40 rpm. (author)

  11. Applicability of the Directed Graph Methodology

    Energy Technology Data Exchange (ETDEWEB)

    Huszti, Jozsef [Institute of Isotope of the Hungarian Academy of Sciences, Budapest (Hungary); Nemeth, Andras [ESRI Hungary, Budapest (Hungary); Vincze, Arpad [Hungarian Atomic Energy Authority, Budapest (Hungary)

    2012-06-15

    Possible methods to construct, visualize and analyse the 'map' of the State's nuclear infrastructure based on different directed graph approaches are proposed. The transportation and the flow network models are described in detail. The use of the possible evaluation methodologies and the use of available software tools to construct and maintain the nuclear 'map' using pre-defined standard building blocks (nuclear facilities) are introduced and discussed.

  12. Application of direct thermometric analysis in iodometry.

    Science.gov (United States)

    Marik-Korda, P; Erdey, L

    1970-12-01

    Elementary chlorine was determined by a thermometric method using potassium iodide as reagent. The temperature rise corresponding to the heat of reaction was proportional to the chlorine content. Iodine formed in the reaction was also determined with sodium thiosulphate. The heat of the chlorine-iodide reaction is about five times that of the iodine-thiosulphate reaction. Direct determination with potassium iodide is simpler and more rapid than the indirect one.

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

    Energy Technology Data Exchange (ETDEWEB)

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

    2014-06-15

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

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

    Energy Technology Data Exchange (ETDEWEB)

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

    2008-01-15

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

  15. Application of Data Mining in direct marketing

    Directory of Open Access Journals (Sweden)

    Dejana Pavlović

    2014-04-01

    Full Text Available The key to successful business operations lies in good communication with clients. There are a growing number of brokers in the financial market who collect excess funds from the clients and perform transfers to those who need the funds. However, many external and internal factors influence the decision on disposal of available funds. This paper identifies and researches into clients’ satisfaction in the banking system. By application of the disclosure of data legality we will try to point to the factors that influence the clients' decision to invest their long-term deposits in the parent bank. Upon classification and clustering, we will interpret and indentify the strengths and weaknesses of the target results. This analysis provides the guidelines through the use of the decision-making tree, application of data mining and the possibility to use a large set of data increases the value and accuracy of this technique. The problem with this technique is accuracy of the data submitted by the client.

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

    Science.gov (United States)

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

    1985-09-01

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

  17. Optimal control novel directions and applications

    CERN Document Server

    Aronna, Maria; Kalise, Dante

    2017-01-01

    Focusing on applications to science and engineering, this book presents the results of the ITN-FP7 SADCO network’s innovative research in optimization and control in the following interconnected topics: optimality conditions in optimal control, dynamic programming approaches to optimal feedback synthesis and reachability analysis, and computational developments in model predictive control. The novelty of the book resides in the fact that it has been developed by early career researchers, providing a good balance between clarity and scientific rigor. Each chapter features an introduction addressed to PhD students and some original contributions aimed at specialist researchers. Requiring only a graduate mathematical background, the book is self-contained. It will be of particular interest to graduate and advanced undergraduate students, industrial practitioners and to senior scientists wishing to update their knowledge.

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

    Directory of Open Access Journals (Sweden)

    Jana Žiarovská

    2018-03-01

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

  19. FDA's Activities Supporting Regulatory Application of "Next Gen" Sequencing Technologies.

    Science.gov (United States)

    Wilson, Carolyn A; Simonyan, Vahan

    2014-01-01

    Applications of next-generation sequencing (NGS) technologies require availability and access to an information technology (IT) infrastructure and bioinformatics tools for large amounts of data storage and analyses. The U.S. Food and Drug Administration (FDA) anticipates that the use of NGS data to support regulatory submissions will continue to increase as the scientific and clinical communities become more familiar with the technologies and identify more ways to apply these advanced methods to support development and evaluation of new biomedical products. FDA laboratories are conducting research on different NGS platforms and developing the IT infrastructure and bioinformatics tools needed to enable regulatory evaluation of the technologies and the data sponsors will submit. A High-performance Integrated Virtual Environment, or HIVE, has been launched, and development and refinement continues as a collaborative effort between the FDA and George Washington University to provide the tools to support these needs. The use of a highly parallelized environment facilitated by use of distributed cloud storage and computation has resulted in a platform that is both rapid and responsive to changing scientific needs. The FDA plans to further develop in-house capacity in this area, while also supporting engagement by the external community, by sponsoring an open, public workshop to discuss NGS technologies and data formats standardization, and to promote the adoption of interoperability protocols in September 2014. Next-generation sequencing (NGS) technologies are enabling breakthroughs in how the biomedical community is developing and evaluating medical products. One example is the potential application of this method to the detection and identification of microbial contaminants in biologic products. In order for the U.S. Food and Drug Administration (FDA) to be able to evaluate the utility of this technology, we need to have the information technology infrastructure and

  20. Direct solar energy and its applications

    International Nuclear Information System (INIS)

    Hamdani, A.J.

    1997-01-01

    Solar energy, which was a utopian dream forty years ago, is today already on the market, particularly for specialized uses and in remote areas. Even solar cells are now on the eve of becoming economically competitive. After a brief account of solar-cell theory, this paper gives the essential details of Photovoltaic Module Manufacturing Technologies, Single Crystal Technology, Fabrication of Wafers, Fabrication of Solar Cell, Photovoltaic Module, Multi Crystalline Silicon, Amorphous Silicon Cell. Semi-conductor based Thin-Film Technology (other than silicon), Copper-Indium Di selenide (IS), Gallium Arsenide, Multi-Junction Devices, as well as Technologies for Improving Conversion Efficiencies, Criteria for high-efficiency Cells and Module Fabrication. It concludes with a section on Direct Utilisation of solar energy, in which a brief description is presented on Solar Thermal Devices, Solar Water Heaters, Calculating hot-water requirements, Solar Stills, Solar Drying, Concentrator Collectors and, finally Measurement of the Solar Resource. At the end, there is a useful Appendix on World-Wide Photovoltaic Cell/Module Manufacturing Capacity Expansion Profile. (author)

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

    International Nuclear Information System (INIS)

    Park, Byeolteo; Myung, Hyun

    2014-01-01

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

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

    Science.gov (United States)

    Park, Byeolteo; Myung, Hyun

    2014-12-01

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

  3. Applications of direct chemical oxidation to demilitarization

    Energy Technology Data Exchange (ETDEWEB)

    Cooper, J.F., LLNL

    1998-06-01

    Research is reported concerning an aqueous process for oxidative destruction of solid- and liquid organic wastes, including ongoing work relevant to demilitarization This process uses acidified ammonium- or sodium peroxydisulfate and operates at ambient pressure and at temperatures of 80- 100 C The oxidant may be regenerated by electrolysis of the sulfate by- product at Pt anodes at roughly 80% coulombic efficiency, even in the presence of inorganic contaminants (e g , nitrate, phosphate or chloride) found in the original waste and entrained in the recycle stream Integral rate constants have been determined for the oxidation of diverse organic compounds at low concentrations (50 ppm, C), with rate constants (based on equivalents) of 0 004-O 02 miri Higher concentrations generally react at a 2-4X higher rate. The process has been carried through full- scale laboratory tests and initial pilot plant tests on chlorinated solvents, using a hydrolysis pretreatment Integral rate data indicate throughput rates of about 200 kg- C/m3-day The process may benefit the demilitarization efforts in various specialized applications destruction of solvents; destruction of trace propellants and explosives in shell casings remaining after bulk removal, destruction of red and pink waters, in situ remediation of soils at open pit burning/detonation sites; and as a regenerative filter for offgas carrying toxic or explosive substances.

  4. Geothermal Direct Heat Applications Program Summary

    Energy Technology Data Exchange (ETDEWEB)

    None

    1981-09-25

    Because of the undefined risk in the development and use of geothermal energy as a thermal energy source, the Department of Energy Division of Geothermal Energy solicited competitive proposals for field experiments in the direct use of geothermal energy. Twenty-two proposals were selected for cost-shared funding with one additional project co-funded by the State of New Mexico. As expected, the critical parameter was developing a viable resource. So far, of the twenty resources drilled, fourteen have proved to be useful resources. These are: Boise, Idaho; Elko heating Company in Nevada; Pagosa Springs, Colorado; Philip School, Philip, South Dakota; St. Mary's Hospital, Pierre, South Dakota; Utah Roses near Salt Lake City; Utah State Prison, Utah; Warm Springs State Hospital, Montana; T-H-S Hospital, Marlin, Texas; Aquafarms International in the Cochella Valley, California; Klamath County YMCA and Klamath Falls in Oregon; Susanville, California and Monroe, utah. Monroe's 164 F and 600 gpm peak flow was inadequate for the planned project, but is expected to be used in a private development. Three wells encountered a resource insufficient for an economical project. These were Madison County at Rexburg, Idaho; Ore-Ida Foods at Ontario, Oregon and Holly Sugar at Brawley, California. Three projects have yet to confirm their resource. The Navarro College well in Corsicana, Texas is being tested; the Reno, Moana, Nevada well is being drilled and the El Centro, California well is scheduled to be drilled in January 1982. The agribusiness project at Kelly Hot Springs was terminated because a significant archeological find was encountered at the proposed site. The Diamond Ring Ranch in South Dakota, and the additional project, Carrie Tingley Hospital in Truth or Consequences, New Mexico both used existing wells. The projects that encountered viable resources have proceeded to design, construct, and in the most advanced projects, to operate geothermal systems for

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

    Directory of Open Access Journals (Sweden)

    Sabrina Weiss

    2016-09-01

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

  6. Next generation sequencing (NGS)technologies and applications

    Energy Technology Data Exchange (ETDEWEB)

    Vuyisich, Momchilo [Los Alamos National Laboratory

    2012-09-11

    NGS technology overview: (1) NGS library preparation - Nucleic acids extraction, Sample quality control, RNA conversion to cDNA, Addition of sequencing adapters, Quality control of library; (2) Sequencing - Clonal amplification of library fragments, (except PacBio), Sequencing by synthesis, Data output (reads and quality); and (3) Data analysis - Read mapping, Genome assembly, Gene expression, Operon structure, sRNA discovery, and Epigenetic analyses.

  7. Power electronic converter systems for direct drive renewable energy applications

    DEFF Research Database (Denmark)

    Chen, Zhe

    2013-01-01

    This chapter presents power electronic conversion systems for wind and marine energy generation applications, in particular, direct drive generator energy conversion systems. Various topologies are presented and system design optimization and reliability are briefly discussed....

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

    Science.gov (United States)

    Scholz, Christian F P; Jensen, Anders

    2017-01-01

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

  9. Chitin and Chitosan as Direct Compression Excipients in Pharmaceutical Applications

    Science.gov (United States)

    Badwan, Adnan A.; Rashid, Iyad; Al Omari, Mahmoud M.H.; Darras, Fouad H.

    2015-01-01

    Despite the numerous uses of chitin and chitosan as new functional materials of high potential in various fields, they are still behind several directly compressible excipients already dominating pharmaceutical applications. There are, however, new attempts to exploit chitin and chitosan in co-processing techniques that provide a product with potential to act as a direct compression (DC) excipient. This review outlines the compression properties of chitin and chitosan in the context of DC pharmaceutical applications. PMID:25810109

  10. Chitin and Chitosan as Direct Compression Excipients in Pharmaceutical Applications

    Directory of Open Access Journals (Sweden)

    Adnan A. Badwan

    2015-03-01

    Full Text Available Despite the numerous uses of chitin and chitosan as new functional materials of high potential in various fields, they are still behind several directly compressible excipients already dominating pharmaceutical applications. There are, however, new attempts to exploit chitin and chitosan in co-processing techniques that provide a product with potential to act as a direct compression (DC excipient. This review outlines the compression properties of chitin and chitosan in the context of DC pharmaceutical applications.

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

    Science.gov (United States)

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

    2016-01-01

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

  12. Applications and Case Studies of the Next-Generation Sequencing Technologies in Food, Nutrition and Agriculture.

    Science.gov (United States)

    Next-generation sequencing technologies are able to produce high-throughput short sequence reads in a cost-effective fashion. The emergence of these technologies has not only facilitated genome sequencing but also changed the landscape of life sciences. Here I survey their major applications ranging...

  13. 42 CFR 86.32 - Application for direct traineeship.

    Science.gov (United States)

    2010-10-01

    ... 42 Public Health 1 2010-10-01 2010-10-01 false Application for direct traineeship. 86.32 Section 86.32 Public Health PUBLIC HEALTH SERVICE, DEPARTMENT OF HEALTH AND HUMAN SERVICES OCCUPATIONAL SAFETY AND HEALTH RESEARCH AND RELATED ACTIVITIES GRANTS FOR EDUCATION PROGRAMS IN OCCUPATIONAL SAFETY AND HEALTH Occupational Safety and Health Direct...

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

    Science.gov (United States)

    Dempsey, David; Suckale, Jenny

    2016-05-01

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

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

    Science.gov (United States)

    Finnerty, J R; Block, B A

    1992-06-01

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

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

    Directory of Open Access Journals (Sweden)

    Cosmas Mwikirize

    2012-12-01

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

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

    Science.gov (United States)

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

    2009-09-01

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

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

    Science.gov (United States)

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

    2012-06-18

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

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

    International Nuclear Information System (INIS)

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

    2009-01-01

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

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

    Energy Technology Data Exchange (ETDEWEB)

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

    2009-09-01

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

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

    Directory of Open Access Journals (Sweden)

    Dimas Alexandre Kliemann

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

  2. Plann: A command-line application for annotating plastome sequences.

    Science.gov (United States)

    Huang, Daisie I; Cronk, Quentin C B

    2015-08-01

    Plann automates the process of annotating a plastome sequence in GenBank format for either downstream processing or for GenBank submission by annotating a new plastome based on a similar, well-annotated plastome. Plann is a Perl script to be executed on the command line. Plann compares a new plastome sequence to the features annotated in a reference plastome and then shifts the intervals of any matching features to the locations in the new plastome. Plann's output can be used in the National Center for Biotechnology Information's tbl2asn to create a Sequin file for GenBank submission. Unlike Web-based annotation packages, Plann is a locally executable script that will accurately annotate a plastome sequence to a locally specified reference plastome. Because it executes from the command line, it is ready to use in other software pipelines and can be easily rerun as a draft plastome is improved.

  3. Applications of High-Throughput Nucleotide Sequencing (PhD)

    DEFF Research Database (Denmark)

    Waage, Johannes

    equally large demands in data handling, analysis and interpretation, perhaps defining the modern challenge of the computational biologist of the post-genomic era. The first part of this thesis consists of a general introduction to the history, common terms and challenges of next generation sequencing......-sequencing, a study of the effects on alternative RNA splicing of KO of the nonsense mediated RNA decay system in Mus, using digital gene expression and a custom-built exon-exon junction mapping pipeline is presented (article I). Evolved from this work, a Bioconductor package, spliceR, for classifying alternative...

  4. Application of Logic to Integer Sequences: A Survey

    Science.gov (United States)

    Makowsky, Johann A.

    Chomsky and Schützenberger showed in 1963 that the sequence d L (n), which counts the number of words of a given length n in a regular language L, satisfies a linear recurrence relation with constant coefficients for n, or equivalently, the generating function g_L(x)=sumn d_L(n) x^n is a rational function. In this talk we survey results concerning sequences a(n) of natural numbers which satisfy linear recurrence relations over ℤ or ℤ m , and

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

    Directory of Open Access Journals (Sweden)

    Philip A. Huebner

    2018-02-01

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

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

    Science.gov (United States)

    Huebner, Philip A.; Willits, Jon A.

    2018-01-01

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

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

    Science.gov (United States)

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

    2016-03-01

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

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

    Directory of Open Access Journals (Sweden)

    Zeng An-Ping

    2004-08-01

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

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

    Directory of Open Access Journals (Sweden)

    Bárbara Angulo

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

  10. Modeling ChIP sequencing in silico with applications.

    Directory of Open Access Journals (Sweden)

    Zhengdong D Zhang

    2008-08-01

    Full Text Available ChIP sequencing (ChIP-seq is a new method for genomewide mapping of protein binding sites on DNA. It has generated much excitement in functional genomics. To score data and determine adequate sequencing depth, both the genomic background and the binding sites must be properly modeled. To develop a computational foundation to tackle these issues, we first performed a study to characterize the observed statistical nature of this new type of high-throughput data. By linking sequence tags into clusters, we show that there are two components to the distribution of tag counts observed in a number of recent experiments: an initial power-law distribution and a subsequent long right tail. Then we develop in silico ChIP-seq, a computational method to simulate the experimental outcome by placing tags onto the genome according to particular assumed distributions for the actual binding sites and for the background genomic sequence. In contrast to current assumptions, our results show that both the background and the binding sites need to have a markedly nonuniform distribution in order to correctly model the observed ChIP-seq data, with, for instance, the background tag counts modeled by a gamma distribution. On the basis of these results, we extend an existing scoring approach by using a more realistic genomic-background model. This enables us to identify transcription-factor binding sites in ChIP-seq data in a statistically rigorous fashion.

  11. Two applications of direct digital down converters in beam diagnostics

    International Nuclear Information System (INIS)

    Powers, Tom; Flood, Roger; Hovater, Curt; Musson, John

    2000-01-01

    The technologies of direct digital down converters, digital frequency synthesis, and digital signal processing are being used in many commercial applications. Because of this commercialization, the component costs are being reduced to the point where they are economically viable for large scale accelerator applications. This paper will discuss two applications of these technologies to beam diagnostics. In the first application the combination of direct digital frequency synthesis and direct digital down converters are coupled with digital signal processor technology in order to maintain the stable gain environment required for a multi-electrode beam position monitoring system. This is done by injecting a CW reference signal into the electronics as part of the front-end circuitry. In the second application direct digital down converters are used to provide a novel approach to the measurement of beam intensity using cavity current monitors. In this system a pair of reference signals are injected into the cavity through an auxiliary port. The beam current is then calculated as the ratio of the beam signal divided by the average of the magnitude of the two reference signals

  12. Technology-based suicide prevention: current applications and future directions.

    Science.gov (United States)

    Luxton, David D; June, Jennifer D; Kinn, Julie T

    2011-01-01

    This review reports on current and emerging technologies for suicide prevention. Technology-based programs discussed include interactive educational and social networking Web sites, e-mail outreach, and programs that use mobile devices and texting. We describe innovative applications such as virtual worlds, gaming, and text analysis that are currently being developed and applied to suicide prevention and outreach programs. We also discuss the benefits and limitations of technology-based applications and discuss future directions for their use.

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

    Science.gov (United States)

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

    2015-01-01

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

  14. Video Enhancement and Dynamic Range Control of HDR Sequences for Automotive Applications

    Directory of Open Access Journals (Sweden)

    Giovanni Ramponi

    2007-01-01

    Full Text Available CMOS video cameras with high dynamic range (HDR output are particularly suitable for driving assistance applications, where lighting conditions can strongly vary, going from direct sunlight to dark areas in tunnels. However, common visualization devices can only handle a low dynamic range, and thus a dynamic range reduction is needed. Many algorithms have been proposed in the literature to reduce the dynamic range of still pictures. Anyway, extending the available methods to video is not straightforward, due to the peculiar nature of video data. We propose an algorithm for both reducing the dynamic range of video sequences and enhancing its appearance, thus improving visual quality and reducing temporal artifacts. We also provide an optimized version of our algorithm for a viable hardware implementation on an FPGA. The feasibility of this implementation is demonstrated by means of a case study.

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

    Science.gov (United States)

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

    2016-03-22

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

  16. Next generation sequencing and its applications in forensic genetics

    DEFF Research Database (Denmark)

    Børsting, Claus; Morling, Niels

    2015-01-01

    articles and presentations at conferences with forensic aspects of NGS. These contributions have demonstrated that NGS offers new possibilities for forensic genetic case work. More information may be obtained from unique samples in a single experiment by analyzing combinations of markers (STRs, SNPs......It has been almost a decade since the first next generation sequencing (NGS) technologies emerged and quickly changed the way genetic research is conducted. Today, full genomes are mapped and published almost weekly and with ever increasing speed and decreasing costs. NGS methods and platforms have...... matured during the last 10 years, and the quality of the sequences has reached a level where NGS is used in clinical diagnostics of humans. Forensic genetic laboratories have also explored NGS technologies and especially in the last year, there has been a small explosion in the number of scientific...

  17. CESAS: Computerized event sequence abstracting system outlines and applications

    International Nuclear Information System (INIS)

    Watanabe, N.; Kobayashi, K.; Fujiki, K.

    1990-01-01

    For the purpose of efficient utilization of the safety-related event information on the nuclear power plants, a new computer software package CESAS has been under development. CESAS is to systematically abstract the event sequence, that is a series of sequential and causal relationships between occurrences, from the event description written in natural language of English. This system is designed to be based on the knowledge engineering technique utilized in the field of natural language processing. The analytical process in this system consists of morphemic, syntactic, semantic, and syntagmatic analyses. At this moment, the first version of CESAS has been developed and applied to several real event descriptions for studying its feasibility. This paper describes the outlines of CESAS and one of analytical results in comparison with a manually-extracted event sequence

  18. Applications of high-throughput sequencing to chromatin structure and function in mammals

    OpenAIRE

    Dunham, Ian

    2009-01-01

    High-throughput DNA sequencing approaches have enabled direct interrogation of chromatin samples from mammalian cells. We are beginning to develop a genome-wide description of nuclear function during development, but further data collection, refinement, and integration are needed.

  19. On direct and indirect methanol fuel cells for transportation applications

    Energy Technology Data Exchange (ETDEWEB)

    Gottesfield, S.

    1996-04-01

    Research on direct oxidation methanol fuel cells (DMFCs) and polymer electrolyte fuel cells (PEFCs) is discussed. Systems considered for transportation applications are addressed. The use of platinum/ruthenium anode electrocatalysts and platinum cathode electrocatalysts in polymer electrolyte DMFCs has resulted in significant performance enhancements.

  20. SU-E-J-216: A Sequence Independent Approach for Quantification of MR Image Deformations From Brachytherapy Applicators

    Energy Technology Data Exchange (ETDEWEB)

    Wieringen, N van; Heerden, L van; Gurney-Champion, O; Kesteren, Z van; Houweling, A; Pieters, B; Bel, A [Academic Medical Center, Amsterdam (Netherlands)

    2015-06-15

    Purpose: MRI is increasingly used as a single imaging modality for brachytherapy treatment planning. The presence of a brachytherapy applicator may cause distortions in the images, especially at higher field strengths. Our aim is to develop a procedure to quantify these distortions theoretically for any MR-sequence and to verify the estimated deformations for clinical sequences. Methods: Image distortions due to perturbation of the B0-field are proportional to the ratio of the induced frequency shift and the read-out bandwidth of the applied sequence. By reconstructing a frequency-shift map from the phase data from a multi-echo sequence, distortions can be calculated for any MR-sequence. Verification of this method for estimating distortions was performed by acquiring images with opposing read-out directions and consequently opposing distortions. The applicator shift can be determined by rigidly matching these images. Clinically, T2W-TSE-images are used for this purpose. For pre-clinical tests, EPI-sequences with narrow read-out bandwidth (19.5–47.5Hz), consequently large distortions, were added to the set of clinical MRsequences. To quantify deformations of the Utrecht Interstitial CT/MR applicator (Elekta Brachytherapy) on a Philips Ingenia 3T MRI, pre-clinical tests were performed in a phantom with the applicator in water, followed by clinical validation. Results: Deformations observed in the narrow bandwidth EPI-images were well predicted using the frequency-shift, the latter giving an overestimation up to 30%/up to 1 voxel. For clinically applied MR-sequences distortions were well below the voxel size. In patient setup distortions determined from the frequency-shift map were at sub-voxel level (<0.7mm). Using T2W-images larger distortions were found (1–2mm). This discrepancy was caused by patient movement between/during acquisition of the T2W-images with opposing read-out directions. Conclusion: Phantom experiments demonstrated the feasibility of a

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

    International Nuclear Information System (INIS)

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

    2003-01-01

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

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

    DEFF Research Database (Denmark)

    Ladefoged, Søren; Birkelund, Svend; Hauge, S

    1995-01-01

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

  3. Application of an E. coli signal sequence as a versatile inclusion body tag.

    Science.gov (United States)

    Jong, Wouter S P; Vikström, David; Houben, Diane; van den Berg van Saparoea, H Bart; de Gier, Jan-Willem; Luirink, Joen

    2017-03-21

    Heterologous protein production in Escherichia coli often suffers from bottlenecks such as proteolytic degradation, complex purification procedures and toxicity towards the expression host. Production of proteins in an insoluble form in inclusion bodies (IBs) can alleviate these problems. Unfortunately, the propensity of heterologous proteins to form IBs is variable and difficult to predict. Hence, fusing the target protein to an aggregation prone polypeptide or IB-tag is a useful strategy to produce difficult-to-express proteins in an insoluble form. When screening for signal sequences that mediate optimal targeting of heterologous proteins to the periplasmic space of E. coli, we observed that fusion to the 39 amino acid signal sequence of E. coli TorA (ssTorA) did not promote targeting but rather directed high-level expression of the human proteins hEGF, Pla2 and IL-3 in IBs. Further analysis revealed that ssTorA even mediated IB formation of the highly soluble endogenous E. coli proteins TrxA and MBP. The ssTorA also induced aggregation when fused to the C-terminus of target proteins and appeared functional as IB-tag in E. coli K-12 as well as B strains. An additive effect on IB-formation was observed upon fusion of multiple ssTorA sequences in tandem, provoking almost complete aggregation of TrxA and MBP. The ssTorA-moiety was successfully used to produce the intrinsically unstable hEGF and the toxic fusion partner SymE, demonstrating its applicability as an IB-tag for difficult-to-express and toxic proteins. We present proof-of-concept for the use of ssTorA as a small, versatile tag for robust E. coli-based expression of heterologous proteins in IBs.

  4. EEC directives and guidelines applicable to radiopharmaceuticals - 1993

    International Nuclear Information System (INIS)

    Cox, P.H.

    1993-01-01

    The manufacture, scale and supply of radiopharmaceuticals in the EEC is regulated by directives that are incorporated into the national laws of the member states. The situation as of 1 January 1993 was not too optimistic, however, as the processing of licensing applications had been completely misjudged. Not one product had been registered as of 1 January. The costs involved are also high and since the European market for radiopharmaceuticals is relatively small, the market cannot afford this. It would appear that the EEC directives are inadquate and too non-specific, so revision is indicated. (orig.)

  5. Direct electroplating of plastic for advanced electrical applications

    DEFF Research Database (Denmark)

    Islam, Aminul; Hansen, Hans Nørgaard; Tang, Peter Torben

    2017-01-01

    Electrodeposition or electroplating is predominantly applied to metallic components. Electroplating of plastics is possible in some cases where an initial electroless plating layer of nickel or copper is made to provide a conductive surface on the plastic part. This paper proposes a method...... for direct electroplating of plastic eliminating the need for slow and expensive processes like electroless metal deposition, PVD coating, painting with conductive inks etc. The results obtained from the test demonstrate the potential of direct electroplating of plastic to enhance the electrical conductivity...... and the use of electroplated plastics for advanced applications like Moulded Interconnect Devices (MIDs)....

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

    Science.gov (United States)

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

    2017-01-05

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

  7. The Microsoft Biology Foundation Applications for High-Throughput Sequencing

    Science.gov (United States)

    Mercer, S.

    2010-01-01

    w9-2 The need for reusable libraries of bioinformatics functions has been recognized for many years and a number of language-specific toolkits have been constructed. Such toolkits have served as valuable nucleation points for the community, promoting the sharing of code and establishing standards. The majority of DNA sequencing machines and many other standard pieces of lab equipment are controlled by PCs using Windows, and a Microsoft genomics toolkit would enable initial processing and quality control to happen closer to the instrumentation and provide opportunities for added-value services within core facilities. The Microsoft Biology Foundation (MBF) is an open source software library, freely available for both commercial and academic use, available as an early-stage betafrom mbf.codeplex.com. This presentation will describe the structure and goals of MBF and demonstrate some of its uses.

  8. Applications of nanotechnology, next generation sequencing and microarrays in biomedical research.

    Science.gov (United States)

    Elingaramil, Sauli; Li, Xiaolong; He, Nongyue

    2013-07-01

    Next-generation sequencing technologies, microarrays and advances in bio nanotechnology have had an enormous impact on research within a short time frame. This impact appears certain to increase further as many biomedical institutions are now acquiring these prevailing new technologies. Beyond conventional sampling of genome content, wide-ranging applications are rapidly evolving for next-generation sequencing, microarrays and nanotechnology. To date, these technologies have been applied in a variety of contexts, including whole-genome sequencing, targeted re sequencing and discovery of transcription factor binding sites, noncoding RNA expression profiling and molecular diagnostics. This paper thus discusses current applications of nanotechnology, next-generation sequencing technologies and microarrays in biomedical research and highlights the transforming potential these technologies offer.

  9. Acidithiobacillus ferrooxidans metabolism: from genome sequence to industrial applications

    Directory of Open Access Journals (Sweden)

    Blake Robert

    2008-12-01

    Full Text Available Abstract Background Acidithiobacillus ferrooxidans is a major participant in consortia of microorganisms used for the industrial recovery of copper (bioleaching or biomining. It is a chemolithoautrophic, γ-proteobacterium using energy from the oxidation of iron- and sulfur-containing minerals for growth. It thrives at extremely low pH (pH 1–2 and fixes both carbon and nitrogen from the atmosphere. It solubilizes copper and other metals from rocks and plays an important role in nutrient and metal biogeochemical cycling in acid environments. The lack of a well-developed system for genetic manipulation has prevented thorough exploration of its physiology. Also, confusion has been caused by prior metabolic models constructed based upon the examination of multiple, and sometimes distantly related, strains of the microorganism. Results The genome of the type strain A. ferrooxidans ATCC 23270 was sequenced and annotated to identify general features and provide a framework for in silico metabolic reconstruction. Earlier models of iron and sulfur oxidation, biofilm formation, quorum sensing, inorganic ion uptake, and amino acid metabolism are confirmed and extended. Initial models are presented for central carbon metabolism, anaerobic metabolism (including sulfur reduction, hydrogen metabolism and nitrogen fixation, stress responses, DNA repair, and metal and toxic compound fluxes. Conclusion Bioinformatics analysis provides a valuable platform for gene discovery and functional prediction that helps explain the activity of A. ferrooxidans in industrial bioleaching and its role as a primary producer in acidic environments. An analysis of the genome of the type strain provides a coherent view of its gene content and metabolic potential.

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

    Directory of Open Access Journals (Sweden)

    Chengwei Luo

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

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

    Science.gov (United States)

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

    2012-01-01

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

  12. γ-Glutamyltranspeptidases: sequence, structure, biochemical properties, and biotechnological applications.

    Science.gov (United States)

    Castellano, Immacolata; Merlino, Antonello

    2012-10-01

    γ-Glutamyltranspeptidases (γ-GTs) are ubiquitous enzymes that catalyze the hydrolysis of γ-glutamyl bonds in glutathione and glutamine and the transfer of the released γ-glutamyl group to amino acids or short peptides. These enzymes are involved in glutathione metabolism and play critical roles in antioxidant defense, detoxification, and inflammation processes. Moreover, γ-GTs have been recently found to be involved in many physiological disorders, such as Parkinson's disease and diabetes. In this review, the main biochemical and structural properties of γ-GTs isolated from different sources, as well as their conformational stability and mechanism of catalysis, are described and examined with the aim of contributing to the discussion on their structure-function relationships. Possible applications of γ-glutamyltranspeptidases in different fields of biotechnology and medicine are also discussed.

  13. Direct Wafer Bonding and Its Application to Waveguide Optical Isolators.

    Science.gov (United States)

    Mizumoto, Tetsuya; Shoji, Yuya; Takei, Ryohei

    2012-05-24

    This paper reviews the direct bonding technique focusing on the waveguide optical isolator application. A surface activated direct bonding technique is a powerful tool to realize a tight contact between dissimilar materials. This technique has the potential advantage that dissimilar materials are bonded at low temperature, which enables one to avoid the issue associated with the difference in thermal expansion. Using this technique, a magneto-optic garnet is successfully bonded on silicon, III-V compound semiconductors and LiNbO₃. As an application of this technique, waveguide optical isolators are investigated including an interferometric waveguide optical isolator and a semileaky waveguide optical isolator. The interferometric waveguide optical isolator that uses nonreciprocal phase shift is applicable to a variety of waveguide platforms. The low refractive index of buried oxide layer in a silicon-on-insulator (SOI) waveguide enhances the magneto-optic phase shift, which contributes to the size reduction of the isolator. A semileaky waveguide optical isolator has the advantage of large fabrication-tolerance as well as a wide operation wavelength range.

  14. Direct Wafer Bonding and Its Application to Waveguide Optical Isolators

    Directory of Open Access Journals (Sweden)

    Ryohei Takei

    2012-05-01

    Full Text Available This paper reviews the direct bonding technique focusing on the waveguide optical isolator application. A surface activated direct bonding technique is a powerful tool to realize a tight contact between dissimilar materials. This technique has the potential advantage that dissimilar materials are bonded at low temperature, which enables one to avoid the issue associated with the difference in thermal expansion. Using this technique, a magneto-optic garnet is successfully bonded on silicon, III-V compound semiconductors and LiNbO3. As an application of this technique, waveguide optical isolators are investigated including an interferometric waveguide optical isolator and a semileaky waveguide optical isolator. The interferometric waveguide optical isolator that uses nonreciprocal phase shift is applicable to a variety of waveguide platforms. The low refractive index of buried oxide layer in a silicon-on-insulator (SOI waveguide enhances the magneto-optic phase shift, which contributes to the size reduction of the isolator. A semileaky waveguide optical isolator has the advantage of large fabrication-tolerance as well as a wide operation wavelength range.

  15. Application of high-throughput sequencing in understanding human oral microbiome related with health and disease

    OpenAIRE

    Chen, Hui; Jiang, Wen

    2014-01-01

    The oral microbiome is one of most diversity habitat in the human body and they are closely related with oral health and disease. As the technique developing,, high throughput sequencing has become a popular approach applied for oral microbial analysis. Oral bacterial profiles have been studied to explore the relationship between microbial diversity and oral diseases such as caries and periodontal disease. This review describes the application of high-throughput sequencing for characterizati...

  16. Application of Patterson-function direct methods to materials characterization.

    Science.gov (United States)

    Rius, Jordi

    2014-09-01

    The aim of this article is a general description of the so-called Patterson-function direct methods (PFDM), from their origin to their present state. It covers a 20-year period of methodological contributions to crystal structure solution, most of them published in Acta Crystallographica Section A. The common feature of these variants of direct methods is the introduction of the experimental intensities in the form of the Fourier coefficients of origin-free Patterson-type functions, which allows the active use of both strong and weak reflections. The different optimization algorithms are discussed and their performances compared. This review focuses not only on those PFDM applications related to powder diffraction data but also on some recent results obtained with electron diffraction tomography data.

  17. Application of Patterson-function direct methods to materials characterization

    Directory of Open Access Journals (Sweden)

    Jordi Rius

    2014-09-01

    Full Text Available The aim of this article is a general description of the so-called Patterson-function direct methods (PFDM, from their origin to their present state. It covers a 20-year period of methodological contributions to crystal structure solution, most of them published in Acta Crystallographica Section A. The common feature of these variants of direct methods is the introduction of the experimental intensities in the form of the Fourier coefficients of origin-free Patterson-type functions, which allows the active use of both strong and weak reflections. The different optimization algorithms are discussed and their performances compared. This review focuses not only on those PFDM applications related to powder diffraction data but also on some recent results obtained with electron diffraction tomography data.

  18. Principle and clinical application of direct dry printer

    International Nuclear Information System (INIS)

    Lin Shaochun; Cheng Xiaomei; Yang Xufeng

    2009-01-01

    It was quite common and practicable that one high speed printer was connected to several DICOM modalities in hospitals with central printing system. For different image quality was demanded by different modalities, image quality should be controled at the printer side, to achieve acceptable high quality medical image on film. The principles and the application of the Direct Dry Printer were discussed in this article as an example. The characteristics of the Direct Dry Printer could produce good film with continuous tone, abundant grayscale and high-quality spatial resolution. It also had a number of' other advantages such as improved structure, higher image quality, faster print speed and more friendly to the environment. (authors)

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

    Science.gov (United States)

    Quinn, Terrance; Sinkala, Zachariah

    2014-01-01

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

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

    Directory of Open Access Journals (Sweden)

    Etchells J Peter

    2009-10-01

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

  1. Stimuli-Directed Helical Chirality Inversion and Bio-Applications

    Directory of Open Access Journals (Sweden)

    Ziyu Lv

    2016-08-01

    Full Text Available Helical structure is a sophisticated ubiquitous motif found in nature, in artificial polymers, and in supramolecular assemblies from microscopic to macroscopic points of view. Significant progress has been made in the synthesis and structural elucidation of helical polymers, nevertheless, a new direction for helical polymeric materials, is how to design smart systems with controllable helical chirality, and further use them to develop chiral functional materials and promote their applications in biology, biochemistry, medicine, and nanotechnology fields. This review summarizes the recent progress in the development of high-performance systems with tunable helical chirality on receiving external stimuli and discusses advances in their applications as drug delivery vesicles, sensors, molecular switches, and liquid crystals. Challenges and opportunities in this emerging area are also presented in the conclusion.

  2. Direct application of geothermal energy in the Republic of Macedonia

    International Nuclear Information System (INIS)

    Dimitrov, Konstantin

    1995-01-01

    The use of geothermal energy for balneology purposes has a history of many centuries. There is also a more than 30 years tradition for heating greenhouses. So called energy crisis of 70-ties and 80-ties provoked geology investigations in order to find possible energy sources, and development of systems for application of low-temperature geothermal water. Tere are a list of projects with direct application of geothermal energy for heating greenhouses, drying agricultural products. heating of public buildings and industrial projects, swimming pools , sanitary warm water preparation, industrial uses, etc. The essential energetic characteristics of different projects are presented in the paper. For the main projects a technical description of characteristics of the heating systems is given, and good technical solutions are underlined. Also the mistakes presented in some projects are listed. (Original)

  3. Nanoparticles in medical applications – a direction of the future?

    Directory of Open Access Journals (Sweden)

    Anna Jung

    2014-06-01

    Full Text Available Methods of producing nanoparticles, called nanotechnologies, have inspired lively interest over the recent years due to the broad possibilities for application of nanoparticles in numerous fields, including electronics, information technology, biotechnology, medicine, pharmacy, cosmetology and others. Nanoparticles are defined as particles which may occur in various shapes and which have at least one dimension smaller than 100 nm. Depending on the process of creation we can differentiate between natural nanoparticles occurring in the environment and designed nanoparticles, which are man-made. Designed nanoparticles are characterised by special physical properties which make them suitable for biomedical applications, among others. An example of such an application is the use of silver nanocomposites, which in a micronised form display a strong bacteriostatic and bactericidal effect. Graphene, the latest achievement of nanotechnology with unique mechanical and physical properties, is another material which raises much interest among researchers. The dynamic development of numerous directions in modern technologies based on nanotechnologies is an indisputable sign of progress. The discovery of the unique properties of nanomaterials opens wide possibilities for numerous applications; however, it also requires comprehensive research to ensure they are safe to use.

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

    Science.gov (United States)

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

    1990-10-23

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

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

    Science.gov (United States)

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

    2017-06-01

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

  6. A roadmap to directed enzyme evolution and screening systems for biotechnological applications

    Directory of Open Access Journals (Sweden)

    Ronny Martínez

    2013-01-01

    Full Text Available Enzymes have been long used in man-made biochemical processes, from brewing and fermentation to current industrial production of fine chemicals. The ever-growing demand for enzymes in increasingly specific applications requires tailoring naturally occurring enzymes to the non-natural conditions found in industrial processes. Relationships between enzyme sequence, structure and activity are far from understood, thus hindering the capacity to design tailored biocatalysts. In the field of protein engineering, directed enzyme evolution is a powerful algorithm to generate and identify novel and improved enzymes through iterative rounds of mutagenesis and screening applying a specific evolutive pressure. In practice, critical checkpoints in directed evolution are: selection of the starting point, generation of the mutant library, development of the screening assay and analysis of the output of the screening campaign. Each step in directed evolution can be performed using conceptually and technically different approaches, all having inherent advantages and challenges. In this article, we present and discuss in a general overview, challenges of designing and performing a directed enzyme evolution campaign, current advances in methods, as well as highlighting some examples of its applications in industrially relevant enzymes.

  7. Directed Abelian algebras and their application to stochastic models.

    Science.gov (United States)

    Alcaraz, F C; Rittenberg, V

    2008-10-01

    With each directed acyclic graph (this includes some D-dimensional lattices) one can associate some Abelian algebras that we call directed Abelian algebras (DAAs). On each site of the graph one attaches a generator of the algebra. These algebras depend on several parameters and are semisimple. Using any DAA, one can define a family of Hamiltonians which give the continuous time evolution of a stochastic process. The calculation of the spectra and ground-state wave functions (stationary state probability distributions) is an easy algebraic exercise. If one considers D-dimensional lattices and chooses Hamiltonians linear in the generators, in finite-size scaling the Hamiltonian spectrum is gapless with a critical dynamic exponent z=D. One possible application of the DAA is to sandpile models. In the paper we present this application, considering one- and two-dimensional lattices. In the one-dimensional case, when the DAA conserves the number of particles, the avalanches belong to the random walker universality class (critical exponent sigma_(tau)=32 ). We study the local density of particles inside large avalanches, showing a depletion of particles at the source of the avalanche and an enrichment at its end. In two dimensions we did extensive Monte-Carlo simulations and found sigma_(tau)=1.780+/-0.005 .

  8. Enamel-Caries Prevention Using Two Applications of Fluoride-Laser Sequence.

    Science.gov (United States)

    Noureldin, Amal; Quintanilla, Ines; Kontogiorgos, Elias; Jones, Daniel

    2016-03-01

    Studies demonstrated a significant synergism between fluoride and laser in reduction of enamel solubility. However, minimal research has focused on testing the sequence of their application and no other research investigated the preventive effect of repeated applications of a combined treatment. This study investigated the effect of two applications of fluoride-laser sequence on the resistance of sound enamel to cariogenic challenge compared to one-time application. Sixty enamel slabs were cut from 10 human incisors, ground flat, polished and coated with nail varnish except a 2 x 2 mm window. Specimens were randomly assigned into five groups of 12 specimens; (CON-) negative-control received no treatment, (CON+) positive-control received pH challenge, (FV) treated with M fluoride varnish, (F-L1) one-application fluoride-varnish followed by CO2 laser-treatment (short-pulsed 10.6 µm, 2.4J/ cm2, 10HZ, 10sec), and (F-L2) two-applications of fluoride varnish-laser treatment. Specimens were left in distilled water for one day between applications. Except CON-, all groups were submitted to pH cycling for 9-days (8 demin/ remin + 1 day remineralisation bath) at 37°C. Enamel demineralization was quantitatively evaluated by measurement of Knoop surface-microhardness (SM H) (50-grams/10 seconds). Data were analyzed using one-way ANOVA (p ≤ 0.05) followed by Duncan's Multiple Range Test. Within the limitations of this study, it was found that one or two applications of fluoride-laser sequence significantly improved resistance of the sound enamel surface to acid attack compared to FV-treated group. Although the two applications of fluoride-laser sequence (F-L1 and F-L2) showed higher SMH values, significant resistance to demineralization was only obtained with repeated applications.

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

    Directory of Open Access Journals (Sweden)

    Joke J F A van Vugt

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

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

    Science.gov (United States)

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

    2018-04-30

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

  11. 3D representations of amino acids—applications to protein sequence comparison and classification

    Directory of Open Access Journals (Sweden)

    Jie Li

    2014-08-01

    Full Text Available The amino acid sequence of a protein is the key to understanding its structure and ultimately its function in the cell. This paper addresses the fundamental issue of encoding amino acids in ways that the representation of such a protein sequence facilitates the decoding of its information content. We show that a feature-based representation in a three-dimensional (3D space derived from amino acid substitution matrices provides an adequate representation that can be used for direct comparison of protein sequences based on geometry. We measure the performance of such a representation in the context of the protein structural fold prediction problem. We compare the results of classifying different sets of proteins belonging to distinct structural folds against classifications of the same proteins obtained from sequence alone or directly from structural information. We find that sequence alone performs poorly as a structure classifier. We show in contrast that the use of the three dimensional representation of the sequences significantly improves the classification accuracy. We conclude with a discussion of the current limitations of such a representation and with a description of potential improvements.

  12. Chemical compound-based direct reprogramming for future clinical applications

    Science.gov (United States)

    Takeda, Yukimasa; Harada, Yoshinori; Yoshikawa, Toshikazu; Dai, Ping

    2018-01-01

    Recent studies have revealed that a combination of chemical compounds enables direct reprogramming from one somatic cell type into another without the use of transgenes by regulating cellular signaling pathways and epigenetic modifications. The generation of induced pluripotent stem (iPS) cells generally requires virus vector-mediated expression of multiple transcription factors, which might disrupt genomic integrity and proper cell functions. The direct reprogramming is a promising alternative to rapidly prepare different cell types by bypassing the pluripotent state. Because the strategy also depends on forced expression of exogenous lineage-specific transcription factors, the direct reprogramming in a chemical compound-based manner is an ideal approach to further reduce the risk for tumorigenesis. So far, a number of reported research efforts have revealed that combinations of chemical compounds and cell-type specific medium transdifferentiate somatic cells into desired cell types including neuronal cells, glial cells, neural stem cells, brown adipocytes, cardiomyocytes, somatic progenitor cells, and pluripotent stem cells. These desired cells rapidly converted from patient-derived autologous fibroblasts can be applied for their own transplantation therapy to avoid immune rejection. However, complete chemical compound-induced conversions remain challenging particularly in adult human-derived fibroblasts compared with mouse embryonic fibroblasts (MEFs). This review summarizes up-to-date progress in each specific cell type and discusses prospects for future clinical application toward cell transplantation therapy. PMID:29739872

  13. Alternatives to electrical cogeneration: The direct application of steam engines

    International Nuclear Information System (INIS)

    Phillips, W.C.

    1993-01-01

    Although small to medium sized industrial facilities are aware of electrical cogeneration, often they are too small for it to be economically justifiable. The direct application of steam turbine power to equipment formerly powered by electric motors, can allow them to use steam capacity to reduce electrical demand and consumption, bypassing cogeneration. Cogeneration converts the heat energy of steam into circular mechanical motion and then converts the circular mechanical motion into electricity. Each conversion entails a loss of energy due to friction and other conversion losses. A substantial amount of the generated electricity is then converted back into circular motion with electric motors, again incurring energy losses. Directly applying the mechanical motion of turbines eliminates both the motion-to-electricity (generator) and the electricity-to-motion (motor) conversion losses. Excess steam capacity during the summer is not unusual for facilities that use steam to provide winter heating. Similarly, most of these facilities experience a large electrical demand peak during the cooling season due to the electricity needed to operate centrifugal chillers. Steam capacity via a turbine to power the chillers can allow the boilers to operate at a higher loading while reducing electrical consumption and demand precisely those periods when demand reduction is most needed. In facilities where the steam generating capacity is sufficient, air compressors provide an appropriate year-round application for turbine power. This paper is the result of an on-going project by the Energy Division, State of North Carolina, Department of Economic and Community Development, in conjunction with the University of North Carolina at Charlotte. The objective of this project is to educate the operating engineers and managers of small to medium sized manufacturing facilities on the technical application and economic justification of steam turbine power

  14. The application of the high throughput sequencing technology in the transposable elements.

    Science.gov (United States)

    Liu, Zhen; Xu, Jian-hong

    2015-09-01

    High throughput sequencing technology has dramatically improved the efficiency of DNA sequencing, and decreased the costs to a great extent. Meanwhile, this technology usually has advantages of better specificity, higher sensitivity and accuracy. Therefore, it has been applied to the research on genetic variations, transcriptomics and epigenomics. Recently, this technology has been widely employed in the studies of transposable elements and has achieved fruitful results. In this review, we summarize the application of high throughput sequencing technology in the fields of transposable elements, including the estimation of transposon content, preference of target sites and distribution, insertion polymorphism and population frequency, identification of rare copies, transposon horizontal transfers as well as transposon tagging. We also briefly introduce the major common sequencing strategies and algorithms, their advantages and disadvantages, and the corresponding solutions. Finally, we envision the developing trends of high throughput sequencing technology, especially the third generation sequencing technology, and its application in transposon studies in the future, hopefully providing a comprehensive understanding and reference for related scientific researchers.

  15. Direct target NOTES: prospective applications for next generation robotic platforms.

    Science.gov (United States)

    Atallah, S; Hodges, A; Larach, S W

    2018-05-01

    A new era in surgical robotics has centered on alternative access to anatomic targets and next generation designs include flexible, single-port systems which follow circuitous rather than straight pathways. Such systems maintain a small footprint and could be utilized for specialized operations based on direct organ target natural orifice transluminal endoscopic surgery (NOTES), of which transanal total mesorectal excision (taTME) is an important derivative. During two sessions, four direct target NOTES operations were conducted on a cadaveric model using a flexible robotic system to demonstrate proof-of-concept of the application of a next generation robotic system to specific types of NOTES operations, all of which required removal of a direct target organ through natural orifice access. These four operations were (a) robotic taTME, (b) robotic transvaginal hysterectomy in conjunction with (c) robotic transvaginal salpingo-oophorectomy, and in an ex vivo model, (d) trans-cecal appendectomy. Feasibility was demonstrated in all cases using the Flex ® Robotic System with Colorectal Drive. During taTME, the platform excursion was 17 cm along a non-linear path; operative time was 57 min for the transanal portion of the dissection. Robotic transvaginal hysterectomy was successfully completed in 78 min with transvaginal extraction of the uterus, although laparoscopic assistance was required. Robotic transvaginal unilateral salpingo-oophorectomy with transvaginal extraction of the ovary and fallopian tube was performed without laparoscopic assistance in 13.5 min. In an ex vivo model, a robotic trans-cecal appendectomy was also successfully performed for the purpose of demonstrating proof-of-concept only; this was completed in 24 min. A flexible robotic system has the potential to access anatomy along circuitous paths, making it a suitable platform for direct target NOTES. The conceptual operations posed could be considered suitable for next generation robotics once

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

    OpenAIRE

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

    2017-01-01

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

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

    OpenAIRE

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

    2013-01-01

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

  18. Controversy and debate on clinical genomics sequencing-paper 1: genomics is not exceptional: rigorous evaluations are necessary for clinical applications of genomic sequencing.

    Science.gov (United States)

    Wilson, Brenda J; Miller, Fiona Alice; Rousseau, François

    2017-12-01

    Next generation genomic sequencing (NGS) technologies-whole genome and whole exome sequencing-are now cheap enough to be within the grasp of many health care organizations. To many, NGS is symbolic of cutting edge health care, offering the promise of "precision" and "personalized" medicine. Historically, research and clinical application has been a two-way street in clinical genetics: research often driven directly by the desire to understand and try to solve immediate clinical problems affecting real, identifiable patients and families, accompanied by a low threshold of willingness to apply research-driven interventions without resort to formal empirical evaluations. However, NGS technologies are not simple substitutes for older technologies and need careful evaluation for use as screening, diagnostic, or prognostic tools. We have concerns across three areas. First, at the moment, analytic validity is unknown because technical platforms are not yet stable, laboratory quality assurance programs are in their infancy, and data interpretation capabilities are badly underdeveloped. Second, clinical validity of genomic findings for patient populations without pre-existing high genetic risk is doubtful, as most clinical experience with NGS technologies relates to patients with a high prior likelihood of a genetic etiology. Finally, we are concerned that proponents argue not only for clinically driven approaches to assessing a patient's genome, but also for seeking out variants associated with unrelated conditions or susceptibilities-so-called "secondary targets"-this is screening on a genomic scale. We argue that clinical uses of genomic sequencing should remain limited to specialist and research settings, that screening for secondary findings in clinical testing should be limited to the maximum extent possible, and that the benefits, harms, and economic implications of their routine use be systematically evaluated. All stakeholders have a responsibility to ensure that

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

    Directory of Open Access Journals (Sweden)

    Vincenza Precone

    2015-01-01

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

  20. Diffusion tensor imaging. Theory, sequence optimization and application in Alzheimer's disease

    International Nuclear Information System (INIS)

    Stieltjes, B.; Schlueter, M.; Hahn, H.K.; Wilhelm, T.; Essig, M.

    2003-01-01

    Diffusion tensor imaging (DTI) offers an in vivo view into the microarchitecture of the brain. Furthermore it allows a three-dimensional reconstruction of fiber tracts. We will discuss the principles of DTI and possibilities for sequence optimization. Finally we will give an overview of DTI and its application in Alzheimer's disease. (orig.) [de

  1. Quantummechanical multi-step direct models for nuclear data applications

    International Nuclear Information System (INIS)

    Koning, A.J.

    1992-10-01

    Various multi-step direct models have been derived and compared on a theoretical level. Subsequently, these models have been implemented in the computer code system KAPSIES, enabling a consistent comparison on the basis of the same set of nuclear parameters and same set of numerical techniques. Continuum cross sections in the energy region between 10 and several hundreds of MeV have successfully been analysed. Both angular distributions and energy spectra can be predicted in an essentially parameter-free manner. It is demonstrated that the quantum-mechanical MSD models (in particular the FKK model) give an improved prediction of pre-equilibrium angular distributions as compared to the experiment-based systematics of Kalbach. This makes KAPSIES a reliable tool for nuclear data applications in the afore-mentioned energy region. (author). 10 refs., 2 figs

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

    Science.gov (United States)

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

    2013-01-01

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

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

    Directory of Open Access Journals (Sweden)

    Hiroko Shimbo

    2014-01-01

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

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

    Science.gov (United States)

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

    2017-09-01

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

  5. Evaluation of second-generation sequencing of 19 dilated cardiomyopathy genes for clinical applications.

    Science.gov (United States)

    Gowrisankar, Sivakumar; Lerner-Ellis, Jordan P; Cox, Stephanie; White, Emily T; Manion, Megan; LeVan, Kevin; Liu, Jonathan; Farwell, Lisa M; Iartchouk, Oleg; Rehm, Heidi L; Funke, Birgit H

    2010-11-01

    Medical sequencing for diseases with locus and allelic heterogeneities has been limited by the high cost and low throughput of traditional sequencing technologies. "Second-generation" sequencing (SGS) technologies allow the parallel processing of a large number of genes and, therefore, offer great promise for medical sequencing; however, their use in clinical laboratories is still in its infancy. Our laboratory offers clinical resequencing for dilated cardiomyopathy (DCM) using an array-based platform that interrogates 19 of more than 30 genes known to cause DCM. We explored both the feasibility and cost effectiveness of using PCR amplification followed by SGS technology for sequencing these 19 genes in a set of five samples enriched for known sequence alterations (109 unique substitutions and 27 insertions and deletions). While the analytical sensitivity for substitutions was comparable to that of the DCM array (98%), SGS technology performed better than the DCM array for insertions and deletions (90.6% versus 58%). Overall, SGS performed substantially better than did the current array-based testing platform; however, the operational cost and projected turnaround time do not meet our current standards. Therefore, efficient capture methods and/or sample pooling strategies that shorten the turnaround time and decrease reagent and labor costs are needed before implementing this platform into routine clinical applications.

  6. Application of genotyping by sequencing technology to a variety of crop breeding programs.

    Science.gov (United States)

    Kim, Changsoo; Guo, Hui; Kong, Wenqian; Chandnani, Rahul; Shuang, Lan-Shuan; Paterson, Andrew H

    2016-01-01

    Since the Arabidopsis genome was completed, draft sequences or pseudomolecules have been published for more than 100 plant genomes including green algae, in large part due to advances in sequencing technologies. Advanced DNA sequencing technologies have also conferred new opportunities for high-throughput low-cost crop genotyping, based on single-nucleotide polymorphisms (SNPs). However, a recurring complication in crop genotyping that differs from other taxa is a higher level of DNA sequence duplication, noting that all angiosperms are thought to have polyploidy in their evolutionary history. In the current article, we briefly review current genotyping methods using next-generation sequencing (NGS) technologies. We also explore case studies of genotyping-by-sequencing (GBS) applications to several crops differing in genome size, organization and breeding system (paleopolyploids, neo-allopolyploids, neo-autopolyploids). GBS typically shows good results when it is applied to an inbred diploid species with a well-established reference genome. However, we have also made some progress toward GBS of outcrossing species lacking reference genomes and of polyploid populations, which still need much improvement. Regardless of some limitations, low-cost and multiplexed genotyping offered by GBS will be beneficial to breed superior cultivars in many crop species. Copyright © 2015 Elsevier Ireland Ltd. All rights reserved.

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

    OpenAIRE

    Gromiha, M. Michael

    2000-01-01

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

  8. HTSstation: a web application and open-access libraries for high-throughput sequencing data analysis.

    Science.gov (United States)

    David, Fabrice P A; Delafontaine, Julien; Carat, Solenne; Ross, Frederick J; Lefebvre, Gregory; Jarosz, Yohan; Sinclair, Lucas; Noordermeer, Daan; Rougemont, Jacques; Leleu, Marion

    2014-01-01

    The HTSstation analysis portal is a suite of simple web forms coupled to modular analysis pipelines for various applications of High-Throughput Sequencing including ChIP-seq, RNA-seq, 4C-seq and re-sequencing. HTSstation offers biologists the possibility to rapidly investigate their HTS data using an intuitive web application with heuristically pre-defined parameters. A number of open-source software components have been implemented and can be used to build, configure and run HTS analysis pipelines reactively. Besides, our programming framework empowers developers with the possibility to design their own workflows and integrate additional third-party software. The HTSstation web application is accessible at http://htsstation.epfl.ch.

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

    Directory of Open Access Journals (Sweden)

    Zakham F

    2013-11-01

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

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

    Science.gov (United States)

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

    2013-01-01

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

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

    International Nuclear Information System (INIS)

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

    2008-01-01

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

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

    Science.gov (United States)

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

    2003-08-01

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

  13. Application of genotyping-by-sequencing on semiconductor sequencing platforms: a comparison of genetic and reference-based marker ordering in barley.

    Directory of Open Access Journals (Sweden)

    Martin Mascher

    Full Text Available The rapid development of next-generation sequencing platforms has enabled the use of sequencing for routine genotyping across a range of genetics studies and breeding applications. Genotyping-by-sequencing (GBS, a low-cost, reduced representation sequencing method, is becoming a common approach for whole-genome marker profiling in many species. With quickly developing sequencing technologies, adapting current GBS methodologies to new platforms will leverage these advancements for future studies. To test new semiconductor sequencing platforms for GBS, we genotyped a barley recombinant inbred line (RIL population. Based on a previous GBS approach, we designed bar code and adapter sets for the Ion Torrent platforms. Four sets of 24-plex libraries were constructed consisting of 94 RILs and the two parents and sequenced on two Ion platforms. In parallel, a 96-plex library of the same RILs was sequenced on the Illumina HiSeq 2000. We applied two different computational pipelines to analyze sequencing data; the reference-independent TASSEL pipeline and a reference-based pipeline using SAMtools. Sequence contigs positioned on the integrated physical and genetic map were used for read mapping and variant calling. We found high agreement in genotype calls between the different platforms and high concordance between genetic and reference-based marker order. There was, however, paucity in the number of SNP that were jointly discovered by the different pipelines indicating a strong effect of alignment and filtering parameters on SNP discovery. We show the utility of the current barley genome assembly as a framework for developing very low-cost genetic maps, facilitating high resolution genetic mapping and negating the need for developing de novo genetic maps for future studies in barley. Through demonstration of GBS on semiconductor sequencing platforms, we conclude that the GBS approach is amenable to a range of platforms and can easily be modified as new

  14. Generation of synthetic sequences of electricity demand: Application in South Australia

    International Nuclear Information System (INIS)

    Magnano, L.; Boland, J.W.

    2007-01-01

    We have developed a model to generate synthetic sequences of half-hourly electricity demand. The generated sequences represent possible realisations of electricity load that could have occurred. Each of the components included in the model has a physical interpretation. These components are yearly and daily seasonality which were modelled using Fourier series, weekly seasonality modelled with dummy variables, and the relationship with current temperature described by polynomial functions of temperature. Finally the stochastic component was modelled with autoregressive moving average (ARMA) processes. These synthetic sequences were developed for two purposes. The first one is to use them as input data in market simulation software. The second one is to build probability distributions of the outputs to calculate probabilistic forecasts. As an application several summers of half-hourly electricity demand were generated and from them the value of demand that is not expected to be exceeded more than once in 10 years was calculated

  15. Ultrafast T2-weighted single shot spin-echo sequences: applications on abdominal and pelvic pathologies

    International Nuclear Information System (INIS)

    Martin, J.; Martin, C.; Falco, J.; Esteban, L.

    1999-01-01

    The magnetic resonance imaging (MRI) sequences that obtain all the data using a sole excitation pulse of 90 degree centigrade, filling the K space in a single repetition time (TR) is known as snap shot or single shot (SS). The SS sequence based on the rapid acquisition with relaxation enhancement (SS-RARE) method, designed by Hening (1) and a variation of it with a half-Fourier reconstruction (SS-HF-RARE (HASTEL)) (2, 3) are capable of obtaining high contrast images in T2, in very short times, that oscillate between one to several seconds. The clinical application of these sequences to abdominal and pelvic pathologies is increasing, providing and improvement in the contrast resolution, but also in the spatial resolution, with a high relation signal/noise ratio, high contrast and absence of movement artifacts. (Author)

  16. Application of native signal sequences for recombinant proteins secretion in Pichia pastoris

    DEFF Research Database (Denmark)

    Borodina, Irina; Do, Duy Duc; Eriksen, Jens C.

    Background Methylotrophic yeast Pichia pastoris is widely used for recombinant protein production, largely due to its ability to secrete correctly folded heterologous proteins to the fermentation medium. Secretion is usually achieved by cloning the recombinant gene after a leader sequence, where...... alpha‐mating factor (MF) prepropeptide from Saccharomyces cerevisiae is most commonly used. Our aim was to test whether signal peptides from P. pastoris native secreted proteins could be used to direct secretion of recombinant proteins. Results Eleven native signal peptides from P. pastoris were tested...... by optimization of expression of three different proteins in P. pastoris. Conclusions Native signal peptides from P. pastoris can be used to direct secretion of recombinant proteins. A novel USER‐based P. pastoris system allows easy cloning of protein‐coding gene with the promoter and leader sequence of choice....

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

    Directory of Open Access Journals (Sweden)

    Kareem Mohideen-Abdul

    2017-06-01

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

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

    Directory of Open Access Journals (Sweden)

    Shota Nakamura

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

  19. Application of direct digital radiography of nasal bone

    International Nuclear Information System (INIS)

    Gao Dengfa; Wang Haijun; Zhang Ailian; Wang Yulin

    2005-01-01

    Objective: To research the application value of direct digital radiograph (DDR ) in nasal bone imaging. Methods: One hundred cases were examined by DDR, 30 cases of them were examined by two methods both DDR and conventional radiography. All digital images were post-processed with 'MUSICA' (Multi-Scale Image Contrast Amplification), incision and largamente, analyzed and diagnosed by experienced two radiologists and two technicians. Results: One hundred cases of nasal bone, soft tissue of nose were showed excellent in DDR, and satisfactory cases were 95 and 92, respectively. Forty-six cases of nasal bone fractures were found. Thirty cases were examined by both DDR and conventional radiography, images of nasal bone, soft tissue of nose were showed, satisfactory cases were 28 in DDR; and satisfactory cases were 6 (χ 2 =20.05, P 2 =15.06, P 2 =5.14, P<0.05) in conventional and digital radiography, respectively. Conclusion: DDR images of nasal bone, soft tissue of nose was excellent, more fractures were discovered than conventional radiography. Image quality of DDR is better than conventional radiography in nasal bone imaging. (authors)

  20. Hybrid sequencing approach applied to human fecal metagenomic clone libraries revealed clones with potential biotechnological applications.

    Science.gov (United States)

    Džunková, Mária; D'Auria, Giuseppe; Pérez-Villarroya, David; Moya, Andrés

    2012-01-01

    Natural environments represent an incredible source of microbial genetic diversity. Discovery of novel biomolecules involves biotechnological methods that often require the design and implementation of biochemical assays to screen clone libraries. However, when an assay is applied to thousands of clones, one may eventually end up with very few positive clones which, in most of the cases, have to be "domesticated" for downstream characterization and application, and this makes screening both laborious and expensive. The negative clones, which are not considered by the selected assay, may also have biotechnological potential; however, unfortunately they would remain unexplored. Knowledge of the clone sequences provides important clues about potential biotechnological application of the clones in the library; however, the sequencing of clones one-by-one would be very time-consuming and expensive. In this study, we characterized the first metagenomic clone library from the feces of a healthy human volunteer, using a method based on 454 pyrosequencing coupled with a clone-by-clone Sanger end-sequencing. Instead of whole individual clone sequencing, we sequenced 358 clones in a pool. The medium-large insert (7-15 kb) cloning strategy allowed us to assemble these clones correctly, and to assign the clone ends to maintain the link between the position of a living clone in the library and the annotated contig from the 454 assembly. Finally, we found several open reading frames (ORFs) with previously described potential medical application. The proposed approach allows planning ad-hoc biochemical assays for the clones of interest, and the appropriate sub-cloning strategy for gene expression in suitable vectors/hosts.

  1. Hybrid sequencing approach applied to human fecal metagenomic clone libraries revealed clones with potential biotechnological applications.

    Directory of Open Access Journals (Sweden)

    Mária Džunková

    Full Text Available Natural environments represent an incredible source of microbial genetic diversity. Discovery of novel biomolecules involves biotechnological methods that often require the design and implementation of biochemical assays to screen clone libraries. However, when an assay is applied to thousands of clones, one may eventually end up with very few positive clones which, in most of the cases, have to be "domesticated" for downstream characterization and application, and this makes screening both laborious and expensive. The negative clones, which are not considered by the selected assay, may also have biotechnological potential; however, unfortunately they would remain unexplored. Knowledge of the clone sequences provides important clues about potential biotechnological application of the clones in the library; however, the sequencing of clones one-by-one would be very time-consuming and expensive. In this study, we characterized the first metagenomic clone library from the feces of a healthy human volunteer, using a method based on 454 pyrosequencing coupled with a clone-by-clone Sanger end-sequencing. Instead of whole individual clone sequencing, we sequenced 358 clones in a pool. The medium-large insert (7-15 kb cloning strategy allowed us to assemble these clones correctly, and to assign the clone ends to maintain the link between the position of a living clone in the library and the annotated contig from the 454 assembly. Finally, we found several open reading frames (ORFs with previously described potential medical application. The proposed approach allows planning ad-hoc biochemical assays for the clones of interest, and the appropriate sub-cloning strategy for gene expression in suitable vectors/hosts.

  2. Applications and challenges of next-generation sequencing in Brassica species.

    Science.gov (United States)

    Wei, Lijuan; Xiao, Meili; Hayward, Alice; Fu, Donghui

    2013-12-01

    Next-generation sequencing (NGS) produces numerous (often millions) short DNA sequence reads, typically varying between 25 and 400 bp in length, at a relatively low cost and in a short time. This revolutionary technology is being increasingly applied in whole-genome, transcriptome, epigenome and small RNA sequencing, molecular marker and gene discovery, comparative and evolutionary genomics, and association studies. The Brassica genus comprises some of the most agro-economically important crops, providing abundant vegetables, condiments, fodder, oil and medicinal products. Many Brassica species have undergone the process of polyploidization, which makes their genomes exceptionally complex and can create difficulties in genomics research. NGS injects new vigor into Brassica research, yet also faces specific challenges in the analysis of complex crop genomes and traits. In this article, we review the advantages and limitations of different NGS technologies and their applications and challenges, using Brassica as an advanced model system for agronomically important, polyploid crops. Specifically, we focus on the use of NGS for genome resequencing, transcriptome sequencing, development of single-nucleotide polymorphism markers, and identification of novel microRNAs and their targets. We present trends and advances in NGS technology in relation to Brassica crop improvement, with wide application for sophisticated genomics research into agronomically important polyploid crops.

  3. Inter frame motion estimation and its application to image sequence compression: an introduction

    International Nuclear Information System (INIS)

    Cremy, C.

    1996-01-01

    With the constant development of new communication technologies like, digital TV, teleconference, and the development of image analysis applications, there is a growing volume of data to manage. Compression techniques are required for the transmission and storage of these data. Dealing with original images would require the use of expansive high bandwidth communication devices and huge storage media. Image sequence compression can be achieved by means of interframe estimation that consists in retrieving redundant information relative to zones where there is little motion between two frames. This paper is an introduction to some motion estimation techniques like gradient techniques, pel-recursive, block-matching, and its application to image sequence compression. (Author) 17 refs

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

    Science.gov (United States)

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

    2012-01-01

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

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

    Science.gov (United States)

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

    2018-04-03

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

  6. Sequence protein identification by randomized sequence database and transcriptome mass spectrometry (SPIDER-TMS): from manual to automatic application of a 'de novo sequencing' approach.

    Science.gov (United States)

    Pascale, Raffaella; Grossi, Gerarda; Cruciani, Gabriele; Mecca, Giansalvatore; Santoro, Donatello; Sarli Calace, Renzo; Falabella, Patrizia; Bianco, Giuliana

    Sequence protein identification by a randomized sequence database and transcriptome mass spectrometry software package has been developed at the University of Basilicata in Potenza (Italy) and designed to facilitate the determination of the amino acid sequence of a peptide as well as an unequivocal identification of proteins in a high-throughput manner with enormous advantages of time, economical resource and expertise. The software package is a valid tool for the automation of a de novo sequencing approach, overcoming the main limits and a versatile platform useful in the proteomic field for an unequivocal identification of proteins, starting from tandem mass spectrometry data. The strength of this software is that it is a user-friendly and non-statistical approach, so protein identification can be considered unambiguous.

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

    Directory of Open Access Journals (Sweden)

    Ivone U. S. Leong

    2014-06-01

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

  8. Identification of coupling direction: Application to cardiorespiratory interaction

    Science.gov (United States)

    Rosenblum, Michael G.; Cimponeriu, Laura; Bezerianos, Anastasios; Patzak, Andreas; Mrowka, Ralf

    2002-04-01

    We consider the problem of experimental detection of directionality of weak coupling between two self-sustained oscillators from bivariate data. We further develop the method introduced by Rosenblum and Pikovsky [Phys. Rev. E 64, 045202 (2001)], suggesting an alternative approach. Next, we consider another framework for identification of directionality, based on the idea of mutual predictability. Our algorithms provide directionality index that shows whether the coupling between the oscillators is unidirectional or bidirectional, and quantifies the asymmetry of bidirectional coupling. We demonstrate the efficiency of three different algorithms in determination of directionality index from short and noisy data. These techniques are then applied to analysis of cardiorespiratory interaction in healthy infants. The results reveal that the direction of coupling between cardiovascular and respiratory systems varies with the age within the first 6 months of life. We find a tendency to change from nearly symmetric bidirectional interaction to nearly unidirectional one (from respiration to the cardiovascular system).

  9. [Application of next-generation semiconductor sequencing technologies in genetic diagnosis of inherited cardiomyopathies].

    Science.gov (United States)

    Zhao, Yue; Zhang, Hong; Xia, Xue-shan

    2015-07-01

    Inherited cardiomyopathy is the most common hereditary cardiac disease. It also causes a significant proportion of sudden cardiac deaths in young adults and athletes. So far, approximately one hundred genes have been reported to be involved in cardiomyopathies through different mechanisms. Therefore, the identification of the genetic basis and disease mechanisms of cardiomyopathies are important for establishing a clinical diagnosis and genetic testing. Next-generation semiconductor sequencing (NGSS) technology platform is a high-throughput sequencer capable of analyzing clinically derived genomes with high productivity, sensitivity and specificity. It was launched in 2010 by Life Technologies of USA, and it is based on a high density semiconductor chip, which was covered with tens of thousands of wells. NGSS has been successfully used in candidate gene mutation screening to identify hereditary disease. In this review, we summarize these genetic variations, challenge and application of NGSS in inherited cardiomyopathy, and its value in disease diagnosis, prevention and treatment.

  10. Genome sequence of three Psychrobacter sp. strains with potential applications in bioremediation

    Directory of Open Access Journals (Sweden)

    Aide Lasa

    2017-06-01

    Full Text Available To date, the genus Psychrobacter consists of 37 recognized species isolated from different sources, however they are more frequently found in cold and other non-polar environments of low water activity. Some strains belonging to the genus have shown different enzymatic activities with potential applications in bioremediation or food industry. In the present study, the whole genome sequences of three Psychrobacter-like strains (C 20.9, Cmf 22.2 and Rd 27.2 isolated from reared clams in Galicia (Spain are described. The sequenced genomes resulted in an assembly size of 3,143,782 bp for C 20.9 isolate, 3,168,467 bp for Cmf 22.2 isolate and 3,028,386 bp for Rd 27.2 isolate. Among the identified coding sequences of the genomes, mercury detoxification and biogeochemistry genes were found, as well as genes related to heavy metals and antibiotic resistance. Also virulence-related features were identified such as the siderophore vibrioferrin or an aerobactin-like siderophore. The phylogenetic analysis of the 16S rRNA gene suggested that these strains may represent novel species of the Psychrobacter genus. The genome sequences of the Psychrobacter sp. strains have been deposited at DDBJ/EMBL/GenBank under the accession numbers MRYA00000000 (Cmf 22.2, MRYB00000000 (Rd 27.2 and MRYC00000000 (C 20.9, and the sequences could be found at the site https://www.ncbi.nlm.nih.gov/bioproject/PRJNA353858.

  11. Application of Sequence-based Methods in Human MicrobialEcology

    Energy Technology Data Exchange (ETDEWEB)

    Weng, Li; Rubin, Edward M.; Bristow, James

    2005-08-29

    Ecologists studying microbial life in the environment have recognized the enormous complexity of microbial diversity for many years, and the development of a variety of culture-independent methods, many of them coupled with high-throughput DNA sequencing, has allowed this diversity to be explored in ever greater detail. Despite the widespread application of these new techniques to the characterization of uncultivated microbes and microbial communities in the environment, their application to human health and disease has lagged behind. Because DNA based-techniques for defining uncultured microbes allow not only cataloging of microbial diversity, but also insight into microbial functions, investigators are beginning to apply these tools to the microbial communities that abound on and within us, in what has aptly been called the second Human Genome Project. In this review we discuss the sequence-based methods for microbial analysis that are currently available and their application to identify novel human pathogens, improve diagnosis of known infectious diseases, and to advance understanding of our relationship with microbial communities that normally reside in and on the human body.

  12. Physically unclonable functions (PUFs) applications, models, and future directions

    CERN Document Server

    Wachsmann, Christian

    2014-01-01

    Today, embedded systems are used in many security-critical applications, from access control, electronic tickets, sensors, and smart devices (e.g., wearables) to automotive applications and critical infrastructures. These systems are increasingly used to produce and process both security-critical and privacy-sensitive data, which bear many security and privacy risks. Establishing trust in the underlying devices and making them resistant to software and hardware attacks is a fundamental requirement in many applications and a challenging, yet unsolved, task. Solutions solely based on software ca

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

    Science.gov (United States)

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

    2014-01-01

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

  14. Direct Deposit Applications filed via the Internet - FY 2016 (53rd week)

    Data.gov (United States)

    Social Security Administration — This dataset provides monthly volumes at the national level from federal fiscal year 2016 for Internet Direct Deposit applications. This dataset includes data from...

  15. Direct energy conversion for IEC fusion for space applications

    International Nuclear Information System (INIS)

    Momota, Hiromu; Nadler, Jon; Miley, George H.

    2000-08-01

    The paper describes a concept of extracting fusion power from D- 3 He fueled IEC (Inertia Electrostatic Configuration) devices. The fusion system consists of a series of fusion modules and direct energy converters at an end or at both ends. This system of multiple units is linear and is connected by a magnetic field. A pair of coils anti-parallel to the magnetic field yields a field-null domain at the center of each unit as required for IEC operation. A stabilizing coil installed between the coil pairs eliminates the strong attractive force between the anti-parallel coils. Accessible regions for charged particle trajectories are essentially isolated from the coil structure. Thus, charged particles are directed along magnetic field lines to the direct energy converter without appreciable losses. A direct energy converter unit designed to be compatible to this unique system is also described. It basically consists of a separator and a traveling wave converter. A separator separates low energy ions and electron from the 14.7 MeV fusion protons and then converts their energy into electricity. In the traveling wave direct energy converter, fusion protons are modulated to form bunches. It couples with a transmission line to couple AC power out. The overall conversion efficiency of this system, combined with E- 3 He IEC cores, is estimated as high as 60%. (author)

  16. Direct energy conversion for IEC fusion for space applications

    Energy Technology Data Exchange (ETDEWEB)

    Momota, Hiromu; Nadler, Jon [National Inst. for Fusion Science, Toki, Gifu (Japan); Miley, George H. [Fusion Studies Laboratory, Urbana, IL (United States)

    2000-08-01

    The paper describes a concept of extracting fusion power from D-{sup 3}He fueled IEC (Inertia Electrostatic Configuration) devices. The fusion system consists of a series of fusion modules and direct energy converters at an end or at both ends. This system of multiple units is linear and is connected by a magnetic field. A pair of coils anti-parallel to the magnetic field yields a field-null domain at the center of each unit as required for IEC operation. A stabilizing coil installed between the coil pairs eliminates the strong attractive force between the anti-parallel coils. Accessible regions for charged particle trajectories are essentially isolated from the coil structure. Thus, charged particles are directed along magnetic field lines to the direct energy converter without appreciable losses. A direct energy converter unit designed to be compatible to this unique system is also described. It basically consists of a separator and a traveling wave converter. A separator separates low energy ions and electron from the 14.7 MeV fusion protons and then converts their energy into electricity. In the traveling wave direct energy converter, fusion protons are modulated to form bunches. It couples with a transmission line to couple AC power out. The overall conversion efficiency of this system, combined with E-{sup 3}He IEC cores, is estimated as high as 60%. (author)

  17. EXTENDE MODEL OF COMPETITIVITY THROUG APPLICATION OF NEW APPROACH DIRECTIVES

    Directory of Open Access Journals (Sweden)

    Slavko Arsovski

    2009-03-01

    Full Text Available The basic subject of this work is the model of new approach impact on quality and safety products, and competency of our companies. This work represents real hypothesis on the basis of expert's experiences, in regard to that the infrastructure with using new approach directives wasn't examined until now, it isn't known which product or industry of Serbia is related to directives of the new approach and CE mark, and it is not known which are effects of the use of the CE mark. This work should indicate existing quality reserves and product's safety, the level of possible competency improvement and increasing the profit by discharging new approach directive requires.

  18. Direct liquid content measurement applicable for He II space cryostats

    International Nuclear Information System (INIS)

    Wanner, M.

    1988-01-01

    A direct calorimetric method for content measurement in the He II cryostat ISO was assessed. A well defined heat pulse into the He II bath causes a small temperature increase which can be measured and directly correlated to the liquid mass through the He II specific heat. To study this method under the potential zero gravity constraints of disconnected liquid volumes a setup was established for investigating heat transfer between separated liquid volumes. The results for different fluid configurations confirm that even for completely disconnected volumes the heat is almost immediately distributed throughout the whole liquid by evaporation and recondensation

  19. Application of GIS in foreign direct investment decision support system

    Science.gov (United States)

    Zhou, Jianlan; Sun, Koumei

    2007-06-01

    It is important to make decisions on how to attract foreign direct investment (FDI) to China and know how the inequality of FDI introduction by locational different provinces. Following background descriptions on China's FDI economic environments and FDI-related policies, this paper demonstrates the uses of geographical information system (GIS) and multi-criterion decision-making (MCDM) framework in solving a spatial multi-objective problem of evaluating and ranking China's provinces for FDI introduction. It implements a foreign direct investment decision support system, which reveals the main determinants of FDI in China and gives some results of regional geographical analysis over spatial data.

  20. On the Farey sequence and its augmentation for applications to image analysis

    Directory of Open Access Journals (Sweden)

    Pratihar Sanjoy

    2017-09-01

    Full Text Available We introduce a novel concept of the augmented Farey table (AFT. Its purpose is to store the ranks of fractions of a Farey sequence in an efficient manner so as to return the rank of any query fraction in constant time. As a result, computations on the digital plane can be crafted down to simple integer operations; for example, the tasks like determining the extent of collinearity of integer points or of parallelism of straight lines—often required to solve many image-analytic problems—can be made fast and efficient through an appropriate AFT-based tool. We derive certain interesting characterizations of an AFT for its efficient generation. We also show how, for a fraction not present in a Farey sequence, the rank of the nearest fraction in that sequence can efficiently be obtained by the regula falsi method from the AFT concerned. To assert its merit, we show its use in two applications—one in polygonal approximation of digital curves and the other in skew correction of engineering drawings in document images. Experimental results indicate the potential of the AFT in such image-analytic applications.

  1. Reprint of "Application of next generation sequencing in clinical microbiology and infection prevention".

    Science.gov (United States)

    Deurenberg, Ruud H; Bathoorn, Erik; Chlebowicz, Monika A; Couto, Natacha; Ferdous, Mithila; García-Cobos, Silvia; Kooistra-Smid, Anna M D; Raangs, Erwin C; Rosema, Sigrid; Veloo, Alida C M; Zhou, Kai; Friedrich, Alexander W; Rossen, John W A

    2017-05-20

    Current molecular diagnostics of human pathogens provide limited information that is often not sufficient for outbreak and transmission investigation. Next generation sequencing (NGS) determines the DNA sequence of a complete bacterial genome in a single sequence run, and from these data, information on resistance and virulence, as well as information for typing is obtained, useful for outbreak investigation. The obtained genome data can be further used for the development of an outbreak-specific screening test. In this review, a general introduction to NGS is presented, including the library preparation and the major characteristics of the most common NGS platforms, such as the MiSeq (Illumina) and the Ion PGM™ (ThermoFisher). An overview of the software used for NGS data analyses used at the medical microbiology diagnostic laboratory in the University Medical Center Groningen in The Netherlands is given. Furthermore, applications of NGS in the clinical setting are described, such as outbreak management, molecular case finding, characterization and surveillance of pathogens, rapid identification of bacteria using the 16S-23S rRNA region, taxonomy, metagenomics approaches on clinical samples, and the determination of the transmission of zoonotic micro-organisms from animals to humans. Finally, we share our vision on the use of NGS in personalised microbiology in the near future, pointing out specific requirements. Copyright © 2017. Published by Elsevier B.V.

  2. Application of next generation sequencing in clinical microbiology and infection prevention.

    Science.gov (United States)

    Deurenberg, Ruud H; Bathoorn, Erik; Chlebowicz, Monika A; Couto, Natacha; Ferdous, Mithila; García-Cobos, Silvia; Kooistra-Smid, Anna M D; Raangs, Erwin C; Rosema, Sigrid; Veloo, Alida C M; Zhou, Kai; Friedrich, Alexander W; Rossen, John W A

    2017-02-10

    Current molecular diagnostics of human pathogens provide limited information that is often not sufficient for outbreak and transmission investigation. Next generation sequencing (NGS) determines the DNA sequence of a complete bacterial genome in a single sequence run, and from these data, information on resistance and virulence, as well as information for typing is obtained, useful for outbreak investigation. The obtained genome data can be further used for the development of an outbreak-specific screening test. In this review, a general introduction to NGS is presented, including the library preparation and the major characteristics of the most common NGS platforms, such as the MiSeq (Illumina) and the Ion PGM™ (ThermoFisher). An overview of the software used for NGS data analyses used at the medical microbiology diagnostic laboratory in the University Medical Center Groningen in The Netherlands is given. Furthermore, applications of NGS in the clinical setting are described, such as outbreak management, molecular case finding, characterization and surveillance of pathogens, rapid identification of bacteria using the 16S-23S rRNA region, taxonomy, metagenomics approaches on clinical samples, and the determination of the transmission of zoonotic micro-organisms from animals to humans. Finally, we share our vision on the use of NGS in personalised microbiology in the near future, pointing out specific requirements. Copyright © 2016 The Author(s). Published by Elsevier B.V. All rights reserved.

  3. Application of HPCN to direct numerical simulation of turbulent flow

    NARCIS (Netherlands)

    Verstappen, RWCP; Veldman, AEP; van Waveren, GM; Hertzberger, B; Sloot, P

    1997-01-01

    This poster shows how HPCN can be used as a path-finding tool for turbulence research. The parallelization of direct numerical simulation of turbulent flow using the data-parallel model and Fortran 95 constructs is treated, both on a shared memory and a distributed memory computer.

  4. Future directions for ferritic/martensitic steels for nuclear applications

    International Nuclear Information System (INIS)

    Klueh, R.L.; Swindeman, R.W.

    2000-01-01

    High-chromium (7-12% Cr) ferritic/martensitic steels are being considered for nuclear applications for both fission and fusion reactors. Conventional 9-12Cr Cr-Mo steels were the first candidates for these applications. For fusion reactors, reduced-activation steels were developed that were patterned on the conventional steels but with molybdenum replaced by tungsten and niobium replaced by tantalum. Both the conventional and reduced-activation steels are considered to have an upper operating temperature limit of about 550degC. For improved reactor efficiency, higher operating temperatures are required. For ferritic/martensitic steels that could meet such requirements, oxide dispersion-strengthened (ODS) steels are being considered. In this paper, the ferritic/martensitic steels that are candidate steels for nuclear applications will be reviewed, the prospect for ODS steel development and the development of steels produced by conventional processes will be discussed. (author)

  5. On avoided words, absent words, and their application to biological sequence analysis.

    Science.gov (United States)

    Almirantis, Yannis; Charalampopoulos, Panagiotis; Gao, Jia; Iliopoulos, Costas S; Mohamed, Manal; Pissis, Solon P; Polychronopoulos, Dimitris

    2017-01-01

    The deviation of the observed frequency of a word w from its expected frequency in a given sequence x is used to determine whether or not the word is avoided . This concept is particularly useful in DNA linguistic analysis. The value of the deviation of w , denoted by [Formula: see text], effectively characterises the extent of a word by its edge contrast in the context in which it occurs. A word w of length [Formula: see text] is a [Formula: see text]-avoided word in x if [Formula: see text], for a given threshold [Formula: see text]. Notice that such a word may be completely absent from x . Hence, computing all such words naïvely can be a very time-consuming procedure, in particular for large k . In this article, we propose an [Formula: see text]-time and [Formula: see text]-space algorithm to compute all [Formula: see text]-avoided words of length k in a given sequence of length n over a fixed-sized alphabet. We also present a time-optimal [Formula: see text]-time algorithm to compute all [Formula: see text]-avoided words (of any length) in a sequence of length n over an integer alphabet of size [Formula: see text]. In addition, we provide a tight asymptotic upper bound for the number of [Formula: see text]-avoided words over an integer alphabet and the expected length of the longest one. We make available an implementation of our algorithm. Experimental results, using both real and synthetic data, show the efficiency and applicability of our implementation in biological sequence analysis. The systematic search for avoided words is particularly useful for biological sequence analysis. We present a linear-time and linear-space algorithm for the computation of avoided words of length k in a given sequence x . We suggest a modification to this algorithm so that it computes all avoided words of x , irrespective of their length, within the same time complexity. We also present combinatorial results with regards to avoided words and absent words.

  6. Application of the accident management information needs methodology to a severe accident sequence

    International Nuclear Information System (INIS)

    Ward, L.W.; Hanson, D.J.; Nelson, W.R.; Solberg, D.E.

    1989-01-01

    The U.S. Nuclear Regulatory Commission (NRC) is conducting an Accident Management Research Program that emphasizes the application of severe accident research results to enhance the capability of plant operating personnel to effectively manage severe accidents. A methodology to identify and assess the information needs of the operating staff of a nuclear power plant during a severe accident has been developed as part of the research program designed to resolve this issue. The methodology identifies the information needs of the plant personnel during a wide range of accident conditions, the existing plant measurements capable of supplying these information needs and what, if any minor additions to instrument and display systems would enhance the capability to manage accidents, known limitations on the capability of these measurements to function properly under the conditions that will be present during a wide range of severe accidents, and areas in which the information systems could mislead plant personnel. This paper presents an application of this methodology to a severe accident sequence to demonstrate its use in identifying the information which is available for management of the event. The methodology has been applied to a severe accident sequence in a Pressurized Water Reactor with a large dry containment. An examination of the capability of the existing measurements was then performed to determine whether the information needs can be supplied

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

    International Nuclear Information System (INIS)

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

    2007-01-01

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

  8. Potential energy savings by using direct current for residential applications

    DEFF Research Database (Denmark)

    Diaz, Enrique Rodriguez; Quintero, Juan Carlos Vasquez; Guerrero, Josep M.

    2017-01-01

    improvement in the power converter units. However, for residential applications, the efficiency is not always improved. A grid connected residential microgrid, with renewable energy sources (RES), energy storage systems (ESS) and local loads, is presented in this work. The microgrid has been modelled...

  9. Application of ring lasers to determine the directions to the poles of Earth's rotation

    International Nuclear Information System (INIS)

    Golyaev, Yu D; Kolbas, Yu Yu

    2012-01-01

    Application of a ring laser to determine the directions to the poles of Earth's rotation is considered. The maximum accuracy of determining the directions is calculated, physical and technical mechanisms that limit the accuracy are analysed, and the instrumental errors are estimated by the example of ring He — Ne lasers with Zeeman biasing. (laser applications and other topics in quantum electronics)

  10. The development of lasers at the CEA Military Applications Direction

    International Nuclear Information System (INIS)

    Coutant, J.

    1997-01-01

    A historical review of the development of lasers and their application at the CEA to the study of plasma inertial confinement in the framework of military applications, is presented. The first solid laser was a ruby laser, and has been used for studying laser-matter interaction, which led to a better knowledge of fusion plasmas. Advancements were achieved with a new lasing medium (neodymium doped glass), the control of pulse duration and shape, parallel setting of several laser chains (OCTAL), the use of glass disks instead of bars (PHEBUS laser)... In the late 70's, power lasers reached the power needed to experiment D-T implosions and give the way to future simulations of the plasma conditions encountered in thermonuclear explosions

  11. SU-E-J-207: Effect of Pulse Sequence Parameters On Geometric Distortions Induced by a Titanium Brachytherapy Applicator

    International Nuclear Information System (INIS)

    Shea, S; Diak, A; Surucu, M; Harkenrider, M; Yacoub, J; Roeske, J; Small, W

    2015-01-01

    Purpose: To investigate the effect of readout bandwidth and voxel size on the appearance of distortion artifacts caused by a titanium brachytherapy applicator. Methods: An acrylic phantom was constructed to rigidly hold a MR conditional, titanium Fletcher-Suit-Delclos-style applicator set (Varian Medical Systems) for imaging on CT (Philips Brilliance) and 1.5T MRI (Siemens Magnetom Aera). Several variants of MRI parameters were tried for 2D T2-weighted turbo spin echo imaging in comparison against the standard clinical protocol with the criteria to keep relative SNR loss less than 20% and imaging time as short as possible. Two 3D sequences were also used for comparison with similar parameters. The applicator tandem was segmented on axial CT images (0.4×0.4×1.5mm 3 resolution) and the CT images were registered to the 3D MR images in Eclipse (Varian). The applicator volume was then overlaid on all MRI sets in 3D-Slicer and distances were measured from the tandem tip to the MRI artifact edge in right/left/superior and anterior/posterior/superior directions from coronal and sagittal 2D acquisitions, respectively, or 3D data reformats. Artifact regions were also manually contoured in coronal/sagittal orientations for area measurements. Results: As would be expected, reductions in voxel size and increases in readout bandwidth reduced artifact size (average max artifact length decreased by 0.95 mm and average max area decrease by 0.27 cm 2 ). Interestingly, bandwidth increases yielded reductions in area (0.19 cm 2 ) and in distance measurements (1 mm) even with voxel increases, as compared to a standard protocol. This could be useful when high performance protocols are not feasible due to long imaging times. Conclusion: We have characterized artifacts caused by cervical brachytherapy applicator across multiple sequence parameters at 1.5T. Future work will focus on finalizing an optimal protocol that balances artifact reduction with imaging time and then testing this new

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

    Science.gov (United States)

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

    2014-04-09

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

  13. Direct model reference adaptive control with application to flexible robots

    Science.gov (United States)

    Steinvorth, Rodrigo; Kaufman, Howard; Neat, Gregory W.

    1992-01-01

    A modification to a direct command generator tracker-based model reference adaptive control (MRAC) system is suggested in this paper. This modification incorporates a feedforward into the reference model's output as well as the plant's output. Its purpose is to eliminate the bounded model following error present in steady state when previous MRAC systems were used. The algorithm was evaluated using the dynamics for a single-link flexible-joint arm. The results of these simulations show a response with zero steady state model following error. These results encourage further use of MRAC for various types of nonlinear plants.

  14. Bi-Directional DC-DC Converter for PHEV Applications

    Energy Technology Data Exchange (ETDEWEB)

    Abas Goodarzi

    2011-01-31

    Plug-In Hybrid Electric Vehicles (PHEV) require high power density energy storage system (ESS) for hybrid operation and high energy density ESS for Electric Vehicle (EV) mode range. However, ESS technologies to maximize power density and energy density simultaneously are not commercially feasible. The use of bi-directional DC-DC converter allows use of multiple energy storage, and the flexible DC-link voltages can enhance the system efficiency and reduce component sizing. This will improve fuel consumption, increase the EV mode range, reduce the total weight, reduce battery initial and life cycle cost, and provide flexibility in system design.

  15. Horizontal Directional Drilling (HDD) for shore approach applications

    Energy Technology Data Exchange (ETDEWEB)

    Smith, Neil [MGI do Brasil Ltda., Rio de Janeiro, RJ (Brazil)

    2003-07-01

    Horizontal directional drilling (HDD) has become a commonly used construction method for pipeline shore approaches. HDD can mitigate environmental impact, provide greater burial depths and minimize construction schedules. The risks that are associated with HDD river crossings, which are generally well recognized, also apply to HDD shore approaches where they are combined with specific risks occurring from working in the marine environment. The shore approach projects of The Bronx and Hunts Point provide good practical examples of the benefits of this technology in spite of the various challenges encountered. (author)

  16. Direct Tax Applications in Relationship Between European Union and Turkey

    OpenAIRE

    YAZARKAN, Hakan; MEZARARKALI, Pınar

    2015-01-01

    European Union (EU) is an economic union that exstipulates common tax policy within the union without interfering the taxes which collected by the members. On the other hand union doesn’t put tax systems of member states to harmonization but has a positive look on efforts convergence. The reason of this is the difference between international tax ratio causes limiting even hindering the capital activities. Turkey which made an application at 31st of July 1959 still can’t become member of EU. ...

  17. Supply chain management models, applications, and research directions

    CERN Document Server

    Pardalos, Panos; Romeijn, H

    2005-01-01

    This work brings together some of the most up to date research in the application of operations research and mathematical modeling te- niques to problems arising in supply chain management and e-Commerce. While research in the broad area of supply chain management enc- passes a wide range of topics and methodologies, we believe this book provides a good snapshot of current quantitative modeling approaches, issues, and trends within the field. Each chapter is a self-contained study of a timely and relevant research problem in supply chain mana- ment. The individual works place a heavy emphasis on the application of modeling techniques to real world management problems. In many instances, the actual results from applying these techniques in practice are highlighted. In addition, each chapter provides important mana- rial insights that apply to general supply chain management practice. The book is divided into three parts. The first part contains ch- ters that address the new and rapidly growing role of the inte...

  18. Graphene directed architecture of fine engineered nanostructures with electrochemical applications

    DEFF Research Database (Denmark)

    Hou, Chengyi; Zhang, Minwei; Halder, Arnab

    2017-01-01

    , and polymers has led to the possibility to create new electroactive and multifunctional nanostructures, which can serve as promising material platforms for electrochemical purposes. However, the precise control and fine-tuning of material structures and properties are still challenging and in demand...... classified nanostructures, including metallic nanostructures, self-assembled organic and supramolecular structures, and fine engineered metal oxides. In these cases, graphene templates either sacrificed during templating synthesis or retained as support for final products. We also discuss remained challenges....... In this review, we aim to highlight some recent efforts devoted to rational design, assembly and fine engineering of electrochemically active nanostructures using graphene or/and its derivatives as soft templates for controlled synthesis and directed growth. We organize the contents according to the chemically...

  19. Performance evaluation of direct methanol fuel cells for portable applications

    Energy Technology Data Exchange (ETDEWEB)

    Rashidi, R.; Dincer, I.; Naterer, G.F. [Faculty of Engineering and Applied Science, University of Ontario Institute of Technology, 2000 Simcoe Street North, Oshawa, Ontario (Canada); Berg, P. [Faculty of Science, University of Ontario Institute of Technology, 2000 Simcoe Street North, Oshawa, Ontario (Canada)

    2009-02-15

    This study examines the feasibility of powering a range of portable devices with a direct methanol fuel cell (DMFC). The analysis includes a comparison between a Li-ion battery and DMFC to supply the power for a laptop, camcorder and a cell phone. A parametric study of the systems for an operational period of 4 years is performed. Under the assumptions made for both the Li-ion battery and DMFC system, the battery cost is lower than the DMFC during the first year of operation. However, by the end of 4 years of operational time, the DMFC system would cost less. The weight and cost comparisons show that the fuel cell system occupies less space than the battery to store a higher amount of energy. The weight of both systems is almost identical. Finally, the CO{sub 2} emissions can be decreased by a higher exergetic efficiency of the DMFC, which leads to improved sustainability. (author)

  20. Neutron spectrometry for reactor applications: status, limitations, and future directions

    International Nuclear Information System (INIS)

    Gold, R.

    1975-08-01

    The ability of ''state-of-the-art'' reactor neutron spectrometry to provide definitive environmental results required for high fluence radiation damage experiments is reviewed. A formal definition of the neutron component is presented as well as general considerations which accrue from both this definition and the existence of the mixed radiation field generally encountered in reactors. A description of four selected methods of reactor neutron spectrometry is included, namely Proton Recoil (PR) methods, Time-Of-Flight (TOF) methods, the 6 Li(n,α) 3 H coincidence method, and Multiple Foil Activation (MFA) methods. These selected methods are compared. Future requirements and directions for reactor neutron spectrometry are discussed. In particular, the needs of future CTR research are stressed and the He 4 - recoil proportional counter spectroscopy method is advanced as a means of meeting these future requirements. 50 references. (auth)

  1. Galaxy tools and workflows for sequence analysis with applications in molecular plant pathology.

    Science.gov (United States)

    Cock, Peter J A; Grüning, Björn A; Paszkiewicz, Konrad; Pritchard, Leighton

    2013-01-01

    The Galaxy Project offers the popular web browser-based platform Galaxy for running bioinformatics tools and constructing simple workflows. Here, we present a broad collection of additional Galaxy tools for large scale analysis of gene and protein sequences. The motivating research theme is the identification of specific genes of interest in a range of non-model organisms, and our central example is the identification and prediction of "effector" proteins produced by plant pathogens in order to manipulate their host plant. This functional annotation of a pathogen's predicted capacity for virulence is a key step in translating sequence data into potential applications in plant pathology. This collection includes novel tools, and widely-used third-party tools such as NCBI BLAST+ wrapped for use within Galaxy. Individual bioinformatics software tools are typically available separately as standalone packages, or in online browser-based form. The Galaxy framework enables the user to combine these and other tools to automate organism scale analyses as workflows, without demanding familiarity with command line tools and scripting. Workflows created using Galaxy can be saved and are reusable, so may be distributed within and between research groups, facilitating the construction of a set of standardised, reusable bioinformatic protocols. The Galaxy tools and workflows described in this manuscript are open source and freely available from the Galaxy Tool Shed (http://usegalaxy.org/toolshed or http://toolshed.g2.bx.psu.edu).

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

    Science.gov (United States)

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

    2016-10-13

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

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

    DEFF Research Database (Denmark)

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

    2015-01-01

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

  4. Single-Cell Whole-Genome Amplification and Sequencing: Methodology and Applications.

    Science.gov (United States)

    Huang, Lei; Ma, Fei; Chapman, Alec; Lu, Sijia; Xie, Xiaoliang Sunney

    2015-01-01

    We present a survey of single-cell whole-genome amplification (WGA) methods, including degenerate oligonucleotide-primed polymerase chain reaction (DOP-PCR), multiple displacement amplification (MDA), and multiple annealing and looping-based amplification cycles (MALBAC). The key parameters to characterize the performance of these methods are defined, including genome coverage, uniformity, reproducibility, unmappable rates, chimera rates, allele dropout rates, false positive rates for calling single-nucleotide variations, and ability to call copy-number variations. Using these parameters, we compare five commercial WGA kits by performing deep sequencing of multiple single cells. We also discuss several major applications of single-cell genomics, including studies of whole-genome de novo mutation rates, the early evolution of cancer genomes, circulating tumor cells (CTCs), meiotic recombination of germ cells, preimplantation genetic diagnosis (PGD), and preimplantation genomic screening (PGS) for in vitro-fertilized embryos.

  5. Zero sequence blocking transformers for multi-pulse rectifier in aerospace applications

    DEFF Research Database (Denmark)

    Yao, Wenli; Blaabjerg, Frede; Zhang, Xiaobin

    2014-01-01

    The power electronics technology plays an even more important role in the aerospace applications of More Electric Aircrafts (MEA). AutoTransformer Rectifier Units (ATRU) have been widely adopted in aircrafts due to its simplicity and reliability. In this paper, Zero Sequence Blocking Transformers...... (ZSBT) are employed in the DC link to realize parallel rectifier bridges for ATRU, being the proposed 24-pulse rectifier. A star-connected autotransformer is used in this topology to divide the primary side voltage into four three-phase voltage groups, among which there is a phase shift of 15......°. The autotransformer then feeds the load through rectifier bridges, which are in parallel with ZSBTs. Compared to the traditional method that is using six interphase transformers to parallel the rectifier bridges; the proposed 24-pulse rectifier only requires four ZSBTs. This will contribute to a reduction of weight...

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

    Science.gov (United States)

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

    2005-12-01

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

  7. WEEE directive application: vitrification of e-waste

    International Nuclear Information System (INIS)

    Silva, A.C.; Pidone, L.; Mello-Castanho, S.R.H.

    2011-01-01

    The aim of the WEEE directive is the electrical and electronic equipment waste (e-waste) mitigation and reduce life-cycle-end environmental impact of the this kind of equipment. Currently applied to electrical and electronic equipment manufacturers and distributors in European Union, it's Pigovian principle based, where the person that place potentially polluting products at the environment, is also legal and financial responsible for the resultant life-cycle-end pollution. This policy is a worldwide trend, and implies a growing demand in the search for new proper waste disposal technological solutions. In this context of broad spectrum, are also entered the medical equipment that make use of electronic devices. This study aims to obtain glasses which can be used as a product of commercial value containing up to 40% by mass of hospital apparatus e-waste. The residues were previously crushed and calcined. Copper and iron aventurine glass were prepared through the modification of the basic composition of soda-lime-borosilicate glass. After the melting temperature of 1300°C, the glasses were characterized by FT-IR and XRD. The chemical stability was evaluated by hydrolytic attack test. The glasses showed a high chemistry and environmental stability, like commercial soda-lime glass, in addition the obtained material present attractive appearance, allowing its use in decoration or architecture products. (author)

  8. Organic Rankine cycle - review and research directions in engine applications

    Science.gov (United States)

    Panesar, Angad

    2017-11-01

    Waste heat to power conversion using Organic Rankine Cycles (ORC) is expected to play an important role in CO2 reductions from diesel engines. Firstly, a review of automotive ORCs is presented focusing on the pure working fluids, thermal architectures and expanders. The discussion includes, but is not limited to: R245fa, ethanol and water as fluids; series, parallel and cascade as architectures; dry saturated, superheated and supercritical as expansion conditions; and scroll, radial turbine and piston as expansion machines. Secondly, research direction in versatile expander and holistic architecture (NOx + CO2) are proposed. Benefits of using the proposed unconventional approaches are quantified using Ricardo Wave and Aspen HYSYS for diesel engine and ORC modelling. Results indicate that, the implementation of versatile piston expander tolerant to two-phase and using cyclopentane can potentially increase the highway drive cycle power by 8%. Furthermore, holistic architecture offering complete utilisation of charge air and exhaust recirculation heat increased the performance noticeably to 5% of engine power at the design point condition.

  9. Application of whole genome shotgun sequencing for detection and characterization of genetically modified organisms and derived products.

    Science.gov (United States)

    Holst-Jensen, Arne; Spilsberg, Bjørn; Arulandhu, Alfred J; Kok, Esther; Shi, Jianxin; Zel, Jana

    2016-07-01

    The emergence of high-throughput, massive or next-generation sequencing technologies has created a completely new foundation for molecular analyses. Various selective enrichment processes are commonly applied to facilitate detection of predefined (known) targets. Such approaches, however, inevitably introduce a bias and are prone to miss unknown targets. Here we review the application of high-throughput sequencing technologies and the preparation of fit-for-purpose whole genome shotgun sequencing libraries for the detection and characterization of genetically modified and derived products. The potential impact of these new sequencing technologies for the characterization, breeding selection, risk assessment, and traceability of genetically modified organisms and genetically modified products is yet to be fully acknowledged. The published literature is reviewed, and the prospects for future developments and use of the new sequencing technologies for these purposes are discussed.

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

    OpenAIRE

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

    2017-01-01

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

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

    Science.gov (United States)

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

    2017-07-06

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

  12. Direct microcontact printing of oligonucleotides for biochip applications

    Directory of Open Access Journals (Sweden)

    Trévisiol E

    2005-07-01

    Full Text Available Abstract Background A critical step in the fabrication of biochips is the controlled placement of probes molecules on solid surfaces. This is currently performed by sequential deposition of probes on a target surface with split or solid pins. In this article, we present a cost-effective procedure namely microcontact printing using stamps, for a parallel deposition of probes applicable for manufacturing biochips. Results Contrary to a previous work, we showed that the stamps tailored with an elastomeric poly(dimethylsiloxane material did not require any surface modification to be able to adsorb oligonucleotides or PCR products. The adsorbed DNA molecules are subsequently printed efficiently on a target surface with high sub-micron resolution. Secondly, we showed that successive stamping is characterized by an exponential decay of the amount of transferred DNA molecules to the surface up the 4th print, then followed by a second regime of transfer that was dependent on the contact time and which resulted in reduced quality of the features. Thus, while consecutive stamping was possible, this procedure turned out to be less reproducible and more time consuming than simply re-inking the stamps between each print. Thirdly, we showed that the hybridization signals on arrays made by microcontact printing were 5 to 10-times higher than those made by conventional spotting methods. Finally, we demonstrated the validity of this microcontact printing method in manufacturing oligonucleotides arrays for mutations recognition in a yeast gene. Conclusion The microcontact printing can be considered as a new potential technology platform to pattern DNA microarrays that may have significant advantages over the conventional spotting technologies as it is easy to implement, it uses low cost material to make the stamp, and the arrays made by this technology are 10-times more sensitive in term of hybridization signals than those manufactured by conventional spotting

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

    Directory of Open Access Journals (Sweden)

    Daniela Maneg

    2016-01-01

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

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

    Science.gov (United States)

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

    2016-01-01

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

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

    Directory of Open Access Journals (Sweden)

    Stafford Phillip

    2009-09-01

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

  16. A DNA Structure-Based Bionic Wavelet Transform and Its Application to DNA Sequence Analysis

    Directory of Open Access Journals (Sweden)

    Fei Chen

    2003-01-01

    Full Text Available DNA sequence analysis is of great significance for increasing our understanding of genomic functions. An important task facing us is the exploration of hidden structural information stored in the DNA sequence. This paper introduces a DNA structure-based adaptive wavelet transform (WT – the bionic wavelet transform (BWT – for DNA sequence analysis. The symbolic DNA sequence can be separated into four channels of indicator sequences. An adaptive symbol-to-number mapping, determined from the structural feature of the DNA sequence, was introduced into WT. It can adjust the weight value of each channel to maximise the useful energy distribution of the whole BWT output. The performance of the proposed BWT was examined by analysing synthetic and real DNA sequences. Results show that BWT performs better than traditional WT in presenting greater energy distribution. This new BWT method should be useful for the detection of the latent structural features in future DNA sequence analysis.

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

    International Nuclear Information System (INIS)

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

    2015-01-01

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

  18. Application of small RNA sequencing to identify microRNAs in acute kidney injury and fibrosis

    Energy Technology Data Exchange (ETDEWEB)

    Pellegrini, Kathryn L. [Department of Medicine, Renal Division, Brigham and Women' s Hospital, Harvard Medical School, Boston, MA (United States); Gerlach, Cory V. [Department of Medicine, Renal Division, Brigham and Women' s Hospital, Harvard Medical School, Boston, MA (United States); Department of Environmental Health, Harvard T.H. Chan School of Public Health, Boston, MA (United States); Laboratory of Systems Pharmacology, Harvard Program in Therapeutic Sciences, Harvard Medical School, Boston, MA (United States); Craciun, Florin L.; Ramachandran, Krithika [Department of Medicine, Renal Division, Brigham and Women' s Hospital, Harvard Medical School, Boston, MA (United States); Bijol, Vanesa [Department of Pathology, Brigham and Women' s Hospital, Harvard Medical School, Boston, MA (United States); Kissick, Haydn T. [Department of Surgery, Urology Division, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA (United States); Vaidya, Vishal S., E-mail: vvaidya@bwh.harvard.edu [Department of Medicine, Renal Division, Brigham and Women' s Hospital, Harvard Medical School, Boston, MA (United States); Department of Environmental Health, Harvard T.H. Chan School of Public Health, Boston, MA (United States); Laboratory of Systems Pharmacology, Harvard Program in Therapeutic Sciences, Harvard Medical School, Boston, MA (United States)

    2016-12-01

    Establishing a microRNA (miRNA) expression profile in affected tissues provides an important foundation for the discovery of miRNAs involved in the development or progression of pathologic conditions. We conducted small RNA sequencing to generate a temporal profile of miRNA expression in the kidneys using a mouse model of folic acid-induced (250 mg/kg i.p.) kidney injury and fibrosis. From the 103 miRNAs that were differentially expressed over the time course (> 2-fold, p < 0.05), we chose to further investigate miR-18a-5p, which is expressed during the acute stage of the injury; miR-132-3p, which is upregulated during transition between acute and fibrotic injury; and miR-146b-5p, which is highly expressed at the peak of fibrosis. Using qRT-PCR, we confirmed the increased expression of these candidate miRNAs in the folic acid model as well as in other established mouse models of acute injury (ischemia/reperfusion injury) and fibrosis (unilateral ureteral obstruction). In situ hybridization confirmed high expression of miR-18a-5p, miR-132-3p and miR-146b-5p throughout the kidney cortex in mice and humans with severe kidney injury or fibrosis. When primary human proximal tubular epithelial cells were treated with model nephrotoxicants such as cadmium chloride (CdCl{sub 2}), arsenic trioxide, aristolochic acid (AA), potassium dichromate (K{sub 2}Cr{sub 2}O{sub 7}) and cisplatin, miRNA-132-3p was upregulated 4.3-fold after AA treatment and 1.5-fold after K{sub 2}Cr{sub 2}O{sub 7} and CdCl{sub 2} treatment. These results demonstrate the application of temporal small RNA sequencing to identify miR-18a, miR-132 and miR-146b as differentially expressed miRNAs during distinct phases of kidney injury and fibrosis progression. - Highlights: • We used small RNA sequencing to identify differentially expressed miRNAs in kidney. • Distinct patterns were found for acute injury and fibrotic stages in the kidney. • Upregulation of miR-18a, -132 and -146b was confirmed in mice

  19. Application of SCALE 6.1 MAVRIC Sequence for Activation Calculation in Reactor Primary Shield Concrete

    International Nuclear Information System (INIS)

    Kim, Yong IL

    2014-01-01

    Activation calculation requires flux information at desired location and reaction cross sections for the constituent elements to obtain production rate of activation products. Generally it is not an easy task to obtain fluxes or reaction rates with low uncertainties in a reasonable time for deep penetration problems by using standard Monte Carlo methods. The MAVRIC (Monaco with Automated Variance Reduction using Importance Calculations) sequence in SCALE 6.1 code package is intended to perform radiation transport on problems that are too challenging for standard, unbiased Monte Carlo methods. And the SCALE code system provides plenty of ENDF reaction types enough to consider almost all activation reactions in the nuclear reactor materials. To evaluate the activation of the important isotopes in primary shield, SCALE 6.1 MAVRIC sequence has been utilized for the KSNP reactor model and the calculated results are compared to the isotopic activity concentration of related standard. Related to the planning for decommission, the activation products in concrete primary shield such as Fe-55, Co-60, Ba-133, Eu-152, and Eu-154 are identified as important elements according to the comparisons with related standard for exemption. In this study, reference data are used for the concrete compositions in the activation calculation to see the applicability of MAVRIC code to the evaluation of activation inventory in the concrete primary shield. The composition data of trace elements as shown in Table 1 are obtained from various US power plant sites and accordingly they have large variations in quantity due to the characteristics of concrete composition. In practical estimation of activation radioactivity for a specific plant related to decommissioning, rigorous chemical analysis of concrete samples of the plant would first have to be performed to get exact information for compositions of concrete. Considering the capability of solving deep penetration transport problems and richness

  20. Applications of a Sequence of Points in Teaching Linear Algebra, Numerical Methods and Discrete Mathematics

    Science.gov (United States)

    Shi, Yixun

    2009-01-01

    Based on a sequence of points and a particular linear transformation generalized from this sequence, two recent papers (E. Mauch and Y. Shi, "Using a sequence of number pairs as an example in teaching mathematics". Math. Comput. Educ., 39 (2005), pp. 198-205; Y. Shi, "Case study projects for college mathematics courses based on a particular…

  1. Reprint of "Application of next generation sequencing in clinical microbiology and infection prevention"

    NARCIS (Netherlands)

    Deurenberg, Ruud H.; Bathoorn, Erik; Chlebowicz, Monika A.; Monge Gomes do Couto, Natacha; Ferdous, Mithila; Garcia-Cobos, Silvia; Kooistra-Smid, Anna M. D.; Raangs, Erwin C.; Rosema, Sigrid; Veloo, Alida C. M.; Zhou, Kai; Friedrich, Alexander W.; Rossen, John W. A.

    2017-01-01

    Current molecular diagnostics of human pathogens provide limited information that is often not sufficient for outbreak and transmission investigation. Next generation sequencing (NGS) determines the DNA sequence of a complete bacterial genome in a single sequence run, and from these data,

  2. Application of next generation sequencing in clinical microbiology and infection prevention

    NARCIS (Netherlands)

    Deurenberg, Ruud H.; Bathoorn, Erik; Chlebowicz, Monika A.; Couto, Natacha; Ferdous, Mithila; Garcia-Cobos, Silvia; Kooistra-Smid, Anna M. D.; Raangs, Erwin C.; Rosema, Sigrid; Veloo, Alida C. M.; Zhou, Kai; Friedrich, Alexander W.; Rossen, John W. A.

    2017-01-01

    Current molecular diagnostics of human pathogens provide limited information that is often not sufficient for outbreak and transmission investigation. Next generation sequencing (NGS) determines the DNA sequence of a complete bacterial genome in a single sequence run, and from these data,

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

    Science.gov (United States)

    Savic, Branislav; Müri, René; Meier, Beat

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

  4. Direct Simulation Monte Carlo Application of the Three Dimensional Forced Harmonic Oscillator Model

    Science.gov (United States)

    2017-12-07

    NUMBER (Include area code) 07 December 2017 Journal Article 24 February 2017 - 31 December 2017 Direct Simulation Monte Carlo Application of the...is proposed. The implementation employs precalculated lookup tables for transition probabilities and is suitable for the direct simulation Monte Carlo...method. It takes into account the microscopic reversibility between the excitation and deexcitation processes , and it satisfies the detailed balance

  5. Smartphone Based Application For Driving Directions With Restaurants On The Way

    Directory of Open Access Journals (Sweden)

    Anup Badhe

    2015-08-01

    Full Text Available Everyday lot of people take a road trip to travel between two points. Each road trip involves driving directions provided in some form by many applications but an essential component to that is food which is sadly missing from all of those. The proposed system tries to encompass the food element into driving directions based on the drivers food preferences

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

    Science.gov (United States)

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

    2018-04-02

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

  7. Ranked solutions to a class of combinatorial optimizations - with applications in mass spectrometry based peptide sequencing

    Science.gov (United States)

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

    2006-03-01

    Typical combinatorial optimizations are NP-hard; however, for a particular class of cost functions the corresponding combinatorial optimizations can be solved in polynomial time. 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 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 fininte 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.

  8. Application potential of sequence stratigraphy to prospecting for sandstone-type uranium deposit in continental depositional basins

    International Nuclear Information System (INIS)

    Li Shengxiang; Chen Zhaobo; Chen Zuyi; Xiang Weidong; Cai Yuqi

    2001-01-01

    Sequence stratigraphy has been widely used in hydrocarbon exploration and development, and great achievements have been achieved. However, its application to the prospecting for sandstone-type uranium deposits is just beginning. The metallogenic characteristics of sandstone-type uranium deposits and those of oil and gas are compared, and the relationship between sandstone-type uranium metallogenesis and the system tracts of sequence stratigraphy is studied. The authors propose that highest and system tracts are the main targets for prospecting interlayer oxidation zone type sandstone uranium deposits, and the incised valleys of low stand system tracts are favourable places for phreatic oxidation zone type sandstone uranium deposits, and transgressive system tracts are generally unfavorable to the formation of in-situ leachable sandstone-type uranium deposits. Finally, the authors look ahead the application potential of sequence stratigraphy to the prospecting for sandstone-type uranium deposits in continental depositional basins

  9. Applicability of the 3D-VIBE sequence to whole brain imaging

    International Nuclear Information System (INIS)

    Makabe, Takeshi; Nakamura, Manami; Moriyama, Ryo

    2009-01-01

    The volumetric interpolated breath-hold examination (VIBE) method has been developed imaging also holds its breath in an abdomen, and to do three-dimensional T1WI in possible time in gradient echo sequence, and applied to dynamic study mainly and planning for time reduction using an interpolation and partial fourier. We considered the condition for imaging to do whole brain as high resolution image using VIBE. Even if base matrix was maintained when an interpolation and partial fourier were used too much excessively by Phantom experiment, the resolution of multiplanar reconstruction (MPR) image fell. There was a limit of the interpolation therefore to maintain the resolution as voxel. Signal-to-noise ratio (SNR) fell by flip angle (FA) increase by the applicability to the head, and peak existed in about 15 deg in contrast-to-noise ratio (CNR) of white matter and gray matter. Therefore by it's clinical and optimizing the imaging condition of VIBE, whole brain, it was imaging possible in about 3 minutes as high resolution image. (author)

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

    Science.gov (United States)

    1990-10-24

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

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

    Directory of Open Access Journals (Sweden)

    Wolfgang Klein

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

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

    Science.gov (United States)

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

    2015-01-01

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

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

    DEFF Research Database (Denmark)

    Hartmeyer, Gitte N; Justesen, Ulrik S

    2010-01-01

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

  14. Development and application of sequence-tagged microsatellite site (STMS) markers in chickpea (Cicer arietinum), banana (Musa spp.) and their major pathogens, Ascochyta rabiei and Mycosphaerella fijiensis

    International Nuclear Information System (INIS)

    Winter, P.; Kaemmer, D.; Paff, T.; Geistlinger, J.; Neu, C.; Kahl, G.

    2001-01-01

    DNA markers of various kinds have found widespread application in many facets of plant breeding and plant pathogen control. Yet another marker type, sequence-tagged microsatellite (STMS) markers, provides the markers of choice for nearly every crop because of their co-dominant nature, reliability, ease of application and high polymorphic information content. We report here on the development of a whole set of STMS markers and the respective, selected primer sequences for two important crops, chickpea (Cicer arietinum L.) and banana (Musa acuminata), and for their most devastating fungal pathogens, Ascochyta rabiei and Mycosphaerella fijiensis, respectively. These markers were generated either by direct screening of size-selected genomic libraries with microsatellite-complementary oligonucleotides, or by enrichment of DNA fragments containing microsatellite sequences. A total of 69 markers for chickpea, 15 markers for M. acuminata, 19 markers for A rabiei and 11 markers for M. fijiensis, selected on the basis of their high information content and ease of use are presented here. These can be applied for mapping of the respective genomes, for various population studies, and cultivar and isolate identification. We further demonstrate that several of these markers can potentially be applied across species boundaries and thus could increase the marker repertoire also for other species of the genus Cicer, Musa and for Ascochyta-type pathogens of bean, and potentially also of lentil and pea. (author)

  15. A Comprehensive Review of Permanent Magnet Transverse Flux Machines for Direct Drive Applications

    Energy Technology Data Exchange (ETDEWEB)

    Muljadi, Eduard [National Renewable Energy Laboratory (NREL), Golden, CO (United States); Husain, Tausif [University of Akron; Hasan, Iftekhar [University of Akron; Sozer, Yilmaz [University of Akron; Husain, Iqbal [North Carolina State University

    2017-11-07

    The use of direct drive machines in renewable and industrial applications are increasing at a rapid rate. Transverse flux machines (TFM) are ideally suited for direct drive applications due to their high torque density. In this paper, a comprehensive review of the permanent magnet (PM) TFMs for direct drive applications is presented. The paper introduces TFMs and their operating principle and then reviews the different type of TFMs proposed in the literature. The TFMs are categorized according to the number of stator sides, types of stator cores and magnet arrangement in the rotor. The review covers different design topologies, materials used for manufacturing, structural and thermal analysis, modeling and design optimization and cogging torque minimization in TFMs. The paper also reviews various applications and comparisons for TFMs that have been presented in the literature.

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

    International Nuclear Information System (INIS)

    Marten-Fuertes, F.

    1995-01-01

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

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

    Science.gov (United States)

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

    2003-11-01

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

  18. Inversion recovery RARE: Clinical application of T2-weighted CSF-suppressed rapid sequence

    International Nuclear Information System (INIS)

    Goetz, G.F.; Hennig, J.; Ziyeh, S.

    1995-01-01

    Inversion-Recovery RARE is a strongly T 2 -weighted fast sequence in which the CSF appears dark. This sequence was used in more than 100 patients. Retrospective analysis of 80 patients with cerebrovascular and inflammatory disease was carried out. The IR-RARE sequence proved to be particularly suitable for identifying small lesions in the neighbourhood of the subarachnoid space. We illustrate the typical contrast provided by this sequence, and describe its characteristics, exemplifying the advantages it offers for the diagnosis of multiple sclerosis, cerebral microangiopathy and brain infarction. (orig.) [de

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

    Energy Technology Data Exchange (ETDEWEB)

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

    1994-07-01

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

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

    Science.gov (United States)

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

    2013-12-01

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

  1. Sequence assembly

    DEFF Research Database (Denmark)

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

    2009-01-01

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

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

    International Nuclear Information System (INIS)

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

    1996-01-01

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

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

    Directory of Open Access Journals (Sweden)

    Janette Schult

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

  4. Application of discrete Fourier inter-coefficient difference for assessing genetic sequence similarity.

    Science.gov (United States)

    King, Brian R; Aburdene, Maurice; Thompson, Alex; Warres, Zach

    2014-01-01

    Digital signal processing (DSP) techniques for biological sequence analysis continue to grow in popularity due to the inherent digital nature of these sequences. DSP methods have demonstrated early success for detection of coding regions in a gene. Recently, these methods are being used to establish DNA gene similarity. We present the inter-coefficient difference (ICD) transformation, a novel extension of the discrete Fourier transformation, which can be applied to any DNA sequence. The ICD method is a mathematical, alignment-free DNA comparison method that generates a genetic signature for any DNA sequence that is used to generate relative measures of similarity among DNA sequences. We demonstrate our method on a set of insulin genes obtained from an evolutionarily wide range of species, and on a set of avian influenza viral sequences, which represents a set of highly similar sequences. We compare phylogenetic trees generated using our technique against trees generated using traditional alignment techniques for similarity and demonstrate that the ICD method produces a highly accurate tree without requiring an alignment prior to establishing sequence similarity.

  5. Optimal control design of turbo spin-echo sequences with applications to parallel-transmit systems

    NARCIS (Netherlands)

    Sbrizzi, Alessandro; Hoogduin, Hans; Hajnal, Joseph V; van den Berg, CAT; Luijten, Peter R; Malik, Shaihan J

    PURPOSE: The design of turbo spin-echo sequences is modeled as a dynamic optimization problem which includes the case of inhomogeneous transmit radiofrequency fields. This problem is efficiently solved by optimal control techniques making it possible to design patient-specific sequences online.

  6. Improvement of methods for large scale sequencing; application to human Xq28

    Energy Technology Data Exchange (ETDEWEB)

    Gibbs, R.A.; Andersson, B.; Wentland, M.A. [Baylor College of Medicine, Houston, TX (United States)] [and others

    1994-09-01

    Sequencing of a one-metabase region of Xq28, spanning the FRAXA and IDS loci has been undertaken in order to investigate the practicality of the shotgun approach for large scale sequencing and as a platform to develop improved methods. The efficiency of several steps in the shotgun sequencing strategy has been increased using PCR-based approaches. An improved method for preparation of M13 libraries has been developed. This protocol combines a previously described adaptor-based protocol with the uracil DNA glycosylase (UDG)-cloning procedure. The efficiency of this procedure has been found to be up to 100-fold higher than that of previously used protocols. In addition the novel protocol is more reliable and thus easy to establish in a laboratory. The method has also been adapted for the simultaneous shotgun sequencing of multiple short fragments by concentrating them before library construction is presented. This protocol is suitable for rapid characterization of cDNA clones. A library was constructed from 15 PCR-amplified and concentrated human cDNA inserts, and the insert sequences could easily be identified as separate contigs during the assembly process and the sequence coverage was even along each fragment. Using this strategy, the fine structures of the FraxA and IDS loci have been revealed and several EST homologies indicating novel expressed sequences have been identified. Use of PCR to close repetitive regions that are difficult to clone was tested by determination of the sequence of a cosmid mapping DXS455 in Xq28, containing a polymorphic VNTR. The region containing the VNTR was not represented in the shotgun library, but by designing PCR primers in the sequences flanking the gap and by cloning and sequencing the PCR product, the fine structure of the VNTR has been determined. It was found to be an AT-rich VNTR with a repeated 25-mer at the center.

  7. Direct application of Padé approximant for solving nonlinear differential equations.

    Science.gov (United States)

    Vazquez-Leal, Hector; Benhammouda, Brahim; Filobello-Nino, Uriel; Sarmiento-Reyes, Arturo; Jimenez-Fernandez, Victor Manuel; Garcia-Gervacio, Jose Luis; Huerta-Chua, Jesus; Morales-Mendoza, Luis Javier; Gonzalez-Lee, Mario

    2014-01-01

    This work presents a direct procedure to apply Padé method to find approximate solutions for nonlinear differential equations. Moreover, we present some cases study showing the strength of the method to generate highly accurate rational approximate solutions compared to other semi-analytical methods. The type of tested nonlinear equations are: a highly nonlinear boundary value problem, a differential-algebraic oscillator problem, and an asymptotic problem. The high accurate handy approximations obtained by the direct application of Padé method shows the high potential if the proposed scheme to approximate a wide variety of problems. What is more, the direct application of the Padé approximant aids to avoid the previous application of an approximative method like Taylor series method, homotopy perturbation method, Adomian Decomposition method, homotopy analysis method, variational iteration method, among others, as tools to obtain a power series solutions to post-treat with the Padé approximant. 34L30.

  8. A Review on Direct Power Control for Applications to Grid Connected PWM Converters

    Directory of Open Access Journals (Sweden)

    T. A. Trivedi

    2015-08-01

    Full Text Available The Direct Power Control strategy has become popular as an alternative to the conventional vector oriented control strategy for grid connected PWM converters. In this paper, Direct Power Control as applied to various applications of grid connected converters is reviewed. The Direct Power Control for PWM rectifiers, Grid Connected DC/AC inverters applications such as renewable energy sources interface, Active Power Filters, Doubly Fed Induction Generators and AC-DC-AC converters are discussed. Control strategies such as Look-Up table based control, predictive control, Virtual Flux DPC, Model based DPC and DPC-Space Vector Modulation are critically reviewed. The effects of various key parameters such as selection of switching vector, sampling time, hysteresis band and grid interfacing on performance of direct power controlled converters are presented.

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

    International Nuclear Information System (INIS)

    Sirianuntapiboon, Suntud; Sansak, Jutarat

    2008-01-01

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

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

    Energy Technology Data Exchange (ETDEWEB)

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

    2008-11-30

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

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

    Science.gov (United States)

    Sirianuntapiboon, Suntud; Sansak, Jutarat

    2008-11-30

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

  12. Direct reform of graphite oxide electrodes by using ambient plasma for supercapacitor applications

    Science.gov (United States)

    Kim, Ho Jun; Jeong, Hae Kyung

    2017-10-01

    Ambient plasma is applied to graphite oxide electrodes directly to improve electrochemical properties for supercapacitor applications. Surface morphology of the electrodes after the plasma treatment changes dramatically and amount of oxygen reduced significantly, demonstrating a reduction effect on the graphite oxide electrode by the ambient plasma. Equivalent series resistance of the electrode also reduced from 108 Ω to 84 Ω after the plasma treatment. Corresponding specific capacitance, therefore, increases from 0.45 F cm-2 to 0.85 F cm-2, proving that the ambient plasma treatment is very efficient, clean, economic, and environment-friendly method to reform the graphite oxide electrodes directly for the supercapacitor applications.

  13. Accurate typing of short tandem repeats from genome-wide sequencing data and its applications.

    Science.gov (United States)

    Fungtammasan, Arkarachai; Ananda, Guruprasad; Hile, Suzanne E; Su, Marcia Shu-Wei; Sun, Chen; Harris, Robert; Medvedev, Paul; Eckert, Kristin; Makova, Kateryna D

    2015-05-01

    Short tandem repeats (STRs) are implicated in dozens of human genetic diseases and contribute significantly to genome variation and instability. Yet profiling STRs from short-read sequencing data is challenging because of their high sequencing error rates. Here, we developed STR-FM, short tandem repeat profiling using flank-based mapping, a computational pipeline that can detect the full spectrum of STR alleles from short-read data, can adapt to emerging read-mapping algorithms, and can be applied to heterogeneous genetic samples (e.g., tumors, viruses, and genomes of organelles). We used STR-FM to study STR error rates and patterns in publicly available human and in-house generated ultradeep plasmid sequencing data sets. We discovered that STRs sequenced with a PCR-free protocol have up to ninefold fewer errors than those sequenced with a PCR-containing protocol. We constructed an error correction model for genotyping STRs that can distinguish heterozygous alleles containing STRs with consecutive repeat numbers. Applying our model and pipeline to Illumina sequencing data with 100-bp reads, we could confidently genotype several disease-related long trinucleotide STRs. Utilizing this pipeline, for the first time we determined the genome-wide STR germline mutation rate from a deeply sequenced human pedigree. Additionally, we built a tool that recommends minimal sequencing depth for accurate STR genotyping, depending on repeat length and sequencing read length. The required read depth increases with STR length and is lower for a PCR-free protocol. This suite of tools addresses the pressing challenges surrounding STR genotyping, and thus is of wide interest to researchers investigating disease-related STRs and STR evolution. © 2015 Fungtammasan et al.; Published by Cold Spring Harbor Laboratory Press.

  14. SU-E-T-661: Quantitative MRI Assessment of a Novel Direction-Modulated Brachytherapy Tandem Applicator for Cervical Cancer

    Energy Technology Data Exchange (ETDEWEB)

    Soliman, A; Elzibak, A; Fatemi, A; Safigholi, H; Leung, E; Ravi, A; Song, W [Sunnybrook Research Institute, Sunnybrook Health Sciences Centre, Toronto, Ontario (Canada); Han, D [Sunnybrook Research Institute, Sunnybrook Health Sciences Centre, Toronto, Ontario (Canada); University of California, San Diego, La Jolla, CA (United States)

    2015-06-15

    Purpose: To quantitatively evaluate the MR image quality of a novel direction modulated brachytherapy (DMBT) tandem applicator for cervical cancer, using the clinical MRI scanning protocol for image guided brachytherapy. Methods: The tungsten alloy-based applicator was placed in a water phantom and clinical imaging protocol was performed. Axial images were acquired using 2D turbo-spin echo (TSE) T2-weighted sequence on a 1.5T GE 450w MR scanner and an 8-channel body coil. As multi-channel receiver coil was used, inhomogeneities in the B1 receive field must be considered before performing the quantification process. Therefore the applicator was removed from the phantom and the whole imaging session was performed again for the water phantom with the same parameters. Images from the two scans were then subtracted, resulting in a difference image that only shows the applicator with its surrounding magnetic susceptibility dipole artifact. Line profiles were drawn and plotted on the difference image at various angles and locations along the tandem. Full width at half maximum (FWHM) was measured at all the line profiles to quantify the extent of the artifact. Additionally, the extent of the artifact along the diameter of the tandem was measured at various angles and locations. Results: After removing the background inhomogeneities of the receiver coil, FWHM of the tandem measured 5.75 ± 0.35 mm (the physical tandem diameter is 5.4 mm). The average extent of the artifacts along the diameter of the tandem measured is 2.14 ± 0.56 mm. In contrast to CT imaging of the same applicator (not shown here), the tandem can be easily identified without additional correction algorithms. Conclusion: This work demonstrated that the novel DMBT tandem applicator has minimal susceptibility artifact in T2-weighted images employed in clinical practice for MRI-guided brachytherapy of cervical cancer.

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

    Directory of Open Access Journals (Sweden)

    Brad Thomas Townsley

    2015-05-01

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

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

    Science.gov (United States)

    Pestaña Nieto, Montserrat; Santolamazza Carbone, Serena

    2009-02-01

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

  17. Application of the Method of Direct Solidification for Obtaining New Materials

    International Nuclear Information System (INIS)

    Grankin, S.S.

    2007-01-01

    The influence of the method of direct solidification on the formation of the material structure has been considered. The main methods of single crystal growth have been described. A considerable influence of the crystal growth parameters (temperature gradient at the front of solidification and the speed of moving of the front of solidification) on the type of the structure and morphology of single crystals has been shown. The examples of application of the method of direct solidification in experimental and industrial production are showed: production of directly crystallized blades for turbines of nuclear power plants and gas-turbine engines

  18. Application of synthetic DNA probes to the analysis of DNA sequence variants in man

    International Nuclear Information System (INIS)

    Wallace, R.B.; Petz, L.D.; Yam, P.Y.

    1986-01-01

    Oligonucleotide probes provide a tool to discriminate between any two alleles on the basis of hybridization. Random sampling of the genome with different oligonucleotide probes should reveal polymorphism in a certain percentage of the cases. In the hope of identifying polymorphic regions more efficiently, we chose to take advantage of the proposed hypermutability of repeated DNA sequences and the specificity of oligonucleotide hybridization. Since, under appropriate conditions, oligonucleotide probes require complete base pairing for hybridization to occur, they will only hybridize to a subset of the members of a repeat family when all members of the family are not identical. The results presented here suggest that oligonucleotide hybridization can be used to extend the genomic sequences that can be tested for the presence of RFLPs. This expands the tools available to human genetics. In addition, the results suggest that repeated DNA sequences are indeed more polymorphic than single-copy sequences. 28 references, 2 figures

  19. An efficient binomial model-based measure for sequence comparison and its application.

    Science.gov (United States)

    Liu, Xiaoqing; Dai, Qi; Li, Lihua; He, Zerong

    2011-04-01

    Sequence comparison is one of the major tasks in bioinformatics, which could serve as evidence of structural and functional conservation, as well as of evolutionary relations. There are several similarity/dissimilarity measures for sequence comparison, but challenges remains. This paper presented a binomial model-based measure to analyze biological sequences. With help of a random indicator, the occurrence of a word at any position of sequence can be regarded as a random Bernoulli variable, and the distribution of a sum of the word occurrence is well known to be a binomial one. By using a recursive formula, we computed the binomial probability of the word count and proposed a binomial model-based measure based on the relative entropy. The proposed measure was tested by extensive experiments including classification of HEV genotypes and phylogenetic analysis, and further compared with alignment-based and alignment-free measures. The results demonstrate that the proposed measure based on binomial model is more efficient.

  20. The application of coloured Petri nets to verification of distributed systems specified by message Sequence Charts

    OpenAIRE

    CHERNENOK S.A.; NEPOMNIASCHY V.A.

    2015-01-01

    The language of message sequence charts (MSC) is a popular scenario-based specification language used to describe the interaction of components in distributed systems. However, the methods for validation of MSC diagrams are underdeveloped. This paper describes a method for translation of MSC diagrams into coloured Petri nets (CPN). The method is applied to the property verification of these diagrams. The considered set of diagram elements is extended by the elements of UML sequence diagrams a...

  1. Molecular diagnosis of Usher syndrome: application of two different next generation sequencing-based procedures.

    Directory of Open Access Journals (Sweden)

    Danilo Licastro

    Full Text Available Usher syndrome (USH is a clinically and genetically heterogeneous disorder characterized by visual and hearing impairments. Clinically, it is subdivided into three subclasses with nine genes identified so far. In the present study, we investigated whether the currently available Next Generation Sequencing (NGS technologies are already suitable for molecular diagnostics of USH. We analyzed a total of 12 patients, most of which were negative for previously described mutations in known USH genes upon primer extension-based microarray genotyping. We enriched the NGS template either by whole exome capture or by Long-PCR of the known USH genes. The main NGS sequencing platforms were used: SOLiD for whole exome sequencing, Illumina (Genome Analyzer II and Roche 454 (GS FLX for the Long-PCR sequencing. Long-PCR targeting was more efficient with up to 94% of USH gene regions displaying an overall coverage higher than 25×, whereas whole exome sequencing yielded a similar coverage for only 50% of those regions. Overall this integrated analysis led to the identification of 11 novel sequence variations in USH genes (2 homozygous and 9 heterozygous out of 18 detected. However, at least two cases were not genetically solved. Our result highlights the current limitations in the diagnostic use of NGS for USH patients. The limit for whole exome sequencing is linked to the need of a strong coverage and to the correct interpretation of sequence variations with a non obvious, pathogenic role, whereas the targeted approach suffers from the high genetic heterogeneity of USH that may be also caused by the presence of additional causative genes yet to be identified.

  2. Molecular Diagnosis of Usher Syndrome: Application of Two Different Next Generation Sequencing-Based Procedures

    Science.gov (United States)

    Licastro, Danilo; Mutarelli, Margherita; Peluso, Ivana; Neveling, Kornelia; Wieskamp, Nienke; Rispoli, Rossella; Vozzi, Diego; Athanasakis, Emmanouil; D'Eustacchio, Angela; Pizzo, Mariateresa; D'Amico, Francesca; Ziviello, Carmela; Simonelli, Francesca; Fabretto, Antonella; Scheffer, Hans; Gasparini, Paolo; Banfi, Sandro; Nigro, Vincenzo

    2012-01-01

    Usher syndrome (USH) is a clinically and genetically heterogeneous disorder characterized by visual and hearing impairments. Clinically, it is subdivided into three subclasses with nine genes identified so far. In the present study, we investigated whether the currently available Next Generation Sequencing (NGS) technologies are already suitable for molecular diagnostics of USH. We analyzed a total of 12 patients, most of which were negative for previously described mutations in known USH genes upon primer extension-based microarray genotyping. We enriched the NGS template either by whole exome capture or by Long-PCR of the known USH genes. The main NGS sequencing platforms were used: SOLiD for whole exome sequencing, Illumina (Genome Analyzer II) and Roche 454 (GS FLX) for the Long-PCR sequencing. Long-PCR targeting was more efficient with up to 94% of USH gene regions displaying an overall coverage higher than 25×, whereas whole exome sequencing yielded a similar coverage for only 50% of those regions. Overall this integrated analysis led to the identification of 11 novel sequence variations in USH genes (2 homozygous and 9 heterozygous) out of 18 detected. However, at least two cases were not genetically solved. Our result highlights the current limitations in the diagnostic use of NGS for USH patients. The limit for whole exome sequencing is linked to the need of a strong coverage and to the correct interpretation of sequence variations with a non obvious, pathogenic role, whereas the targeted approach suffers from the high genetic heterogeneity of USH that may be also caused by the presence of additional causative genes yet to be identified. PMID:22952768

  3. A new method for detecting signal regions in ordered sequences of real numbers, and application to viral genomic data.

    Science.gov (United States)

    Gog, Julia R; Lever, Andrew M L; Skittrall, Jordan P

    2018-01-01

    We present a fast, robust and parsimonious approach to detecting signals in an ordered sequence of numbers. Our motivation is in seeking a suitable method to take a sequence of scores corresponding to properties of positions in virus genomes, and find outlying regions of low scores. Suitable statistical methods without using complex models or making many assumptions are surprisingly lacking. We resolve this by developing a method that detects regions of low score within sequences of real numbers. The method makes no assumptions a priori about the length of such a region; it gives the explicit location of the region and scores it statistically. It does not use detailed mechanistic models so the method is fast and will be useful in a wide range of applications. We present our approach in detail, and test it on simulated sequences. We show that it is robust to a wide range of signal morphologies, and that it is able to capture multiple signals in the same sequence. Finally we apply it to viral genomic data to identify regions of evolutionary conservation within influenza and rotavirus.

  4. Application of a time-dependent coalescence process for inferring the history of population size changes from DNA sequence data.

    Science.gov (United States)

    Polanski, A; Kimmel, M; Chakraborty, R

    1998-05-12

    Distribution of pairwise differences of nucleotides from data on a sample of DNA sequences from a given segment of the genome has been used in the past to draw inferences about the past history of population size changes. However, all earlier methods assume a given model of population size changes (such as sudden expansion), parameters of which (e.g., time and amplitude of expansion) are fitted to the observed distributions of nucleotide differences among pairwise comparisons of all DNA sequences in the sample. Our theory indicates that for any time-dependent population size, N(tau) (in which time tau is counted backward from present), a time-dependent coalescence process yields the distribution, p(tau), of the time of coalescence between two DNA sequences randomly drawn from the population. Prediction of p(tau) and N(tau) requires the use of a reverse Laplace transform known to be unstable. Nevertheless, simulated data obtained from three models of monotone population change (stepwise, exponential, and logistic) indicate that the pattern of a past population size change leaves its signature on the pattern of DNA polymorphism. Application of the theory to the published mtDNA sequences indicates that the current mtDNA sequence variation is not inconsistent with a logistic growth of the human population.

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

    Science.gov (United States)

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

    2005-01-01

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

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

    Directory of Open Access Journals (Sweden)

    Francesco Ferrari

    2013-11-01

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

  7. The clinical application of genome-wide sequencing for monogenic diseases in Canada: Position Statement of the Canadian College of Medical Geneticists.

    Science.gov (United States)

    Boycott, Kym; Hartley, Taila; Adam, Shelin; Bernier, Francois; Chong, Karen; Fernandez, Bridget A; Friedman, Jan M; Geraghty, Michael T; Hume, Stacey; Knoppers, Bartha M; Laberge, Anne-Marie; Majewski, Jacek; Mendoza-Londono, Roberto; Meyn, M Stephen; Michaud, Jacques L; Nelson, Tanya N; Richer, Julie; Sadikovic, Bekim; Skidmore, David L; Stockley, Tracy; Taylor, Sherry; van Karnebeek, Clara; Zawati, Ma'n H; Lauzon, Julie; Armour, Christine M

    2015-07-01

    provide genetic counselling and obtain informed consent prior to undertaking clinical genome-wide sequencing. Counselling should include discussion of the limitations of testing, likelihood and implications of diagnosis and incidental findings, and the potential need for further analysis to facilitate clinical interpretation, including studies performed in a research setting. These recommendations will be routinely re-evaluated as knowledge of diagnostic and clinical utility of clinical genome-wide sequencing improves. While the document was developed to direct practice in Canada, the applicability of the statement is broader and will be of interest to clinicians and health jurisdictions internationally. Published by the BMJ Publishing Group Limited. For permission to use (where not already granted under a licence) please go to http://group.bmj.com/group/rights-licensing/permissions.

  8. The clinical application of genome-wide sequencing for monogenic diseases in Canada: Position Statement of the Canadian College of Medical Geneticists

    Science.gov (United States)

    Boycott, Kym; Hartley, Taila; Adam, Shelin; Bernier, Francois; Chong, Karen; Fernandez, Bridget A; Friedman, Jan M; Geraghty, Michael T; Hume, Stacey; Knoppers, Bartha M; Laberge, Anne-Marie; Majewski, Jacek; Mendoza-Londono, Roberto; Meyn, M Stephen; Michaud, Jacques L; Nelson, Tanya N; Richer, Julie; Sadikovic, Bekim; Skidmore, David L; Stockley, Tracy; Taylor, Sherry; van Karnebeek, Clara; Zawati, Ma'n H; Lauzon, Julie; Armour, Christine M

    2015-01-01

    other than those linked to the primary indication; and (3) clinicians should provide genetic counselling and obtain informed consent prior to undertaking clinical genome-wide sequencing. Counselling should include discussion of the limitations of testing, likelihood and implications of diagnosis and incidental findings, and the potential need for further analysis to facilitate clinical interpretation, including studies performed in a research setting. These recommendations will be routinely re-evaluated as knowledge of diagnostic and clinical utility of clinical genome-wide sequencing improves. While the document was developed to direct practice in Canada, the applicability of the statement is broader and will be of interest to clinicians and health jurisdictions internationally. PMID:25951830

  9. 75 FR 78980 - Application to Export Electric Energy; Direct Energy Marketing, Inc.

    Science.gov (United States)

    2010-12-17

    ... Marketing, Inc. AGENCY: Office of Electricity Delivery and Energy Reliability, DOE. ACTION: Notice of Application. SUMMARY: Direct Energy Marketing, Inc. (DEMI) has applied to renew its authority to transmit..., Federal power marketing agencies, and other entities within the United States. The existing international...

  10. Direct Write Printing on Thin and Flexible Substrates for Space Applications

    Science.gov (United States)

    Paquette, Beth

    2016-01-01

    This presentation describes the work done on direct-write printing conductive traces for a flexible detector application. A Repeatability Plan was established to define detector requirements, material and printer selections, printing facilities, and tests to verify requirements are met. Designs were created for the detector, and printed using an aerosol jet printer. Testing for requirement verification is ongoing.

  11. Design considerations for permanent magnet direct drive generators for wind energy applications

    NARCIS (Netherlands)

    Jassal, A.K.; Polinder, H.; Damen, M.E.C.; Versteegh, K.

    2012-01-01

    Permanent Magnet Direct Drive (PMDD) generators offer very high force density, high efficiency and low number of components. Due to these advantages, PMDD generators are getting popular in the wind energy industry especially for offshore application. Presence of permanent magnets gives magnetic

  12. Functionalized ormosil scaffolds processed by direct laser polymerization for application in tissue engineering

    DEFF Research Database (Denmark)

    Matei, A.; Schou, Jørgen; Canulescu, Stela

    2013-01-01

    Synthesized N,N′-(methacryloyloxyethyl triehtoxy silyl propyl carbamoyl-oxyhexyl)-urea hybrid methacrylate was polymerized by direct laser polymerization using femtosecond laser pulses with the aim of using it for subsequent applications in tissue engineering. The as-obtained scaffolds were...

  13. Application of Six Thinking Hats with the Theme „Profession of Sociologist”. Transcript of the Sequence of Green Hat

    Directory of Open Access Journals (Sweden)

    Gheorghe Onuţ

    2009-12-01

    Full Text Available The study is the transcription of the sequence of green hat from the application of the creative technique Six Thinking Hats (Edward de Bono’s creation that I did at the workshop with the theme „Profession of Sociologist”, of the international colloquium of social sciences ACUM 2008. The colloquium ACUM is the most important of the scientific manifestations organized by the Faculty of Law and Sociology of „Transilvania” University of Braşov.

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

    Directory of Open Access Journals (Sweden)

    Nicholas J Schurch

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

  15. SU-G-IeP1-09: MRI Evaluation of a Direction-Modulated Brachytherapy (DMBT) Tandem Applicator for Cervical Cancer On 3T

    Energy Technology Data Exchange (ETDEWEB)

    Soliman, A; Safigholi, H [Sunnybrook Research Institute, Toronto, ON (Canada); Sunnybrook Health Sciences Centre, Toronto, ON (Canada); Han, D [University of California San Francisco, San Francisco, CA (United States); Elzibak, A; Mashouf, S; Owrangi, A; Ravi, A [Sunnybrook Health Sciences Centre, Toronto, ON (Canada); University of Toronto, Toronto, ON (Canada); Song, W [Sunnybrook Research Institute, Toronto, ON (Canada); Sunnybrook Health Sciences Centre, Toronto, ON (Canada); University of Toronto, Toronto, ON (Canada)

    2016-06-15

    Purpose: To assess image quality and artifact extent of a novel direction modulated brachytherapy (DMBT) tandem applicator on a 3T MRI using various clinical imaging sequences. Methods: The tandem applicator is composed of a tungsten alloy with 6 peripheral grooves covered with a PEEK tip. An MR-compatible phantom with similar dimensions to the female pelvis was manufactured. To visually assess the spatial shift of the applicator’s tip, a mountable radial-fiducial with 4 plastic rods, each of 3mm diameter, was designed to tightly fit on the applicator. The rods are separated by 16 mm and mounted at 90-degree relative to one another. The pelvis phantom was filled with a solution of MnCl2 to mimic T2 relaxation time of the cervix (60-80 ms at 3T).Imaging was performed on a 3T Philips Achieva using a 16-channel Torso coil array. Four MR sequences were tested: T2-weighted fast spin-echo (T2w-FSE), proton density weighted FSE (PDw-FSE), T1-weighted FSE (T1w-FSE) and T1 weighted spoiled gradient echo (T1w-GE). The spatial resolution was kept the same between all sequences: 0.6 × 0.6 × 3 mm{sup 3} with no slice gaps. Para-sagittal images were acquired with the applicator fixed at a 30-degree angle anterior to the B0- field to mimic clinical settings. Results: Minimal artifacts were observed on T2w-FSE, PDw-FSE and T1-FSE, while significant artifacts were seen on T1w-GE images. Artifacts induced in all 3 FSE sequences did not hinder accurate localisation of the tip and the applicator boundaries. The drift of the applicator’s centreline from the radial fiducials was measured and found to be < 1 mm for the 3 FSE sequences. Conclusion: The tungsten–based DMBT applicator can be potentially used on 3T with various clinical sequences without inducing significant artifacts. Further validation on patients as well as the evaluation of relative SNR among the different sequences is required.

  16. Application of Quaternion in improving the quality of global sequence alignment scores for an ambiguous sequence target in Streptococcus pneumoniae DNA

    Science.gov (United States)

    Lestari, D.; Bustamam, A.; Novianti, T.; Ardaneswari, G.

    2017-07-01

    DNA sequence can be defined as a succession of letters, representing the order of nucleotides within DNA, using a permutation of four DNA base codes including adenine (A), guanine (G), cytosine (C), and thymine (T). The precise code of the sequences is determined using DNA sequencing methods and technologies, which have been developed since the 1970s and currently become highly developed, advanced and highly throughput sequencing technologies. So far, DNA sequencing has greatly accelerated biological and medical research and discovery. However, in some cases DNA sequencing could produce any ambiguous and not clear enough sequencing results that make them quite difficult to be determined whether these codes are A, T, G, or C. To solve these problems, in this study we can introduce other representation of DNA codes namely Quaternion Q = (PA, PT, PG, PC), where PA, PT, PG, PC are the probability of A, T, G, C bases that could appear in Q and PA + PT + PG + PC = 1. Furthermore, using Quaternion representations we are able to construct the improved scoring matrix for global sequence alignment processes, by applying a dot product method. Moreover, this scoring matrix produces better and higher quality of the match and mismatch score between two DNA base codes. In implementation, we applied the Needleman-Wunsch global sequence alignment algorithm using Octave, to analyze our target sequence which contains some ambiguous sequence data. The subject sequences are the DNA sequences of Streptococcus pneumoniae families obtained from the Genebank, meanwhile the target DNA sequence are received from our collaborator database. As the results we found the Quaternion representations improve the quality of the sequence alignment score and we can conclude that DNA sequence target has maximum similarity with Streptococcus pneumoniae.

  17. Applicability of Ion Torrent Colon and Lung sequencing panel on circulating cell-free DNA

    DEFF Research Database (Denmark)

    Demuth, Christina; Tranberg Madsen, Anne; Larsen, Anne Winther

    of targeted sequencing have been optimised for clinical use on FFPE, e.g. the Ion Torrent Colon and Lung panel. The size of DNA extracted from FFPE tissue is comparable with that from cfDNA. We therefore investigated the performance of the clinically relevant Ion Torrent Colon and Lung panel on cfDNA. Methods...... a baseline for the panel. Lastly, the panel was tested on 52 patient samples. Patient plasma samples are from a previously collected cohort of EGFR wild-type non-small cell lung cancer patients (ClinicalTrial.gov: NCT02043002) All samples were sequenced using the Ion Torrent Oncomine Solid Tumor DNA kit...... (Colon and Lung panel) from Thermo Fisher. Sample preparation was performed using the Ion Torrent Chef and sequencing was performed on the Personal Genome Machine (PGM) system. Data was analyzed using the Torrent Suite software, and variants called by Ion Reporter. Results: No somatic mutations were...

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

    Science.gov (United States)

    Sirianuntapiboon, Suntud; Sadahiro, Ohmomo; Salee, Paneeta

    2007-10-01

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

  19. Application of massively parallel sequencing to genetic diagnosis in multiplex families with idiopathic sensorineural hearing impairment.

    Directory of Open Access Journals (Sweden)

    Chen-Chi Wu

    Full Text Available Despite the clinical utility of genetic diagnosis to address idiopathic sensorineural hearing impairment (SNHI, the current strategy for screening mutations via Sanger sequencing suffers from the limitation that only a limited number of DNA fragments associated with common deafness mutations can be genotyped. Consequently, a definitive genetic diagnosis cannot be achieved in many families with discernible family history. To investigate the diagnostic utility of massively parallel sequencing (MPS, we applied the MPS technique to 12 multiplex families with idiopathic SNHI in which common deafness mutations had previously been ruled out. NimbleGen sequence capture array was designed to target all protein coding sequences (CDSs and 100 bp of the flanking sequence of 80 common deafness genes. We performed MPS on the Illumina HiSeq2000, and applied BWA, SAMtools, Picard, GATK, Variant Tools, ANNOVAR, and IGV for bioinformatics analyses. Initial data filtering with allele frequencies (0.95 prioritized 5 indels (insertions/deletions and 36 missense variants in the 12 multiplex families. After further validation by Sanger sequencing, segregation pattern, and evolutionary conservation of amino acid residues, we identified 4 variants in 4 different genes, which might lead to SNHI in 4 families compatible with autosomal dominant inheritance. These included GJB2 p.R75Q, MYO7A p.T381M, KCNQ4 p.S680F, and MYH9 p.E1256K. Among them, KCNQ4 p.S680F and MYH9 p.E1256K were novel. In conclusion, MPS allows genetic diagnosis in multiplex families with idiopathic SNHI by detecting mutations in relatively uncommon deafness genes.

  20. Application of Ammonium Persulfate for Selective Oxidation of Guanines for Nucleic Acid Sequencing

    Directory of Open Access Journals (Sweden)

    Yafen Wang

    2017-07-01

    Full Text Available Nucleic acids can be sequenced by a chemical procedure that partially damages the nucleotide positions at their base repetition. Many methods have been reported for the selective recognition of guanine. The accurate identification of guanine in both single and double regions of DNA and RNA remains a challenging task. Herein, we present a new, non-toxic and simple method for the selective recognition of guanine in both DNA and RNA sequences via ammonium persulfate modification. This strategy can be further successfully applied to the detection of 5-methylcytosine by using PCR.

  1. Application of the linear-quadratic model with incomplete repair to radionuclide directed therapy

    International Nuclear Information System (INIS)

    Millar, W.T.; Glasgow Univ.

    1991-01-01

    The LQ model has now been extended to include a general time varying dose rate profile, and the equations can be readily evaluated if an exponential radiation damage repair process is assumed. These equations are applicable to radionuclide directed therapy, including brachytherapy. Kinetic uptake data obtained during radionuclide directed therapy may therefore be used to determine the radiobiological dosimetry of the target and non-target tissues. Also, preliminary tracer studies may be used to pre-plan the radionuclide directed therapy, provided that tracer and therapeutic amounts of the radionuclide carrier are identically processed by the tissues. It is also shown that continuous radionuclide therapy will induce less damage in late-responding tissues than 2 Gy/fraction external beam therapy if the ratio of the maximum dose rate and the sublethal damage repair half-life in the tissue is less than 1.0 Gy. Similar inequalities may be derived for β-particle radionuclide directed therapy. (author)

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

    Directory of Open Access Journals (Sweden)

    Prakash Radhakrishnan

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

  3. DHCVIM - a direct heating containment vessel interactions module: applications to Sandia National Laboratories Surtsey experiments

    International Nuclear Information System (INIS)

    Ginsberg, T.; Tutu, N.K.

    1987-01-01

    Direct containment heating is the mechanism of severe nuclear reactor accident containment loading that results from transfer of thermal and chemical energy from high-temperature, finely divided, molten core material to the containment atmosphere. The direct heating containment vessel interactions module (DHCVIM) has been developed at Brookhaven National Laboratory to model the mechanisms of containment loading resulting from the direct heating accident sequence. The calculational procedure is being used at present to model the Sandia National Laboratories one-tenth-scale Surtsey direct containment heating experiments. The objective of the code is to provide a test bed for detailed modeling of various aspects of the thermal, chemical, and hydrodynamic interactions that are expected to occur in three regions of a containment building: reactor cavity, intermediate subcompartments, and containment dome. Major emphasis is placed on the description of reactor cavity dynamics. This paper summarizes the modeling principles that are incorporated in DHCVIM and presents a prediction of the Surtsey Test DCH-2 that was made prior to execution of the experiment

  4. A Simplified Method for Gene Knockout and Direct Screening of Recombinant Clones for Application in Paenibacillus polymyxa.

    Directory of Open Access Journals (Sweden)

    Seong-Bin Kim

    Full Text Available Paenibacillus polymyxa is a bacterium widely used in agriculture, industry, and environmental remediation because it has multiple functions including nitrogen fixation and produces various biologically active compounds. Among these compounds are the antibiotics polymyxins, and the bacterium is currently being reassessed for medical application. However, a lack of genetic tools for manipulation of P. polymyxa has limited our understanding of the biosynthesis of these compounds.To facilitate an understanding of the genetic determinants of the bacterium, we have developed a system for marker exchange mutagenesis directly on competent cells of P. polymyxa under conditions where homologous recombination is enhanced by denaturation of the suicide plasmid DNA. To test this system, we targeted P. polymyxa α-and β-amylase genes for disruption. Chloramphenicol or erythromycin resistance genes were inserted into the suicide plasmid pGEM7Z-f+ (Promega. To mediate homologous recombination and replacement of the targeted genes with the antibiotic resistance genes nucleotide sequences of the α-and β-amylase genes were cloned into the plasmid flanking the antibiotic resistance genes.We have created a simple system for targeted gene deletion in P. polymyxa E681. We propose that P. polymyxa isogenic mutants could be developed using this system of marker exchange mutagenesis. α-and β-amylase genes provide a useful tool for direct recombinant screening in P. polymyxa.

  5. Next-Generation DNA Sequencing of VH/VL Repertoires: A Primer and Guide to Applications in Single-Domain Antibody Discovery.

    Science.gov (United States)

    Henry, Kevin A

    2018-01-01

    Immunogenetic analyses of expressed antibody repertoires are becoming increasingly common experimental investigations and are critical to furthering our understanding of autoimmunity, infectious disease, and cancer. Next-generation DNA sequencing (NGS) technologies have now made it possible to interrogate antibody repertoires to unprecedented depths, typically by sequencing of cDNAs encoding immunoglobulin variable domains. In this chapter, we describe simple, fast, and reliable methods for producing and sequencing multiplex PCR amplicons derived from the variable regions (V H , V H H or V L ) of rearranged immunoglobulin heavy and light chain genes using the Illumina MiSeq platform. We include complete protocols and primer sets for amplicon sequencing of V H /V H H/V L repertoires directly from human, mouse, and llama lymphocytes as well as from phage-displayed V H /V H H/V L libraries; these can be easily be adapted to other types of amplicons with little modification. The resulting amplicons are diverse and representative, even using as few as 10 3 input B cells, and their generation is relatively inexpensive, requiring no special equipment and only a limited set of primers. In the absence of heavy-light chain pairing, single-domain antibodies are uniquely amenable to NGS analyses. We present a number of applications of NGS technology useful in discovery of single-domain antibodies from phage display libraries, including: (i) assessment of library functionality; (ii) confirmation of desired library randomization; (iii) estimation of library diversity; and (iv) monitoring the progress of panning experiments. While the case studies presented here are of phage-displayed single-domain antibody libraries, the principles extend to other types of in vitro display libraries.

  6. Draft genome sequence of Pseudomonas corrugata, a phytopathogenic bacterium with potential industrial applications.

    Science.gov (United States)

    Licciardello, G; Jackson, R W; Bella, P; Strano, C P; Catara, A F; Arnold, D L; Venturi, V; Silby, M W; Catara, V

    2014-04-10

    Pseudomonas corrugata was first described as the causal agent of a tomato disease called 'pith necrosis' yet it is considered as a biological resource in various fields such as biocontrol of plant diseases and production of industrially promising microbial biopolymers (mcl-PHA). Here we report the first draft genome sequence of this species. Copyright © 2014 Elsevier B.V. All rights reserved.

  7. Application of sequence stratigraphy to carbonate reservoir prediction, Early Palaeozoic eastern Warburton basin, South Australia

    Energy Technology Data Exchange (ETDEWEB)

    Xiaowen S.; Stuart, W.J.

    1996-12-31

    The Early Palaeozoic Warburton Basin underlies the gas and oil producing Cooper and Eromanga Basins. Postdepositional tectonism created high potential fracture porosities, complicating the stratigraphy and making reservoir prediction difficult. Sequence stratigraphy integrating core, cuttings, well-log, seismic and biostratigraphic data has recognized a carbonate-dominated to mixed carbonate/siliciclastic supersequence comprising several depositional sequences. Biostratigraphy based on trilobites and conodonts ensures reliable well and seismic correlations across structurally complex areas. Lithofacies interpretation indicates sedimentary environments ranging from carbonate inner shelf, peritidal, shelf edge, deep outer shelf and slope to basin. Log facies show gradually upward shallowing trends or abrupt changes indicating possible sequence boundaries. With essential depositional models and sequence analysis from well data, seismic facies suggest general reflection configurations including parallel-continuous layered patterns indicating uniform neuritic shelf, and mounded structures suggesting carbonate build-ups and pre-existing volcanic relief. Seismic stratigraphy also reveals inclined slope and onlapping margins of a possibly isolated platform geometry. The potential reservoirs are dolomitized carbonates containing oomoldic, vuggy, intercrystalline and fracture porosities in lowstand systems tracts either on carbonate mounds and shelf crests or below shelf edge. The source rock is a deep basinal argillaceous mudstone, and the seal is fine-grained siltstone/shale of the transgressive system tract.

  8. Application of sequence stratigraphy to carbonate reservoir prediction, Early Palaeozoic eastern Warburton basin, South Australia

    Energy Technology Data Exchange (ETDEWEB)

    Xiaowen S.; Stuart, W.J.

    1996-01-01

    The Early Palaeozoic Warburton Basin underlies the gas and oil producing Cooper and Eromanga Basins. Postdepositional tectonism created high potential fracture porosities, complicating the stratigraphy and making reservoir prediction difficult. Sequence stratigraphy integrating core, cuttings, well-log, seismic and biostratigraphic data has recognized a carbonate-dominated to mixed carbonate/siliciclastic supersequence comprising several depositional sequences. Biostratigraphy based on trilobites and conodonts ensures reliable well and seismic correlations across structurally complex areas. Lithofacies interpretation indicates sedimentary environments ranging from carbonate inner shelf, peritidal, shelf edge, deep outer shelf and slope to basin. Log facies show gradually upward shallowing trends or abrupt changes indicating possible sequence boundaries. With essential depositional models and sequence analysis from well data, seismic facies suggest general reflection configurations including parallel-continuous layered patterns indicating uniform neuritic shelf, and mounded structures suggesting carbonate build-ups and pre-existing volcanic relief. Seismic stratigraphy also reveals inclined slope and onlapping margins of a possibly isolated platform geometry. The potential reservoirs are dolomitized carbonates containing oomoldic, vuggy, intercrystalline and fracture porosities in lowstand systems tracts either on carbonate mounds and shelf crests or below shelf edge. The source rock is a deep basinal argillaceous mudstone, and the seal is fine-grained siltstone/shale of the transgressive system tract.

  9. Growth Plate Flow and Metabolism Screening Using MR: A New Application for Specialized MR Sequences

    DEFF Research Database (Denmark)

    Shiguetomi Medina, Juan Manuel; Stødkilde-Jørgensen, Hans; Rahbek, Ole

    . Methods Four normal pig frozen tibiae were studied. Tomography, MR T1 and T2 sequences were performed and compared. Apparent Diffusion Coefficient and Surface Tension Images were also performed and analyzed. Finally, methylmethacrylate embedding histology was performed using hematoxylin-eosin, toluidine...

  10. No Reference Prediction of Quality Metrics for H.264 Compressed Infrared Image Sequences for UAV Applications

    DEFF Research Database (Denmark)

    Hossain, Kabir; Mantel, Claire; Forchhammer, Søren

    2018-01-01

    The framework for this research work is the acquisition of Infrared (IR) images from Unmanned Aerial Vehicles (UAV). In this paper we consider the No-Reference (NR) prediction of Full Reference Quality Metrics for Infrared (IR) video sequences which are compressed and thus distorted by an H.264...

  11. Joining Movement Sequences: Modified Dynamic Movement Primitives for Robotics Applications Exemplified on Handwriting

    DEFF Research Database (Denmark)

    Kulvicius, Tomas; Ning, K.; Tamosiunaite, M.

    2012-01-01

    to simulated handwriting generation, which are also shown on a robot, where an adaptive algorithm is used to learn trajectories from human demonstration. These results demonstrate that the new method is a feasible alternative for joining of movement sequences, which has a high potential for all robotics...

  12. Applications of statistical physics and information theory to the analysis of DNA sequences

    Science.gov (United States)

    Grosse, Ivo

    2000-10-01

    DNA carries the genetic information of most living organisms, and the of genome projects is to uncover that genetic information. One basic task in the analysis of DNA sequences is the recognition of protein coding genes. Powerful computer programs for gene recognition have been developed, but most of them are based on statistical patterns that vary from species to species. In this thesis I address the question if there exist universal statistical patterns that are different in coding and noncoding DNA of all living species, regardless of their phylogenetic origin. In search for such species-independent patterns I study the mutual information function of genomic DNA sequences, and find that it shows persistent period-three oscillations. To understand the biological origin of the observed period-three oscillations, I compare the mutual information function of genomic DNA sequences to the mutual information function of stochastic model sequences. I find that the pseudo-exon model is able to reproduce the mutual information function of genomic DNA sequences. Moreover, I find that a generalization of the pseudo-exon model can connect the existence and the functional form of long-range correlations to the presence and the length distributions of coding and noncoding regions. Based on these theoretical studies I am able to find an information-theoretical quantity, the average mutual information (AMI), whose probability distributions are significantly different in coding and noncoding DNA, while they are almost identical in all studied species. These findings show that there exist universal statistical patterns that are different in coding and noncoding DNA of all studied species, and they suggest that the AMI may be used to identify genes in different living species, irrespective of their taxonomic origin.

  13. Comparative study and application of MR sialography using different pulse sequences

    International Nuclear Information System (INIS)

    Shi Ruihua; Qi Jianping; Feng Dingyi; Zou Mingli; Hu Junwu; Zhu Wenzhen; Xia Liming; Wang Chengyuan

    2004-01-01

    Objective: To evaluate the accuracy of MR sialography in demonstrating the main salivary duct systems by using a series of pulse sequences and stimulation of salivation by vitamin C. Methods: MR sialography was prospectively performed with STIR, heavily T 2 weighted FSE, and SS FSE sequences in 17 patients suspected with salivary duct abnormalities and 13 volunteers, respectively, and MR sialography was further performed in 16 patients after vitamin C stimulation. The results of the above three sequences were compared with each other. Results: The main salivary gland duct was depicted in all cases by any of the mentioned sequence. The STIR images were significantly superior to SS FSE and heavily T 2 weighted FSE images for demonstrating the salivary duct system, followed by heavily T 2 weighted FSE images. On STIR images, first- and second- order intraglandular branches were clearly depicted in all cases, and the thinnest branches were about 0.8 mm. On heavily T 2 weighted FSE images, the first-order and the second-order intraglandular branches were delineated in 25 of 30 and 18 of 30 cases, respectively. But on SS FSE images, only 20 to 30 first-order and 10 of 30 second-order intraglandular branches could be detected. MR sialography with vitamin C stimulation revealed the good visualization of the salivary duct system, and the ducts became wider than before. In 7 cases with acute sialadenitis, the main duct became slightly wider and the distal ducts were dilated; In 7 cases with benign tumor, the ducts were displaced but remained continuous; The duct in one patients with submandibular gland cancer showed destruction and discontinuity. The ducts of one patient with Sjogren syndrome and one with sialidosis displayed normal. Conclusion: MR sialography with evoked salivation is noninvasive and allows delineation of both normal and abnormal parotid and submandibular gland duct systems, and the images are especially better on STIR sequence

  14. Application of Ion Torrent Sequencing to the Assessment of the Effect of Alkali Ballast Water Treatment on Microbial Community Diversity

    Science.gov (United States)

    Fujimoto, Masanori; Moyerbrailean, Gregory A.; Noman, Sifat; Gizicki, Jason P.; Ram, Michal L.; Green, Phyllis A.; Ram, Jeffrey L.

    2014-01-01

    The impact of NaOH as a ballast water treatment (BWT) on microbial community diversity was assessed using the 16S rRNA gene based Ion Torrent sequencing with its new 400 base chemistry. Ballast water samples from a Great Lakes ship were collected from the intake and discharge of both control and NaOH (pH 12) treated tanks and were analyzed in duplicates. One set of duplicates was treated with the membrane-impermeable DNA cross-linking reagent propidium mono-azide (PMA) prior to PCR amplification to differentiate between live and dead microorganisms. Ion Torrent sequencing generated nearly 580,000 reads for 31 bar-coded samples and revealed alterations of the microbial community structure in ballast water that had been treated with NaOH. Rarefaction analysis of the Ion Torrent sequencing data showed that BWT using NaOH significantly decreased microbial community diversity relative to control discharge (pbased principal coordinate analysis (PCoA) plots and UPGMA tree analysis revealed that NaOH-treated ballast water microbial communities differed from both intake communities and control discharge communities. After NaOH treatment, bacteria from the genus Alishewanella became dominant in the NaOH-treated samples, accounting for alkali ballast water treatment in reducing ballast water microbial diversity and demonstrated the application of new Ion Torrent sequencing techniques to microbial community studies. PMID:25222021

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

    Science.gov (United States)

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

    2013-09-23

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

  16. Functionalized Ormosil Scaffolds Processed by Direct Laser Polymerization for Application in Tissue Engineering

    DEFF Research Database (Denmark)

    Matei, A.; Schou, Jørgen; Canulescu, Stela

    The N,N’-(methacryloyloxyethyl triehtoxy silyl propyl carbamoyl-oxyhexyl)-urea hybrid methacrylate for applications in tissue engineering was synthesized and afterwards polymerized by direct laser polymerization using femtosecond laser pulses with the aim of using it for further applications...... in tissue engineering. The as-obtained scaffolds were modified either by low pressure argon plasma treatment or by using two different proteins (lysozyme, fibrinogen). For improved adhesion, the proteins were deposited by matrix assisted pulsed laser evaporation. The functionalized structures were tested...

  17. Advanced directions of peaceful applications of nuclear energy in the Republic of Azerbaijan

    International Nuclear Information System (INIS)

    Garibov, A.A.

    2006-01-01

    Full text: Application of nuclear energy is actual during last years due to depletion of organic sources of row materials. Therefore, each country develops the programs on peaceful application of nuclear energy and using alternative as well as other energy sources on the basis of the analysis of fuel-energy balance and energy demand state. The Republic of Azerbaijan has huge hydrocarbon resources and alternative energy sources. However, taking into account the fact that hydrocarbon resources can cover increasing energy demand at maximum 50-60 years and renewable energy sources can not meet large energy demand during near future then the discovering of advanced ways on peaceful application of nuclear energy is of great importance. Since the seventies of the twentieth century, wide spectrum of scientific researches on the discovering advanced ways on peaceful application of nuclear energy are carried out in the Republic of Azerbaijan. Among them it is necessary to mark the following directions: radiation modification of the properties of polymers, absorbents, catalysts, metals and alloys, semiconductors, dielectrics, ferroelectrics and various devices; radiation oil-chemistry processes; radiation polymerization; radiation-heterogeneous processes; atomic-hydrogen energy; scientific problems of radiation safety and nuclear security; discovering possibilities for using radiation technologies in the solution of environmental problems; radiation sciences of materials and radiation physics; radiation biology and medicine; application of isotope sources in medicine; application of isotope in oil-gas industry; application of isotope sources in radiography and different fields of technique

  18. Application of next-generation sequencing methods for microbial monitoring of anaerobic digestion of lignocellulosic biomass.

    Science.gov (United States)

    Bozan, Mahir; Akyol, Çağrı; Ince, Orhan; Aydin, Sevcan; Ince, Bahar

    2017-09-01

    The anaerobic digestion of lignocellulosic wastes is considered an efficient method for managing the world's energy shortages and resolving contemporary environmental problems. However, the recalcitrance of lignocellulosic biomass represents a barrier to maximizing biogas production. The purpose of this review is to examine the extent to which sequencing methods can be employed to monitor such biofuel conversion processes. From a microbial perspective, we present a detailed insight into anaerobic digesters that utilize lignocellulosic biomass and discuss some benefits and disadvantages associated with the microbial sequencing techniques that are typically applied. We further evaluate the extent to which a hybrid approach incorporating a variation of existing methods can be utilized to develop a more in-depth understanding of microbial communities. It is hoped that this deeper knowledge will enhance the reliability and extent of research findings with the end objective of improving the stability of anaerobic digesters that manage lignocellulosic biomass.

  19. Optimal pseudorandom sequence selection for online c-VEP based BCI control applications

    DEFF Research Database (Denmark)

    Isaksen, Jonas L.; Mohebbi, Ali; Puthusserypady, Sadasivan

    2017-01-01

    to predict the chance of completion and accuracy score. Results: No specific pseudorandom sequence showed superior accuracy on the group basis. When isolating the individual performances with the highest accuracy, time consumption per identification was not significantly increased. The Accuracy Score aids...... is a laborious process. Aims: This study aimed to suggest an efficient method for choosing the optimal stimulus sequence based on a fast test and simple measures to increase the performance and minimize the time consumption for research trials. Methods: A total of 21 healthy subjects were included in an online...... wheelchair control task and completed the same task using stimuli based on the m-code, the gold-code, and the Barker-code. Correct/incorrect identification and time consumption were obtained for each identification. Subject-specific templates were characterized and used in a forward-step first-order model...

  20. Regularity dimension of sequences and its application to phylogenetic tree reconstruction

    International Nuclear Information System (INIS)

    Pham, Tuan D.

    2012-01-01

    The concept of dimension is a central development of chaos theory for studying nonlinear dynamical systems. Different types of dimensions have been derived to interpret different geometrical or physical observations. Approximate entropy and its modified methods have been introduced for studying regularity and complexity of time-series data in physiology and biology. Here, the concept of power laws and entropy measure are adopted to develop the regularity dimension of sequences to model a mathematical relationship between the frequency with which information about signal regularity changes in various scales. The proposed regularity dimension is applied to reconstruct phylogenetic trees using mitochondrial DNA (mtDNA) sequences for the family Hominidae, which can be validated according to the hypothesized evolutionary relationships between organisms.

  1. Real time application of whole genome sequencing for outbreak investigation - What is an achievable turnaround time?

    Science.gov (United States)

    McGann, Patrick; Bunin, Jessica L; Snesrud, Erik; Singh, Seema; Maybank, Rosslyn; Ong, Ana C; Kwak, Yoon I; Seronello, Scott; Clifford, Robert J; Hinkle, Mary; Yamada, Stephen; Barnhill, Jason; Lesho, Emil

    2016-07-01

    Whole genome sequencing (WGS) is increasingly employed in clinical settings, though few assessments of turnaround times (TAT) have been performed in real-time. In this study, WGS was used to investigate an unfolding outbreak of vancomycin resistant Enterococcus faecium (VRE) among 3 patients in the ICU of a tertiary care hospital. Including overnight culturing, a TAT of just 48.5 h for a comprehensive report was achievable using an Illumina Miseq benchtop sequencer. WGS revealed that isolates from patient 2 and 3 differed from that of patient 1 by a single nucleotide polymorphism (SNP), indicating nosocomial transmission. However, the unparalleled resolution provided by WGS suggested that nosocomial transmission involved two separate events from patient 1 to patient 2 and 3, and not a linear transmission suspected by the time line. Rapid TAT's are achievable using WGS in the clinical setting and can provide an unprecedented level of resolution for outbreak investigations. Published by Elsevier Inc.

  2. Organism-specific rRNA capture system for application in next-generation sequencing.

    Directory of Open Access Journals (Sweden)

    Sai-Kam Li

    Full Text Available RNA-sequencing is a powerful tool in studying RNomics. However, the highly abundance of ribosomal RNAs (rRNA and transfer RNA (tRNA have predominated in the sequencing reads, thereby hindering the study of lowly expressed genes. Therefore, rRNA depletion prior to sequencing is often performed in order to preserve the subtle alteration in gene expression especially those at relatively low expression levels. One of the commercially available methods is to use DNA or RNA probes to hybridize to the target RNAs. However, there is always a concern with the non-specific binding and unintended removal of messenger RNA (mRNA when the same set of probes is applied to different organisms. The degree of such unintended mRNA removal varies among organisms due to organism-specific genomic variation. We developed a computer-based method to design probes to deplete rRNA in an organism-specific manner. Based on the computation results, biotinylated-RNA-probes were produced by in vitro transcription and were used to perform rRNA depletion with subtractive hybridization. We demonstrated that the designed probes of 16S rRNAs and 23S rRNAs can efficiently remove rRNAs from Mycobacterium smegmatis. In comparison with a commercial subtractive hybridization-based rRNA removal kit, using organism-specific probes is better in preserving the RNA integrity and abundance. We believe the computer-based design approach can be used as a generic method in preparing RNA of any organisms for next-generation sequencing, particularly for the transcriptome analysis of microbes.

  3. Highly directional transurethral ultrasound applicators with rotational control for MRI-guided prostatic thermal therapy

    Energy Technology Data Exchange (ETDEWEB)

    Ross, Anthony B [Thermal Therapy Research Group, UCSF Radiation Oncology, San Francisco, CA (United States); Diederich, Chris J [Thermal Therapy Research Group, UCSF Radiation Oncology, San Francisco, CA (United States); Nau, William H [Thermal Therapy Research Group, UCSF Radiation Oncology, San Francisco, CA (United States); Gill, Harcharan [Department of Urology, Stanford University, Stanford, CA (United States); Bouley, Donna M [Department of Comparative Medicine, Stanford University, Stanford, CA (United States); Daniel, Bruce [Department of Radiology, Stanford University, Stanford, CA (United States); Rieke, Viola [Department of Radiology, Stanford University, Stanford, CA (United States); Butts, R Kim [Department of Radiology, Stanford University, Stanford, CA (United States); Sommer, Graham [Department of Radiology, Stanford University, Stanford, CA (United States)

    2004-01-21

    Transurethral ultrasound applicators with highly directional energy deposition and rotational control were investigated for precise treatment of benign prostatic hyperplasia (BPH) and adenocarcinoma of the prostate (CaP). Two types of catheter-based applicators were fabricated, using either sectored tubular (3.5 mm OD x 10 mm) or planar transducers (3.5 mm x 10 mm). They were constructed to be MRI compatible, minimally invasive and allow for manual rotation of the transducer array within a 10 mm cooling balloon. In vivo evaluations of the applicators were performed in canine prostates (n 3) using MRI guidance (0.5 T interventional magnet). MR temperature imaging (MRTI) utilizing the proton resonance frequency shift method was used to acquire multiple-slice temperature overlays in real time for monitoring and guiding the thermal treatments. Post-treatment T1-weighted contrast-enhanced imaging and triphenyl tetrazolium chloride stained tissue sections were used to define regions of tissue coagulation. Single sonications with the tubular applicator ) produced coagulated zones covering a wedge of the prostate extending from 1-2 mm outside the urethra to the outer boundary of the gland (16 mm radial coagulation). Single sonications with the planar applicator (15-20 W, 10 min, {approx}8 MHz) generated thermal lesions of {approx}30 extending to the prostate boundary. Multiple sequential sonications (sweeping) of a planar applicator (12 W with eight rotations of 30 each) demonstrated controllable coagulation of a 270 contiguous section of the prostate extending to the capsule boundary. The feasibility of using highly directional transurethral ultrasound applicators with rotational capabilities to selectively coagulate regions of the prostate while monitoring and controlling the treatments with MRTI was demonstrated in this study.

  4. [Artificial muscle and its prospect in application for direct cardiac compression assist].

    Science.gov (United States)

    Dong, Jing; Yang, Ming; Zheng, Zhejun; Yan, Guozheng

    2008-12-01

    Artificial heart is an effective device in solving insufficient native heart supply for heart transplant, and the research and application of novel actuators play an important role in the development of artificial heart. In this paper, artificial muscle is introduced as the actuators of direct cardiac compression assist, and some of its parameters are compared with those of native heart muscle. The open problems are also discussed.

  5. Application of a Software tool for Evaluating Human Factors in Accident Sequences

    International Nuclear Information System (INIS)

    Queral, Cesar; Exposito, Antonio; Gonzalez, Isaac; Quiroga, Juan Antonio; Ibarra, Aitor; Hortal, Javier; Hulsund, John-Einar; Nilsen, Svein

    2006-01-01

    The Probabilistic Safety Assessment (PSA) includes the actions of the operator like elements in the set of the considered protection performances during accident sequences. Nevertheless, its impact throughout a sequence is not analyzed in a dynamic way. In this sense, it is convenient to make more detailed studies about its importance in the dynamics of the sequences, letting make studies of sensitivity respect to the human reliability and the response times. For this reason, the CSN is involved in several activities oriented to develop a new safety analysis methodology, the Integrated Safety Assessment (ISA), which must be able to incorporate operator actions in conventional thermo-hydraulic (TH) simulations. One of them is the collaboration project between CSN, HRP and the DSE-UPM that started in 2003. In the framework of this project, a software tool has been developed to incorporate operator actions in TH simulations. As a part of the ISA, this tool permits to quantify human error probabilities (HEP) and to evaluate its impact in the final state of the plant. Independently, it can be used for evaluating the impact of the execution by operators of procedures and guidelines in the final state of the plant and the evaluation of the allowable response times for the manual actions of the operator. The results obtained in the first pilot case are included in this paper. (authors)

  6. Sequence spaces [Formula: see text] and [Formula: see text] with application in clustering.

    Science.gov (United States)

    Khan, Mohd Shoaib; Alamri, Badriah As; Mursaleen, M; Lohani, Qm Danish

    2017-01-01

    Distance measures play a central role in evolving the clustering technique. Due to the rich mathematical background and natural implementation of [Formula: see text] distance measures, researchers were motivated to use them in almost every clustering process. Beside [Formula: see text] distance measures, there exist several distance measures. Sargent introduced a special type of distance measures [Formula: see text] and [Formula: see text] which is closely related to [Formula: see text]. In this paper, we generalized the Sargent sequence spaces through introduction of [Formula: see text] and [Formula: see text] sequence spaces. Moreover, it is shown that both spaces are BK -spaces, and one is a dual of another. Further, we have clustered the two-moon dataset by using an induced [Formula: see text]-distance measure (induced by the Sargent sequence space [Formula: see text]) in the k-means clustering algorithm. The clustering result established the efficacy of replacing the Euclidean distance measure by the [Formula: see text]-distance measure in the k-means algorithm.

  7. [Sequence analysis of LEAFY homologous gene from Dendrobium moniliforme and application for identification of medicinal Dendrobium].

    Science.gov (United States)

    Xing, Wen-Rui; Hou, Bei-Wei; Guan, Jing-Jiao; Luo, Jing; Ding, Xiao-Yu

    2013-04-01

    The LEAFY (LFY) homologous gene of Dendrobium moniliforme (L.) Sw. was cloned by new primers which were designed based on the conservative region of known sequences of orchid LEAFY gene. Partial LFY homologous gene was cloned by common PCR, then we got the complete LFY homologous gene Den LFY by Tail-PCR. The complete sequence of DenLFY gene was 3 575 bp which contained three exons and two introns. Using BLAST method, comparison analysis among the exon of LFY homologous gene indicted that the DenLFY gene had high identity with orchids LFY homologous, including the related fragment of PhalLFY (84%) in Phalaenopsis hybrid cultivar, LFY homologous gene in Oncidium (90%) and in other orchid (over 80%). Using MP analysis, Dendrobium is found to be the sister to Oncidium and Phalaenopsis. Homologous analysis demonstrated that the C-terminal amino acids were highly conserved. When the exons and introns were separately considered, exons and the sequence of amino acid were good markers for the function research of DenLFY gene. The second intron can be used in authentication research of Dendrobium based on the length polymorphism between Dendrobium moniliforme and Dendrobium officinale.

  8. Plann: A command-line application for annotating plastome sequences1

    Science.gov (United States)

    Huang, Daisie I.; Cronk, Quentin C. B.

    2015-01-01

    Premise of the study: Plann automates the process of annotating a plastome sequence in GenBank format for either downstream processing or for GenBank submission by annotating a new plastome based on a similar, well-annotated plastome. Methods and Results: Plann is a Perl script to be executed on the command line. Plann compares a new plastome sequence to the features annotated in a reference plastome and then shifts the intervals of any matching features to the locations in the new plastome. Plann’s output can be used in the National Center for Biotechnology Information’s tbl2asn to create a Sequin file for GenBank submission. Conclusions: Unlike Web-based annotation packages, Plann is a locally executable script that will accurately annotate a plastome sequence to a locally specified reference plastome. Because it executes from the command line, it is ready to use in other software pipelines and can be easily rerun as a draft plastome is improved. PMID:26312193

  9. Application of ion torrent sequencing to the assessment of the effect of alkali ballast water treatment on microbial community diversity.

    Science.gov (United States)

    Fujimoto, Masanori; Moyerbrailean, Gregory A; Noman, Sifat; Gizicki, Jason P; Ram, Michal L; Green, Phyllis A; Ram, Jeffrey L

    2014-01-01

    The impact of NaOH as a ballast water treatment (BWT) on microbial community diversity was assessed using the 16S rRNA gene based Ion Torrent sequencing with its new 400 base chemistry. Ballast water samples from a Great Lakes ship were collected from the intake and discharge of both control and NaOH (pH 12) treated tanks and were analyzed in duplicates. One set of duplicates was treated with the membrane-impermeable DNA cross-linking reagent propidium mono-azide (PMA) prior to PCR amplification to differentiate between live and dead microorganisms. Ion Torrent sequencing generated nearly 580,000 reads for 31 bar-coded samples and revealed alterations of the microbial community structure in ballast water that had been treated with NaOH. Rarefaction analysis of the Ion Torrent sequencing data showed that BWT using NaOH significantly decreased microbial community diversity relative to control discharge (pPCoA) plots and UPGMA tree analysis revealed that NaOH-treated ballast water microbial communities differed from both intake communities and control discharge communities. After NaOH treatment, bacteria from the genus Alishewanella became dominant in the NaOH-treated samples, accounting for microbial community structure between PMA-processed and non-PMA samples occurred in intake water samples, which exhibited a significantly higher amount of PMA-sensitive cyanobacteria/chloroplast 16S rRNA than their corresponding non-PMA total DNA samples. The community assembly obtained using Ion Torrent sequencing was comparable to that obtained from a subset of samples that were also subjected to 454 pyrosequencing. This study showed the efficacy of alkali ballast water treatment in reducing ballast water microbial diversity and demonstrated the application of new Ion Torrent sequencing techniques to microbial community studies.

  10. Criteria for confirming sequence periodicity identified by Fourier transform analysis: application to GCR2, a candidate plant GPCR?

    Science.gov (United States)

    Illingworth, Christopher J R; Parkes, Kevin E; Snell, Christopher R; Mullineaux, Philip M; Reynolds, Christopher A

    2008-03-01

    Methods to determine periodicity in protein sequences are useful for inferring function. Fourier transformation is one approach but care is required to ensure the periodicity is genuine. Here we have shown that empirically-derived statistical tables can be used as a measure of significance. Genuine protein sequences data rather than randomly generated sequences were used as the statistical backdrop. The method has been applied to G-protein coupled receptor (GPCR) sequences, by Fourier transformation of hydrophobicity values, codon frequencies and the extent of over-representation of codon pairs; the latter being related to translational step times. Genuine periodicity was observed in the hydrophobicity whereas the apparent periodicity (as inferred from previously reported measures) in the translation step times was not validated statistically. GCR2 has recently been proposed as the plant GPCR receptor for the hormone abscisic acid. It has homology to the Lanthionine synthetase C-like family of proteins, an observation confirmed by fold recognition. Application of the Fourier transform algorithm to the GCR2 family revealed strongly predicted seven fold periodicity in hydrophobicity, suggesting why GCR2 has been reported to be a GPCR, despite negative indications in most transmembrane prediction algorithms. The underlying multiple sequence alignment, also required for the Fourier transform analysis of periodicity, indicated that the hydrophobic regions around the 7 GXXG motifs commence near the C-terminal end of each of the 7 inner helices of the alpha-toroid and continue to the N-terminal region of the helix. The results clearly explain why GCR2 has been understandably but erroneously predicted to be a GPCR.

  11. The effect of Zn, N and P application on nutrient uptake in wheat-maize sequence using isotopic techniques

    International Nuclear Information System (INIS)

    Tehrani, M.M.; Sachdev, P.; Sachdev, M.S.

    2006-01-01

    A pot experiment was conducted at the Nuclear Research Laboratory , Indian Agricultural Research Institute, New Delhi in 2000-2001. The experiment was 3x3x3 factorial in Completely Randomized Design (CRD) with three replications. Fertilizers were applied as three levels of zinc 0. 2.5 and 5 mg Zn kg -1 as ZnSO 4 , three levels of phosphorus 0, 7.5 and 15 mg P kg -1 through KH 2 PO 4 and three levels of nitrogen 30, 60 and 90 mg N kg -1 as urea. Zn fertilizer was not applied for the second crop in sequence. The amount of available Zn in soil decreased by the application of P and N, but increased by the Zn application. The P application increased the available pool of P in soil, but the zinc levels had no effect on it. Data revealed that the P application decreased the Zn concentration in plant tissue for both the crops. The per cent N utilization decreased drastically with increasing rate of N application from N 30 to N 90 in wheat. The highest level of P application resulted in least total Zn uptake, per cent Zndff, fertilizer Zn uptake and per cent Zn utilized from fertilizer. The no zinc application showed the highest value of Zn application to the wheat crop. The highest values of total P uptake, per cent Pdff, fertilizer uptake and per cent P utilized from fertilizer in the succeeding crop of maize were observed with residual effect of Zn 5 among three levels of Zn application to the first crop of maize. (author)

  12. Comparison of Burrows-Wheeler transform-based mapping algorithms used in high-throughput whole-genome sequencing: application to Illumina data for livestock genomes

    Science.gov (United States)

    Ongoing developments and cost decreases in next-generation sequencing (NGS) technologies have led to an increase in their application, which has greatly enhanced the fields of genetics and genomics. Mapping sequence reads onto a reference genome is a fundamental step in the analysis of NGS data. Eff...

  13. Risk evaluation method for faults by engineering approach. (2) Application concept of margin analysis utilizing accident sequences

    International Nuclear Information System (INIS)

    Kamiya, Masanobu; Kanaida, Syuuji; Kamiya, Kouichi; Sato, Kunihiko; Kuroiwa, Katsuya

    2016-01-01

    The influence of the fault displacement on the facility should to be evaluated not only by the activity of the fault but also by obtaining risk information by considering scenarios including such as the frequency and the degree of the hazard, which should be an appropriate approach for nuclear safety. An applicable concept of margin analysis utilizing accident sequences for evaluating the influence of the fault displacement is proposed. By use of this analysis, we can evaluate of the safety functions and margin for core damage, verify the efficiency of equipment of portable type and make a decision to take additional measures to reduce the risk by using obtained risk information. (author)

  14. The Application of Next Generation Sequencing Technology on Noninvasive Prenatal Test

    DEFF Research Database (Denmark)

    Jiang, Hui

    There are nearly 7000 rare diseases that have been reported in the world. Although most of them occur with a frequency of less than one in 2000, in total about 6% of the population suffers from rare diseases. These rare diseases are often caused by changes in genes, which is currently lack of eff...... diseases and monogenetic diseases in a noninvasively manner. The new approach has great potential to be wildly used in the worldwide with the decreasing in sequencing costs, and therefore play an incredible role to prevent rare diseases....

  15. Modeling of Video Sequences by Gaussian Mixture: Application in Motion Estimation by Block Matching Method

    Directory of Open Access Journals (Sweden)

    Abdenaceur Boudlal

    2010-01-01

    Full Text Available This article investigates a new method of motion estimation based on block matching criterion through the modeling of image blocks by a mixture of two and three Gaussian distributions. Mixture parameters (weights, means vectors, and covariance matrices are estimated by the Expectation Maximization algorithm (EM which maximizes the log-likelihood criterion. The similarity between a block in the current image and the more resembling one in a search window on the reference image is measured by the minimization of Extended Mahalanobis distance between the clusters of mixture. Performed experiments on sequences of real images have given good results, and PSNR reached 3 dB.

  16. Direct push driven in situ color logging tool (CLT): technique, analysis routines, and application

    Science.gov (United States)

    Werban, U.; Hausmann, J.; Dietrich, P.; Vienken, T.

    2014-12-01

    Direct push technologies have recently seen a broad development providing several tools for in situ parameterization of unconsolidated sediments. One of these techniques is the measurement of soil colors - a proxy information that reveals to soil/sediment properties. We introduce the direct push driven color logging tool (CLT) for real-time and depth-resolved investigation of soil colors within the visible spectrum. Until now, no routines exist on how to handle high-resolved (mm-scale) soil color data. To develop such a routine, we transform raw data (CIEXYZ) into soil color surrogates of selected color spaces (CIExyY, CIEL*a*b*, CIEL*c*h*, sRGB) and denoise small-scale natural variability by Haar and Daublet4 wavelet transformation, gathering interpretable color logs over depth. However, interpreting color log data as a single application remains challenging. Additional information, such as site-specific knowledge of the geological setting, is required to correlate soil color data to specific layers properties. Hence, we exemplary provide results from a joint interpretation of in situ-obtained soil color data and 'state-of-the-art' direct push based profiling tool data and discuss the benefit of additional data. The developed routine is capable of transferring the provided information obtained as colorimetric data into interpretable color surrogates. Soil color data proved to correlate with small-scale lithological/chemical changes (e.g., grain size, oxidative and reductive conditions), especially when combined with additional direct push vertical high resolution data (e.g., cone penetration testing and soil sampling). Thus, the technique allows enhanced profiling by means of providing another reproducible high-resolution parameter for analysis subsurface conditions. This opens potential new areas of application and new outputs for such data in site investigation. It is our intention to improve color measurements by means method of application and data

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

    Directory of Open Access Journals (Sweden)

    Vanessa eKrause

    2016-01-01

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

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

    Science.gov (United States)

    Trivedi, Chintan A.; Bollmann, Johann H.

    2013-01-01

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

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

    Directory of Open Access Journals (Sweden)

    Chintan A Trivedi

    2013-05-01

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

  20. Applications of direct-to-consumer hearing devices for adults with hearing loss: a review

    Science.gov (United States)

    Manchaiah, Vinaya; Taylor, Brian; Dockens, Ashley L; Tran, Nicole R; Lane, Kayla; Castle, Mariana; Grover, Vibhu

    2017-01-01

    Background This systematic literature review is aimed at investigating applications of direct-to-consumer hearing devices for adults with hearing loss. This review discusses three categories of direct-to-consumer hearing devices: 1) personal sound amplification products (PSAPs), 2) direct-mail hearing aids, and 3) over-the-counter (OTC) hearing aids. Method A literature review was conducted using EBSCOhost and included the databases CINAHL, MEDLINE, and PsycINFO. After applying prior agreed inclusion and exclusion criteria, 13 reports were included in the review. Results Included studies fell into three domains: 1) electroacoustic characteristics, 2) consumer surveys, and 3) outcome evaluations. Electroacoustic characteristics of these devices vary significantly with some meeting the stringent acoustic criteria used for hearing aids, while others producing dangerous output levels (ie, over 120-dB sound pressure level). Low-end (or low-cost) devices were typically poor in acoustic quality and did not meet gain levels necessary for most adult and elderly hearing loss patterns (eg, presbycusis), especially in high frequencies. Despite direct-mail hearing aids and PSAPs being associated with lower satisfaction when compared to hearing aids purchased through hearing health care professionals, consumer surveys suggest that 5%–19% of people with hearing loss purchase hearing aids through direct-mail or online. Studies on outcome evaluation suggest positive outcomes of OTC devices in the elderly population. Of note, OTC outcomes appear better when a hearing health care professional supports these users. Conclusion While some direct-to-consumer hearing devices have the capability to produce adverse effects due to production of dangerously high sound levels and internal noise, the existing literature suggests that there are potential benefits of these devices. Research of direct-to-consumer hearing devices is limited, and current published studies are of weak quality. Much

  1. Versatile Gene-Specific Sequence Tags for Arabidopsis Functional Genomics: Transcript Profiling and Reverse Genetics Applications

    Science.gov (United States)

    Hilson, Pierre; Allemeersch, Joke; Altmann, Thomas; Aubourg, Sébastien; Avon, Alexandra; Beynon, Jim; Bhalerao, Rishikesh P.; Bitton, Frédérique; Caboche, Michel; Cannoot, Bernard; Chardakov, Vasil; Cognet-Holliger, Cécile; Colot, Vincent; Crowe, Mark; Darimont, Caroline; Durinck, Steffen; Eickhoff, Holger; de Longevialle, Andéol Falcon; Farmer, Edward E.; Grant, Murray; Kuiper, Martin T.R.; Lehrach, Hans; Léon, Céline; Leyva, Antonio; Lundeberg, Joakim; Lurin, Claire; Moreau, Yves; Nietfeld, Wilfried; Paz-Ares, Javier; Reymond, Philippe; Rouzé, Pierre; Sandberg, Goran; Segura, Maria Dolores; Serizet, Carine; Tabrett, Alexandra; Taconnat, Ludivine; Thareau, Vincent; Van Hummelen, Paul; Vercruysse, Steven; Vuylsteke, Marnik; Weingartner, Magdalena; Weisbeek, Peter J.; Wirta, Valtteri; Wittink, Floyd R.A.; Zabeau, Marc; Small, Ian

    2004-01-01

    Microarray transcript profiling and RNA interference are two new technologies crucial for large-scale gene function studies in multicellular eukaryotes. Both rely on sequence-specific hybridization between complementary nucleic acid strands, inciting us to create a collection of gene-specific sequence tags (GSTs) representing at least 21,500 Arabidopsis genes and which are compatible with both approaches. The GSTs were carefully selected to ensure that each of them shared no significant similarity with any other region in the Arabidopsis genome. They were synthesized by PCR amplification from genomic DNA. Spotted microarrays fabricated from the GSTs show good dynamic range, specificity, and sensitivity in transcript profiling experiments. The GSTs have also been transferred to bacterial plasmid vectors via recombinational cloning protocols. These cloned GSTs constitute the ideal starting point for a variety of functional approaches, including reverse genetics. We have subcloned GSTs on a large scale into vectors designed for gene silencing in plant cells. We show that in planta expression of GST hairpin RNA results in the expected phenotypes in silenced Arabidopsis lines. These versatile GST resources provide novel and powerful tools for functional genomics. PMID:15489341

  2. Direct analysis in real time-Mass spectrometry (DART-MS) in forensic and security applications.

    Science.gov (United States)

    Pavlovich, Matthew J; Musselman, Brian; Hall, Adam B

    2018-03-01

    Over the last decade, direct analysis in real time (DART) has emerged as a viable method for fast, easy, and reliable "ambient ionization" for forensic analysis. The ability of DART to generate ions from chemicals that might be present at the scene of a criminal activity, whether they are in the gas, liquid, or solid phase, with limited sample preparation has made the technology a useful analytical tool in numerous forensic applications. This review paper summarizes many of those applications, ranging from the analysis of trace evidence to security applications, with a focus on providing the forensic scientist with a resource for developing their own applications. The most common uses for DART in forensics are in studying seized drugs, drugs of abuse and their metabolites, bulk and detonated explosives, toxic chemicals, chemical warfare agents, inks and dyes, and commercial plant and animal products that have been adulterated for economic gain. This review is meant to complement recent reviews that have described the fundamentals of the ionization mechanism and the general use of DART. We describe a wide range of forensic applications beyond the field of analyzing drugs of abuse, which dominates the literature, including common experimental and data analysis methods. © 2016 Wiley Periodicals, Inc. Mass Spec Rev 37:171-187, 2018. © 2016 Wiley Periodicals, Inc.

  3. [Application of single nucleotide polymorphism-microarray and target gene sequencing in the study of genetic etiology of children with unexplained intellectual disability or developmental delay].

    Science.gov (United States)

    Gao, Z J; Jiang, Q; Cheng, D Z; Yan, X X; Chen, Q; Xu, K M

    2016-10-02

    Objective: To evaluate the application of single nucleotide polymorphism (SNP)-microarray and target gene sequencing technology in the clinical molecular genetic diagnosis of unexplained intellectual disability(ID) or developmental delay (DD). Method: Patients with ID or DD were recruited in the Department of Neurology, Affiliated Children's Hospital of Capital Institute of Pediatrics between September 2015 and February 2016. The intellectual assessment of the patients was performed using 0-6-year-old pediatric examination table of neuropsychological development or Wechsler intelligence scale (>6 years). Patients with a DQ less than 49 or IQ less than 51 were included in this study. The patients were scanned by SNP-array for detection of genomic copy number variations (CNV), and the revealed genomic imbalance was confirmed by quantitative real time-PCR. Candidate gene mutation screening was carried out by target gene sequencing technology.Causal mutations or likely pathogenic variants were verified by polymerase chain reaction and direct sequencing. Result: There were 15 children with ID or DD enrolled, 9 males and 6 females. The age of these patients was 7 months-16 years and 9 months. SNP-array revealed that two of the 15 patients had genomic CNV. Both CNV were de novo micro deletions, one involved 11q24.1q25 and the other micro deletion located on 21q22.2q22.3. Both micro deletions were proved to have a clinical significance due to their association with ID, brain DD, unusual faces etc. by querying Decipher database. Thirteen patients with negative findings in SNP-array were consequently examined with target gene sequencing technology, genotype-phenotype correlation analysis and genetic analysis. Five patients were diagnosed with monogenic disorder, two were diagnosed with suspected genetic disorder and six were still negative. Conclusion: Sequential use of SNP-array and target gene sequencing technology can significantly increase the molecular genetic etiologic

  4. Experiences with High-Level Programming Directives for Porting Applications to GPUs

    International Nuclear Information System (INIS)

    Ding, Wei; Chapman, Barbara; Sankaran, Ramanan; Graham, Richard L.

    2012-01-01

    HPC systems now exploit GPUs within their compute nodes to accelerate program performance. As a result, high-end application development has become extremely complex at the node level. In addition to restructuring the node code to exploit the cores and specialized devices, the programmer may need to choose a programming model such as OpenMP or CPU threads in conjunction with an accelerator programming model to share and manage the difference node resources. This comes at a time when programmer productivity and the ability to produce portable code has been recognized as a major concern. In order to offset the high development cost of creating CUDA or OpenCL kernels, directives have been proposed for programming accelerator devices, but their implications are not well known. In this paper, we evaluate the state of the art accelerator directives to program several applications kernels, explore transformations to achieve good performance, and examine the expressiveness and performance penalty of using high-level directives versus CUDA. We also compare our results to OpenMP implementations to understand the benefits of running the kernels in the accelerator versus CPU cores.

  5. Persistence of malathion residues in stored milled rice: Direct and indirect applications

    International Nuclear Information System (INIS)

    Arshad, J.H.

    1990-01-01

    Two experiments were carried out: (i) to study the persistence of malathion residues in stored milled rice following multiple applications of 14 C-malathion to the bagged rice and (ii) to determine the degradation of malathion in stored milled rice and stored paddy following direct and single application of 14 C-malathion. The storage conditions were similar to those found in the local rice godowns. Three applications of malathion to the bagged milled rice resulted in the accumulation of malathion and its metabolites in and/or on the rice grains over the storage period. After 9 months' storage, ca. 4% of the total applied radioactivity, which amounted to 10 μg/g equivalent of 14 C residues, were found in and/or on the grains. About one fourth of the residue remained as the unchanged parent compound. On the other hand, when 14 C-malathion at the 10 ppm level was mixed directly with the milled rice or paddy prior to storage, the amount of malathion (recovered in the chloroform extracts) decreased from 6.2 μg/g at zero time to 2.9 μg/g after 3 months' storage for the milled rice samples. The major metabolite in the milled rice and paddy samples was malathion monocarboxylic acid with trace amounts of malathion dicarboxylic acid and malaoxon. (author). 5 refs, 3 tabs

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

    Science.gov (United States)

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

    2010-09-01

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

  7. Development of an accident sequence precursor methodology and its application to significant accident precursors

    Energy Technology Data Exchange (ETDEWEB)

    Jang, Seung Hyun; Park, Sung Hyun; Jae, Moo Sung [Dept. of of Nuclear Engineering, Hanyang University, Seoul (Korea, Republic of)

    2017-03-15

    The systematic management of plant risk is crucial for enhancing the safety of nuclear power plants and for designing new nuclear power plants. Accident sequence precursor (ASP) analysis may be able to provide risk significance of operational experience by using probabilistic risk assessment to evaluate an operational event quantitatively in terms of its impact on core damage. In this study, an ASP methodology for two operation mode, full power and low power/shutdown operation, has been developed and applied to significant accident precursors that may occur during the operation of nuclear power plants. Two operational events, loss of feedwater and steam generator tube rupture, are identified as ASPs. Therefore, the ASP methodology developed in this study may contribute to identifying plant risk significance as well as to enhancing the safety of nuclear power plants by applying this methodology systematically.

  8. Gapped sequence alignment using artificial neural networks: application to the MHC class I system

    DEFF Research Database (Denmark)

    Andreatta, Massimo; Nielsen, Morten

    2016-01-01

    . On this relatively simple system, we developed a sequence alignment method based on artificial neural networks that allows insertions and deletions in the alignment. Results: We show that prediction methods based on alignments that include insertions and deletions have significantly higher performance than methods...... trained on peptides of single lengths. Also, we illustrate how the location of deletions can aid the interpretation of the modes of binding of the peptide-MHC, as in the case of long peptides bulging out of the MHC groove or protruding at either terminus. Finally, we demonstrate that the method can learn...... the length profile of different MHC molecules, and quantified the reduction of the experimental effort required to identify potential epitopes using our prediction algorithm. Availability and implementation: The NetMHC-4.0 method for the prediction of peptide-MHC class I binding affinity using gapped...

  9. A xylanase gene directly cloned from the genomic DNA of alkaline wastewater sludge showing application potential in the paper industry.

    Science.gov (United States)

    Zhao, Yanyu; Luo, Huiying; Meng, Kun; Shi, Pengjun; Wang, Guozeng; Yang, Peilong; Yuan, Tiezheng; Yao, Bin

    2011-09-01

    A xylanase gene, aws-2x, was directly cloned from the genomic DNA of the alkaline wastewater sludge using degenerated PCR and modified TAIL-PCR. The deduced amino acid sequence of AWS-2x shared the highest identity (60%) with the xylanase from Chryseobacterium gleum belonging to the glycosyl hydrolase GH family 10. Recombinant AWS-2x was expressed in Escherichia coli BL21 (DE3) and purified to electrophoretic homogeneity. The enzyme showed maximal activity at pH 7.5 and 55 °C, maintained more than 50% of maximal activity when assayed at pH 9.0, and was stable over a wide pH range from 4.0 to 11.0. The specific activity of AWS-2x towards hardwood xylan (beechwood and birchwood xylan) was significantly higher than that to cereal xylan (oat spelt xylan and wheat arabinoxylan). These properties make AWS-2x a potential candidate for application in the pulp and paper industry.

  10. Stepwise integral scaling method for severe accident analysis and its application to corium dispersion in direct containment heating

    International Nuclear Information System (INIS)

    Ishii, M.; Zhang, G.; No, H. C.; Eltwila, F.

    1994-01-01

    Accident sequences which lead to severe core damage and to possible radioactive fission products into the environment have a very low probability. However, the interest in this area increased significantly due to the occurrence of the small break loss-of-coolant accident at TMI-2 which led to partial core damage, and of the Chernobyl accident in the former USSR which led to extensive core disassembly and significant release of fission products over several countries. In particular, the latter accident raised the international concern over the potential consequences of severe accidents in nuclear reactor systems. One of the significant shortcomings in the analyses of severe accidents is the lack of well-established and reliable scaling criteria for various multiphase flow phenomena. However, the scaling criteria are essential to the severe accident, because the full scale tests are basically impossible to perform. They are required for (1) designing scaled down or simulation experiments, (2) evaluating data and extrapolating the data to prototypic conditions, and (3) developing correctly scaled physical models and correlations. In view of this, a new scaling method is developed for the analysis of severe accidents. Its approach is quite different from the conventional methods. In order to demonstrate its applicability, this new stepwise integral scaling method has been applied to the analysis of the corium dispersion problem in the direct containment heating. ((orig.))

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

    Directory of Open Access Journals (Sweden)

    Corti Stefania

    2011-03-01

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

  12. Applications of direct-to-consumer hearing devices for adults with hearing loss: a review

    Directory of Open Access Journals (Sweden)

    Manchaiah V

    2017-05-01

    Full Text Available Vinaya Manchaiah,1–4 Brian Taylor,5 Ashley L Dockens,1 Nicole R Tran,1 Kayla Lane,1 Mariana Castle,1 Vibhu Grover1 1Department of Speech and Hearing Sciences, Lamar University, Beaumont, TX, USA; 2The Swedish Institute for Disability Research, Department of Behavioural Sciences and Learning, Linköping University, Linköping, Sweden; 3Audiology India, Mysore, 4Department of Speech and Hearing, School of Allied Health Sciences, Manipal University, Manipal, India; 5Taylor Audio LLC, Minneapolis, MN, USA Background: This systematic literature review is aimed at investigating applications of direct-to-consumer hearing devices for adults with hearing loss. This review discusses three categories of direct-to-consumer hearing devices: 1 personal sound amplification products (PSAPs, 2 direct-mail hearing aids, and 3 over-the-counter (OTC hearing aids.Method: A literature review was conducted using EBSCOhost and included the databases CINAHL, MEDLINE, and PsycINFO. After applying prior agreed inclusion and exclusion criteria, 13 reports were included in the review.Results: Included studies fell into three domains: 1 electroacoustic characteristics, 2 consumer surveys, and 3 outcome evaluations. Electroacoustic characteristics of these devices vary significantly with some meeting the stringent acoustic criteria used for hearing aids, while others producing dangerous output levels (ie, over 120-dB sound pressure level. Low-end (or low-cost devices were typically poor in acoustic quality and did not meet gain levels necessary for most adult and elderly hearing loss patterns (eg, presbycusis, especially in high frequencies. Despite direct-mail hearing aids and PSAPs being associated with lower satisfaction when compared to hearing aids purchased through hearing health care professionals, consumer surveys suggest that 5%–19% of people with hearing loss purchase hearing aids through direct-mail or online. Studies on outcome evaluation suggest positive

  13. A Quasi-Linear Behavioral Model and an Application to Self-Directed Learning

    Science.gov (United States)

    Ponton, Michael K.; Carr, Paul B.

    1999-01-01

    A model is presented that describes the relationship between one's knowledge of the world and the concomitant personal behaviors that serve as a mechanism to obtain desired outcomes. Integrated within this model are the differing roles that outcomes serve as motivators and as modifiers to one's worldview. The model is dichotomized between general and contextual applications. Because learner self-directedness (a personal characteristic) involves cognition and affection while self-directed learning (a pedagogic process) encompasses conation, behavior and introspection, the model can be dichotomized again in another direction. Presented also are the roles that cognitive motivation theories play in moving an individual through this behavioral model and the roles of wishes, self-efficacy, opportunity and self-influence.

  14. Gold nanoparticle arrays directly grown on nanostructured indium tin oxide electrodes: Characterization and electroanalytical application

    International Nuclear Information System (INIS)

    Zhang Jingdong; Oyama, Munetaka

    2005-01-01

    This work describes an improved seed-mediated growth approach for the direct attachment and growth of mono-dispersed gold nanoparticles on nanostructured indium tin oxide (ITO) surfaces. It was demonstrated that, when the seeding procedure of our previously reported seed-mediated growth process on an ITO surface was modified, the density of gold nanospheres directly grown on the surface could be highly improved, while the emergence of nanorods was restrained. By field emission scanning electron microscopy (FE-SEM) and cyclic voltammetry, the growth of gold nanoparticles with increasing growth time on the defect sites of nanostructured ITO surface was monitored. Using a [Fe(China) 6 ] 3- /[Fe(China) 6 ] 4- redox probe, the increasingly facile heterogeneous electron transfer kinetics resulting from the deposition and growth of gold nanoparticle arrays was observed. The as-prepared gold nanoparticle arrays exhibited high catalytic activity toward the electrooxidation of nitric oxide, which could provide electroanalytical application for nitric oxide sensing

  15. Nuclear Material Accountability Applications of a Continuous Energy and Direction Gamma Ray Detector

    International Nuclear Information System (INIS)

    Gerts, David; Bean, Robert; Paff, Marc

    2010-01-01

    The Idaho National Laboratory has recently developed a detector system based on the principle of a Wilson cloud chamber that gives the original energy and direction to a gamma ray source. This detector has the properties that the energy resolution is continuous and the direction to the source can be resolved to desired fidelity. Furthermore, the detector has low power requirements, is durable, operates in widely varying environments, and is relatively cheap to produce. This detector is expected, however, to require significant time to perform measurements. To mitigate the significant time for measurements, the detector is expected to scale to very large sizes with a linear increase in cost. For example, the proof of principle detector is approximately 30,000 cm3. This work describes the technical results that lead to these assertions. Finally, the applications of this detector are described in the context of nuclear material accountability.

  16. Application of N-doped graphene modified carbon ionic liquid electrode for direct electrochemistry of hemoglobin.

    Science.gov (United States)

    Sun, Wei; Dong, Lifeng; Deng, Ying; Yu, Jianhua; Wang, Wencheng; Zhu, Qianqian

    2014-06-01

    Nitrogen-doped graphene (NG) was synthesized and used for the investigation on direct electrochemistry of hemoglobin (Hb) with a carbon ionic liquid electrode as the substrate electrode. Due to specific characteristics of NG such as excellent electrocatalytic property and large surface area, direct electron transfer of Hb was realized with enhanced electrochemical responses appearing. Electrochemical behaviors of Hb on the NG modified electrode were carefully investigated with the electrochemical parameters calculated. The Hb modified electrode exhibited excellent electrocatalytic reduction activity toward different substrates, such as trichloroacetic acid and H2O2, with wider dynamic range and lower detection limit. These findings show that NG can be used for the preparation of chemically modified electrodes with improved performance and has potential applications in electrochemical sensing. Copyright © 2014 Elsevier B.V. All rights reserved.

  17. Training sequence design for MIMO channels : An application-oriented approach

    NARCIS (Netherlands)

    Katselis, D.; Rojas, C.R.; Bengtsson, M.; Bjornson, E.; Bombois, X.; Shariati, N.; Jansson, M.; Hjalmarsson, H.

    2013-01-01

    In this paper, the problem of training optimization for estimating a multiple-input multiple-output (MIMO) flat fading channel in the presence of spatially and temporally correlated Gaussian noise is studied in an application-oriented setup. So far, the problem of MIMO channel estimation has mostly

  18. 76 FR 28990 - Ultra High Throughput Sequencing for Clinical Diagnostic Applications-Approaches To Assess...

    Science.gov (United States)

    2011-05-19

    ... Web cast of the public meeting, you must register online at http://www.fda.gov/MedicalDevices/News... technologies are currently extensively used in research and are entering clinical diagnostic use; they are... technologies for clinical applications, appropriate evaluation tools (e.g., standards, well established...

  19. Adapting Team-Based Learning for Application in the Basic Electric Circuit Theory Sequence

    Science.gov (United States)

    O'Connell, Robert M.

    2015-01-01

    Team-based learning (TBL) is a form of student-centered active learning in which students independently study new conceptual material before it is treated in the classroom, and then subsequently spend considerable classroom time working in groups on increasingly challenging problems and applications based on that new material. TBL provides…

  20. Application of large-scale sequencing to marker discovery in plants

    Indian Academy of Sciences (India)

    2012-10-15

    Oct 15, 2012 ... mate-pair libraries (large insert libraries), RNA-Seq data, reduced ... range of different applications for SGS have been developed and applied to marker ..... duced by human selection for desirable grain qualities. A total of 399 ...

  1. Integrated multi sensors and camera video sequence application for performance monitoring in archery

    Science.gov (United States)

    Taha, Zahari; Arif Mat-Jizat, Jessnor; Amirul Abdullah, Muhammad; Muazu Musa, Rabiu; Razali Abdullah, Mohamad; Fauzi Ibrahim, Mohamad; Hanafiah Shaharudin, Mohd Ali

    2018-03-01

    This paper explains the development of a comprehensive archery performance monitoring software which consisted of three camera views and five body sensors. The five body sensors evaluate biomechanical related variables of flexor and extensor muscle activity, heart rate, postural sway and bow movement during archery performance. The three camera views with the five body sensors are integrated into a single computer application which enables the user to view all the data in a single user interface. The five body sensors’ data are displayed in a numerical and graphical form in real-time. The information transmitted by the body sensors are computed with an embedded algorithm that automatically transforms the summary of the athlete’s biomechanical performance and displays in the application interface. This performance will be later compared to the pre-computed psycho-fitness performance from the prefilled data into the application. All the data; camera views, body sensors; performance-computations; are recorded for further analysis by a sports scientist. Our developed application serves as a powerful tool for assisting the coach and athletes to observe and identify any wrong technique employ during training which gives room for correction and re-evaluation to improve overall performance in the sport of archery.

  2. Hydrothermal research and development assessment. Task Force report: projections for direct-heat applications

    Energy Technology Data Exchange (ETDEWEB)

    1982-04-01

    Low and moderate temperature hydrothermal resources suitable for direct-heat applications have been identified in 37 states. The extent to which three resources might be used over the next 20 years were evaluated and the probable impact of Federal programs on hydrothermal resource utilization was assessed. The use types that comprise the bulk of the market were determined. Representative firms and municipalities were interviewed to determine their willingness to use hydrothermal energy, and to determine the investment decision criteria that would influence their actions. (MHR)

  3. Superior quality diamond heel inserts improve cutting structure and seal life in abrasive and directional applications

    Energy Technology Data Exchange (ETDEWEB)

    Cobb, Tyler; Scott, Dan; Nelms, Derek [Society of Petroleum Engineers (United States)

    2011-07-01

    In the oil and gas industry, continuous improvements over the last century have led to the development of increasingly efficient drilling equipment. Among the new technologies is the polycrystalline diamond compact bit which has become more efficient than roller cone bits for several applications; the utilization of roller cone bits is now restricted to tough applications such as directional drilling and drilling through hard and abrasive formations. The aim of this paper is to present the development of improved roller cone bits using new designs and diamond inserts of superior quality. Two case studies on the use of improved roller cone bits are presented herein. Results showed that the novel diamond inserts combined with the design improvements provide better wear resistance. This paper demonstrated that roller cone bits have achieved greater reliability and longevity thanks to the new generation of diamond inserts and to design improvements.

  4. A liquid crystal polymer membrane MEMS sensor for flow rate and flow direction sensing applications

    International Nuclear Information System (INIS)

    Kottapalli, A G P; Tan, C W; Olfatnia, M; Miao, J M; Barbastathis, G; Triantafyllou, M

    2011-01-01

    The paper reports the design, fabrication and experimental results of a liquid crystal polymer (LCP) membrane-based pressure sensor for flow rate and flow direction sensing applications. Elaborate experimental testing results demonstrating the sensors' performance as an airflow sensor have been illustrated and validated with theory. MEMS sensors using LCP as a membrane structural material show higher sensitivity and reliability over silicon counterparts. The developed device is highly robust for harsh environment applications such as atmospheric wind flow monitoring and underwater flow sensing. A simple, low-cost and repeatable fabrication scheme has been developed employing low temperatures. The main features of the sensor developed in this work are a LCP membrane with integrated thin film gold piezoresistors deposited on it. The sensor developed demonstrates a good sensitivity of 3.695 mV (ms −1 ) −1 , large operating range (0.1 to >10 ms −1 ) and good accuracy in measuring airflow with an average error of only 3.6% full-scale in comparison with theory. Various feasible applications of the developed sensor have been demonstrated with experimental results. The sensor was tested for two other applications—in clinical diagnosis for breath rate, breath velocity monitoring, and in underwater applications for object detection by sensing near-field spatial flow pressure

  5. Adaptive Basis Selection for Exponential Family Smoothing Splines with Application in Joint Modeling of Multiple Sequencing Samples

    OpenAIRE

    Ma, Ping; Zhang, Nan; Huang, Jianhua Z.; Zhong, Wenxuan

    2017-01-01

    Second-generation sequencing technologies have replaced array-based technologies and become the default method for genomics and epigenomics analysis. Second-generation sequencing technologies sequence tens of millions of DNA/cDNA fragments in parallel. After the resulting sequences (short reads) are mapped to the genome, one gets a sequence of short read counts along the genome. Effective extraction of signals in these short read counts is the key to the success of sequencing technologies. No...

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

    Science.gov (United States)

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

    2014-09-04

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

  7. Application of ion torrent sequencing to the assessment of the effect of alkali ballast water treatment on microbial community diversity.

    Directory of Open Access Journals (Sweden)

    Masanori Fujimoto

    Full Text Available The impact of NaOH as a ballast water treatment (BWT on microbial community diversity was assessed using the 16S rRNA gene based Ion Torrent sequencing with its new 400 base chemistry. Ballast water samples from a Great Lakes ship were collected from the intake and discharge of both control and NaOH (pH 12 treated tanks and were analyzed in duplicates. One set of duplicates was treated with the membrane-impermeable DNA cross-linking reagent propidium mono-azide (PMA prior to PCR amplification to differentiate between live and dead microorganisms. Ion Torrent sequencing generated nearly 580,000 reads for 31 bar-coded samples and revealed alterations of the microbial community structure in ballast water that had been treated with NaOH. Rarefaction analysis of the Ion Torrent sequencing data showed that BWT using NaOH significantly decreased microbial community diversity relative to control discharge (p<0.001. UniFrac distance based principal coordinate analysis (PCoA plots and UPGMA tree analysis revealed that NaOH-treated ballast water microbial communities differed from both intake communities and control discharge communities. After NaOH treatment, bacteria from the genus Alishewanella became dominant in the NaOH-treated samples, accounting for <0.5% of the total reads in intake samples but more than 50% of the reads in the treated discharge samples. The only apparent difference in microbial community structure between PMA-processed and non-PMA samples occurred in intake water samples, which exhibited a significantly higher amount of PMA-sensitive cyanobacteria/chloroplast 16S rRNA than their corresponding non-PMA total DNA samples. The community assembly obtained using Ion Torrent sequencing was comparable to that obtained from a subset of samples that were also subjected to 454 pyrosequencing. This study showed the efficacy of alkali ballast water treatment in reducing ballast water microbial diversity and demonstrated the application of new

  8. Genome wide characterization of simple sequence repeats in watermelon genome and their application in comparative mapping and genetic diversity analysis.

    Science.gov (United States)

    Zhu, Huayu; Song, Pengyao; Koo, Dal-Hoe; Guo, Luqin; Li, Yanman; Sun, Shouru; Weng, Yiqun; Yang, Luming

    2016-08-05

    clustered in another group. Furthermore, structure analysis was consistent with the dendrogram indicating the 134 watermelon accessions were classified into two populations. The large number of genome wide SSR markers developed herein from the watermelon genome provides a valuable resource for genetic map construction, QTL exploration, map-based gene cloning and marker-assisted selection in watermelon which has a very narrow genetic base and extremely low polymorphism among cultivated lines. Furthermore, the cross-species transferable SSR markers identified herein should also have practical uses in many applications in species of Cucurbitaceae family whose whole genome sequences are not yet available.

  9. Application of Next Generation Sequencing in Mammalian Embryogenomics: Lessons Learned from Endogenous Betaretroviruses of Sheep

    Science.gov (United States)

    Spencer, Thomas E.; Palmarini, Massimo

    2012-01-01

    Endogenous retroviruses (ERVs) are present in the genome of all vertebrates and are remnants of ancient exogenous retroviral infections of the host germline transmitted vertically from generation to generation. The sheep genome contains 27 JSRV-related endogenous betaretroviruses (enJSRVs) related to the pathogenic Jaagsiekte sheep retrovirus (JSRV) that have been integrating in the host genome for the last 5 to 7 million years. The exogenous JSRV is a causative agent of a transmissible lung cancer in sheep, and enJSRVs are able to protect the host against JSRV infection. In sheep, the enJSRVs are most abundantly expressed in the uterine epithelia as well as in the conceptus (embryo and associated extraembryonic membranes) trophectoderm. Sixteen of the 27 enJSRV loci contain an envelope (env) gene with an intact open reading frame, and in utero loss-of-function experiments found the enJSRVs Env to be essential for trophoblast outgrowth and conceptus elongation. Collectively, available evidence supports the ideas that genes captured from ancestral retroviruses were pivotal in the acquisition of new, important functions in mammalian evolution and were positively selected for biological roles in genome plasticity, protection of the host against infection of related pathogenic and exogenous retroviruses, and a convergent physiological role in placental morphogenesis and thus mammalian reproduction. The discovery of ERVs in mammals was initially based on molecular cloning discovery techniques and will be boosted forward by next generation sequencing technologies and in silico discovery techniques. PMID:22951118

  10. Application of Tandem Two-Dimensional Mass Spectrometry for Top-Down Deep Sequencing of Calmodulin.

    Science.gov (United States)

    Floris, Federico; Chiron, Lionel; Lynch, Alice M; Barrow, Mark P; Delsuc, Marc-André; O'Connor, Peter B

    2018-06-04

    Two-dimensional mass spectrometry (2DMS) involves simultaneous acquisition of the fragmentation patterns of all the analytes in a mixture by correlating their precursor and fragment ions by modulating precursor ions systematically through a fragmentation zone. Tandem two-dimensional mass spectrometry (MS/2DMS) unites the ultra-high accuracy of Fourier transform ion cyclotron resonance (FT-ICR) MS/MS and the simultaneous data-independent fragmentation of 2DMS to achieve extensive inter-residue fragmentation of entire proteins. 2DMS was recently developed for top-down proteomics (TDP), and applied to the analysis of calmodulin (CaM), reporting a cleavage coverage of about ~23% using infrared multiphoton dissociation (IRMPD) as fragmentation technique. The goal of this work is to expand the utility of top-down protein analysis using MS/2DMS in order to extend the cleavage coverage in top-down proteomics further into the interior regions of the protein. In this case, using MS/2DMS, the cleavage coverage of CaM increased from ~23% to ~42%. Graphical Abstract Two-dimensional mass spectrometry, when applied to primary fragment ions from the source, allows deep-sequencing of the protein calmodulin.

  11. Design Considerations of a Transverse Flux Machine for Direct-Drive Wind Turbine Applications: Preprint

    Energy Technology Data Exchange (ETDEWEB)

    Husain, Tausif; Hasan, Iftekhar; Sozer, Yilmaz; Husain, Iqbal; Muljadi, Eduard

    2017-01-01

    This paper presents the design considerations of a double-sided transverse flux machine (TFM) for direct-drive wind turbine applications. The TFM has a modular structure with quasi-U stator cores and ring windings. The rotor is constructed with ferrite magnets in a flux-concentrating arrangement to achieve high air gap flux density. The design considerations for this TFM with respect to initial sizing, pole number selection, key design ratios, and pole shaping are presented in this paper. Pole number selection is critical in the design process of a TFM because it affects both the torque density and power factor under fixed magnetic and changing electrical loading. Several key design ratios are introduced to facilitate the design procedure. The effect of pole shaping on back-emf and inductance is also analyzed. These investigations provide guidance toward the required design of a TFM for direct-drive applications. The analyses are carried out using analytical and three-dimensional finite element analysis. A prototype is under construction for experimental verification.

  12. A Reconfigurable WiMAX Antenna for Directional and Broadside Application

    Directory of Open Access Journals (Sweden)

    M. Jusoh

    2013-01-01

    Full Text Available A novel reconfigurable compact patch array antenna for directional and broadside application is proposed. The presented antenna has successfully been able to function for directional beam at 320° or 35° and divisive broadside beam at 43° and 330°. This is realized in the unique form of aperture coupled spiral feeding technique and positioning of the radiating elements at 0°, 90,° and 180°. The switchable feature is effectively performed by the configuration of three PIN diodes. All PIN diodes are positioned at the specific location of the aperture coupled structure. It is discovered in simulation that the switches can be represented with a copper strip line or touchstone (TS block . The proposed antenna design operates at 2.37 GHz to 2.41 GHz and has a maximum gain of 6.4 dB and efficiency of 85.97%. Such antenna produces a broadside HPBW with a wider bandwidth covering from −90° to 90° compared to the normal microstrip antenna which could only provide HPBW of −50° to 50°. Moreover, the proposed antenna has small physical dimension of 100 mm by 100 mm. The simulation and measurement results have successfully exhibited the idea of the presented antenna performance. Therefore, the antenna is sufficiently competent in the smart WiMAX antenna application.

  13. Patient’s Cross-border Mobility Directive: Application, Performance and Perceptions Two Years after Transposition

    Directory of Open Access Journals (Sweden)

    Riedel Rafał

    2016-10-01

    Full Text Available This paper seeks to analyse the directive on the application of patients’ rights in cross-border healthcare. Two years after the transposition, it is time for first evaluations of its application, performance and perception. The analysis consists of three major elements: reconstruction of the legal scope and subject matter of the new legislation, conclusions of the evaluative reports monitoring its implementation and performance as well as the public opinion polls revealing the EU citizens’ perception of its details. These three components combined together deliver a picture of the state of play about the pan-European cross-border patients’ mobility. The bottomline conclusions negatively verify the supposition present in some earlier literature on patients’ cross-border mobility that the directive has a transformative potential leading towards the creation of truly competitive pan-European medical market. After two years of its operation, there is still no increased patients’ mobility across EU internal borders observed. As regards the speculations for the future, there are only some weak symptoms identified and they may result in intensified cross-border mobility for healthcare.

  14. A rank-based sequence aligner with applications in phylogenetic analysis.

    Directory of Open Access Journals (Sweden)

    Liviu P Dinu

    Full Text Available Recent tools for aligning short DNA reads have been designed to optimize the trade-off between correctness and speed. This paper introduces a method for assigning a set of short DNA reads to a reference genome, under Local Rank Distance (LRD. The rank-based aligner proposed in this work aims to improve correctness over speed. However, some indexing strategies to speed up the aligner are also investigated. The LRD aligner is improved in terms of speed by storing [Formula: see text]-mer positions in a hash table for each read. Another improvement, that produces an approximate LRD aligner, is to consider only the positions in the reference that are likely to represent a good positional match of the read. The proposed aligner is evaluated and compared to other state of the art alignment tools in several experiments. A set of experiments are conducted to determine the precision and the recall of the proposed aligner, in the presence of contaminated reads. In another set of experiments, the proposed aligner is used to find the order, the family, or the species of a new (or unknown organism, given only a set of short Next-Generation Sequencing DNA reads. The empirical results show that the aligner proposed in this work is highly accurate from a biological point of view. Compared to the other evaluated tools, the LRD aligner has the important advantage of being very accurate even for a very low base coverage. Thus, the LRD aligner can be considered as a good alternative to standard alignment tools, especially when the accuracy of the aligner is of high importance. Source code and UNIX binaries of the aligner are freely available for future development and use at http://lrd.herokuapp.com/aligners. The software is implemented in C++ and Java, being supported on UNIX and MS Windows.

  15. [Application of Next Generation Sequencing for AML/MDS Diagnosis and Treatment].

    Science.gov (United States)

    Cheng, Huan-Chen; Liu, Sheng-Wei; Liu, Yu; Zhao, Xue-Fei; Li, Wei; Qiu, Lin; Ma, Jun

    2017-12-01

    To detect the mutations of AML/MDS- related genes by using next generation sequencing (NGS), to analyze the mutation levels of each genes in the AML/MDS and the sensitivity of NGS, and to evaluate the feasibility of gene mutations for monitoring the MRD and predicating the progression of diseases. The specimens were collected from primary AML (68 cases) and MDS (57 cases) patients from August 2015 to June 2016 in the Harbin Institute of Hematology and Oncology. The mutations of 22 related genes were detected by using AML/MDS-NGS chips. TET2 gene showed the highest mutation rate in AML (55.9%) and MDS (56.1%). The gene mutations were as follows: CEBPA (11.8%), DNMT3A (7.4%), C-KIT (7.4%) and FLT3-ITD (7.4%) in AML, and U2AF1 (10.5%) and SRSF2 (10.5%) in MDS. All the genes had specific mutation sites except TP53 and CEBPA. The mutations of FLT3, C-KIT and CEBPA became negative in the 5 AML patients in remission when compared with those at primary attack, but the mutation rate of TET2 gene was not obviously changed, whereas the mutation rate of the 5 MDS patients was not significantly changed. The new gene mutations appeared in 3 MDS patients with disease progression, but the mutation rate was not changed significantly in the disease progression. The gene mutation rate still has not been changed significantly even after remission. Both AML and MDS have their own specific mutated genes and sites. Some gene mutations, such as CEBPA, can be used as an effective indicator to monitoring MRD in AML patients, but those only used for the evaluation of the disease progression and prognosis in MDS patients.

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

    Directory of Open Access Journals (Sweden)

    Bahram Nasr Isfahani

    2006-09-01

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

  17. Near-term Forecasting of Solar Total and Direct Irradiance for Solar Energy Applications

    Science.gov (United States)

    Long, C. N.; Riihimaki, L. D.; Berg, L. K.

    2012-12-01

    variability. This new system could be a long term economical solution for solar energy applications.xample of SW Flux Analysis global hemispheric (light blue) and direct (yellow) clear-sky shortwave (SW) along with corresponding actual global hemispheric (blue) and direct (red) SW, and the corresponding fractional sky cover (black, right Y-axis). Note in afternoon about 40-50% of the global SW is available, yet most times there is no direct SW.

  18. Omni Directional Multimaterial Soft Cylindrical Actuator and Its Application as a Steerable Catheter.

    Science.gov (United States)

    Gul, Jahan Zeb; Yang, Young Jin; Su, Kim Young; Choi, Kyung Hyun

    2017-09-01

    Soft actuators with complex range of motion lead to strong interest in applying devices like biomedical catheters and steerable soft pipe inspectors. To facilitate the use of soft actuators in devices where controlled, complex, precise, and fast motion is required, a structurally controlled Omni directional soft cylindrical actuator is fabricated in a modular way using multilayer composite of polylactic acid based conductive Graphene, shape memory polymer, shape memory alloy, and polyurethane. Multiple fabrication techniques are discussed step by step that mainly include fused deposition modeling based 3D printing, dip coating, and UV curing. A mathematical control model is used to generate patterned electrical signals for the Omni directional deformations. Characterizations like structural control, bending, recovery, path, and thermal effect are carried out with and without load (10 g) to verify the new cylindrical design concept. Finally, the application of Omni directional actuator as a steerable catheter is explored by fabricating a scaled version of carotid artery through 3D printing using a semitransparent material.

  19. PHYSICAL ATTRIBUTES OF SOIL AFTER SWINE WASTEWATER APPLICATION AS COVER FERTILIZER ON MAIZE CROP AND BLACK OATS SEQUENCE

    Directory of Open Access Journals (Sweden)

    FÁBIO PALCZEWSKI PACHECO

    2017-01-01

    Full Text Available The rate of swine wastewater application (SW in agricultural production could result in the replacement of chemical fertilizers. However, SW destroys soil physical properties by decreasing pore bulk, which negatively affects both crop yield and development. In this context, this study aimed at monitoring the influence of swine wastewater as a cover fertilizer in maize and black oats in sequence on soil physical properties. Five application rates (0, 100, 200, 300 and 537 m3ha - 1 equivalent to 0, 11.2, 22.3, 33.5 and 60 kg ha-1 N, respectively, based on the average nitrogen concentration in SW were tested with four replications each. In the studied area, soil porosity, density, and water content, before maize sowing and at the end of the cycles of maize and black oats, were determined by the volumetric ring method. Data were submitted for regression analyses. There was a reduction in the macroporosity and total porosity of the soil when the SW application rate, before maize cultivation, was higher. The introduction of black oats helped to improve the physical quality of the soil and reduced the compaction of the surface layer from 0 to 15 cm and 100 to 300 m3 ha-1 SW rates.

  20. Alignment of Short Reads: A Crucial Step for Application of Next-Generation Sequencing Data in Precision Medicine

    Directory of Open Access Journals (Sweden)

    Hao Ye

    2015-11-01

    Full Text Available Precision medicine or personalized medicine has been proposed as a modernized and promising medical strategy. Genetic variants of patients are the key information for implementation of precision medicine. Next-generation sequencing (NGS is an emerging technology for deciphering genetic variants. Alignment of raw reads to a reference genome is one of the key steps in NGS data analysis. Many algorithms have been developed for alignment of short read sequences since 2008. Users have to make a decision on which alignment algorithm to use in their studies. Selection of the right alignment algorithm determines not only the alignment algorithm but also the set of suitable parameters to be used by the algorithm. Understanding these algorithms helps in selecting the appropriate alignment algorithm for different applications in precision medicine. Here, we review current available algorithms and their major strategies such as seed-and-extend and q-gram filter. We also discuss the challenges in current alignment algorithms, including alignment in multiple repeated regions, long reads alignment and alignment facilitated with known genetic variants.

  1. In- and Ga-based inorganic double perovskites with direct bandgaps for photovoltaic applications.

    Science.gov (United States)

    Dai, Jun; Ma, Liang; Ju, Minggang; Huang, Jinsong; Zeng, Xiao Cheng

    2017-08-16

    Double perovskites in the form of A 2 B'B''X 6 (A = Cs, B' = Ag, B'' = Bi) have been reported as potential alternatives to lead-containing organometal trihalide perovskites. However, all double perovskites synthesized to date exhibit indirect bandgaps >1.95 eV, which are undesirable for photovoltaic and optoelectronic applications. Herein, we report a comprehensive computer-aided screening of In- and Ga-based double perovskites for potential photovoltaic applications. To this end, several preconditions are implemented for the screening of optimal candidates, which include structural stability, electronic bandgaps, and optical absorption. Importantly, four In- and Ga-based double perovskites are identified to possess direct bandgaps within the desirable range of 0.9-1.6 eV for photovoltaic applications. Dominant optical absorption of the four double perovskites is found to be in the UV range. The structural and thermal stability of the four double perovskites are examined using both the empirical Goldschmidt ratio and convex-hull calculations. Only Cs 2 AgInBr 6 is predicted to be thermodynamically stable.

  2. A survey of direct inversion methods having possible application to tunnel detection

    International Nuclear Information System (INIS)

    Mager, R.D.

    1985-01-01

    Within recent years there has been considerable interest in the development of geophysical methods for the location of hidden underground tunnels and cavities. Consideration of this problem has been motivated by military applications, such as the detection of shallow man-made tunnels and arm caches, as well as civilian applications such as detection of limestone cavities in karst terrain and the mapping of abandoned mine workings. There are also applications for in-situ coal gasification and for the monitoring of nuclear waste disposal sites. The most reliable method presently used to map these underground anomalies has been direct detection by closely spaced drilling. However, the high cost of drilling renders this method impractical except for detailed and localized mapping, and certainly unfeasible for any type of broad-scale reconnaissance activity. Largely motivated by petroleum and mineral exploration needs, however, the seismic industry has seen a virtual revolution in acquisition and processing techniques within the past ten years. Paralleling these developments have been corresponding developments in acoustical imaging and non-destructive testing. Researchers in the field of inverse scattering have produced a number of new methods for target imaging from backscattered reflection data

  3. Packaging of high-power bars for optical pumping and direct applications

    Science.gov (United States)

    Heinemann, Stefan; An, Haiyan; Barnowski, Tobias; Jiang, John; Negoita, Viorel; Roff, Robert; Vethake, Thilo; Boucke, Konstantin; Treusch, Georg

    2015-03-01

    Continuous cost reduction, improved reliability and modular platform guide the design of our next generation heatsink and packaging process. Power scaling from a single device effectively lowers the cost, while electrical insulation of the heatsink, low junction temperature and hard solder enable high reliability. We report on the latest results for scaling the output power of bars for optical pumping and materials processing. The epitaxial design and geometric structures are specific for the application, while packaging with minimum thermal impedance, low stress and low smile are generic features. The isolated heatsink shows a thermal impedance of 0.2 K/W and the maximum output power is limited by the requirement of a junction temperature of less than 68oC for high reliability. Low contact impedance are addressed for drive currents of 300 A. For pumping applications, bars with a fill factor of 60% are deployed emitting more than 300 W of output power with an efficiency of about 55% and 8 bars are arranged in a compact pump module emitting 2 kW of collimated power suitable for pumping disk lasers. For direct applications we target coupling kilowatts of output powers into fibers of 100 μm diameter with 0.1 NA based on dense wavelength multiplexing. Low fill factor bars with large optical waveguide and specialized coating also emit 300 W.

  4. Application and outcomes of therapy combining transcranial direct current stimulation and virtual reality: a systematic review.

    Science.gov (United States)

    Massetti, Thais; Crocetta, Tânia Brusque; Silva, Talita Dias da; Trevizan, Isabela Lopes; Arab, Claudia; Caromano, Fátima Aparecida; Monteiro, Carlos Bandeira de Mello

    2017-08-01

    To evaluate the methods and major outcomes of transcranial direct current stimulation (tDCS) combined with virtual reality (VR) therapy in randomized controlled trials. A systematic review was performed following PRISMA guidelines using PubMed, PubMed Central, Web of Science and CAPES periodic databases, with no time restriction. The studies were screened for the following inclusion criteria: human subjects, combination of VR and tDCS methods, and randomized controlled study design. All potentially relevant articles were independently reviewed by two researchers, who reached a consensus on which articles met the inclusion criteria. The PEDro scale was used to evaluate the studies. Eleven studies were included, all of which utilized a variety of tDCS and VR application methods. The main outcomes were found to be beneficial in intervention groups of different populations, including improvements in body sway, gait, stroke recovery, pain management and vegetative reactions. The use of tDCS combined with VR showed positive results in both healthy and impaired patients. Future studies with larger sample sizes and homogeneous participants are required to confirm the benefits of tDCS and VR. Implications for Rehabilitation tDCS with VR intervention can be an alternative to traditional rehabilitation programs. tDCS with VR is a promising type of intervention with a variety of positive effects. Application of tDCS with VR is appropriated to both healthy and impaired patients. There is no consensus of tDCS with VR application.

  5. The Development of an UAV Borne Direct Georeferenced Photogrammetric Platform for Ground Control Point Free Applications

    Directory of Open Access Journals (Sweden)

    Chien-Hsun Chu

    2012-07-01

    Full Text Available To facilitate applications such as environment detection or disaster monitoring, the development of rapid low cost systems for collecting near real time spatial information is very critical. Rapid spatial information collection has become an emerging trend for remote sensing and mapping applications. In this study, a fixed-wing Unmanned Aerial Vehicle (UAV-based spatial information acquisition platform that can operate in Ground Control Point (GCP free environments is developed and evaluated. The proposed UAV based photogrammetric platform has a Direct Georeferencing (DG module that includes a low cost Micro Electro Mechanical Systems (MEMS Inertial Navigation System (INS/ Global Positioning System (GPS integrated system. The DG module is able to provide GPS single frequency carrier phase measurements for differential processing to obtain sufficient positioning accuracy. All necessary calibration procedures are implemented. Ultimately, a flight test is performed to verify the positioning accuracy in DG mode without using GCPs. The preliminary results of positioning accuracy in DG mode illustrate that horizontal positioning accuracies in the x and y axes are around 5 m at 300 m flight height above the ground. The positioning accuracy of the z axis is below 10 m. Therefore, the proposed platform is relatively safe and inexpensive for collecting critical spatial information for urgent response such as disaster relief and assessment applications where GCPs are not available.

  6. mrsFAST-Ultra: a compact, SNP-aware mapper for high performance sequencing applications.

    Science.gov (United States)

    Hach, Faraz; Sarrafi, Iman; Hormozdiari, Farhad; Alkan, Can; Eichler, Evan E; Sahinalp, S Cenk

    2014-07-01

    High throughput sequencing (HTS) platforms generate unprecedented amounts of data that introduce challenges for processing and downstream analysis. While tools that report the 'best' mapping location of each read provide a fast way to process HTS data, they are not suitable for many types of downstream analysis such as structural variation detection, where it is important to report multiple mapping loci for each read. For this purpose we introduce mrsFAST-Ultra, a fast, cache oblivious, SNP-aware aligner that can handle the multi-mapping of HTS reads very efficiently. mrsFAST-Ultra improves mrsFAST, our first cache oblivious read aligner capable of handling multi-mapping reads, through new and compact index structures that reduce not only the overall memory usage but also the number of CPU operations per alignment. In fact the size of the index generated by mrsFAST-Ultra is 10 times smaller than that of mrsFAST. As importantly, mrsFAST-Ultra introduces new features such as being able to (i) obtain the best mapping loci for each read, and (ii) return all reads that have at most n mapping loci (within an error threshold), together with these loci, for any user specified n. Furthermore, mrsFAST-Ultra is SNP-aware, i.e. it can map reads to reference genome while discounting the mismatches that occur at common SNP locations provided by db-SNP; this significantly increases the number of reads that can be mapped to the reference genome. Notice that all of the above features are implemented within the index structure and are not simple post-processing steps and thus are performed highly efficiently. Finally, mrsFAST-Ultra utilizes multiple available cores and processors and can be tuned for various memory settings. Our results show that mrsFAST-Ultra is roughly five times faster than its predecessor mrsFAST. In comparison to newly enhanced popular tools such as Bowtie2, it is more sensitive (it can report 10 times or more mappings per read) and much faster (six times or

  7. Myocardial tagging by Cardiovascular Magnetic Resonance: evolution of techniques--pulse sequences, analysis algorithms, and applications

    Directory of Open Access Journals (Sweden)

    Ibrahim El-Sayed H

    2011-07-01

    Full Text Available Abstract Cardiovascular magnetic resonance (CMR tagging has been established as an essential technique for measuring regional myocardial function. It allows quantification of local intramyocardial motion measures, e.g. strain and strain rate. The invention of CMR tagging came in the late eighties, where the technique allowed for the first time for visualizing transmural myocardial movement without having to implant physical markers. This new idea opened the door for a series of developments and improvements that continue up to the present time. Different tagging techniques are currently available that are more extensive, improved, and sophisticated than they were twenty years ago. Each of these techniques has different versions for improved resolution, signal-to-noise ratio (SNR, scan time, anatomical coverage, three-dimensional capability, and image quality. The tagging techniques covered in this article can be broadly divided into two main categories: 1 Basic techniques, which include magnetization saturation, spatial modulation of magnetization (SPAMM, delay alternating with nutations for tailored excitation (DANTE, and complementary SPAMM (CSPAMM; and 2 Advanced techniques, which include harmonic phase (HARP, displacement encoding with stimulated echoes (DENSE, and strain encoding (SENC. Although most of these techniques were developed by separate groups and evolved from different backgrounds, they are in fact closely related to each other, and they can be interpreted from more than one perspective. Some of these techniques even followed parallel paths of developments, as illustrated in the article. As each technique has its own advantages, some efforts have been made to combine different techniques together for improved image quality or composite information acquisition. In this review, different developments in pulse sequences and related image processing techniques are described along with the necessities that led to their invention

  8. CRISPR-Cas9 technology: applications in genome engineering, development of sequence-specific antimicrobials, and future prospects.

    Science.gov (United States)

    de la Fuente-Núñez, César; Lu, Timothy K

    2017-02-20

    The development of CRISPR-Cas9 technology has revolutionized our ability to edit DNA and to modulate expression levels of genes of interest, thus providing powerful tools to accelerate the precise engineering of a wide range of organisms. In addition, the CRISPR-Cas system can be harnessed to design "precision" antimicrobials that target bacterial pathogens in a DNA sequence-specific manner. This capability will enable killing of drug-resistant microbes by selectively targeting genes involved in antibiotic resistance, biofilm formation and virulence. Here, we review the origins and mechanistic basis of CRISPR-Cas systems, discuss how this technology can be leveraged to provide a range of applications in both eukaryotic and prokaryotic systems, and finish by outlining limitations and future prospects.

  9. Time sequence analysis of flickering auroras. I - Application of Fourier analysis. [in atmosphere

    Science.gov (United States)

    Berkey, F. T.; Silevitch, M. B.; Parsons, N. R.

    1980-01-01

    Using a technique that enables one to digitize the brightness of auroral displays from individual fields of a video signal, we have analyzed the frequency content of flickering aurora. Through the application of Fourier analysis to our data, we have found that flickering aurora contains a wide range of enhanced frequencies, although the dominant frequency enhancement generally occurs in the range 6-12 Hz. Each incidence of flickering that we observed was associated with increased radio wave absorption. Furthermore, we have found that flickering occurs in bright auroral surges, the occurrence of which is not limited to the 'breakup' phase of auroral substorms. Our results are interpreted in terms of a recently proposed theory of fluctuating double layers that accounts for a number of the observational features.

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

    Science.gov (United States)

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

    2013-09-01

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

  11. Application of a Pore Fraction Hot Tearing Model to Directionally Solidified and Direct Chill Cast Aluminum Alloys

    Science.gov (United States)

    Dou, Ruifeng; Phillion, A. B.

    2016-08-01

    Hot tearing susceptibility is commonly assessed using a pressure drop equation in the mushy zone that includes the effects of both tensile deformation perpendicular to the thermal gradient as well as shrinkage feeding. In this study, a Pore Fraction hot tearing model, recently developed by Monroe and Beckermann (JOM 66:1439-1445, 2014), is extended to additionally include the effect of strain rate parallel to the thermal gradient. The deformation and shrinkage pore fractions are obtained on the basis of the dimensionless Niyama criterion and a scaling variable method. First, the model is applied to the binary Al-Cu system under conditions of directional solidification. It is shown that for the same Niyama criterion, a decrease in the cooling rate increases both the deformation and shrinkage pore fractions because of an increase in the time spent in the brittle temperature region. Second, the model is applied to the industrial aluminum alloy AA5182 as part of a finite element simulation of the Direct Chill (DC) casting process. It is shown that an increase in the casting speed during DC casting increases the deformation and shrinkage pore fractions, causing the maximum point of pore fraction to move towards the base of the casting. These results demonstrate that including the strain rate parallel to the thermal gradient significantly improves the predictive quality of hot tearing criteria based on the pressure drop equation.

  12. SU-F-J-163: In Vivo Quantification of Sequence Parameter Effect On Geometric Distortion Caused by Implanted Titanium Brachytherapy Applicator

    Energy Technology Data Exchange (ETDEWEB)

    Sullivan, T; Diak, A; Surucu, M; Yacoub, J; Harkenrider, M; Shea, S [Loyola University Chicago, Maywood, IL (United States)

    2016-06-15

    Purpose: The use of MR to plan and evaluate brachytherapy treatment for cervical cancer is increasing given the availability of MR conditional or safe applicators and MRI’s proven superiority to CT for characterizing soft tissue lesions. The titanium applicators, however, cause geometric distortions or imaging artifacts, which reduce the utility of MRI for dosimetry. We sought to quantify the observed volume of the same applicator on a previously optimized T2 sequence in comparison to the conventional T2 sequence and CT obtained for brachytherapy planning. Methods: Prior work with testing in phantoms showed that increases in readout bandwidth yielded reductions in artifact area and distortion measurements even with voxel increases. Following IRB approval, nine patients with titanium tandem & ovoid applicator (Varian Medical Systems) in place were scanned with a standard periprocedural protocol which included sagittal T2 fast spin echo (FSE) acquisition (res 0.98×0.78×4.0 mm{sup 3}; BW 200Hz). An additional T2-weighted FSE sequence (res 0.98×0.98×3–4 mm{sup 3}; BW500Hz) with increased readout bandwidth, readout voxel size, and echo train length was added to the protocol. Volume measurements of the applicator (from tip to cervical stop) were hand-segmented in Velocity AI 3.1 (Velocity Medical Solutions) for the two T2 FSE sequences and a planning CT obtained shortly after MRI. Differences were analyzed using a paired t-test. Results: Average apparent volumes of the applicator on standard T2 sequence, decreased bandwidth T2 sequence and CT were 5.922±1.283 cm{sup 3}, 4.544±1.524 cm3, and 2.304±0.509 cm{sup 3} respectively. Conclusion: Apparent volumes of a brachytherapy applicator can be compared in vivo. The modified sequence results in decreased apparent size of the cervical applicator. Both MR sequence volumes were larger than the planning CT, which was expected. Future work will focus on the diagnostic quality of the new sequence and quantifying any

  13. INTERGEO - Central/East European Collaboration Network on direct application of geothermal energy

    Energy Technology Data Exchange (ETDEWEB)

    Popovski, K [Central/East European Collaboration Network on Direct Application of Geothermal Energy, Bitola (Yugoslavia); Arpasi, M [International Geothermal Association - European Branch, Budapest (Hungary)

    1997-12-01

    A proposal for organisation of a Network to be known as INTERGEO is presented, which should extend and reinforce the cooperation for the development of the direct application of geothermal energy between the developed EC countries and the ones of the so called Central/East European region. Unter the term `developed countries` for this particular energy source utilisation mainly Italy, France and Germany should be understood. The Central/East European region consists the following countries: Albania, Bosnia and Herzegovina, Bulgaria, Belarus, Croatia, Czech Republic, Estonia, Hungary, Latvia, Lituania, Macedonia, Moldova, Poland, Roumania, Slovenia, Slovakia, Turkey, Ukraine and Yugoslavia. The idea itself, the need and possibilities for organisation, possible plan of action and expected benefits for the EC and Central/East European countries are elaborated in order to come to the conclusions for the proposal justifiableness and feasibility for realisation. (orig.)

  14. SHAPE SELECTIVE NANO-CATALYSTS: TOWARD DIRECT METHANOL FUEL CELLS APPLICATIONS

    Energy Technology Data Exchange (ETDEWEB)

    Murph, S.

    2010-06-16

    A series of bimetallic core-shell-alloy type Au-Pt nanomaterials with various morphologies, aspect ratios and compositions, were produced in a heterogenous epitaxial fashion. Gold nanoparticles with well-controlled particle size and shape, e.g. spheres, rods and cubes, were used as 'seeds' for platinum growth in the presence of a mild reducing agent, ascorbic acid and a cationic surfactant cethyltrimethyl ammonium bromide (CTAB). The reactions take place in air and water, and are quick, economical and amenable for scaling up. The synthesized nanocatalysts were characterized by electron microscopy techniques and energy dispersive X-ray analysis. Nafion membranes were embedded with the Au-Pt nanomaterials and analyzed by atomic force microscopy (AFM) and scanning electron microscopy (SEM) for their potential in direct methanol fuel cells applications.

  15. Application of an EGR system in a direct injection diesel engine to reduce NOx emissions

    Science.gov (United States)

    De Serio, D.; De Oliveira, A.; Sodré, J. R.

    2016-09-01

    This work presents the application of an exhaust gas recirculation (EGR) system in a direct injection diesel engine operating with diesel oil containing 7% biodiesel (B7). EGR rates of up to 10% were applied with the primary aim to reduce oxides of nitrogen (NOx) emissions. The experiments were conducted in a 44 kW diesel power generator to evaluate engine performance and emissions for different load settings. The use of EGR caused a peak pressure reduction during the combustion process and a decrease in thermal efficiency, mainly at high engine loads. A reduction of NOx emissions of up to 26% was achieved, though penalizing carbon monoxide (CO) and total hydrocarbons (THC) emissions.

  16. Indocyanine green enhanced surgery; principle, clinical applications and future research directions

    Directory of Open Access Journals (Sweden)

    Catalin Alius

    2018-05-01

    Full Text Available Over the past decade a new emergent technology has become very popular in all fields of surgery using Indocyanine green and near infrared fluorescent optical systems. This revolutionary approach overlaps conventional and near infrared images to produce highly informative intraoperative images on the anatomy and physiology of various tissues. Near infrared fluorescence is employed for perioperative angiography in vascular mapping, assessment of anastomoses, location of sentinel lymph nodes and delineation of biliary tree anatomy, highlighting tumours and metastatic deposits, improving surgical techniques and for many other uses. A lot of researchers have reported better surgical outcomes and technique innovations facilitated by this novel technology which although in its early stages, it lights up great interest worldwide. This article reviews the principle of the method, the properties of the fluorescent dye, the main clinical applications and discusses future research directions.

  17. Redox cofactor engineering in industrial microorganisms: strategies, recent applications and future directions.

    Science.gov (United States)

    Liu, Jiaheng; Li, Huiling; Zhao, Guangrong; Caiyin, Qinggele; Qiao, Jianjun

    2018-05-01

    NAD and NADP, a pivotal class of cofactors, which function as essential electron donors or acceptors in all biological organisms, drive considerable catabolic and anabolic reactions. Furthermore, they play critical roles in maintaining intracellular redox homeostasis. However, many metabolic engineering efforts in industrial microorganisms towards modification or introduction of metabolic pathways, especially those involving consumption, generation or transformation of NAD/NADP, often induce fluctuations in redox state, which dramatically impede cellular metabolism, resulting in decreased growth performance and biosynthetic capacity. Here, we comprehensively review the cofactor engineering strategies for solving the problematic redox imbalance in metabolism modification, as well as their features, suitabilities and recent applications. Some representative examples of in vitro biocatalysis are also described. In addition, we briefly discuss how tools and methods from the field of synthetic biology can be applied for cofactor engineering. Finally, future directions and challenges for development of cofactor redox engineering are presented.

  18. Out-of-plane platforms with bi-directional thermal bimorph actuation for transducer applications

    KAUST Repository

    Conchouso Gonzalez, David

    2015-04-01

    This paper reports on the Buckled Cantilever Platform (BCP) that allows the manipulation of the out of plane structures through the adjustment of the pitch angle using thermal bimorph micro-Actuators. Due to the micro-fabrication process used, the bimorph actuators can be designed to move in both: Counter Clockwise (CCW) and Clockwise (CW) directions with a resolution of up to 110 μm/V, with smallest step in the range of nanometers. Thermal and electrical characterization of the thermal bimorph actuators showed low influence in the platforms temperature and low power consumption (< 35μW) mainly due to the natural isolation of the structure. Tip displacements larger than 500μm were achieved. The precise angle adjustment achieved through these mechanisms makes them optimal for a range of different MEMS applications, like optical benches and low frequency sweeping sensors and antennas. © 2015 IEEE.

  19. A study of a direct-injection stratified-charge rotary engine for motor vehicle application

    Science.gov (United States)

    Kagawa, Ryoji; Okazaki, Syunki; Somyo, Nobuhiro; Akagi, Yuji

    1993-03-01

    A study of a direct-injection stratified-charge system (DISC), as applied to a rotary engine (RE) for motor vehicle usage, was undertaken. The goals of this study were improved fuel consumption and reduced exhaust emissions. These goals were thought feasible due to the high thermal efficiency associated with the DISC-RE. This was the first application of this technology to a motor vehicle engine. Stable ignition and ideal stratification systems were developed by means of numerical calculations, air-fuel mixture measurements, and actual engine tests. The use of DISC resulted in significantly improved fuel consumption and reduced exhaust emissions. The use of an exhaust gas recirculating system was studied and found to be beneficial in NOx reduction.

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

    International Nuclear Information System (INIS)

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

    1996-01-01

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

  1. Directional ratio based on parabolic molecules and its application to the analysis of tubular structures

    Science.gov (United States)

    Labate, Demetrio; Negi, Pooran; Ozcan, Burcin; Papadakis, Manos

    2015-09-01

    As advances in imaging technologies make more and more data available for biomedical applications, there is an increasing need to develop efficient quantitative algorithms for the analysis and processing of imaging data. In this paper, we introduce an innovative multiscale approach called Directional Ratio which is especially effective to distingush isotropic from anisotropic structures. This task is especially useful in the analysis of images of neurons, the main units of the nervous systems which consist of a main cell body called the soma and many elongated processes called neurites. We analyze the theoretical properties of our method on idealized models of neurons and develop a numerical implementation of this approach for analysis of fluorescent images of cultured neurons. We show that this algorithm is very effective for the detection of somas and the extraction of neurites in images of small circuits of neurons.

  2. Characterization of Polyethylene-Graft-Sulfonated Polyarylsulfone Proton Exchange Membranes for Direct Methanol Fuel Cell Applications.

    Science.gov (United States)

    Kim, Hyung Kyu; Zhang, Gang; Nam, Changwoo; Chung, T C Mike

    2015-12-04

    This paper examines polymer film morphology and several important properties of polyethylene-graft-sulfonated polyarylene ether sulfone (PE-g-s-PAES) proton exchange membranes (PEMs) for direct methanol fuel cell applications. Due to the extreme surface energy differences between a semi-crystalline and hydrophobic PE backbone and several amorphous and hydrophilic s-PAES side chains, the PE-g-s-PAES membrane self-assembles into a unique morphology, with many proton conductive s-PAES channels embedded in the stable and tough PE matrix and a thin hydrophobic PE layer spontaneously formed on the membrane surfaces. In the bulk, these membranes show good mechanical properties (tensile strength >30 MPa, Young's modulus >1400 MPa) and low water swelling (λ 3 mmol/g in the s-PAES domains. On the surface, the thin hydrophobic and semi-crystalline PE layer shows some unusual barrier (protective) properties. In addition to exhibiting higher through-plane conductivity (up to 160 mS/cm) than in-plane conductivity, the PE surface layer minimizes methanol cross-over from anode to cathode with reduced fuel loss, and stops the HO• and HO₂• radicals, originally formed at the anode, entering into PEM matrix. Evidently, the thin PE surface layer provides a highly desirable protecting layer for PEMs to reduce fuel loss and increase chemical stability. Overall, the newly developed PE-g-s-PAES membranes offer a desirable set of PEM properties, including conductivity, selectivity, mechanical strength, stability, and cost-effectiveness for direct methanol fuel cell applications.

  3. Characterization of Polyethylene-Graft-Sulfonated Polyarylsulfone Proton Exchange Membranes for Direct Methanol Fuel Cell Applications

    Directory of Open Access Journals (Sweden)

    Hyung Kyu Kim

    2015-12-01

    Full Text Available This paper examines polymer film morphology and several important properties of polyethylene-graft-sulfonated polyarylene ether sulfone (PE-g-s-PAES proton exchange membranes (PEMs for direct methanol fuel cell applications. Due to the extreme surface energy differences between a semi-crystalline and hydrophobic PE backbone and several amorphous and hydrophilic s-PAES side chains, the PE-g-s-PAES membrane self-assembles into a unique morphology, with many proton conductive s-PAES channels embedded in the stable and tough PE matrix and a thin hydrophobic PE layer spontaneously formed on the membrane surfaces. In the bulk, these membranes show good mechanical properties (tensile strength >30 MPa, Young’s modulus >1400 MPa and low water swelling (λ < 15 even with high IEC >3 mmol/g in the s-PAES domains. On the surface, the thin hydrophobic and semi-crystalline PE layer shows some unusual barrier (protective properties. In addition to exhibiting higher through-plane conductivity (up to 160 mS/cm than in-plane conductivity, the PE surface layer minimizes methanol cross-over from anode to cathode with reduced fuel loss, and stops the HO• and HO2• radicals, originally formed at the anode, entering into PEM matrix. Evidently, the thin PE surface layer provides a highly desirable protecting layer for PEMs to reduce fuel loss and increase chemical stability. Overall, the newly developed PE-g-s-PAES membranes offer a desirable set of PEM properties, including conductivity, selectivity, mechanical strength, stability, and cost-effectiveness for direct methanol fuel cell applications.

  4. Application of Direct Assessment Approaches and Methodologies to Cathodically Protected Nuclear Waste Transfer Lines

    International Nuclear Information System (INIS)

    Dahl, Megan M.; Pikas, Joseph; Edgemon, Glenn L.; Philo, Sarah

    2013-01-01

    The U.S. Department of Energy's (DOE) Hanford Site is responsible for the safe storage, retrieval, treatment, and disposal of approximately 54 million gallons (204 million liters) of radioactive waste generated since the site's inception in 1943. Today, the major structures involved in waste management at Hanford include 149 carbon steel single-shell tanks, 28 carbon-steel double-shell tanks, plus a network of buried metallic transfer lines and ancillary systems (pits, vaults, catch tanks, etc.) required to store, retrieve, and transfer waste within the tank farm system. Many of the waste management systems at Hanford are still in use today. In response to uncertainties regarding the structural integrity of these systems,' an independent, comprehensive integrity assessment of the Hanford Site piping system was performed. It was found that regulators do not require the cathodically protected pipelines located within the Hanford Site to be assessed by External Corrosion Direct Assessment (ECDA) or any other method used to ensure integrity. However, a case study is presented discussing the application of the direct assessment process on pipelines in such a nuclear environment. Assessment methodology and assessment results are contained herein. An approach is described for the monitoring, integration of outside data, and analysis of this information in order to identify whether coating deterioration accompanied by external corrosion is a threat for these waste transfer lines

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

    Directory of Open Access Journals (Sweden)

    Head Steven R

    2011-06-01

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

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

    Energy Technology Data Exchange (ETDEWEB)

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

    1978-01-01

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

  7. Application of natural gas to the direct reduction of iron ore

    Energy Technology Data Exchange (ETDEWEB)

    1975-05-01

    The Gas Committee of the U.N. Economic Commission for Europe evaluated the potentials of natural gas for direct reduction of iron ore. The report, based essentially on that by the Italian representative E. Pasero with comments and observations from experts of the other member countries, indicated the general tendency of the iron and steel industry to use natural gas to reduce production costs by reducing coke consumption. By the end of 1972, gas consumption by these industries was reported at 38.8 billion Btu/ton (10.79 Gcal/m ton) by the Steel Committee of the U.N. Economic Commission at the symposium on the economic and technical aspects of the direct reduction of iron ore, held in September 1972 in Bucharest. In comparison, coke consumption was 9.5 billion Btu/ton (2.64 Gcal/m ton) steel, liquid hydrocarbons 3.1 billion Btu (0.85 Gcal), and electricity 16.1 billion Btu (4.46 Gcal). Natural gas was used mainly for ore reduction and generation of the reducing gas in-shaft furnaces with backdraft heating circulation, fixed-bed furances (Hyl type), and fluidized-bed reactors. Processes include the Midrex (shaft furnace), H.I.B. (fluidized bed), and Novalfer (fluidized bed). These processes are used to obtain 4.5 million tons/yr of iron sponge for the production of steel in electric furnaces. The natural gas outlook for direct reduction of iron will depend on local conditions and fuel availability. Its industrial application has been most successful in mini-steel installations, especially in the U.S., Japan, and Western Europe, and it is recommended for developing countries with no steel-industry basis.

  8. Optimization of parameter values for complex pulse sequences by simulated annealing: application to 3D MP-RAGE imaging of the brain.

    Science.gov (United States)

    Epstein, F H; Mugler, J P; Brookeman, J R

    1994-02-01

    A number of pulse sequence techniques, including magnetization-prepared gradient echo (MP-GRE), segmented GRE, and hybrid RARE, employ a relatively large number of variable pulse sequence parameters and acquire the image data during a transient signal evolution. These sequences have recently been proposed and/or used for clinical applications in the brain, spine, liver, and coronary arteries. Thus, the need for a method of deriving optimal pulse sequence parameter values for this class of sequences now exists. Due to the complexity of these sequences, conventional optimization approaches, such as applying differential calculus to signal difference equations, are inadequate. We have developed a general framework for adapting the simulated annealing algorithm to pulse sequence parameter value optimization, and applied this framework to the specific case of optimizing the white matter-gray matter signal difference for a T1-weighted variable flip angle 3D MP-RAGE sequence. Using our algorithm, the values of 35 sequence parameters, including the magnetization-preparation RF pulse flip angle and delay time, 32 flip angles in the variable flip angle gradient-echo acquisition sequence, and the magnetization recovery time, were derived. Optimized 3D MP-RAGE achieved up to a 130% increase in white matter-gray matter signal difference compared with optimized 3D RF-spoiled FLASH with the same total acquisition time. The simulated annealing approach was effective at deriving optimal parameter values for a specific 3D MP-RAGE imaging objective, and may be useful for other imaging objectives and sequences in this general class.

  9. Landscape Valuation of Environmental Amenities throughoutthe Application of Direct and Indirect Methods

    Directory of Open Access Journals (Sweden)

    Luís Loures

    2015-01-01

    Full Text Available Landscape design, construction and management should no longer be the result of superficial approaches based exclusively on designers’ and planners’ ideas. This research starts with the assumption that the aesthetic component constitutes an essential attribute for better understanding and evaluating landscapes. This study analyzes the aesthetic quality and economic valuation of the Lower Guadiana river landscape, through the application of direct and indirect landscape evaluation methods. In order to gauge not only experts’ opinion, it is supported by the application of public participation techniques about the opinion and perceptions of the site visitors/users. The present research considered the analysis of six landscape subunits regarding landscape quality, fragility and visual absorption capacity. The obtained results showed that there are significant differences between the perceptions of the general public and experts’ analysis. Touristic Complexes and Golf Courses had high visual quality, while Agricultural and Production Areas had high visual fragility. Moreover, the performed analysis made clear that the combined use of landscape assessment methods is suited to this type of study, since it enables quantifying the value of existence, management and maintenance of a particular environmental assets and/or services.

  10. Characterizing U.S. Heat Demand for Potential Application of Geothermal Direct Use: Preprint

    Energy Technology Data Exchange (ETDEWEB)

    McCabe, Kevin; Gleason, Michael; Reber, Tim; Young, Katherine R.

    2016-10-01

    In this paper, we assess the U.S. demand for low-temperature thermal energy at the county resolution for four major end-use sectors: residential buildings, commercial buildings, manufacturing facilities, and agricultural facilities. Existing, publicly available data on the U.S. thermal demand market are characterized by coarse spatial resolution, with assessments typically at the state-level or larger. For many uses, these data are sufficient; however, our research was motivated by an interest in assessing the potential demand for direct use (DU) of low-temperature (30 degrees to 150 degrees C) geothermal heat. The availability and quality of geothermal resources for DU applications are highly spatially heterogeneous; therefore, to assess the potential market for these resources, it is necessary to understand the spatial variation in demand for low-temperature resources at a local resolution. This paper presents the datasets and methods we used to develop county-level estimates of the thermal demand for the residential, commercial, manufacturing, and agricultural sectors. Although this analysis was motivated by an interest in geothermal energy deployment, the results are likely to have broader applications throughout the energy industry. The county-resolution thermal demand data developed in this study for four major U.S. sectors may have far-reaching implications for building technologies, industrial processes, and various distributed renewable energy thermal resources (e.g. biomass, solar).

  11. The Direct Georeferencing Application and Performance Analysis of Uav Helicopter in Gcp-Free Area

    Science.gov (United States)

    Lo, C. F.; Tsai, M. L.; Chiang, K. W.; Chu, C. H.; Tsai, G. J.; Cheng, C. K.; El-Sheimy, N.; Ayman, H.

    2015-08-01

    There are many disasters happened because the weather changes extremely in these years. To facilitate applications such as environment detection or monitoring becomes very important. Therefore, the development of rapid low cost systems for collecting near real-time spatial information is very critical. Rapid spatial information collection has become an emerging trend for remote sensing and mapping applications. This study develops a Direct Georeferencing (DG) based Unmanned Aerial Vehicle (UAV) helicopter photogrammetric platform where an Inertial Navigation System (INS)/Global Navigation Satellite System (GNSS) integrated Positioning and Orientation System (POS) system is implemented to provide the DG capability of the platform. The performance verification indicates that the proposed platform can capture aerial images successfully. A flight test is performed to verify the positioning accuracy in DG mode without using Ground Control Points (GCP). The preliminary results illustrate that horizontal DG positioning accuracies in the x and y axes are around 5 meter with 100 meter flight height. The positioning accuracy in the z axis is less than 10 meter. Such accuracy is good for near real-time disaster relief. The DG ready function of proposed platform guarantees mapping and positioning capability even in GCP free environments, which is very important for rapid urgent response for disaster relief. Generally speaking, the data processing time for the DG module, including POS solution generalization, interpolation, Exterior Orientation Parameters (EOP) generation, and feature point measurements, is less than 1 hour.

  12. Dramatics and education: Different directions and approaches to the application of drama/theatre techniques

    Directory of Open Access Journals (Sweden)

    Stamenković Ivana

    2015-01-01

    Full Text Available This paper describes, from the perspective of drama pedagogy, two basic directions in the application of drama and/or theatre techniques in the educational context which mainly differ primarily according to who applies them in practice with children and the young - teachers or professional actors.. Then the most prominent approaches of individual authors are singled out from each agent. Although there are certain similarities among them, we wanted also to show their differences, evident in theoretical, pedagogical and practical orientations. In this context the opinions about the importance of dramatics for education, and about the effects of the use of different approaches, levels and the ways of the application of drama/theatre techniques are singled out, showing at the same time different roles, levels and ways of participating students. This theme is important for promoting dramatics pedagogy, which is not at a high level of development in our country, in spite of the fact that many authors are engaged in theoretical and/or practical work in this area.

  13. Spatiotemporal Fusion of Multisource Remote Sensing Data: Literature Survey, Taxonomy, Principles, Applications, and Future Directions

    Directory of Open Access Journals (Sweden)

    Xiaolin Zhu

    2018-03-01

    Full Text Available Satellite time series with high spatial resolution is critical for monitoring land surface dynamics in heterogeneous landscapes. Although remote sensing technologies have experienced rapid development in recent years, data acquired from a single satellite sensor are often unable to satisfy our demand. As a result, integrated use of data from different sensors has become increasingly popular in the past decade. Many spatiotemporal data fusion methods have been developed to produce synthesized images with both high spatial and temporal resolutions from two types of satellite images, frequent coarse-resolution images, and sparse fine-resolution images. These methods were designed based on different principles and strategies, and therefore show different strengths and limitations. This diversity brings difficulties for users to choose an appropriate method for their specific applications and data sets. To this end, this review paper investigates literature on current spatiotemporal data fusion methods, categorizes existing methods, discusses the principal laws underlying these methods, summarizes their potential applications, and proposes possible directions for future studies in this field.

  14. Application of habitat thresholds in conservation: Considerations, limitations, and future directions

    Directory of Open Access Journals (Sweden)

    Yntze van der Hoek

    2015-01-01

    Full Text Available Habitat thresholds are often interpreted as the minimum required area of habitat, and subsequently promoted as conservation targets in natural resource policies and planning. Unfortunately, several recent reviews and messages of caution on the application of habitat thresholds in conservation have largely fallen on deaf ears, leading to a dangerous oversimplification and generalization of the concept. We highlight the prevalence of oversimplification/over-generalization of results from habitat threshold studies in policy documentation, the consequences of such over-generalization, and directions for habitat threshold studies that have conservation applications without risking overgeneralization. We argue that in order to steer away from misapplication of habitat thresholds in conservation, we should not focus on generalized nominal habitat values (i.e., amounts or percentages of habitat, but on the use of habitat threshold modeling for comparative exercises of area-sensitivity or the identification of environmental dangers. In addition, we should remain focused on understanding the processes and mechanisms underlying species responses to habitat change. Finally, studies could that focus on deriving nominal value threshold amounts should do so only if the thresholds are detailed, species-specific, and translated to conservation targets particular to the study area only.

  15. Characterizing U.S. Heat Demand Market for Potential Application of Geothermal Direct Use

    Energy Technology Data Exchange (ETDEWEB)

    McCabe, Kevin; Gleason, Michael; Reber, Tim; Young, Katherine R.

    2017-05-01

    In this paper, we assess the U.S. demand for low-temperature thermal energy at the county resolution for four major end-use sectors: residential buildings, commercial buildings, manufacturing facilities, and agricultural facilities. Existing, publicly available data on the U.S. thermal demand market are characterized by coarse spatial resolution, with assessments typically at the state-level or larger. For many uses, these data are sufficient; however, our research was motivated by an interest in assessing the potential demand for direct use (DU) of low-temperature (30 degrees to 150 degrees C) geothermal heat. The availability and quality of geothermal resources for DU applications are highly spatially heterogeneous; therefore, to assess the potential market for these resources, it is necessary to understand the spatial variation in demand for low-temperature resources at a local resolution. This paper presents the datasets and methods we used to develop county-level estimates of the thermal demand for the residential, commercial, manufacturing, and agricultural sectors. Although this analysis was motivated by an interest in geothermal energy deployment, the results are likely to have broader applications throughout the energy industry. The county-resolution thermal demand data developed in this study for four major U.S. sectors may have far-reaching implications for building technologies, industrial processes, and various distributed renewable energy thermal resources (e.g. biomass, solar).

  16. Warthog: A MOOSE-Based Application for the Direct Code Coupling of BISON and PROTEUS

    Energy Technology Data Exchange (ETDEWEB)

    McCaskey, Alexander J. [Oak Ridge National Lab. (ORNL), Oak Ridge, TN (United States); Slattery, Stuart [Oak Ridge National Lab. (ORNL), Oak Ridge, TN (United States); Billings, Jay Jay [Oak Ridge National Lab. (ORNL), Oak Ridge, TN (United States)

    2015-09-01

    The Nuclear Energy Advanced Modeling and Simulation (NEAMS) program from the Department of Energy's Office of Nuclear Energy provides a robust toolkit for the modeling and simulation of current and future advanced nuclear reactor designs. This toolkit provides these technologies organized across product lines: two divisions targeted at fuels and end-to-end reactor modeling, and a third for integration, coupling, and high-level workflow management. The Fuels Product Line and the Reactor Product line provide advanced computational technologies that serve each respective field well, however, their current lack of integration presents a major impediment to future improvements of simulation solution fidelity. There is a desire for the capability to mix and match tools across Product Lines in an effort to utilize the best from both to improve NEAMS modeling and simulation technologies. This report details a new effort to provide this Product Line interoperability through the development of a new application called Warthog. This application couples the BISON Fuel Performance application from the Fuels Product Line and the PROTEUS Core Neutronics application from the Reactors Product Line in an effort to utilize the best from all parts of the NEAMS toolkit and improve overall solution fidelity of nuclear fuel simulations. To achieve this, Warthog leverages as much prior work from the NEAMS program as possible, and in doing so, enables interoperability between the disparate MOOSE and SHARP frameworks, and the libMesh and MOAB mesh data formats. This report describes this work in full. We begin with a detailed look at the individual NEAMS framework technologies used and developed in the various Product Lines, and the current status of their interoperability. We then introduce the Warthog application: its overall architecture and the ways it leverages the best existing tools from across the NEAMS toolkit to enable BISON-PROTEUS integration. Furthermore, we show how

  17. Enrichment of denitrifying methanotrophic bacteria for application after direct low-temperature anaerobic sewage treatment

    Energy Technology Data Exchange (ETDEWEB)

    Kampman, Christel, E-mail: christel.kampman@wur.nl [Sub-department of Environmental Technology, Wageningen University, P.O. Box 17, 6700 AA, Wageningen (Netherlands); Hendrickx, Tim L.G. [Sub-department of Environmental Technology, Wageningen University, P.O. Box 17, 6700 AA, Wageningen (Netherlands); Luesken, Francisca A.; Alen, Theo A. van; Op den Camp, Huub J.M.; Jetten, Mike S.M. [Department of Microbiology, Institute for Water and Wetland Research, Radboud University Nijmegen, Heyendaalseweg 135, 6525 AJ Nijmegen (Netherlands); Zeeman, Grietje; Buisman, Cees J.N.; Temmink, Hardy [Sub-department of Environmental Technology, Wageningen University, P.O. Box 17, 6700 AA, Wageningen (Netherlands)

    2012-08-15

    Highlights: Black-Right-Pointing-Pointer A new concept for low-temperature anaerobic sewage treatment is proposed. Black-Right-Pointing-Pointer In this concept, denitrification and methane oxidation are performed by Methylomirabilis oxyfera. Black-Right-Pointing-Pointer The bacteria were enriched from fresh water sediment using sequencing fed-batch reactors. Black-Right-Pointing-Pointer The volumetric consumption rate has to be increased by an order of magnitude for practical application. Black-Right-Pointing-Pointer Further research should focus on systems with improved biomass retention. - Abstract: Despite many advantages of anaerobic sewage treatment over conventional activated sludge treatment, it has not yet been applied in temperate zones. This is especially because effluent from low-temperature anaerobic treatment contains nitrogen and dissolved methane. The presence of nitrogen and methane offers the opportunity to develop a reactor in which methane is used as electron donor for denitrification. Such a reactor could be used in a new concept for low-temperature anaerobic sewage treatment, consisting of a UASB-digester system, a reactor for denitrification coupled to anaerobic methane oxidation, and a nitritation reactor. In the present study denitrifying methanotrophic bacteria similar to 'Candidatus Methylomirabilis oxyfera' were enriched. Maximum volumetric nitrite consumption rates were 33.5 mg NO{sub 2}{sup -}-N/L d (using synthetic medium) and 37.8 mg NO{sub 2}{sup -}-N/L d (using medium containing effluent from a sewage treatment plant), which are similar to the maximum rate reported so far. Though the goal was to increase the rates, in both reactors, after reaching these maximum rates, volumetric nitrite consumption rates decreased in time. Results indicate biomass washout may have significantly decelerated enrichment. Therefore, to obtain higher volumetric consumption rates, further research should focus on systems with complete biomass

  18. Enrichment of denitrifying methanotrophic bacteria for application after direct low-temperature anaerobic sewage treatment

    International Nuclear Information System (INIS)

    Kampman, Christel; Hendrickx, Tim L.G.; Luesken, Francisca A.; Alen, Theo A. van; Op den Camp, Huub J.M.; Jetten, Mike S.M.; Zeeman, Grietje; Buisman, Cees J.N.; Temmink, Hardy

    2012-01-01

    Highlights: ► A new concept for low-temperature anaerobic sewage treatment is proposed. ► In this concept, denitrification and methane oxidation are performed by Methylomirabilis oxyfera. ► The bacteria were enriched from fresh water sediment using sequencing fed-batch reactors. ► The volumetric consumption rate has to be increased by an order of magnitude for practical application. ► Further research should focus on systems with improved biomass retention. - Abstract: Despite many advantages of anaerobic sewage treatment over conventional activated sludge treatment, it has not yet been applied in temperate zones. This is especially because effluent from low-temperature anaerobic treatment contains nitrogen and dissolved methane. The presence of nitrogen and methane offers the opportunity to develop a reactor in which methane is used as electron donor for denitrification. Such a reactor could be used in a new concept for low-temperature anaerobic sewage treatment, consisting of a UASB-digester system, a reactor for denitrification coupled to anaerobic methane oxidation, and a nitritation reactor. In the present study denitrifying methanotrophic bacteria similar to ‘Candidatus Methylomirabilis oxyfera’ were enriched. Maximum volumetric nitrite consumption rates were 33.5 mg NO 2 − -N/L d (using synthetic medium) and 37.8 mg NO 2 − -N/L d (using medium containing effluent from a sewage treatment plant), which are similar to the maximum rate reported so far. Though the goal was to increase the rates, in both reactors, after reaching these maximum rates, volumetric nitrite consumption rates decreased in time. Results indicate biomass washout may have significantly decelerated enrichment. Therefore, to obtain higher volumetric consumption rates, further research should focus on systems with complete biomass retention.

  19. 37 CFR 1.823 - Requirements for nucleotide and/or amino acid sequences as part of the application.

    Science.gov (United States)

    2010-07-01

    ... may not include material other than part of the sequence listing. A fixed-width font should be used... integer expressing the number of bases or amino acid residues M. Type Whether presented sequence molecule is DNA, RNA, or PRT (protein). If a nucleotide sequence contains both DNA and RNA fragments, the type...

  20. Directed shift of vaginal microbiota induced by vaginal application of sucrose gel in rhesus macaques.

    Science.gov (United States)

    Hu, Kai-tao; Zheng, Jin-xin; Yu, Zhi-jian; Chen, Zhong; Cheng, Hang; Pan, Wei-guang; Yang, Wei-zhi; Wang, Hong-yan; Deng, Qi-wen; Zeng, Zhong-ming

    2015-04-01

    Sucrose gel was used to treat bacterial vaginosis in a phase III clinical trial. However, the changes of vaginal flora after treatment were only examined by Nugent score in that clinical trial, While the vaginal microbiota of rhesus macaques is characterized by anaerobic, Gram-negative bacteria, few lactobacilli, and pH levels above 4.6, similar to the microbiota of patients with bacterial vaginosis. This study is aimed to investigate the change of the vaginal microbiota of rehsus macaques after topical use of sucrose gel to reveal more precisely the bacterial population shift after the topical application of sucrose gel. Sixteen rhesus macaques were treated with 0.5 g sucrose gel vaginally and three with 0.5 g of placebo gel. Vaginal swabs were collected daily following treatment. Vaginal pH levels and Nugent scores were recorded. The composition of the vaginal micotbiota was tested by V3∼V4 16S rDNA metagenomic sequencing. Dynamic changes in the Lactobacillus genus were analyzed by qPCR. The vaginal microbiota of rhesus macaques are dominated by anaerobic Gram-negative bacteria, with few lactobacilli and high pH levels above 4.6. After five days' treatment with topical sucrose gel, the component percentage of Lactobacillus in vaginal microbiota increased from 1.31% to 81.59%, while the component percentage of Porphyromonas decreased from 18.60% to 0.43%, Sneathia decreased from 15.09% to 0.89%, Mobiluncus decreased from 8.23% to 0.12%, etc.. The average vaginal pH values of 16 rhesus macaques of the sucrose gel group decreased from 5.4 to 3.89. There were no significant changes in microbiota and vaginal pH observed in the placebo group. Rhesus macaques can be used as animal models of bacterial vaginosis to develop drugs and test treatment efficacy. Furthermore, the topical application of sucrose gel induced the shifting of vaginal flora of rhesus macaques from a BV kind of flora to a lactobacilli-dominating flora. Copyright © 2015 The Authors. Published by

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

    Science.gov (United States)

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

    2017-01-01

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

  2. Comprehensive transcriptome assembly of Chickpea (Cicer arietinum L. using sanger and next generation sequencing platforms: development and applications.

    Directory of Open Access Journals (Sweden)

    Himabindu Kudapa

    Full Text Available A comprehensive transcriptome assembly of chickpea has been developed using 134.95 million Illumina single-end reads, 7.12 million single-end FLX/454 reads and 139,214 Sanger expressed sequence tags (ESTs from >17 genotypes. This hybrid transcriptome assembly, referred to as Cicer arietinumTranscriptome Assembly version 2 (CaTA v2, available at http://data.comparative-legumes.org/transcriptomes/cicar/lista_cicar-201201, comprising 46,369 transcript assembly contigs (TACs has an N50 length of 1,726 bp and a maximum contig size of 15,644 bp. Putative functions were determined for 32,869 (70.8% of the TACs and gene ontology assignments were determined for 21,471 (46.3%. The new transcriptome assembly was compared with the previously available chickpea transcriptome assemblies as well as to the chickpea genome. Comparative analysis of CaTA v2 against transcriptomes of three legumes - Medicago, soybean and common bean, resulted in 27,771 TACs common to all three legumes indicating strong conservation of genes across legumes. CaTA v2 was also used for identification of simple sequence repeats (SSRs and intron spanning regions (ISRs for developing molecular markers. ISRs were identified by aligning TACs to the Medicago genome, and their putative mapping positions at chromosomal level were identified using transcript map of chickpea. Primer pairs were designed for 4,990 ISRs, each representing a single contig for which predicted positions are inferred and distributed across eight linkage groups. A subset of randomly selected ISRs representing all eight chickpea linkage groups were validated on five chickpea genotypes and showed 20% polymorphism with average polymorphic information content (PIC of 0.27. In summary, the hybrid transcriptome assembly developed and novel markers identified can be used for a variety of applications such as gene discovery, marker-trait association, diversity analysis etc., to advance genetics research and breeding

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

    Directory of Open Access Journals (Sweden)

    Panté Nelly

    2009-06-01

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

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

    Science.gov (United States)

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

  5. Putting instruction sequences into effect

    NARCIS (Netherlands)

    Bergstra, J.A.

    2011-01-01

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

  6. Conceptual design report for a Direct Hydrogen Proton Exchange Membrane Fuel Cell for transportation application

    Energy Technology Data Exchange (ETDEWEB)

    NONE

    1995-09-05

    This report presents the conceptual design for a Direct-Hydrogen-Fueled Proton Exchange Membrane (PEM) Fuel Cell System for transportation applications. The design is based on the initial selection of the Chrysler LH sedan as the target vehicle with a 50 kW (gross) PEM Fuel Cell Stack (FCS) as the primary power source, a battery-powered Load Leveling Unit (LLU) for surge power requirements, an on-board hydrogen storage subsystem containing high pressure gaseous storage, a Gas Management Subsystem (GMS) to manage the hydrogen and air supplies for the FCS, and electronic controllers to control the electrical system. The design process has been dedicated to the use of Design-to-Cost (DTC) principles. The Direct Hydrogen-Powered PEM Fuel Cell Stack Hybrid Vehicle (DPHV) system is designed to operate on the Federal Urban Driving Schedule (FUDS) and Hiway Cycles. These cycles have been used to evaluate the vehicle performance with regard to range and hydrogen usage. The major constraints for the DPHV vehicle are vehicle and battery weight, transparency of the power system and drive train to the user, equivalence of fuel and life cycle costs to conventional vehicles, and vehicle range. The energy and power requirements are derived by the capability of the DPHV system to achieve an acceleration from 0 to 60 MPH within 12 seconds, and the capability to achieve and maintain a speed of 55 MPH on a grade of seven percent. The conceptual design for the DPHV vehicle is shown in a figure. A detailed description of the Hydrogen Storage Subsystem is given in section 4. A detailed description of the FCS Subsystem and GMS is given in section 3. A detailed description of the LLU, selection of the LLU energy source, and the power controller designs is given in section 5.

  7. Application of infiltrated LSCM-GDC oxide anode in direct carbon/coal fuel cells.

    Science.gov (United States)

    Yue, Xiangling; Arenillas, Ana; Irvine, John T S

    2016-08-15

    Hybrid direct carbon/coal fuel cells (HDCFCs) utilise an anode based upon a molten carbonate salt with an oxide conducting solid electrolyte for direct carbon/coal conversion. They can be fuelled by a wide range of carbon sources, and offer higher potential chemical to electrical energy conversion efficiency and have the potential to decrease CO2 emissions compared to coal-fired power plants. In this study, the application of (La, Sr)(Cr, Mn)O3 (LSCM) and (Gd, Ce)O2 (GDC) oxide anodes was explored in a HDCFC system running with two different carbon fuels, an organic xerogel and a raw bituminous coal. The electrochemical performance of the HDCFC based on a 1-2 mm thick 8 mol% yttria stabilised zirconia (YSZ) electrolyte and the GDC-LSCM anode fabricated by wet impregnation procedures was characterized and discussed. The infiltrated oxide anode showed a significantly higher performance than the conventional Ni-YSZ anode, without suffering from impurity formation under HDCFC operation conditions. Total polarisation resistance (Rp) reached 0.8-0.9 Ω cm(2) from DCFC with an oxide anode on xerogel and bituminous coal at 750 °C, with open circuit voltage (OCV) values in the range 1.1-1.2 V on both carbon forms. These indicated the potential application of LSCM-GDC oxide anode in HDCFCs. The chemical compatibility of LSCM/GDC with carbon/carbonate investigation revealed the emergence of an A2BO4 type oxide in place of an ABO3 perovskite structure in the LSCM in a reducing environment, due to Li attack as a result of intimate contact between the LSCM and Li2CO3, with GDC being stable under identical conditions. Such reaction between LSCM and Li2CO3 was not observed on a LSCM-YSZ pellet treated with Li-K carbonate in 5% H2/Ar at 700 °C, nor on a GDC-LSCM anode after HDCFC operation. The HDCFC durability tests of GDC-LSCM oxide on a xerogel and on raw bituminous coal were performed under potentiostatic operation at 0.7 V at 750 °C. The degradation mechanisms were

  8. High-Throughput Sequencing, a VersatileWeapon to Support Genome-Based Diagnosis in Infectious Diseases: Applications to Clinical Bacteriology

    Directory of Open Access Journals (Sweden)

    Ségolène Caboche

    2014-04-01

    Full Text Available The recent progresses of high-throughput sequencing (HTS technologies enable easy and cost-reduced access to whole genome sequencing (WGS or re-sequencing. HTS associated with adapted, automatic and fast bioinformatics solutions for sequencing applications promises an accurate and timely identification and characterization of pathogenic agents. Many studies have demonstrated that data obtained from HTS analysis have allowed genome-based diagnosis, which has been consistent with phenotypic observations. These proofs of concept are probably the first steps toward the future of clinical microbiology. From concept to routine use, many parameters need to be considered to promote HTS as a powerful tool to help physicians and clinicians in microbiological investigations. This review highlights the milestones to be completed toward this purpose.

  9. Use of nuclear space technology of direct energy conversion for terrestrial application

    International Nuclear Information System (INIS)

    Chitaykin, V.I.; Meleta, Ye.A.; Yarygin, V.I.; Mikheyev, A.S.; Tulin, S.M.

    2000-01-01

    In due time the SSC RF-IPPE exercised the scientific supervision and directly participated in the development, fabrication, space flight test and maintenance of the direct energy conversion nuclear power plants (NPP) for space application under the 'BUK' and 'TOPAZ' programs. We have used the acquired experience and the high technologies developed for the 'BUK' NPP with a thermoelectric conversion of thermal (nuclear) energy into electrical one in the development under the order of RAO 'GAZPROM' of the natural gas fired self contained thermoelectric current sources (AIT-500) and heat and electricity sources (TEP-500). These are intended for electrochemical rust protection of gas pipelines and for the electricity and heat supply to the telemetric and microwave-link systems located along the gas pipelines. Of special interest at the moment are the new developments of self contained current sources with the electrical output of ∼500 Wel for new gas pipelines being constructed under the projects such as the 'Yamal-Europe' project. The electrochemical rust protection of gas pipelines laying on unsettled and non-electrified territory of arctic regions of Russia is performed by means of the so-called Cathodic Protection Stations (CPS). Accounting for a complex of rather rigid requirements imposed by arctic operating conditions, the most attractive sources of electricity supply to the CPS are the thermoelectric heat-into-electricity converters and the generators (TEG). This paper deals with the essential results of the development, investigation and testing of unconventional TEGs using the low-temperature bismuth-tellurium thermoelectric batteries assembled together as tubular thermoelectric batteries with a radial ring geometry built into the gas-heated thermoelectric modules, which are collected to make up either the thermoelectric plants for heat and electricity supply or the self contained power sources. One of the peculiarities of these plants is the combination of

  10. Direct diode lasers and their advantages for materials processing and other applications

    Science.gov (United States)

    Fritsche, Haro; Ferrario, Fabio; Koch, Ralf; Kruschke, Bastian; Pahl, Ulrich; Pflueger, Silke; Grohe, Andreas; Gries, Wolfgang; Eibl, Florian; Kohl, Stefanie; Dobler, Michael

    2015-03-01

    The brightness of diode lasers is improving continuously and has recently started to approach the level of some solid state lasers. The main technology drivers over the last decade were improvements of the diode laser output power and divergence, enhanced optical stacking techniques and system design, and most recently dense spectral combining. Power densities at the work piece exceed 1 MW/cm2 with commercially available industrial focus optics. These power densities are sufficient for cutting and welding as well as ablation. Single emitter based diode laser systems further offer the advantage of fast current modulation due their lower drive current compared to diode bars. Direct diode lasers may not be able to compete with other technologies as fiber or CO2-lasers in terms of maximum power or beam quality. But diode lasers offer a range of features that are not possible to implement in a classical laser. We present an overview of those features that will make the direct diode laser a very valuable addition in the near future, especially for the materials processing market. As the brightness of diode lasers is constantly improving, BPP of less than 5mm*mrad have been reported with multikW output power. Especially single emitter-based diode lasers further offer the advantage of very fast current modulation due to their low drive current and therefore low drive voltage. State of the art diode drivers are already demonstrated with pulse durations of direct current control allows pulses of several microseconds with hundreds of watts average power. Spot sizes of less than 100 μm are obtained at the work piece. Such a diode system allows materials processing with a pulse parameter range that is hardly addressed by any other laser system. High productivity material ablation with cost effective lasers is enabled. The wide variety of wavelengths, high brightness, fast power modulation and high efficiency of diode lasers results in a strong pull of existing markets, but

  11. Sensitivity enhanced NMR spectroscopy by quenching scalar coupling mediated relaxation: Application to the direct observation of hydrogen bonds in 13C/15N-labeled proteins

    Energy Technology Data Exchange (ETDEWEB)

    Liu Aizhuo; Hu Weidong; Qamar, Seema; Majumdar, Ananya [Memorial Sloan-Kettering Cancer Center, Cellular Biochemistry and Biophysics Program (United States)

    2000-05-15

    In this paper, we demonstrate that the sensitivity of triple-resonance NMR experiments can be enhanced significantly through quenching scalar coupling mediated relaxation by using composite-pulse decoupling (CPD) or an adiabatic decoupling sequence on aliphatic, in particular alpha-carbons in {sup 13}C/{sup 15}N-labeled proteins. The CPD-HNCO experiment renders 50% sensitivity enhancement over the conventional CT-HNCO experiment performed on a 12 kDa FK506 binding protein, when a total of 266 ms of amide nitrogen-carbonyl carbon defocusing and refocusing periods is employed. This is a typical time period for the direct detection of hydrogen bonds in proteins via trans-hydrogen bond {sup 3h}J{sub NC'} couplings. The experimental data fit theoretical analysis well. The significant enhancement in sensitivity makes the experiment more applicable to larger-sized proteins without resorting to perdeuteration.

  12. Rapid Diagnostics of Onboard Sequences

    Science.gov (United States)

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

    2012-01-01

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

  13. Ammonia Volatilization from Urea-Application Influenced Germination and Early Seedling Growth of Dry Direct-Seeded Rice

    Directory of Open Access Journals (Sweden)

    Xiaoli Qi

    2012-01-01

    Full Text Available Poor seed germination and early seedling growth associated with urea-induced soil ammonia volatilization are major constraints in the adoption of dry direct-seeded rice. To directly examine soil ammonia volatilization and its damage to seed germination and early seedling growth of dry direct-seeded rice when urea is applied at seeding, two Petri-dish incubation experiments and a field experiment were conducted. Ammonia volatilization due to urea application significantly reduced seed germination and early seedling growth of dry direct-seedling rice. NBPT significantly reduced ammonia volatilization following urea application. The application of ammonium sulfate, instead of urea at seeding, may mitigate poor crop establishment of dry direct-seeded rice. Root growth of dry direct-seeded rice was more seriously inhibited by soil ammonia volatilization than that of shoot. Results suggest that roots are more sensitive to soil ammonia toxicity than shoots in dry direct-seeded rice system when N is applied as urea at seeding.

  14. Dosimetric characterization of a bi-directional micromultileaf collimator for stereotactic applications.

    Science.gov (United States)

    Bucciolini, M; Russo, S; Banci Buonamici, F; Pini, S; Silli, P

    2002-07-01

    A 6 MV photon beam from Linac SL75-5 has been collimated with a new micromultileaf device that is able to shape the field in the two orthogonal directions with four banks of leaves. This is the first clinical installation of the collimator and in this paper the dosimetric characterization of the system is reported. The dosimetric parameters required by the treatment planning system used for the dose calculation in the patient are: tissue maximum ratios, output factors, transmission and leakage of the leaves, penumbra values. Ionization chambers, silicon diode, radiographic films, and LiF thermoluminescent dosimeters have been employed for measurements of absolute dose and beam dosimetric data. Measurements with different dosimeters supply results in reasonable agreement among them and consistent with data available in literature for other models of micromultileaf collimator; that permits the use of the measured parameters for clinical applications. The discrepancies between results obtained with the different detectors (around 2%) for the analyzed parameters can be considered an indication of the accuracy that can be reached by current stereotactic dosimetry.

  15. Direct chemical grafted curcumin on halloysite nanotubes as dual-responsive prodrug for pharmacological applications.

    Science.gov (United States)

    Massaro, M; Amorati, R; Cavallaro, G; Guernelli, S; Lazzara, G; Milioto, S; Noto, R; Poma, P; Riela, S

    2016-04-01

    Covalently functionalized halloysite nanotubes (HNTs) were successfully employed as dual-responsive nanocarriers for curcumin (Cur). Particularly, we synthesized HNT-Cur prodrug with a controlled curcumin release on dependence of both intracellular glutathione (GSH) and pH conditions. In order to obtain HNT-Cur produgs, halloysite was firstly functionalized with cysteamine through disulphide linkage. Afterwards, curcumin molecules were chemically conjugated to the amino end groups of halloysite via Schiff's base formation. The successful functionalization of halloysite was proved by thermogravimetric analysis, FT-IR spectroscopy, dynamic light scattering and scanning electron microscopy. Experimental data confirmed the presence of curcumin on HNT external surface. Moreover, we investigated the kinetics of curcumin release by UV-vis spectroscopy, which highlighted that HNT-Cur prodrug possesses dual stimuli-responsive ability upon exposure to GSH-rich or acidic environment. In vitro antiproliferative and antioxidant properties of HNT-Cur prodrug were studied with the aim to explore their potential applications in pharmaceutics. This work puts forward an efficient strategy to prepare halloysite based nanocarriers with controlled drug delivery capacity through direct chemical grafting with stimuli-responsive linkage. Copyright © 2016 Elsevier B.V. All rights reserved.

  16. Acceleration of cardiovascular MRI using parallel imaging: basic principles, practical considerations, clinical applications and future directions

    International Nuclear Information System (INIS)

    Niendorf, T.; Sodickson, D.

    2006-01-01

    Cardiovascular Magnetic Resonance (CVMR) imaging has proven to be of clinical value for non-invasive diagnostic imaging of cardiovascular diseases. CVMR requires rapid imaging; however, the speed of conventional MRI is fundamentally limited due to its sequential approach to image acquisition, in which data points are collected one after the other in the presence of sequentially-applied magnetic field gradients and radiofrequency coils to acquire multiple data points simultaneously, and thereby to increase imaging speed and efficiency beyond the limits of purely gradient-based approaches. The resulting improvements in imaging speed can be used in various ways, including shortening long examinations, improving spatial resolution and anatomic coverage, improving temporal resolution, enhancing image quality, overcoming physiological constraints, detecting and correcting for physiologic motion, and streamlining work flow. Examples of these strategies will be provided in this review, after some of the fundamentals of parallel imaging methods now in use for cardiovascular MRI are outlined. The emphasis will rest upon basic principles and clinical state-of-the art cardiovascular MRI applications. In addition, practical aspects such as signal-to-noise ratio considerations, tailored parallel imaging protocols and potential artifacts will be discussed, and current trends and future directions will be explored. (orig.)

  17. Palladium-alloy catalysts as ethanol tolerant cathodes for direct alcohol fuel cell applications

    Energy Technology Data Exchange (ETDEWEB)

    Savadogo, O. [Ecole Polytechnique de Montreal, Montreal, PQ (Canada). Laboratoire de nouveaux materiaux pour l' energie et l' electrochimie; Varela, F.J.R. [Centro de Investigacion y de Estudios Avanzados, Coahuila (Mexico). Unidad Saltillo

    2008-07-01

    Recent studies have demonstrated that electroactive palladium (Pd) and Pd-alloy catalysts prepared using a sputtering technique possess a similar degree of activity as platinum (Pt) electrodes. This study demonstrated that Pd and Pd-alloys show a high degree of tolerance to ethanol during oxygen reduction reaction (ORR) processes. The onset potential of the ORR process in the presence of 0.5M of ethanol decreased by only 33 mV and 18 mV on Pd and Pd-cobalt (Co) catalysts. Linear sweep voltammetry experiments showed that no peak current density caused by the electro-oxidation of ethanol was observed in the Pd-based catalysts. The selective behaviour of the Pd and Pd-Co catalysts was attributed to a slow rate of adsorption of the ethanol as well as the presence of reaction intermediates on the catalytic surface. Results suggested that the Pd and Pd-Co catalysts are suitable candidates for direct alcohol fuel cell applications. 10 refs., 2 figs.

  18. Direct Radiofrequency Application Improves Pain and Gait in Collagenase-Induced Acute Achilles Tendon Injury

    Directory of Open Access Journals (Sweden)

    Yun-Pu Tsai

    2013-01-01

    Full Text Available Radiofrequency (RF is often used as a supplementary and alternative method to alleviate pain for chronic tendinopathy. Whether or how it would work for acute tendon injury is not addressed in the literatures. Through detailed pain and gait monitoring, we hypothesized that collagenase-induce acute tendinopathy model may be able to answer these questions. Gait parameters, including time, distance, and range of motion, were recorded and analyzed using a walking track equipped with a video-based system. Expression of substance P (SP, calcitonin gene related peptide (CGRP, and galanin were used as pain markers. Beta-III tubulin and Masson trichrome staining were used as to evaluate nerve sprouting, matrix tension, and degeneration in the tendon. Of fourteen analyzed parameters, RF significantly improved stance phase, step length, preswing, and intermediary toe-spread of gait. Improved gait related to the expression of substance P, CGRP, and reduced nerve fiber sprouting and matrix tension, but not galanin. The study indicates that direct RF application may be a valuable approach to improve gait and pain in acute tendon injury. Altered gait parameters may be used as references to evaluate therapeutic outcomes of RF or other treatment plan for tendinopathy.

  19. Quality by design approach: application of artificial intelligence techniques of tablets manufactured by direct compression.

    Science.gov (United States)

    Aksu, Buket; Paradkar, Anant; de Matas, Marcel; Ozer, Ozgen; Güneri, Tamer; York, Peter

    2012-12-01

    The publication of the International Conference of Harmonization (ICH) Q8, Q9, and Q10 guidelines paved the way for the standardization of quality after the Food and Drug Administration issued current Good Manufacturing Practices guidelines in 2003. "Quality by Design", mentioned in the ICH Q8 guideline, offers a better scientific understanding of critical process and product qualities using knowledge obtained during the life cycle of a product. In this scope, the "knowledge space" is a summary of all process knowledge obtained during product development, and the "design space" is the area in which a product can be manufactured within acceptable limits. To create the spaces, artificial neural networks (ANNs) can be used to emphasize the multidimensional interactions of input variables and to closely bind these variables to a design space. This helps guide the experimental design process to include interactions among the input variables, along with modeling and optimization of pharmaceutical formulations. The objective of this study was to develop an integrated multivariate approach to obtain a quality product based on an understanding of the cause-effect relationships between formulation ingredients and product properties with ANNs and genetic programming on the ramipril tablets prepared by the direct compression method. In this study, the data are generated through the systematic application of the design of experiments (DoE) principles and optimization studies using artificial neural networks and neurofuzzy logic programs.

  20. Mould design and manufacturing considerations of honeycomb biocomposites with transverse fibre direction for aerospace application

    Science.gov (United States)

    Manan, N. H.; Majid, D. L.; Romli, F. I.

    2016-10-01

    Sandwich structures with honeycomb core are known to significantly improve stiffness at lower weight and possess high flexural rigidity. They have found wide applications in aerospace as part of the primary structures, as well as the interior paneling and floors. High performance aluminum and aramid are the typical materials used for the purpose of honeycomb core whereas in other industries, materials such as fibre glass, carbon fibre, Nomex and also Kevlar reinforced with polymer are used. Recently, growing interest in developing composite structures with natural fibre reinforcement has also spurred research in natural fibre honeycomb material. The majority of the researches done, however, have generally emphasized on the usage of random chopped fibre and only a few are reported on development of honeycomb structure using unidirectional fibre as the reinforcement. This is mainly due to its processing difficulties, which often involve several stages to account for the arrangement of fibres and curing. Since the use of unidirectional fibre supports greater strength compared to random chopped fibre, a single-stage process in conjunction with vacuum infusion is suggested with a mould design that supports fibre arrangement in the direction of honeycomb loading.

  1. Pipeline integrity management in an urban environment supported by an External Corrosion Direct Assessment (ECDA) application

    Energy Technology Data Exchange (ETDEWEB)

    Dus, Pedro Luiz; Valente, Antonio Carlos Rodrigues [Companhia de Gas de Sao Paulo (COMGAS), Sao Paulo, SP (Brazil); Valdes, Alberto [GE Oil and Gas-PII Pipeline Solutions, Houston, TX (United States)

    2009-07-01

    COMGAS is the largest natural gas distributing company in Brazil, having more than 700,000 costumers. Gas delivery to this customer base is achieved through a network of high-pressure steel pipelines (17 and 35 bar) with around 1,100 km (690 miles) in length, the majority operating inside urban areas. The Integrity Management of this network is a particularly difficult task since neither pigging nor hydrostatic testing can be used to inspect the existing pipelines. Direct Assessment (DA) is the only assessment technique available at the moment. As an initial stage COMGAS has implemented an innovative project called SIA (Sistema de Integridade de Ativos). SIA combines functionality targeted for guiding and implementing an External Corrosion Assessment (ECDA) procedure, with full data alignment and integration, corporate policies on safety and dedicated reporting capabilities. Seamless interaction between SIA and the existing Operations GIS system was a key specification requirement for the construction of the system. This paper describes the lessons learned during the implementation of the ECDA module of the SIA, the first application experiences of the ECDA process with the support of the module and the initial benefits obtained from the use of the new Integrity Management System. (author)

  2. Direct Georeferencing of a Pushbroom, Lightweight Hyperspectral System for Mini-UAV Applications

    Directory of Open Access Journals (Sweden)

    Marion Jaud

    2018-01-01

    Full Text Available Hyperspectral imagery has proven its potential in many research applications, especially in the field of environmental sciences. Currently, hyperspectral imaging is generally performed by satellite or aircraft platforms, but mini-UAV (Unmanned Aerial Vehicle platforms (<20 kg are now emerging. On such platforms, payload restrictions are critical, so sensors must be selected according to stringent specifications. This article presents the integration of a light pushbroom hyperspectral sensor onboard a multirotor UAV, which we have called Hyper-DRELIO (Hyperspectral DRone for Environmental and LIttoral Observations. This article depicts the system design: the UAV platform, the imaging module, the navigation module, and the interfacing between the different elements. Pushbroom sensors offer a better combination of spatial and spectral resolution than full-frame cameras. Nevertheless, data georectification has to be performed line by line, the quality of direct georeferencing being limited by mechanical stability, good timing accuracy, and the resolution and accuracy of the proprioceptive sensors. A georegistration procedure is proposed for geometrical pre-processing of hyperspectral data. The specifications of Hyper-DRELIO surveys are described through two examples of surveys above coastal or inland waters, with different flight altitudes. This system can collect hyperspectral data in VNIR (Visible and Near InfraRed domain above small study sites (up to about 4 ha with both high spatial resolution (<10 cm and high spectral resolution (1.85 nm and with georectification accuracy on the order of 1 to 2 m.

  3. Direct high-frequency modulation of VCSELs and applications in fibre optic RF and microwave links

    International Nuclear Information System (INIS)

    Larsson, Anders; Carlsson, Christina; Gustavsson, Johan; Haglund, Asa; Modh, Peter; Bengtsson, Joergen

    2004-01-01

    With the rapid development of wireless communication networks there is an increasing demand for efficient and cost-effective transmission and distribution of RF signals. Fibre optic RF links, employing directly modulated semiconductor lasers, provide many of the desired characteristics for such distribution systems and in the search for cost-effective solutions, the vertical cavity surface emitting laser (VCSEL) is of interest. It has therefore been the purpose of this work to investigate whether 850 nm VCSELs fulfil basic performance requirements for fibre optic RF links operating in the low-GHz range. The performance of single- and multimode oxide confined VCSELs has been compared, in order to pin-point limitations and to find the optimum design. Fibre optic RF links using VCSELs and multimode fibres have been assembled and evaluated with respect to performance characteristics of importance for wireless communication systems. We have found that optimized single-mode VCSELs provide the highest performance and that links using such VCSELs and high-bandwidth multimode fibres satisfy the requirements in a number of applications, including cellular systems for mobile communication and wireless local area networks

  4. Application of the Beta Coefficient in the Market of Direct residential Real Estate Investments

    Directory of Open Access Journals (Sweden)

    Wolski Rafał

    2014-07-01

    Full Text Available The beta coefficient is one of the most popular indices used in contemporary finances. Despite the fact that there are justified doubts connected with its application, it is currently difficult to imagine a situation in which the cost of capital would be calculated without the use of the CAPM model. Thus, an attempt at answering the question whether and to what degree beta may be used in the real estate market constitutes an interesting problem. This is because on the one hand, the formal structure suggests that beta should not be used for assets which are not included in the benchmark but, on the other hand, such a benchmark should, at least theoretically, contain all market assets. Therefore, a decision was made to have a closer look at this issue, with the analysis of the possibility of using the beta coefficient in the residential real estate market set as the objective. Using the database of prices in the direct real estate investment created by the NBP, a comparison was conducted with regard to features of undertaken investments on the basis of an analysis of systematic risk calculated using selected indices available on the Polish market.

  5. Sensing methanol concentration in direct methanol fuel cell with total harmonic distortion: Theory and application

    International Nuclear Information System (INIS)

    Mao Qing; Krewer, Ulrike

    2012-01-01

    The nonlinear frequency response of a direct methanol fuel cell (DMFC) is studied by analyzing the total harmonic distortion (THD) spectra. The dependence of the THD spectra on methanol concentration and methanol oxidation kinetics is investigated by means of both simulation and experiment. Simulation using a continuous stirred tank reactor network model suggests that the methanol concentration profile in the anode has a strong impact on the THD spectra. The experimentally observed nonlinear behavior of the DMFC anode can be qualitatively reproduced with a model containing a three-step methanol oxidation mechanism with Kauranen–Frumkin/Temkin kinetics. Both experiment and simulation results show that THD value has a monotonic correlation with methanol concentration at certain frequencies and its sensitivity to concentration is improved with increased current amplitude. The monotonic relationship enables the THD to sense the methanol concentration level by the DMFC itself, which is of mayor interest for the portable application as an external sensor for the system can be omitted.

  6. Nonparametric combinatorial sequence models.

    Science.gov (United States)

    Wauthier, Fabian L; Jordan, Michael I; Jojic, Nebojsa

    2011-11-01

    This work considers biological sequences that exhibit combinatorial structures in their composition: groups of positions of the aligned sequences are "linked" and covary as one unit across sequences. If multiple such groups exist, complex interactions can emerge between them. Sequences of this kind arise frequently in biology but methodologies for analyzing them are still being developed. This article presents a nonparametric prior on sequences which allows combinatorial structures to emerge and which induces a posterior distribution over factorized sequence representations. We carry out experiments on three biological sequence families which indicate that combinatorial structures are indeed present and that combinatorial sequence models can more succinctly describe them than simpler mixture models. We conclude with an application to MHC binding prediction which highlights the utility of the posterior distribution over sequence representations induced by the prior. By integrating out the posterior, our method compares favorably to leading binding predictors.

  7. Round table about the application in France of the new EURATOM directive establishing the basic radioprotection standards

    International Nuclear Information System (INIS)

    Godet, Jean-Luc; Lahaye, Thierry; Bernard, Herve

    2014-06-01

    Started in 2008, the updating works of the existing EURATOM directives are now completed with the publication in December 5, 2013 of the new 2013/59 Euratom Directive in the Official Journal of the European Union. The new directive establishes the basic protection standards relative to the health protection against ionizing radiation exposure hazards. This update allows to consolidate 5 existing directives, to take into consideration the recommendations of the International Commission on Radiological Protection (ICRP) published in 2007 (ICRP Publication 103), and to ensure consistency between the European framework with the new IAEA basic standards published in 2011. From January 17, 2014, France has a period of 4 years to transpose the new directive into national right and thus, to adjust the French national regulation included in the health, labor and environment laws to the European and international standards. This document brings together the 3 presentations (slides) made at this round table and dealing with: 1 - The transposition of Euratom directive 2013/59/ relative to basic radioprotection standards (J.L. Godet); 2 - The application in France of the new Euratom directive (T. Lahaye); 3 - A nuclear operator point of view regarding the daily application of Directive 2013-59 (H. Bernard)

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

    Directory of Open Access Journals (Sweden)

    Qingshan Xu

    2017-07-01

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

  9. Characterizing Ductile Damage and Failure: Application of the Direct Current Potential Drop Method to Uncracked Tensile Specimens

    OpenAIRE

    Brinnel, V.; Döbereiner, B.; Münstermann, Sebastian

    2014-01-01

    Modern high-strength steels exhibit excellent ductility properties but their application is hindered by traditional design rules. A characterization of necessary safety margins for the ductile failure of these steels is therefore required. Direct observation of ductile damage within tests is currently not possible, only limited measurements can be made with synchrotron or X-ray radiation facilities. The direct current potential drop (DCPD) method can determine ductile crack propagation with l...

  10. Hybrid Large Eddy Simulation / Reynolds Averaged Navier-Stokes Modeling in Directed Energy Applications

    Science.gov (United States)

    Zilberter, Ilya Alexandrovich

    In this work, a hybrid Large Eddy Simulation / Reynolds-Averaged Navier Stokes (LES/RANS) turbulence model is applied to simulate two flows relevant to directed energy applications. The flow solver blends the Menter Baseline turbulence closure near solid boundaries with a Lenormand-type subgrid model in the free-stream with a blending function that employs the ratio of estimated inner and outer turbulent length scales. A Mach 2.2 mixing nozzle/diffuser system representative of a gas laser is simulated under a range of exit pressures to assess the ability of the model to predict the dynamics of the shock train. The simulation captures the location of the shock train responsible for pressure recovery but under-predicts the rate of pressure increase. Predicted turbulence production at the wall is found to be highly sensitive to the behavior of the RANS turbulence model. A Mach 2.3, high-Reynolds number, three-dimensional cavity flow is also simulated in order to compute the wavefront aberrations of an optical beam passing thorough the cavity. The cavity geometry is modeled using an immersed boundary method, and an auxiliary flat plate simulation is performed to replicate the effects of the wind-tunnel boundary layer on the computed optical path difference. Pressure spectra extracted on the cavity walls agree with empirical predictions based on Rossiter's formula. Proper orthogonal modes of the wavefront aberrations in a beam originating from the cavity center agree well with experimental data despite uncertainty about in flow turbulence levels and boundary layer thicknesses over the wind tunnel window. Dynamic mode decomposition of a planar wavefront spanning the cavity reveals that wavefront distortions are driven by shear layer oscillations at the Rossiter frequencies; these disturbances create eddy shocklets that propagate into the free-stream, creating additional optical wavefront distortion.

  11. Sesamin from Cuscuta palaestina natural plant extracts: Directions for new prospective applications.

    Science.gov (United States)

    Abu-Lafi, Saleh; Makhamra, Sadam; Rayan, Ibrahim; Barriah, Waseim; Nasser, Ahmed; Abu Farkh, Basheer; Rayan, Anwar

    2018-01-01

    The aim of this study is to disclose the potential bioactive components of Cuscuta palaestina, a native parasitic natural plant of flora palaestina and to open direction towards new prospective application. GC-MS analysis identified 18 components in the methanolic extract of C. palaestina for the first time. The most appealing among them are Sesamin and two other phytosterols (Campesterol and Stigmasterol), all of which are documented in the scientific literature for their anticancer activity. Quantitation of Sesamin extracted from C. palaestina by HPLC-PDA with the use of three organic solvents showed that the Sesamin content in the methanolic extract was the highest. Following the disclosure of Sesamin presence in C. palaestina, we raised the question of whether it is produced naturally in C. palaestina or acquired from the host plant. The quantitation of Sesamin in C. palaestina was performed while being with five different host plants, and was compared with the amount of Sesamin in C. palaestina grown alone. The findings reveal that Sesamin is an endogenous secondary metabolite in C. palaestina. Thus, further studies are required to prove if C. palaestina can be used as an alternative source of anticancer phytochemicals, mainly Sesamin, and if proteins in the Sesamin production pathway could be valid biological targets for the development of novel and selective pesticides for control/ eradication of C. palaestina and maybe some other Cuscuta species. As well, the findings from this study raise a big question of whether inferring Sesamin production in C. palaestina could reduce its attack ability to host plants.

  12. Application of ultrasonic extraction method in the preparation of the directive action beverage from black currant

    Directory of Open Access Journals (Sweden)

    N. S. Rodionova

    2016-01-01

    Full Text Available The article presents the results of experimental determination of physical-and chemical parameters, the amount of anthocyanins, the definition of color and organoleptic characteristics of the beverage prepared with ultrasonic extraction method in comparison with the fruit-drink, obtained according to traditional recipe. Black currant was chosen the main raw material for the development of the beverage production technology. It is characterized by a high content of bioactive components that increase the adaptive abilities of human body. The purpose is to use ultrasonic extraction method in the preparation of functionally directed actions beverages. Extractor with submerged ultrasonic emitter was used as an experimental device. The essence of its operation is as follows: a mixture of the extractant and the plant substrate in different ratios was loaded into a container with the emitter, then the ultrasonic generator was turned on. The vibrations of ultrasonic frequency (22 kHz made high-frequency mechanical vibrations that caused the formation of intense cavitation areas and diffuse dissolution of cell substrates in the extractant in the treated mixture. The ultrasonic extraction technique involves brief contact of berries and extractant (up to 15 minutes upon application of ultrasonic vibrations. With an increase in exposure time, the yield of biologically active substances increases to reach an equilibrium state corresponding to the most complete exhaustion of raw materials. All this leads to a significant acceleration of the transition from the active ingredients from the raw materials into the extractant to obtain a product with improved physical - and chemical, organoleptic characteristics, as well as a higher antioxidant activity.

  13. Construction of a virtual Mycobacterium tuberculosis consensus genome and its application to data from a next generation sequencer.

    Science.gov (United States)

    Okumura, Kayo; Kato, Masako; Kirikae, Teruo; Kayano, Mitsunori; Miyoshi-Akiyama, Tohru

    2015-03-20

    Although Mycobacterium tuberculosis isolates are consisted of several different lineages and the epidemiology analyses are usually assessed relative to a particular reference genome, M. tuberculosis H37Rv, which might introduce some biased results. Those analyses are essentially based genome sequence information of M. tuberculosis and could be performed in sillico in theory, with whole genome sequence (WGS) data available in the databases and obtained by next generation sequencers (NGSs). As an approach to establish higher resolution methods for such analyses, whole genome sequences of the M. tuberculosis complexes (MTBCs) strains available on databases were aligned to construct virtual reference genome sequences called the consensus sequence (CS), and evaluated its feasibility in in sillico epidemiological analyses. The consensus sequence (CS) was successfully constructed and utilized to perform phylogenetic analysis, evaluation of read mapping efficacy, which is crucial for detecting single nucleotide polymorphisms (SNPs), and various MTBC typing methods virtually including spoligotyping, VNTR, Long sequence polymorphism and Beijing typing. SNPs detected based on CS, in comparison with H37Rv, were utilized in concatemer-based phylogenetic analysis to determine their reliability relative to a phylogenetic tree based on whole genome alignment as the gold standard. Statistical comparison of phylogenic trees based on CS with that of H37Rv indicated the former showed always better results that that of later. SNP detection and concatenation with CS was advantageous because the frequency of crucial SNPs distinguishing among strain lineages was higher than those of H37Rv. The number of SNPs detected was lower with the consensus than with the H37Rv sequence, resulting in a significant reduction in computational time. Performance of each virtual typing was satisfactory and accorded with those published when those are available. These results indicated that virtual CS

  14. Evaluation of the usefulness of smartphone-directed applications for measuring heart rate and arrhythmia detection

    Directory of Open Access Journals (Sweden)

    Michał Witkowski

    2017-12-01

    Conclusions: The majority of the free applications, available for smartphones, are able to measure HR precisely in patients with sinus rhythm, while in patients with AF, the exact measurement is significantly impeded by HR deficits. Only one out of 16 applications was able to measure HR in a patient with AF. None of the available applications could detect AF.

  15. Effect of directed-spray glyphosate applications on survival and growth of planted oaks after three growing seasons

    Science.gov (United States)

    Andrew B. Self; Andrew W. Ezell; Josh L. Moree; Rory O. Thornton

    2013-01-01

    Thousands of acres of oak (Quercus spp.) plantations are established across the South annually. Survival and growth of these plantings have been less than desirable. Several techniques have been utilized in attempts to achieve improved success in these areas. One such technique that has been recommended is the application of directed-spray herbicide...

  16. Design of an Axial-Flux permanent magnet machine for an in-wheel direct drive application

    NARCIS (Netherlands)

    Bastiaens, K.; Jansen, J.W.; Jumayev, S.; Lomonova, E.A.

    2017-01-01

    This paper concerns the optimization and comparison of six different axial-flux permanent magnet (AFPM) machine topologies for an in-wheel direct drive application. The objective of the optimization is to reach maximum power density, which is of essence for an in-wheel motor. The machine topologies

  17. Small-World Optimization Algorithm and Its Application in a Sequencing Problem of Painted Body Storage in a Car Company

    Directory of Open Access Journals (Sweden)

    Tian Zhipeng

    2015-01-01

    Full Text Available In the car company, the painted body storage (PBS is set up between the paint shop and the assembly shop. It stores the vehicles in production and reorders the vehicles sequence. To improve production efficiency of assembly shop, a mathematical model is developed aiming at minimizing the consumption rate of options and the total overtime and idle time. As the PBS sequencing process contains upstream sequence inbound and downstream sequence outbound, this paper proposes an algorithm with two phases. In the first phase, the discrete small-world optimization algorithm (DSWOA is applied to schedule the inbound sequence by employing the short-range nodes and the long-range nodes in order to realize the global searching. In the second phase, the heuristic algorithm is applied to schedule the outbound sequencing. The proposed model and algorithm are applied in an automobile enterprise. The results indicate that the two-phase algorithm is suitable for the PBS sequencing problem and the DSWOA has a better searching performance than GA in this problem. The sensitivity of model parameters is analyzed as well.

  18. Application of Space Vector Modulation in Direct Torque Control of PMSM

    Directory of Open Access Journals (Sweden)

    Michal Malek

    2008-01-01

    Full Text Available The paper deals with an improvement of direct torque control method for permanent magnet synchronous motor drives. Electrical torque distortion of the machine under original direct torque control is relatively high and if proper measures are taken it can be substantially decreased. The proposed solution here is to combine direct torque control with the space vector modulation technique. Such approach can eliminate torque distortion while preserving the simplicity of the original method.

  19. Direct heat applications of geothermal energy in The Geysers/Clear Lake region. Volume I. Geotechnical assessment, agribusiness applications, socioeconomic assessment, engineering assessment. Final report

    Energy Technology Data Exchange (ETDEWEB)

    1977-08-01

    The different uses to which geothermal heat and fluids could be applied as a direct utilization of resource or as heat utilization are explored. The following aspects are covered: geotechnical assessment, agricultural and industrial applications, socioeconomic assessment, and engineering assessment. (MHR)

  20. Evaluation of available phosphorus and cadmium associated with phosphate rock for direct application

    International Nuclear Information System (INIS)

    Chien, S.H.

    2002-01-01

    Three greenhouse experiments were conducted to evaluate available P and Cd associated with the use of phosphate rock (PR) for direct application. These experiments were: (1) 'Estimation of Phosphorus Availability to Maize and Cowpea From Phosphate Rock as Enhanced by Water-Soluble Phosphorus'; (2) 'Modified Iron Oxide-Impregnated Paper Strip (Pi) Test for Soils Treated With Phosphate Fertilizers'; and (3) 'Effect of Acidulation of High Cadmium Containing Phosphate Rocks on Cadmium Uptake by Upland Rice'. In the first experiment, a medium-reactive Central Florida phosphate rock (PR) was used. The effectiveness of P sources in terms of increasing dry-matter yield and P uptake followed the order of TSP≥(PR+TSP)>PR for maize and TSP=(TSP+PR)>PR for cowpea. P uptake from PR in the presence of TSP was higher than P uptake from PR applied alone. With respect to P uptake from PR applied alone, the corresponding relative increase in P uptake from PR due to TSP influence was 165% for maize and 72% for cowpea. In the second experiment, a highly reactive North Carolina PR was used. Both Bray I and the Pi test (with CaCl 2 ) underestimated available P from PR with respect to TSP. Available P estimated by the Pi test with KCl was more closely related to P uptake with both PR and TSP. More P was extracted from PR by the Pi test with KCl than with CaCl 2 , whereas no effect was observed for TSP. In the third experiment, a low-reactive Togo PR and a highly reactive North Carolina PR were used. Both PRs were fully acidulated to SSP and Togo PR was also partially acidulated with H 2 SO 4 at 50% level to PAPR. Cd uptake by rice grain followed the order of NC-SSP > NC-PR and Togo-SSP > Togo PAPR > Togo PR. The results also showed that most of the Cd uptake was retained in rice root and straw. Total uptake of Cd, Ca, and P by the rice plant was higher from NC-PR than from Togo-PR. Cd concentration in rice grain showed no significant difference between NC-PR and Togo-PR, whereas Cd

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

    NARCIS (Netherlands)

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

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

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

    DEFF Research Database (Denmark)

    Martin, P; Heiskari, N; Zhou, J

    1998-01-01

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

  3. A Review on the Applications of Next Generation Sequencing Technologies as Applied to Food-Related Microbiome Studies

    Directory of Open Access Journals (Sweden)

    Yu Cao

    2017-09-01

    Full Text Available The development of next generation sequencing (NGS techniques has enabled researchers to study and understand the world of microorganisms from broader and deeper perspectives. The contemporary advances in DNA sequencing technologies have not only enabled finer characterization of bacterial genomes but also provided deeper taxonomic identification of complex microbiomes which in its genomic essence is the combined genetic material of the microorganisms inhabiting an environment, whether the environment be a particular body econiche (e.g., human intestinal contents or a food manufacturing facility econiche (e.g., floor drain. To date, 16S rDNA sequencing, metagenomics and metatranscriptomics are the three basic sequencing strategies used in the taxonomic identification and characterization of food-related microbiomes. These sequencing strategies have used different NGS platforms for DNA and RNA sequence identification. Traditionally, 16S rDNA sequencing has played a key role in understanding the taxonomic composition of a food-related microbiome. Recently, metagenomic approaches have resulted in improved understanding of a microbiome by providing a species-level/strain-level characterization. Further, metatranscriptomic approaches have contributed to the functional characterization of the complex interactions between different microbial communities within a single microbiome. Many studies have highlighted the use of NGS techniques in investigating the microbiome of fermented foods. However, the utilization of NGS techniques in studying the microbiome of non-fermented foods are limited. This review provides a brief overview of the advances in DNA sequencing chemistries as the technology progressed from first, next and third generations and highlights how NGS provided a deeper understanding of food-related microbiomes with special focus on non-fermented foods.

  4. The cluster index of regularly varying sequences with applications to limit theory for functions of multivariate Markov chains

    DEFF Research Database (Denmark)

    Mikosch, Thomas Valentin; Wintenberger, Olivier

    2014-01-01

    We introduce the cluster index of a multivariate stationary sequence and characterize the index in terms of the spectral tail process. This index plays a major role in limit theory for partial sums of sequences. We illustrate the use of the cluster index by characterizing infinite variance stable...... limit distributions and precise large deviation results for sums of multivariate functions acting on a stationary Markov chain under a drift condition....

  5. A Review on the Applications of Next Generation Sequencing Technologies as Applied to Food-Related Microbiome Studies

    Science.gov (United States)

    Cao, Yu; Fanning, Séamus; Proos, Sinéad; Jordan, Kieran; Srikumar, Shabarinath

    2017-01-01

    The development of next generation sequencing (NGS) techniques has enabled researchers to study and understand the world of microorganisms from broader and deeper perspectives. The contemporary advances in DNA sequencing technologies have not only enabled finer characterization of bacterial genomes but also provided deeper taxonomic identification of complex microbiomes which in its genomic essence is the combined genetic material of the microorganisms inhabiting an environment, whether the environment be a particular body econiche (e.g., human intestinal contents) or a food manufacturing facility econiche (e.g., floor drain). To date, 16S rDNA sequencing, metagenomics and metatranscriptomics are the three basic sequencing strategies used in the taxonomic identification and characterization of food-related microbiomes. These sequencing strategies have used different NGS platforms for DNA and RNA sequence identification. Traditionally, 16S rDNA sequencing has played a key role in understanding the taxonomic composition of a food-related microbiome. Recently, metagenomic approaches have resulted in improved understanding of a microbiome by providing a species-level/strain-level characterization. Further, metatranscriptomic approaches have contributed to the functional characterization of the complex interactions between different microbial communities within a single microbiome. Many studies have highlighted the use of NGS techniques in investigating the microbiome of fermented foods. However, the utilization of NGS techniques in studying the microbiome of non-fermented foods are limited. This review provides a brief overview of the advances in DNA sequencing chemistries as the technology progressed from first, next and third generations and highlights how NGS provided a deeper understanding of food-related microbiomes with special focus on non-fermented foods. PMID:29033905

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

    Science.gov (United States)

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

    2002-07-01

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

  7. Residual, direct and cumulative effect of zinc application on wheat and rice yield under rice-wheat syst

    Directory of Open Access Journals (Sweden)

    R. Khan

    2009-05-01

    Full Text Available Zinc (Zn deficiency is prevalent particularly on calcareous soils of arid and semiarid region. A field experiment was conducted to investigate the direct, residual and cumulative effect of zinc on the yield of wheat and rice in permanent layout for two consecutive years, 2004-05 and 2005-06 at Arid Zone Research Institute D.I. Khan. Soil under study was deficient in Zn (0.8 mg kg-1. Effect of Zn on yield, Zn concentrations in leaf and soils were assessed using wheat variety Naseer-2000 and rice variety IRRI-6. Three rates of Zn, ranging from 0 to 10 kg ha-1 in soil, were applied as zinc sulphate (ZnSO4. 7H2O along with basal dose fertilization of nitrogen, phosphorus and potassium. Mature leaf and soil samples were collected at panicle initiation stage. The results showed that grain yield of wheat and rice was significantly increased by the direct application of 5 and 10 kg Zn ha-1. Highest grain yield of wheat (5467 kg ha-1 was recorded with the direct application of 10 kg Zn ha-1 while 4994 kg ha-1 was recorded with the cumulative application of 10 kg Zn ha-1 but the yield increase due to residual effect of Zn was statistically lower than the cumulative effect of Zn. Maximum paddy yield was recorded with the cumulative application ofZn followed by residual and direct applied 10 and 5 kg Zn kg ha-1, respectively. Zn concentration in soils ranged from 0.3 to 1.5 mg kg-1 in wheat and 0.24 to 2.40 mg kg-1 in rice, while in leaves it ranged from 18-48 mg kg-1 in wheat and 15-52 mg kg-1 in rice. The concentration of Zn in soil and leaves increased due to the treatments in the order; cumulative > residual > direct effect > control (without Zn. The yield attributes like 1000- grain weight, number of spikes, spike length and plant height were increased by the residual, direct and cumulative effect of Zn levels; however, the magnitude of increase was higher in cumulative effect than residual and direct effect of Zn, respectively. Under Zn-deficient soil

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

    DEFF Research Database (Denmark)

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

    2002-01-01

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

  9. Application of the EC pressure equipment directive in the gas industry; Die Anwendung der EG-Druckgeraeterichtlinie in der Gaswirtschaft

    Energy Technology Data Exchange (ETDEWEB)

    Bueschel, K. [Deutscher Verein des Gas- und Wasserfaches e.V., Bonn (Germany); John, M. [Karlsruhe Univ. (T.H.) (Germany). DVGW-Forschungsstelle am Engler-Bunte-Institut; Wasser, U. [Bundesverband der Deutschen Gas- und Wasserwirtschaft e.V., Bonn (Germany)

    2000-07-01

    The EC Pressure Equipment Directive primarily concerns that broad range of equipment that falls under the Equipment Safety Act and its regulations on pressure vessels, boilers etc. Meanwhile, however, the mainstream view is that also some equipment of the gas industry is affected although its pipeline systems have been excluded from the Directive. The interpretation of the Directive must take into account this background in order to reach satisfactory conclusions in the actual application of the Directive to the components of the gas industry. (orig.) [German] Die EG-Druckgeraeterichtlinie betrifft primaer jenes grosse Geraetespektrum, das unter das Geraetesicherheitsgesetz und dessen Verordnungen zu Druckbehaeltern, Dampfkesseln etc. faellt. Inzwischen herrscht jedoch die Meinung vor, dass auch bestimmte Anlagenteile der Gaswirtschaft erfasst werden, obwohl deren Rohrleitungssysteme von der Richtlinie ausgenommen worden sind. Die Auslegung der Richtlinie muss diesen Hintergrund beachten, um zu befriedigenden Aussagen bei ihrer konkreten Anwendung auf die Komponenten der Gaswirtschaft zu gelangen. (orig.)

  10. Direct methods for vision-based robot control : application and implementation

    NARCIS (Netherlands)

    Pieters, R.S.

    2013-01-01

    With the growing interest of integrating robotics into everyday life and industry, the requirements towards the quality and quantity of applications grows equally hard. This trend is profoundly recognized in applications involving visual perception. Whereas visual sensing in home environments tend

  11. Advancements in high-power high-brightness laser bars and single emitters for pumping and direct diode application

    Science.gov (United States)

    An, Haiyan; Jiang, Ching-Long J.; Xiong, Yihan; Zhang, Qiang; Inyang, Aloysius; Felder, Jason; Lewin, Alexander; Roff, Robert; Heinemann, Stefan; Schmidt, Berthold; Treusch, Georg

    2015-03-01

    We have continuously optimized high fill factor bar and packaging design to increase power and efficiency for thin disc laser system pump application. On the other hand, low fill factor bars packaged on the same direct copper bonded (DCB) cooling platform are used to build multi-kilowatt direct diode laser systems. We have also optimized the single emitter designs for fiber laser pump applications. In this paper, we will give an overview of our recent advances in high power high brightness laser bars and single emitters for pumping and direct diode application. We will present 300W bar development results for our next generation thin disk laser pump source. We will also show recent improvements on slow axis beam quality of low fill factor bar and its application on performance improvement of 4-5 kW TruDiode laser system with BPP of 30 mm*mrad from a 600 μm fiber. Performance and reliability results of single emitter for multiemitter fiber laser pump source will be presented as well.

  12. Direct chemical synthesis of MnO2 nanowhiskers on MXene surfaces for supercapacitor applications

    KAUST Repository

    Baby, Rakhi Raghavan; Ahmed, Bilal; Anjum, Dalaver H.; Alshareef, Husam N.

    2016-01-01

    Transition metal carbides (MXenes) are an emerging class of two dimensional (2D) materials with promising electrochemical energy storage performance. Herein, for the first time, by direct chemical synthesis, nanocrystalline ε-MnO2 whiskers were

  13. Are ‘Agent’ Exclusion Clauses a Legitimate Application of the EU Database Directive?

    Directory of Open Access Journals (Sweden)

    Jimi Groom

    2004-03-01

    Full Text Available This article explores the implications of the implementation of the European Database Directive in the area of autonomous agents and the use of exclusion tools in the part of database owners to stop agents accessing their works.

  14. Are Agent Exclusion Clauses a Legitimate Application of the EU Database Directive?

    OpenAIRE

    Jimi Groom

    2004-01-01

    This article explores the implications of the implementation of the European Database Directive in the area of autonomous agents and the use of exclusion tools in the part of database owners to stop agents accessing their works.

  15. Progress Towards the Development of a Traveling Wave Direct Energy Converter for Aneutronic Fusion Propulsion Applications

    Science.gov (United States)

    Tarditi, A. G.; Chap, A.; Wolinsky, J.; Scott, J. H.

    2015-01-01

    A coordinated experimental and theory/simulation effort has been carried out to investigate the physics of the Traveling Wave Direct Energy Converter (TWDEC), a scheme that has been proposed in the past for the direct conversion into electricity of the kinetic energy of an ion beam generated from fusion reactions. This effort has been focused in particular on the TWDEC process in the high density beam regime, thus accounting for the ion beam expansion due to its space charge.

  16. Experience of the application of direct democracy and mediate participation’s possibilities in territorial communities of Ukraine

    Directory of Open Access Journals (Sweden)

    N. M. Nahorna

    2016-10-01

    Taking into consideration such situation, the application of direct democracy and mediate participation’s possibilities in territorial communities of Ukraine appears to be more and more relevant for scientifically theoretical apprehension and practical introduction of the modern Ukraine’s political life. Thus, we consider that the improvement of the mechanisms of direct democracy and mediate citizens’ participation should become an important task of state’s policy in the process of raise of the Ukrainian political system efficiency. At the present stage of political transformations they are an actual instrument of influencing the population, aimed at the increase of control of the governmental institutions between the elections periods. Indisputably, such experience of the application of direct democracy and mediate participation’s possibilities in territorial communities of Ukraine together with the necessary improvement of legal sphere and the raise of the efficiency of the direct democracy’s mechanisms practical implementation will positively influence the development of social and political life and will allow to use the main means of the realization of direct democracy at the local level and at the national level effectively and will stimulate the participation of population in the political process.

  17. Development of Highly Informative Genome-Wide Single Sequence Repeat Markers for Breeding Applications in Sesame and Construction of a Web Resource: SisatBase

    Directory of Open Access Journals (Sweden)

    Komivi Dossa

    2017-08-01

    Full Text Available The sequencing of the full nuclear genome of sesame (Sesamum indicum L. provides the platform for functional analyses of genome components and their application in breeding programs. Although the importance of microsatellites markers or simple sequence repeats (SSR in crop genotyping, genetics, and breeding applications is well established, only a little information exist concerning SSRs at the whole genome level in sesame. In addition, SSRs represent a suitable marker type for sesame molecular breeding in developing countries where it is mainly grown. In this study, we identified 138,194 genome-wide SSRs of which 76.5% were physically mapped onto the 13 pseudo-chromosomes. Among these SSRs, up to three primers pairs were supplied for 101,930 SSRs and used to in silico amplify the reference genome together with two newly sequenced sesame accessions. A total of 79,957 SSRs (78% were polymorphic between the three genomes thereby suggesting their promising use in different genomics-assisted breeding applications. From these polymorphic SSRs, 23 were selected and validated to have high polymorphic potential in 48 sesame accessions from different growing areas of Africa. Furthermore, we have developed an online user-friendly database, SisatBase (http://www.sesame-bioinfo.org/SisatBase/, which provides free access to SSRs data as well as an integrated platform for functional analyses. Altogether, the reference SSR and SisatBase would serve as useful resources for genetic assessment, genomic studies, and breeding advancement in sesame, especially in developing countries.

  18. Application of the PROMETHEE technique to determine depression outlet location and flow direction in DEM

    Science.gov (United States)

    Chou, Tien-Yin; Lin, Wen-Tzu; Lin, Chao-Yuan; Chou, Wen-Chieh; Huang, Pi-Hui

    2004-02-01

    With the fast growing progress of computer technologies, spatial information on watersheds such as flow direction, watershed boundaries and the drainage network can be automatically calculated or extracted from a digital elevation model (DEM). The stubborn problem that depressions exist in DEMs has been frequently encountered while extracting the spatial information of terrain. Several filling-up methods have been proposed for solving depressions. However, their suitability for large-scale flat areas is inadequate. This study proposes a depression watershed method coupled with the Preference Ranking Organization METHod for Enrichment Evaluations (PROMETHEEs) theory to determine the optimal outlet and calculate the flow direction in depressions. Three processing procedures are used to derive the depressionless flow direction: (1) calculating the incipient flow direction; (2) establishing the depression watershed by tracing the upstream drainage area and determining the depression outlet using PROMETHEE theory; (3) calculating the depressionless flow direction. The developed method was used to delineate the Shihmen Reservoir watershed located in Northern Taiwan. The results show that the depression watershed method can effectively solve the shortcomings such as depression outlet differentiating and looped flow direction between depressions. The suitability of the proposed approach was verified.

  19. Rotation sequence to report humerothoracic kinematics during 3D motion involving large horizontal component: application to the tennis forehand drive.

    Science.gov (United States)

    Creveaux, Thomas; Sevrez, Violaine; Dumas, Raphaël; Chèze, Laurence; Rogowski, Isabelle

    2018-03-01

    The aim of this study was to examine the respective aptitudes of three rotation sequences (Y t X f 'Y h '', Z t X f 'Y h '', and X t Z f 'Y h '') to effectively describe the orientation of the humerus relative to the thorax during a movement involving a large horizontal abduction/adduction component: the tennis forehand drive. An optoelectronic system was used to record the movements of eight elite male players, each performing ten forehand drives. The occurrences of gimbal lock, phase angle discontinuity and incoherency in the time course of the three angles defining humerothoracic rotation were examined for each rotation sequence. Our results demonstrated that no single sequence effectively describes humerothoracic motion without discontinuities throughout the forehand motion. The humerothoracic joint angles can nevertheless be described without singularities when considering the backswing/forward-swing and the follow-through phases separately. Our findings stress that the sequence choice may have implications for the report and interpretation of 3D joint kinematics during large shoulder range of motion. Consequently, the use of Euler/Cardan angles to represent 3D orientation of the humerothoracic joint in sport tasks requires the evaluation of the rotation sequence regarding singularity occurrence before analysing the kinematic data, especially when the task involves a large shoulder range of motion in the horizontal plane.

  20. APPLICABILITY ANALYSIS OF THE PHASE CORRELATION ALGORITHM FOR STABILIZATION OF VIDEO FRAMES SEQUENCES FOR CAPILLARY BLOOD FLOW

    Directory of Open Access Journals (Sweden)

    K. A. Karimov

    2016-05-01

    Full Text Available Videocapillaroscopy is a convenient and non-invasive method of blood flow parameters recovery in the capillaries. Capillaries position can vary at recorded video sequences due to the registration features of capillary blood flow. Stabilization algorithm of video capillary blood flow based on phase correlation is proposed and researched. This algorithm is compared to the known algorithms of video frames stabilization with full-frame superposition and with key points. Programs, based on discussed algorithms, are compared under processing the experimentally recorded video sequences of human capillaries and under processing of computer-simulated sequences of video frames with the specified offset. The full-frame superposition algorithm provides high quality of stabilization; however, the program based on this algorithm requires significant computational resources. Software implementation of the algorithm based on the detection of the key points is characterized by good performance, but provides low quality of stabilization for video sequences capillary blood flow. Algorithm based on phase correlation method provides high quality of stabilization and program realization of this algorithm requires minimal computational resources. It is shown that the phase correlation algorithm is the most useful for stabilization of video sequences for capillaries blood flow. Obtained findings can be used in the software for biomedical diagnostics.

  1. A WiFi Tracking Device Printed Directly on Textile for Wearable Electronics Applications

    KAUST Repository

    Krykpayev, Bauyrzhan

    2015-12-01

    Wearable technology is quickly becoming commonplace in our everyday life - fit-ness and health monitors, smart watches, and Google Glass, just to name a few. It is very clear that in near future the wearable technology will only grow. One of the biggest wearable fields is the E-textiles. E-textiles empower clothes with new functionality by enhancing fabrics with electronics and interconnects. The main obstacle to the development of E-textile field is the relative difficulty and large tolerance in its manufacturing as compared to the standard circuit production. Current methods such as the application of conductive foils, embroidering of conductive wires and treatment with conductive coatings do not possess efficient, fast and reliable mass production traits inherent to the electronic industry. On the other hand, the method of conductive printing on textile has the potential to unlock the efficiency similar to PCB production, due to its roll-to-roll and reel-to-reel printing capabilities. Further-more, printing on textiles is a common practice to realize graphics, artwork, etc. and thus adaptability to conductive ink printing will be relatively easier. Even though conductive printing is a fully additive process, the end circuit layout is very similar to the one produced via PCB manufacture. However, due to high surface roughness and porosity of textiles, efficient and reliable printing on textile has remained elusive. Direct conductive printing on textile is possible but only on specialized dense and tightly interwoven fabrics. Such fabrics are usually uncommon and expensive. Another option is to employ an interface layer that flattens the textile surface, thus allowing printing on it. The interface layer method can be used with a variety of textiles such as polyester/cotton that can be found in any store, making this method promising for wearable electronics. Very few examples and that too of simple structures such as a line, square patch or electrode have been

  2. Enhancement of Hybrid SPEEK Based Polymer–Cyclodextrin-Silica Inorganic Membrane for Direct Methanol Fuel Cell Application

    Directory of Open Access Journals (Sweden)

    Tutuk Djoko Kusworo

    2017-06-01

      Keywords: Direct Methanol Fuel Cell, Poly(ether ether ketone, cyclodextrin-silica, sulfonation, ionic conductivity. Article History: Received January 18th 2017; Received in revised form April 21st 2017; Accepted June 22nd 2017; Available online How to Cite This Article: Kusworo, T.D., Hakim, M.F. and Hadiyanto, H. (2017 Enhancement of Hybrid SPEEK Based Polymer–Cyclodextrin-Silica Inorganic Membrane for Direct Methanol Fuel Cell Application. International Journal of Renewable Energy Development, 6(2, 165-170. https://doi.org/10.14710/ijred.6.2.165-170

  3. Application of nanodisc technology for direct electrochemical investigation of plant cytochrome P450s and their NADPH P450 oxidoreductase

    DEFF Research Database (Denmark)

    Bavishi, Krutika; Laursen, Tomas; Martinez, Karen Laurence

    2016-01-01

    Direct electrochemistry of cytochrome P450 containing systems has primarily focused on investigating enzymes from microbes and animals for bio-sensing applications. Plant P450s receive electrons from NADPH P450 oxidoreductase (POR) to orchestrate the bio-synthesis of a plethora of commercially...... was electro-catalytically active while the P450s generated hydrogen peroxide (H2O2). These nanodisc-based investigations lay the prospects and guidelines for construction of a simplified platform to perform mediator-free, direct electrochemistry of non-engineered cytochromes P450 under native-like conditions...

  4. Direct heat applications of geothermal energy in The Geysers/Clear Lake region. Volume I. Geotechnical assessment, agribusiness applications, socioeconomic assessment, engineering assessment. Final report

    Energy Technology Data Exchange (ETDEWEB)

    1976-08-01

    Discussion is presented under the following section headings: background and some technical characteristics of geothermal resources; geology and geohydrology, geophysics, and, conclusions regarding availability of geothermal energy for nonelectric uses; agricultural assessment of Lake County, site assessment for potential agricultural development, analysis of potential agricultural applications, special application of low cost geothermal energy to algae harvesting, development of an integrated agribusiness, geothermal complex in Lake County, analysis of individual enterprises, and, recommendations for subsequent work; demographic characteristics, economic condition and perspective of Lake County, economic impact of geothermal in Lake County, social and economic factors related to geothermal resource development, socioeconomic impact of nonelectric uses of geothermal energy, and, identification of direct heat applications of geothermal energy for Lake County based on selected interviews; cost estimate procedure, example, justification of procedure, and, typical costs and conclusions; and, recommended prefeasibility and feasibility studies related to construction of facilities for nonelectric applications of geothermal resource utilization. (JGB)

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

    Directory of Open Access Journals (Sweden)

    Inácio JAL

    2005-01-01

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

  6. Self-start manual for direct use applications of geothermal resources

    Energy Technology Data Exchange (ETDEWEB)

    Christiansen, C.C.

    1978-07-01

    The process essential to resource assessment and acquisition, candidate application screening, community needs assessment, community acceptance testing, market assessment, regulation, environmental repoting and permitting, siting, technology status, and financing options are presented.

  7. Application of next-generation sequencing for rapid marker development in molecular plant breeding: a case study on anthracnose disease resistance in Lupinus angustifolius L.

    Directory of Open Access Journals (Sweden)

    Yang Huaan

    2012-07-01

    fingerprinting method for marker-assisted selection in the Australian national lupin breeding program. Conclusions We demonstrated that more than 30 molecular markers linked to a target gene of agronomic trait of interest can be identified from a small portion (1/8 of one sequencing run on HiSeq2000 by applying NGS based RAD sequencing in marker development. The markers developed by the strategy described in this study are all co-dominant SNP markers, which can readily be converted into high throughput multiplex format or low-cost, simple PCR-based markers desirable for large scale marker implementation in plant breeding programs. The high density and closely linked molecular markers associated with a target trait help to overcome a major bottleneck for implementation of molecular markers on a wide range of germplasm in breeding programs. We conclude that application of NGS based RAD sequencing as DNA fingerprinting is a very rapid and cost-effective strategy for marker development in molecular plant breeding. The strategy does not require any prior genome knowledge or molecular information for the species under investigation, and it is applicable to other plant species.

  8. Roche genome sequencer FLX based high-throughput sequencing of ancient DNA

    DEFF Research Database (Denmark)

    Alquezar-Planas, David E; Fordyce, Sarah Louise

    2012-01-01

    Since the development of so-called "next generation" high-throughput sequencing in 2005, this technology has been applied to a variety of fields. Such applications include disease studies, evolutionary investigations, and ancient DNA. Each application requires a specialized protocol to ensure...... that the data produced is optimal. Although much of the procedure can be followed directly from the manufacturer's protocols, the key differences lie in the library preparation steps. This chapter presents an optimized protocol for the sequencing of fossil remains and museum specimens, commonly referred...

  9. Exact distribution of a pattern in a set of random sequences generated by a Markov source: applications to biological data

    Directory of Open Access Journals (Sweden)

    Regad Leslie

    2010-01-01

    Full Text Available Abstract Background In bioinformatics it is common to search for a pattern of interest in a potentially large set of rather short sequences (upstream gene regions, proteins, exons, etc.. Although many methodological approaches allow practitioners to compute the distribution of a pattern count in a random sequence generated by a Markov source, no specific developments have taken into account the counting of occurrences in a set of independent sequences. We aim to address this problem by deriving efficient approaches and algorithms to perform these computations both for low and high complexity patterns in the framework of homogeneous or heterogeneous Markov models. Results The latest advances in the field allowed us to use a technique of optimal Markov chain embedding based on deterministic finite automata to introduce three innovative algorithms. Algorithm 1 is the only one able to deal with heterogeneous models. It also permits to avoid any product of convolution of the pattern distribution in individual sequences. When working with homogeneous models, Algorithm 2 yields a dramatic reduction in the complexity by taking advantage of previous computations to obtain moment generating functions efficiently. In the particular case of low or moderate complexity patterns, Algorithm 3 exploits power computation and binary decomposition to further reduce the time complexity to a logarithmic scale. All these algorithms and their relative interest in comparison with existing ones were then tested and discussed on a toy-example and three biological data sets: structural patterns in protein loop structures, PROSITE signatures in a bacterial proteome, and transcription factors in upstream gene regions. On these data sets, we also compared our exact approaches to the tempting approximation that consists in concatenating the sequences in the data set into a single sequence. Conclusions Our algorithms prove to be effective and able to handle real data sets with

  10. Exact distribution of a pattern in a set of random sequences generated by a Markov source: applications to biological data.

    Science.gov (United States)

    Nuel, Gregory; Regad, Leslie; Martin, Juliette; Camproux, Anne-Claude

    2010-01-26

    In bioinformatics it is common to search for a pattern of interest in a potentially large set of rather short sequences (upstream gene regions, proteins, exons, etc.). Although many methodological approaches allow practitioners to compute the distribution of a pattern count in a random sequence generated by a Markov source, no specific developments have taken into account the counting of occurrences in a set of independent sequences. We aim to address this problem by deriving efficient approaches and algorithms to perform these computations both for low and high complexity patterns in the framework of homogeneous or heterogeneous Markov models. The latest advances in the field allowed us to use a technique of optimal Markov chain embedding based on deterministic finite automata to introduce three innovative algorithms. Algorithm 1 is the only one able to deal with heterogeneous models. It also permits to avoid any product of convolution of the pattern distribution in individual sequences. When working with homogeneous models, Algorithm 2 yields a dramatic reduction in the complexity by taking advantage of previous computations to obtain moment generating functions efficiently. In the particular case of low or moderate complexity patterns, Algorithm 3 exploits power computation and binary decomposition to further reduce the time complexity to a logarithmic scale. All these algorithms and their relative interest in comparison with existing ones were then tested and discussed on a toy-example and three biological data sets: structural patterns in protein loop structures, PROSITE signatures in a bacterial proteome, and transcription factors in upstream gene regions. On these data sets, we also compared our exact approaches to the tempting approximation that consists in concatenating the sequences in the data set into a single sequence. Our algorithms prove to be effective and able to handle real data sets with multiple sequences, as well as biological patterns of

  11. ZnO/Cu nanocomposite: a platform for direct electrochemistry of enzymes and biosensing applications.

    Science.gov (United States)

    Yang, Chi; Xu, Chunxiang; Wang, Xuemei

    2012-03-06

    Unique structured nanomaterials can facilitate the direct electron transfer between redox proteins and the electrodes. Here, in situ directed growth on an electrode of a ZnO/Cu nanocomposite was prepared by a simple corrosion approach, which enables robust mechanical adhesion and electrical contact between the nanostructured ZnO and the electrodes. This is great help to realize the direct electron transfer between the electrode surface and the redox protein. SEM images demonstrate that the morphology of the ZnO/Cu nanocomposite has a large specific surface area, which is favorable to immobilize the biomolecules and construct biosensors. Using glucose oxidase (GOx) as a model, this ZnO/Cu nanocomposite is employed for immobilization of GOx and the construction of the glucose biosensor. Direct electron transfer of GOx is achieved at ZnO/Cu nanocomposite with a high heterogeneous electron transfer rate constant of 0.67 ± 0.06 s(-1). Such ZnO/Cu nanocomposite provides a good matrix for direct electrochemistry of enzymes and mediator-free enzymatic biosensors.

  12. FOREIGN DIRECT INVESTMENT AND ECONOMIC PROGRESS:APPLICATION OF A DYNAMIC MODEL

    Directory of Open Access Journals (Sweden)

    Cyril A. Ogbokor

    2018-01-01

    Full Text Available Capital movements,whether in the form of foreign direct investment or foreignportfolio investment are considered to have a positive multiplier effect on theeconomy.The study contributes to the empirical literature by investigatingwhether foreign direct investment affects economic growth using Namibia as atest centre.The study made use ofvector autoregression methodto examine thisrelationship.A quarterly data covering 1990:Q1 to 2014:Q4 was employed.Theresults found cointegratingrelationships among the four variables that wereinvestigated. The estimated long-run equation also suggests a positive relationshipamongst the variables that have been examined in the study. Surprisingly, noevidence of causality was found pertaining tothe variables assessed in the study.Moreover, real exchange rate and net foreign direct investment contributed moretowards innovations in economic growth during the forecast horizon compared tothe openness index. The study concludes by crafting opportunities for furtherinquiries.

  13. A clinical application of laser direction in anastomosis for inferior canalicular laceration

    Institute of Scientific and Technical Information of China (English)

    LIANG Tao; ZHAO Ke-xiao; ZHANG Ling-yun

    2006-01-01

    Objective:To study the therapeutic efficiency and effecacy of laser-directing approach on searching for the nasal broken end of lacerated lacrimal canaliculus in anastomosis for canalicular laceration.Methods: Forty-nine patients ( 49 eyes ) suffering from traumatic inferior canalicular laceration were divided into control group and laser-directing group. The distance between the lacrimal punctum and the nasal broken end of lacerated lacrimal canaliculus was more than 6 mm. During the course of management of eyelid trauma, the patients were treated by canalicular anastomosis operation with traditional method and laser-directing method in searching for the nasal broken end of lacerated lacrimal canaliculus respectively. The silicone tube of 1 mm diameter was intubated in the lacrimal passage as a stent for 4 to 6months.Results: In the laser-directing group, the mean time in searching for the nasal broken end of lacerated lacrimal canaliculus was (5.75 ± 1.49) minutes and the mean time of operation was (49.21±3.37) minutes; both were significantly shorter than that of the control group(P <0.01). The cure rate of the laser-directing group was96.55 %, higher than that of the control group but without statistical significance (P > 0.05).Conclusions: The laser-directing method is much quicker and more convenient to searching for the nasal broken end of the lacerated lacrimal canaliculus than the traditional approach, and patients suffer less pain and damaging in canalicular anastomosis operation.

  14. Feasibility study on applicability of direct contact heat transfer SGs or FBRs

    International Nuclear Information System (INIS)

    Kinoshita, Izumi; Nishi, Yoshihisa; Furuya, Masahiro

    1997-01-01

    As a candidate of an innovative steam generator for fast breeder reactors, heat exchanger with direct contact heat transfer between melting alloy and water was proposed. The objectives of this study are to obtain the technical feasibility of this concept, to evaluate the heat transfer characteristics of direct contact heat transfer and to estimate the size and volume of this SG. Followings are main results. (1) In the case of sodium tube failure, it is considered that steam and water will not enter into the primary sodium under appropriate countermeasures. (2) Under the condition of temperature and pressure of SG for FBRs, the phenomenon such as vapor explosion is not take place in this SG concept. (3) as a result of material compatibility test and analysis, it is considered that 9Cr-1Mo steel and 21/4cr-1Mo steel will be a candidate structural material. (4) It is considered that the production of oxides by the chemical reaction between melting alloy and water is mitigated by dissolving hydrogen gas in feed water. (5) The fundamental direct contact heat transfer characteristics between a melting alloy and water is obtained in following two regions. One is the evaporating region and the other is the superheating region. The effect of the system pressure on the heat transfer characteristics and the required degree of superheat of a melting alloy above the water saturation temperature are evaluated during direct contact heat transfer experiments by injecting water into a high temperature melting alloy. (6) Due to the high heat transfer performance of direct contact heat transfer, it is found that compact steam generation section will be expected. However, because of the characteristics of direct contact heat exchanger, achievement of high efficiency was difficult. In order to make a good use of this SG concept, improvement of efficiency is necessary. (author)

  15. Direct and vicarious violent victimization and juvenile delinquency: an application of general strain theory.

    Science.gov (United States)

    Lin, Wen-Hsu; Cochran, John K; Mieczkowski, Thomas

    2011-01-01

    Using a national probability sample of adolescents (12–17), this study applies general strain theory to how violent victimization, vicarious violent victimization, and dual violent victimization affect juvenile violent/property crime and drug use. In addition, the mediating effect and moderating effect of depression, low social control, and delinquent peer association on the victimization–delinquency relationship is also examined. Based on SEM analyses and contingency tables, the results indicate that all three types of violent victimization have significant and positive direct effects on violent/property crime and drug use. In addition, the expected mediating effects and moderating effects are also found. Limitations and future directions are discussed.

  16. Direct hyperpolarization of micro- and nanodiamonds for bioimaging applications - Considerations on particle size, functionalization and polarization loss

    Science.gov (United States)

    Kwiatkowski, Grzegorz; Jähnig, Fabian; Steinhauser, Jonas; Wespi, Patrick; Ernst, Matthias; Kozerke, Sebastian

    2018-01-01

    Due to the inherently long relaxation time of 13C spins in diamond, the nuclear polarization enhancement obtained with dynamic nuclear polarization can be preserved for a time on the order of about one hour, opening up an opportunity to use diamonds as a new class of long-lived contrast agents. The present communication explores the feasibility of using 13C spins in directly hyperpolarized diamonds for MR imaging including considerations for potential in vivo applications.

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

    Science.gov (United States)

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

    2011-01-01

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

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

    DEFF Research Database (Denmark)

    Hansen, Trine; Skånseng, Beate; Hoorfar, Jeffrey

    2013-01-01

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

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

    Science.gov (United States)

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

    1993-11-01

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

  20. Ni2P Makes Application of the PtRu Catalyst Much Stronger in Direct Methanol Fuel Cells.

    Science.gov (United States)

    Chang, Jinfa; Feng, Ligang; Liu, Changpeng; Xing, Wei

    2015-10-12

    PtRu is regarded as the best catalyst for direct methanol fuel cells, but the performance decay resulting from the loss of Ru seriously hinders commercial applications. Herein, we demonstrated that the presence of Ni2 P largely reduces Ru loss, which thus makes the application of PtRu much stronger in direct methanol fuel cells. Outstanding catalytic activity and stability were observed by cyclic voltammetry. Upon integrating the catalyst material into a practical direct methanol fuel cell, the highest maximum power density was achieved on the PtRu-Ni2P/C catalyst among the reference catalysts at different temperatures. A maximum power density of 69.9 mW cm(-2) at 30 °C was obtained on PtRu-Ni2P/C, which is even higher than the power density of the state-of-the-art commercial PtRu catalyst at 70 °C (63.1 mW cm(-2)). Moreover, decay in the performance resulting from Ru loss was greatly reduced owing to the presence of Ni2 P, which is indicative of very promising applications. © 2015 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.