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Sample records for random sequences reconsidered

  1. absolutely regular random sequences

    Directory of Open Access Journals (Sweden)

    Michel Harel

    1996-01-01

    Full Text Available In this paper, the central limit theorems for the density estimator and for the integrated square error are proved for the case when the underlying sequence of random variables is nonstationary. Applications to Markov processes and ARMA processes are provided.

  2. Permutation Entropy for Random Binary Sequences

    Directory of Open Access Journals (Sweden)

    Lingfeng Liu

    2015-12-01

    Full Text Available In this paper, we generalize the permutation entropy (PE measure to binary sequences, which is based on Shannon’s entropy, and theoretically analyze this measure for random binary sequences. We deduce the theoretical value of PE for random binary sequences, which can be used to measure the randomness of binary sequences. We also reveal the relationship between this PE measure with other randomness measures, such as Shannon’s entropy and Lempel–Ziv complexity. The results show that PE is consistent with these two measures. Furthermore, we use PE as one of the randomness measures to evaluate the randomness of chaotic binary sequences.

  3. Nonlinear deterministic structures and the randomness of protein sequences

    CERN Document Server

    Huang Yan Zhao

    2003-01-01

    To clarify the randomness of protein sequences, we make a detailed analysis of a set of typical protein sequences representing each structural classes by using nonlinear prediction method. No deterministic structures are found in these protein sequences and this implies that they behave as random sequences. We also give an explanation to the controversial results obtained in previous investigations.

  4. Reconsidering the generation time hypothesis based on nuclear ribosomal ITS sequence comparisons in annual and perennial angiosperms.

    Science.gov (United States)

    Soria-Hernanz, David F; Fiz-Palacios, Omar; Braverman, John M; Hamilton, Matthew B

    2008-12-29

    Differences in plant annual/perennial habit are hypothesized to cause a generation time effect on divergence rates. Previous studies that compared rates of divergence for internal transcribed spacer (ITS1 and ITS2) sequences of nuclear ribosomal DNA (nrDNA) in angiosperms have reached contradictory conclusions about whether differences in generation times (or other life history features) are associated with divergence rate heterogeneity. We compared annual/perennial ITS divergence rates using published sequence data, employing sampling criteria to control for possible artifacts that might obscure any actual rate variation caused by annual/perennial differences. Relative rate tests employing ITS sequences from 16 phylogenetically-independent annual/perennial species pairs rejected rate homogeneity in only a few comparisons, with annuals more frequently exhibiting faster substitution rates. Treating branch length differences categorically (annual faster or perennial faster regardless of magnitude) with a sign test often indicated an excess of annuals with faster substitution rates. Annuals showed an approximately 1.6-fold rate acceleration in nucleotide substitution models for ITS. Relative rates of three nuclear loci and two chloroplast regions for the annual Arabidopsis thaliana compared with two closely related Arabidopsis perennials indicated that divergence was faster for the annual. In contrast, A. thaliana ITS divergence rates were sometimes faster and sometimes slower than the perennial. In simulations, divergence rate differences of at least 3.5-fold were required to reject rate constancy in > 80 % of replicates using a nucleotide substitution model observed for the combination of ITS1 and ITS2. Simulations also showed that categorical treatment of branch length differences detected rate heterogeneity > 80% of the time with a 1.5-fold or greater rate difference. Although rate homogeneity was not rejected in many comparisons, in cases of significant rate

  5. Simulations Using Random-Generated DNA and RNA Sequences

    Science.gov (United States)

    Bryce, C. F. A.

    1977-01-01

    Using a very simple computer program written in BASIC, a very large number of random-generated DNA or RNA sequences are obtained. Students use these sequences to predict complementary sequences and translational products, evaluate base compositions, determine frequencies of particular triplet codons, and suggest possible secondary structures.…

  6. Entropy and long-range correlations in random symbolic sequences

    CERN Document Server

    Melnik, S S

    2014-01-01

    The goal of this paper is to develop an estimate for the entropy of random long-range correlated symbolic sequences with elements belonging to a finite alphabet. As a plausible model, we use the high-order additive stationary ergodic Markov chain. Supposing that the correlations between random elements of the chain are weak we express the differential entropy of the sequence by means of the symbolic pair correlation function. We also examine an algorithm for estimating the differential entropy of finite symbolic sequences. We show that the entropy contains two contributions, the correlation and fluctuation ones. The obtained analytical results are used for numerical evaluation of the entropy of written English texts and DNA nucleotide sequences. The developed theory opens the way for constructing a more consistent and sophisticated approach to describe the systems with strong short- and weak long-range correlations.

  7. Humans cannot consciously generate random numbers sequences: Polemic study.

    Science.gov (United States)

    Figurska, Małgorzata; Stańczyk, Maciej; Kulesza, Kamil

    2008-01-01

    It is widely believed, that randomness exists in Nature. In fact such an assumption underlies many scientific theories and is embedded in the foundations of quantum mechanics. Assuming that this hypothesis is valid one can use natural phenomena, like radioactive decay, to generate random numbers. Today, computers are capable of generating the so-called pseudorandom numbers. Such series of numbers are only seemingly random (bias in the randomness quality can be observed). Question whether people can produce random numbers, has been investigated by many scientists in the recent years. The paper "Humans can consciously generate random numbers sequences..." published recently in Medical Hypotheses made claims that were in many ways contrary to state of art; it also stated far-reaching hypotheses. So, we decided to repeat the experiments reported, with special care being taken of proper laboratory procedures. Here, we present the results and discuss possible implications in computer and other sciences.

  8. Classification of periodic, chaotic and random sequences using ...

    Indian Academy of Sciences (India)

    ities of different datasets. Entropy cannot differentiate between chaotic and random sequences while ApEn and LZ cannot distinguish between weak and strong chaos. Figure 1. 95% confidence interval for mean LZ complexity of 50 samples of length. 20 using four bins. Pramana – J. Phys., Vol. 84, No. 3, March 2015. 367 ...

  9. Peptide based diagnostics: are random-sequence peptides more useful than tiling proteome sequences?

    Science.gov (United States)

    Navalkar, Krupa Arun; Johnston, Stephan Albert; Stafford, Phillip

    2015-02-01

    Diagnostics using peptide ligands have been available for decades. However, their adoption in diagnostics has been limited, not because of poor sensitivity but in many cases due to diminished specificity. Numerous reports suggest that protein-based rather than peptide-based disease detection is more specific. We examined two different approaches to peptide-based diagnostics using Coccidioides (aka Valley Fever) as the disease model. Although the pathogen was discovered more than a century ago, a highly sensitive diagnostic remains unavailable. We present a case study where two different approaches to diagnosing Valley Fever were used: first, overlapping Valley Fever epitopes representing immunodominant Coccidioides antigens were tiled using a microarray format of presynthesized peptides. Second, a set of random sequence peptides identified using a 10,000 peptide immunosignaturing microarray was compared for sensitivity and specificity. The scientific hypothesis tested was that actual epitope peptides from Coccidioides would provide sufficient sensitivity and specificity as a diagnostic. Results demonstrated that random sequence peptides exhibited higher accuracy when classifying different stages of Valley Fever infection vs. epitope peptides. The epitope peptide array did provide better performance than the existing immunodiffusion array, but when directly compared to the random sequence peptides, reported lower overall accuracy. This study suggests that there are competing aspects of antibody recognition that involve conservation of pathogen sequence and aspects of mimotope recognition and amino acid substitutions. These factors may prove critical when developing the next generation of high-performance immunodiagnostics. Copyright © 2014 Elsevier B.V. All rights reserved.

  10. Random Sequence for Optimal Low-Power Laser Generated Ultrasound

    Science.gov (United States)

    Vangi, D.; Virga, A.; Gulino, M. S.

    2017-08-01

    Low-power laser generated ultrasounds are lately gaining importance in the research world, thanks to the possibility of investigating a mechanical component structural integrity through a non-contact and Non-Destructive Testing (NDT) procedure. The ultrasounds are, however, very low in amplitude, making it necessary to use pre-processing and post-processing operations on the signals to detect them. The cross-correlation technique is used in this work, meaning that a random signal must be used as laser input. For this purpose, a highly random and simple-to-create code called T sequence, capable of enhancing the ultrasound detectability, is introduced (not previously available at the state of the art). Several important parameters which characterize the T sequence can influence the process: the number of pulses Npulses , the pulse duration δ and the distance between pulses dpulses . A Finite Element FE model of a 3 mm steel disk has been initially developed to analytically study the longitudinal ultrasound generation mechanism and the obtainable outputs. Later, experimental tests have shown that the T sequence is highly flexible for ultrasound detection purposes, making it optimal to use high Npulses and δ but low dpulses . In the end, apart from describing all phenomena that arise in the low-power laser generation process, the results of this study are also important for setting up an effective NDT procedure using this technology.

  11. Random-breakage mapping method applied to human DNA sequences

    Science.gov (United States)

    Lobrich, M.; Rydberg, B.; Cooper, P. K.; Chatterjee, A. (Principal Investigator)

    1996-01-01

    The random-breakage mapping method [Game et al. (1990) Nucleic Acids Res., 18, 4453-4461] was applied to DNA sequences in human fibroblasts. The methodology involves NotI restriction endonuclease digestion of DNA from irradiated calls, followed by pulsed-field gel electrophoresis, Southern blotting and hybridization with DNA probes recognizing the single copy sequences of interest. The Southern blots show a band for the unbroken restriction fragments and a smear below this band due to radiation induced random breaks. This smear pattern contains two discontinuities in intensity at positions that correspond to the distance of the hybridization site to each end of the restriction fragment. By analyzing the positions of those discontinuities we confirmed the previously mapped position of the probe DXS1327 within a NotI fragment on the X chromosome, thus demonstrating the validity of the technique. We were also able to position the probes D21S1 and D21S15 with respect to the ends of their corresponding NotI fragments on chromosome 21. A third chromosome 21 probe, D21S11, has previously been reported to be close to D21S1, although an uncertainty about a second possible location existed. Since both probes D21S1 and D21S11 hybridized to a single NotI fragment and yielded a similar smear pattern, this uncertainty is removed by the random-breakage mapping method.

  12. PRIMITIVE MATRICES AND GENERATORS OF PSEUDO RANDOM SEQUENCES OF GALOIS

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    A. Beletsky

    2014-04-01

    Full Text Available In theory and practice of information cryptographic protection one of the key problems is the forming a binary pseudo-random sequences (PRS with a maximum length with acceptable statistical characteristics. PRS generators are usually implemented by linear shift register (LSR of maximum period with linear feedback [1]. In this paper we extend the concept of LSR, assuming that each of its rank (memory cell can be in one of the following condition. Let’s call such registers “generalized linear shift register.” The research goal is to develop algorithms for constructing Galois and Fibonacci generalized matrix of n-order over the field , which uniquely determined both the structure of corresponding generalized of n-order LSR maximal period, and formed on their basis Galois PRS generators of maximum length. Thus the article presents the questions of formation the primitive generalized Fibonacci and Galois arbitrary order matrix over the prime field . The synthesis of matrices is based on the use of irreducible polynomials of degree and primitive elements of the extended field generated by polynomial. The constructing methods of Galois and Fibonacci conjugated primitive matrices are suggested. The using possibilities of such matrices in solving the problem of constructing generalized generators of Galois pseudo-random sequences are discussed.

  13. Random Whole Metagenomic Sequencing for Forensic Discrimination of Soils

    Science.gov (United States)

    Khodakova, Anastasia S.; Smith, Renee J.; Burgoyne, Leigh; Abarno, Damien; Linacre, Adrian

    2014-01-01

    Here we assess the ability of random whole metagenomic sequencing approaches to discriminate between similar soils from two geographically distinct urban sites for application in forensic science. Repeat samples from two parklands in residential areas separated by approximately 3 km were collected and the DNA was extracted. Shotgun, whole genome amplification (WGA) and single arbitrarily primed DNA amplification (AP-PCR) based sequencing techniques were then used to generate soil metagenomic profiles. Full and subsampled metagenomic datasets were then annotated against M5NR/M5RNA (taxonomic classification) and SEED Subsystems (metabolic classification) databases. Further comparative analyses were performed using a number of statistical tools including: hierarchical agglomerative clustering (CLUSTER); similarity profile analysis (SIMPROF); non-metric multidimensional scaling (NMDS); and canonical analysis of principal coordinates (CAP) at all major levels of taxonomic and metabolic classification. Our data showed that shotgun and WGA-based approaches generated highly similar metagenomic profiles for the soil samples such that the soil samples could not be distinguished accurately. An AP-PCR based approach was shown to be successful at obtaining reproducible site-specific metagenomic DNA profiles, which in turn were employed for successful discrimination of visually similar soil samples collected from two different locations. PMID:25111003

  14. Random whole metagenomic sequencing for forensic discrimination of soils.

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    Anastasia S Khodakova

    Full Text Available Here we assess the ability of random whole metagenomic sequencing approaches to discriminate between similar soils from two geographically distinct urban sites for application in forensic science. Repeat samples from two parklands in residential areas separated by approximately 3 km were collected and the DNA was extracted. Shotgun, whole genome amplification (WGA and single arbitrarily primed DNA amplification (AP-PCR based sequencing techniques were then used to generate soil metagenomic profiles. Full and subsampled metagenomic datasets were then annotated against M5NR/M5RNA (taxonomic classification and SEED Subsystems (metabolic classification databases. Further comparative analyses were performed using a number of statistical tools including: hierarchical agglomerative clustering (CLUSTER; similarity profile analysis (SIMPROF; non-metric multidimensional scaling (NMDS; and canonical analysis of principal coordinates (CAP at all major levels of taxonomic and metabolic classification. Our data showed that shotgun and WGA-based approaches generated highly similar metagenomic profiles for the soil samples such that the soil samples could not be distinguished accurately. An AP-PCR based approach was shown to be successful at obtaining reproducible site-specific metagenomic DNA profiles, which in turn were employed for successful discrimination of visually similar soil samples collected from two different locations.

  15. Equivalent Conditions of Complete Convergence for Weighted Sums of Sequences of Negatively Dependent Random Variables

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    Mingle Guo

    2012-01-01

    Full Text Available The complete convergence for weighted sums of sequences of negatively dependent random variables is investigated. By applying moment inequality and truncation methods, the equivalent conditions of complete convergence for weighted sums of sequences of negatively dependent random variables are established. These results not only extend the corresponding results obtained by Li et al. (1995, Gut (1993, and Liang (2000 to sequences of negatively dependent random variables, but also improve them.

  16. Design of Long Period Pseudo-Random Sequences from the Addition of m -Sequences over 𝔽 p

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    Ren Jian

    2004-01-01

    Full Text Available Pseudo-random sequence with good correlation property and large linear span is widely used in code division multiple access (CDMA communication systems and cryptology for reliable and secure information transmission. In this paper, sequences with long period, large complexity, balance statistics, and low cross-correlation property are constructed from the addition of m -sequences with pairwise-prime linear spans (AMPLS. Using m -sequences as building blocks, the proposed method proved to be an efficient and flexible approach to construct long period pseudo-random sequences with desirable properties from short period sequences. Applying the proposed method to 𝔽 2 , a signal set ( ( 2 n − 1 ( 2 m − 1 , ( 2 n + 1 ( 2 m + 1 , ( 2 ( n + 1 / 2 + 1 ( 2 ( m + 1 / 2 + 1 is constructed.

  17. Distributions on unbounded moment spaces and random moment sequences

    OpenAIRE

    Dette, Holger; Nagel, Jan

    2012-01-01

    In this paper we define distributions on moment spaces corresponding to measures on the real line with an unbounded support. We identify these distributions as limiting distributions of random moment vectors defined on compact moment spaces and as distributions corresponding to random spectral measures associated with the Jacobi, Laguerre and Hermite ensemble from random matrix theory. For random vectors on the unbounded moment spaces we prove a central limit theorem where the centering vecto...

  18. A Novel Method for Increasing the Entropy of a Sequence of Independent, Discrete Random Variables

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    Mieczyslaw Jessa

    2015-10-01

    Full Text Available In this paper, we propose a novel method for increasing the entropy of a sequence of independent, discrete random variables with arbitrary distributions. The method uses an auxiliary table and a novel theorem that concerns the entropy of a sequence in which the elements are a bitwise exclusive-or sum of independent discrete random variables.

  19. Cryptographic pseudo-random sequences from the chaotic Hénon ...

    Indian Academy of Sciences (India)

    Pseudo-random number sequences are useful in many applications including Monte-Carlo simulation, spread spectrum ... a pseudo-random binary sequence from the two-dimensional chaotic Hénon map is explored. ... is the Hénon map, a two-dimensional discrete-time nonlinear dynamical system represented by the state ...

  20. Natural vs. random protein sequences: Discovering combinatorics properties on amino acid words.

    Science.gov (United States)

    Santoni, Daniele; Felici, Giovanni; Vergni, Davide

    2016-02-21

    Casual mutations and natural selection have driven the evolution of protein amino acid sequences that we observe at present in nature. The question about which is the dominant force of proteins evolution is still lacking of an unambiguous answer. Casual mutations tend to randomize protein sequences while, in order to have the correct functionality, one expects that selection mechanisms impose rigid constraints on amino acid sequences. Moreover, one also has to consider that the space of all possible amino acid sequences is so astonishingly large that it could be reasonable to have a well tuned amino acid sequence indistinguishable from a random one. In order to study the possibility to discriminate between random and natural amino acid sequences, we introduce different measures of association between pairs of amino acids in a sequence, and apply them to a dataset of 1047 natural protein sequences and 10,470 random sequences, carefully generated in order to preserve the relative length and amino acid distribution of the natural proteins. We analyze the multidimensional measures with machine learning techniques and show that, to a reasonable extent, natural protein sequences can be differentiated from random ones. Copyright © 2015 Elsevier Ltd. All rights reserved.

  1. Interstellar Panspermia Reconsidered

    Science.gov (United States)

    Zubrin, R.

    The absence of free-living microorganisms simpler than bacteria on Earth is evidence that life did not originate on Earth, but immigrated. The question then arises as to whether life was imported from a point of origin in our solar system, most likely Mars, of whether the solar system was seeded from interstellar sources. The search for fossil or extant prebacterial organisms (prebacteria) on Mars can resolve this question. However, to understand the likelihood of interstellar panspermia, we also need to consider whether the Earth itself has served as an efficient source for the spread of microorganisms. Close encounters with other stars due to random stellar motion occur with a frequency of 1/20 Myr, in fair agreement with the observed frequency of major impact events and mass extinctions. Such events are estimated to eject unsterilized material into interstellar space at a time-averaged rate of 10 tonnes per year. A number of mechanisms for the interstellar dissemination of bacteria along with this material are considered. It is shown that transmission of microbial life from one solar system to another is highly probable.

  2. Quantifying biodiversity and asymptotics for a sequence of random strings.

    Science.gov (United States)

    Koyano, Hitoshi; Kishino, Hirohisa

    2010-06-01

    We present a methodology for quantifying biodiversity at the sequence level by developing the probability theory on a set of strings. Further, we apply our methodology to the problem of quantifying the population diversity of microorganisms in several extreme environments and digestive organs and reveal the relation between microbial diversity and various environmental parameters.

  3. Inter simple sequence repeats (ISSR) and random amplified ...

    African Journals Online (AJOL)

    21 of 30 random amplified polymorphic DNA (RAPD) primers produced 220 reproducible bands with average of 10.47 bands per primer and 80.12% of polymorphism. OPR02 primer showed the highest number of effective allele (Ne), Shannon index (I) and genetic diversity (H). Some of the cultivars had specific bands, ...

  4. Random Coding Bounds for DNA Codes Based on Fibonacci Ensembles of DNA Sequences

    Science.gov (United States)

    2008-07-01

    Highway, Suite 1204, Arlington, VA 22202-4302, and to the Office of Management and Budget, Paperwork Reduction Project (0704-0188) Washington, DC...COVERED (From - To) 6 Jul 08 – 11 Jul 08 4. TITLE AND SUBTITLE RANDOM CODING BOUNDS FOR DNA CODES BASED ON FIBONACCI ENSEMBLES OF DNA SEQUENCES...sequences which are generalizations of the Fibonacci sequences. 15. SUBJECT TERMS DNA Codes, Fibonacci Ensembles, DNA Computing, Code Optimization 16

  5. Prediction of Protein Hotspots from Whole Protein Sequences by a Random Projection Ensemble System

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    Jinjian Jiang

    2017-07-01

    Full Text Available Hotspot residues are important in the determination of protein-protein interactions, and they always perform specific functions in biological processes. The determination of hotspot residues is by the commonly-used method of alanine scanning mutagenesis experiments, which is always costly and time consuming. To address this issue, computational methods have been developed. Most of them are structure based, i.e., using the information of solved protein structures. However, the number of solved protein structures is extremely less than that of sequences. Moreover, almost all of the predictors identified hotspots from the interfaces of protein complexes, seldom from the whole protein sequences. Therefore, determining hotspots from whole protein sequences by sequence information alone is urgent. To address the issue of hotspot predictions from the whole sequences of proteins, we proposed an ensemble system with random projections using statistical physicochemical properties of amino acids. First, an encoding scheme involving sequence profiles of residues and physicochemical properties from the AAindex1 dataset is developed. Then, the random projection technique was adopted to project the encoding instances into a reduced space. Then, several better random projections were obtained by training an IBk classifier based on the training dataset, which were thus applied to the test dataset. The ensemble of random projection classifiers is therefore obtained. Experimental results showed that although the performance of our method is not good enough for real applications of hotspots, it is very promising in the determination of hotspot residues from whole sequences.

  6. Prediction of Protein Hotspots from Whole Protein Sequences by a Random Projection Ensemble System

    Science.gov (United States)

    Jiang, Jinjian; Wang, Nian; Chen, Peng; Zheng, Chunhou; Wang, Bing

    2017-01-01

    Hotspot residues are important in the determination of protein-protein interactions, and they always perform specific functions in biological processes. The determination of hotspot residues is by the commonly-used method of alanine scanning mutagenesis experiments, which is always costly and time consuming. To address this issue, computational methods have been developed. Most of them are structure based, i.e., using the information of solved protein structures. However, the number of solved protein structures is extremely less than that of sequences. Moreover, almost all of the predictors identified hotspots from the interfaces of protein complexes, seldom from the whole protein sequences. Therefore, determining hotspots from whole protein sequences by sequence information alone is urgent. To address the issue of hotspot predictions from the whole sequences of proteins, we proposed an ensemble system with random projections using statistical physicochemical properties of amino acids. First, an encoding scheme involving sequence profiles of residues and physicochemical properties from the AAindex1 dataset is developed. Then, the random projection technique was adopted to project the encoding instances into a reduced space. Then, several better random projections were obtained by training an IBk classifier based on the training dataset, which were thus applied to the test dataset. The ensemble of random projection classifiers is therefore obtained. Experimental results showed that although the performance of our method is not good enough for real applications of hotspots, it is very promising in the determination of hotspot residues from whole sequences. PMID:28718782

  7. An empirical study of the complexity and randomness of prediction error sequences

    Science.gov (United States)

    Ratsaby, Joel

    2011-07-01

    We investigate a population of binary mistake sequences that result from learning with parametric models of different order. We obtain estimates of their error, algorithmic complexity and divergence from a purely random Bernoulli sequence. We study the relationship of these variables to the learner's information density parameter which is defined as the ratio between the lengths of the compressed to uncompressed files that contain the learner's decision rule. The results indicate that good learners have a low information density ρ while bad learners have a high ρ. Bad learners generate mistake sequences that are atypically complex or diverge stochastically from a purely random Bernoulli sequence. Good learners generate typically complex sequences with low divergence from Bernoulli sequences and they include mistake sequences generated by the Bayes optimal predictor. Based on the static algorithmic interference model of [18] the learner here acts as a static structure which "scatters" the bits of an input sequence (to be predicted) in proportion to its information density ρ thereby deforming its randomness characteristics.

  8. Do natural proteins differ from random sequences polypeptides? Natural vs. random proteins classification using an evolutionary neural network.

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    Davide De Lucrezia

    Full Text Available Are extant proteins the exquisite result of natural selection or are they random sequences slightly edited by evolution? This question has puzzled biochemists for long time and several groups have addressed this issue comparing natural protein sequences to completely random ones coming to contradicting conclusions. Previous works in literature focused on the analysis of primary structure in an attempt to identify possible signature of evolutionary editing. Conversely, in this work we compare a set of 762 natural proteins with an average length of 70 amino acids and an equal number of completely random ones of comparable length on the basis of their structural features. We use an ad hoc Evolutionary Neural Network Algorithm (ENNA in order to assess whether and to what extent natural proteins are edited from random polypeptides employing 11 different structure-related variables (i.e. net charge, volume, surface area, coil, alpha helix, beta sheet, percentage of coil, percentage of alpha helix, percentage of beta sheet, percentage of secondary structure and surface hydrophobicity. The ENNA algorithm is capable to correctly distinguish natural proteins from random ones with an accuracy of 94.36%. Furthermore, we study the structural features of 32 random polypeptides misclassified as natural ones to unveil any structural similarity to natural proteins. Results show that random proteins misclassified by the ENNA algorithm exhibit a significant fold similarity to portions or subdomains of extant proteins at atomic resolution. Altogether, our results suggest that natural proteins are significantly edited from random polypeptides and evolutionary editing can be readily detected analyzing structural features. Furthermore, we also show that the ENNA, employing simple structural descriptors, can predict whether a protein chain is natural or random.

  9. Assessing randomness and complexity in human motion trajectories through analysis of symbolic sequences

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    Zhen ePeng

    2014-03-01

    Full Text Available Complexity is a hallmark of intelligent behavior consisting both of regular patterns and random variation. To quantitatively assess the complexity and randomness of human motion, we designed a motor task in which we translated subjects' motion trajectories into strings of symbol sequences. In the first part of the experiment participants were asked to perform self-paced movements to create repetitive patterns, copy pre-specified letter sequences, and generate random movements. To investigate whether the degree of randomness can be manipulated, in the second part of the experiment participants were asked to perform unpredictable movements in the context of a pursuit game, where they received feedback from an online Bayesian predictor guessing their next move. We analyzed symbol sequences representing subjects' motion trajectories with five common complexity measures: predictability, compressibility, approximate entropy, Lempel-Ziv complexity, as well as effective measure complexity. We found that subjects’ self-created patterns were the most complex, followed by drawing movements of letters and self-paced random motion. We also found that participants could change the randomness of their behavior depending on context and feedback. Our results suggest that humans can adjust both complexity and regularity in different movement types and contexts and that this can be assessed with information-theoretic measures of the symbolic sequences generated from movement trajectories.

  10. INSTRUCTIONAL CONFERENCE ON THE THEORY OF STOCHASTIC PROCESSES: Controlled random sequences and Markov chains

    Science.gov (United States)

    Yushkevich, A. A.; Chitashvili, R. Ya

    1982-12-01

    CONTENTSIntroduction Chapter I. Foundations of the general theory of controlled random sequences and Markov chains with the expected reward criterion § 1. Controlled random sequences, Markov chains, and models § 2. Necessary and sufficient conditions for optimality § 3. The Bellman equation for the value function and the existence of (ε-) optimal strategies Chapter II. Some problems in the theory of controlled homogeneous Markov chains § 4. Description of the solutions of the Bellman equation, a characterization of the value function, and the Bellman operator § 5. Sufficiency of stationary strategies in homogeneous Markov models § 6. The lexicographic Bellman equation References

  11. The algorithm of random length sequences synthesis for frame synchronization of digital television systems

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    Аndriy V. Sadchenko

    2015-12-01

    Full Text Available Digital television systems need to ensure that all digital signals processing operations are performed simultaneously and consistently. Frame synchronization dictated by the need to match phases of transmitter and receiver so that it would be possible to identify the start of a frame. As a frame synchronization signals are often used long length binary sequence with good aperiodic autocorrelation function. Aim: This work is dedicated to the development of the algorithm of random length sequences synthesis. Materials and Methods: The paper provides a comparative analysis of the known sequences, which can be used at present as synchronization ones, revealed their advantages and disadvantages. This work proposes the algorithm for the synthesis of binary synchronization sequences of random length with good autocorrelation properties based on noise generator with a uniform distribution law of probabilities. A "white noise" semiconductor generator is proposed to use as the initial material for the synthesis of binary sequences with desired properties. Results: The statistical analysis of the initial implementations of the "white noise" and synthesized sequences for frame synchronization of digital television is conducted. The comparative analysis of the synthesized sequences with known ones was carried out. The results show the benefits of obtained sequences in compare with known ones. The performed simulations confirm the obtained results. Conclusions: Thus, the search algorithm of binary synchronization sequences with desired autocorrelation properties received. According to this algorithm, the sequence can be longer in length and without length limitations. The received sync sequence can be used for frame synchronization in modern digital communication systems that will increase their efficiency and noise immunity.

  12. Theoretical study of polymeric mixtures with different sequence statistics. I. Ising class: Linear random copolymers with different statistical sequences and ternary blends of linear random copolymers with homopolymers

    Energy Technology Data Exchange (ETDEWEB)

    Qi, Shuyan [Department of Chemical Engineering, Department of Chemistry, and Materials Science Division, Lawrence Berkeley National Laboratory, University of California, Berkeley, California 94720 (United States); Chakraborty, Arup K. [Department of Chemical Engineering, Department of Chemistry, and Materials Science Division, Lawrence Berkeley National Laboratory, University of California, Berkeley, California 94720 (United States)

    2000-01-15

    We derive a Landau free energy functional for polymeric mixtures containing components with different sequence statistics. We then apply this general field theory to two mixtures that belong to the Ising universality class: mixtures of two different linear random copolymers, and ternary systems of linear random copolymers and two homopolymers. We discuss the instability conditions for the homogeneous state of these mixtures, and calculate the structure factors for different components in the homogeneous state. The structure factors show interesting features which can directly be compared with scattering experiments carried out with selectively deuterated samples. We also work out the eigenmodes representing the least stable concentration fluctuations for these mixtures. The nature of these concentration fluctuations provides information regarding the ordered phases and the kinetic pathways that lead to them. We find various demixing modes for different characteristics of the two mixtures (e.g., average compositions, statistical correlation lengths, and volume fractions). (c) 2000 American Institute of Physics.

  13. rMotifGen: random motif generator for DNA and protein sequences

    Directory of Open Access Journals (Sweden)

    Hardin C Timothy

    2007-08-01

    Full Text Available Abstract Background Detection of short, subtle conserved motif regions within a set of related DNA or amino acid sequences can lead to discoveries about important regulatory domains such as transcription factor and DNA binding sites as well as conserved protein domains. In order to help assess motif detection algorithms on motifs with varying properties and levels of conservation, we have developed a computational tool, rMotifGen, with the sole purpose of generating a number of random DNA or protein sequences containing short sequence motifs. Each motif consensus can be user-defined, randomly generated, or created from a position-specific scoring matrix (PSSM. Insertions and mutations within these motifs are created according to user-defined parameters and substitution matrices. The resulting sequences can be helpful in mutational simulations and in testing the limits of motif detection algorithms. Results Two implementations of rMotifGen have been created, one providing a graphical user interface (GUI for random motif construction, and the other serving as a command line interface. The second implementation has the added advantages of platform independence and being able to be called in a batch mode. rMotifGen was used to construct sample sets of sequences containing DNA motifs and amino acid motifs that were then tested against the Gibbs sampler and MEME packages. Conclusion rMotifGen provides an efficient and convenient method for creating random DNA or amino acid sequences with a variable number of motifs, where the instance of each motif can be incorporated using a position-specific scoring matrix (PSSM or by creating an instance mutated from its corresponding consensus using an evolutionary model based on substitution matrices. rMotifGen is freely available at: http://bioinformatics.louisville.edu/brg/rMotifGen/.

  14. The Effect of Interference on Temporal Order Memory for Random and Fixed Sequences in Nondemented Older Adults

    Science.gov (United States)

    Tolentino, Jerlyn C.; Pirogovsky, Eva; Luu, Trinh; Toner, Chelsea K.; Gilbert, Paul E.

    2012-01-01

    Two experiments tested the effect of temporal interference on order memory for fixed and random sequences in young adults and nondemented older adults. The results demonstrate that temporal order memory for fixed and random sequences is impaired in nondemented older adults, particularly when temporal interference is high. However, temporal order…

  15. Expressed sequence tags of randomly selected cDNA clones from Eucalyptus globulus-Pisolithus tinctorius ectomycorrhiza.

    Science.gov (United States)

    Tagu, D; Martin, F

    1995-01-01

    Random sequencing of cDNA clones from Eucalyptus globulus-Pisolithus tinctorius ectomycorrhizal tissues was carried out to generate expressed sequence tags (ESTs). Database comparisons revealed that 42% of the cDNAs corresponded to previously sequenced genes. These ESTs represent efficient molecular markers to analyze changes in gene expression during the formation of the ectomycorrhizal symbiosis.

  16. NullSeq: A Tool for Generating Random Coding Sequences with Desired Amino Acid and GC Contents.

    Directory of Open Access Journals (Sweden)

    Sophia S Liu

    2016-11-01

    Full Text Available The existence of over- and under-represented sequence motifs in genomes provides evidence of selective evolutionary pressures on biological mechanisms such as transcription, translation, ligand-substrate binding, and host immunity. In order to accurately identify motifs and other genome-scale patterns of interest, it is essential to be able to generate accurate null models that are appropriate for the sequences under study. While many tools have been developed to create random nucleotide sequences, protein coding sequences are subject to a unique set of constraints that complicates the process of generating appropriate null models. There are currently no tools available that allow users to create random coding sequences with specified amino acid composition and GC content for the purpose of hypothesis testing. Using the principle of maximum entropy, we developed a method that generates unbiased random sequences with pre-specified amino acid and GC content, which we have developed into a python package. Our method is the simplest way to obtain maximally unbiased random sequences that are subject to GC usage and primary amino acid sequence constraints. Furthermore, this approach can easily be expanded to create unbiased random sequences that incorporate more complicated constraints such as individual nucleotide usage or even di-nucleotide frequencies. The ability to generate correctly specified null models will allow researchers to accurately identify sequence motifs which will lead to a better understanding of biological processes as well as more effective engineering of biological systems.

  17. No evidence that mRNAs have lower folding free energies than random sequences with the same dinucleotide distribution

    DEFF Research Database (Denmark)

    Workman, Christopher; Krogh, Anders Stærmose

    1999-01-01

    This work investigates whether mRNA has a lower estimated folding free energy than random sequences. The free energy estimates are calculated by the mfold program for prediction of RNA secondary structures. For a set of 46 mRNAs it is shown that the predicted free energy is not significantly...... different from random sequences with the same dinucleotide distribution. For random sequences with the same mononucleotide distribution it has previously been shown that the native mRNA sequences have a lower predicted free energy, which indicates a more stable structure than random sequences. However......, dinucleotide content is important when assessing the significance of predicted free energy as the physical stability of RNA secondary structure is known to depend on dinucleotide base stacking energies. Even known RNA secondary structures, like tRNAs, can be shown to have predicted free energies...

  18. Reconsidering evil : confronting Reflections with Confessions

    NARCIS (Netherlands)

    Schaafsma, Esther Petruschka

    2006-01-01

    The notion of evil is not undisputed in contemporary philosophy and theology. Reconsidering Evil attempts a regauging of this notion by comparing four different approaches to the theme of evil. Paul Ricœur’s approach via symbols of evil provides a focus that enables an analysis and comparison of the

  19. A sequence-based method to predict the impact of regulatory variants using random forest.

    Science.gov (United States)

    Liu, Qiao; Gan, Mingxin; Jiang, Rui

    2017-03-14

    Most disease-associated variants identified by genome-wide association studies (GWAS) exist in noncoding regions. In spite of the common agreement that such variants may disrupt biological functions of their hosting regulatory elements, it remains a great challenge to characterize the risk of a genetic variant within the implicated genome sequence. Therefore, it is essential to develop an effective computational model that is not only capable of predicting the potential risk of a genetic variant but also valid in interpreting how the function of the genome is affected with the occurrence of the variant. We developed a method named kmerForest that used a random forest classifier with k-mer counts to predict accessible chromatin regions purely based on DNA sequences. We demonstrated that our method outperforms existing methods in distinguishing known accessible chromatin regions from random genomic sequences. Furthermore, the performance of our method can further be improved with the incorporation of sequence conservation features. Based on this model, we assessed importance of the k-mer features by a series of permutation experiments, and we characterized the risk of a single nucleotide polymorphism (SNP) on the function of the genome using the difference between the importance of the k-mer features affected by the occurrence of the SNP. We conducted a series of experiments and showed that our model can well discriminate between pathogenic and normal SNPs. Particularly, our model correctly prioritized SNPs that are proved to be enriched for the binding sites of FOXA1 in breast cancer cell lines from previous studies. We presented a novel method to interpret functional genetic variants purely base on DNA sequences. The proposed k-mer based score offers an effective means of measuring the impact of SNPs on the function of the genome, and thus shedding light on the identification of genetic risk factors underlying complex traits and diseases.

  20. Random amino acid mutations and protein misfolding lead to Shannon limit in sequence-structure communication.

    Directory of Open Access Journals (Sweden)

    Andreas Martin Lisewski

    2008-09-01

    Full Text Available The transmission of genomic information from coding sequence to protein structure during protein synthesis is subject to stochastic errors. To analyze transmission limits in the presence of spurious errors, Shannon's noisy channel theorem is applied to a communication channel between amino acid sequences and their structures established from a large-scale statistical analysis of protein atomic coordinates. While Shannon's theorem confirms that in close to native conformations information is transmitted with limited error probability, additional random errors in sequence (amino acid substitutions and in structure (structural defects trigger a decrease in communication capacity toward a Shannon limit at 0.010 bits per amino acid symbol at which communication breaks down. In several controls, simulated error rates above a critical threshold and models of unfolded structures always produce capacities below this limiting value. Thus an essential biological system can be realistically modeled as a digital communication channel that is (a sensitive to random errors and (b restricted by a Shannon error limit. This forms a novel basis for predictions consistent with observed rates of defective ribosomal products during protein synthesis, and with the estimated excess of mutual information in protein contact potentials.

  1. Random amino acid mutations and protein misfolding lead to Shannon limit in sequence-structure communication.

    Science.gov (United States)

    Lisewski, Andreas Martin

    2008-09-01

    The transmission of genomic information from coding sequence to protein structure during protein synthesis is subject to stochastic errors. To analyze transmission limits in the presence of spurious errors, Shannon's noisy channel theorem is applied to a communication channel between amino acid sequences and their structures established from a large-scale statistical analysis of protein atomic coordinates. While Shannon's theorem confirms that in close to native conformations information is transmitted with limited error probability, additional random errors in sequence (amino acid substitutions) and in structure (structural defects) trigger a decrease in communication capacity toward a Shannon limit at 0.010 bits per amino acid symbol at which communication breaks down. In several controls, simulated error rates above a critical threshold and models of unfolded structures always produce capacities below this limiting value. Thus an essential biological system can be realistically modeled as a digital communication channel that is (a) sensitive to random errors and (b) restricted by a Shannon error limit. This forms a novel basis for predictions consistent with observed rates of defective ribosomal products during protein synthesis, and with the estimated excess of mutual information in protein contact potentials.

  2. Cardiorespiratory Kinetics Determined by Pseudo-Random Binary Sequences - Comparisons between Walking and Cycling.

    Science.gov (United States)

    Koschate, J; Drescher, U; Thieschäfer, L; Heine, O; Baum, K; Hoffmann, U

    2016-12-01

    This study aims to compare cardiorespiratory kinetics as a response to a standardised work rate protocol with pseudo-random binary sequences between cycling and walking in young healthy subjects. Muscular and pulmonary oxygen uptake (V̇O2) kinetics as well as heart rate kinetics were expected to be similar for walking and cycling. Cardiac data and V̇O2 of 23 healthy young subjects were measured in response to pseudo-random binary sequences. Kinetics were assessed applying time series analysis. Higher maxima of cross-correlation functions between work rate and the respective parameter indicate faster kinetics responses. Muscular V̇O2 kinetics were estimated from heart rate and pulmonary V̇O2 using a circulatory model. Muscular (walking vs. cycling [mean±SD in arbitrary units]: 0.40±0.08 vs. 0.41±0.08) and pulmonary V̇O2 kinetics (0.35±0.06 vs. 0.35±0.06) were not different, although the time courses of the cross-correlation functions of pulmonary V̇O2 showed unexpected biphasic responses. Heart rate kinetics (0.50±0.14 vs. 0.40±0.14; P=0.017) was faster for walking. Regarding the biphasic cross-correlation functions of pulmonary V̇O2 during walking, the assessment of muscular V̇O2 kinetics via pseudo-random binary sequences requires a circulatory model to account for cardio-dynamic distortions. Faster heart rate kinetics for walking should be considered by comparing results from cycle and treadmill ergometry. © Georg Thieme Verlag KG Stuttgart · New York.

  3. Interference Suppression Performance of Automotive UWB Radars Using Pseudo Random Sequences

    Directory of Open Access Journals (Sweden)

    I. Pasya

    2015-12-01

    Full Text Available Ultra wideband (UWB automotive radars have attracted attention from the viewpoint of reducing traffic accidents. The performance of automotive radars may be degraded by interference from nearby radars using the same frequency. In this study, a scenario where two cars pass each other on a road was considered. Considering the utilization of cross-polarization, the desired-to-undesired signal power ratio (DUR was found to vary approximately from -10 to 30 dB. Different pseudo random sequences were employed for spectrum spreading the different radar signals to mitigate the interference effects. This paper evaluates the interference suppression provided by maximum length sequence (MLS and Gold sequence (GS through numerical simulations of the radar’s performance in terms of probability of false alarm and probability of detection. It was found that MLS and GS yielded nearly the same performance when the DUR is -10 dB (worst case; for example when fixing the probability of false alarm to 0.0001, the probabilities of detection were 0.964 and 0.946 respectively. The GS are more advantageous than MLS due to larger number of different sequences having the same length in GS than in MLS.

  4. Partial summations of stationary sequences of non-Gaussian random variables

    DEFF Research Database (Denmark)

    Mohr, Gunnar; Ditlevsen, Ove Dalager

    1996-01-01

    The distribution of the sum of a finite number of identically distributed random variables is in many cases easily determined given that the variables are independent. The moments of any order of the sum can always be expressed by the moments of the single term without computational problems...... of convergence of the distribution of a sum (or an integral) of mutually dependent random variables to the Gaussian distribution. The paper is closely related to the work in Ditlevsen el al. [Ditlevsen, O., Mohr, G. & Hoffmeyer, P. Integration of non-Gaussian fields. Prob. Engng Mech 11 (1996) 15-23](2)........ However, in the case of dependency between the terms even calculation of a few of the first moments of the sum presents serious computational problems. By use of computerized symbol manipulations it is practicable to obtain exact moments of partial sums of stationary sequences of mutually dependent...

  5. The evolution of proteins from random amino acid sequences: II. Evidence from the statistical distributions of the lengths of modern protein sequences.

    Science.gov (United States)

    White, S H

    1994-04-01

    This paper continues an examination of the hypothesis that modern proteins evolved from random heteropeptide sequences. In support of the hypothesis, White and Jacobs (1993, J Mol Evol 36:79-95) have shown that any sequence chosen randomly from a large collection of nonhomologous proteins has a 90% or better chance of having a lengthwise distribution of amino acids that is indistinguishable from the random expectation regardless of amino acid type. The goal of the present study was to investigate the possibility that the random-origin hypothesis could explain the lengths of modern protein sequences without invoking specific mechanisms such as gene duplication or exon splicing. The sets of sequences examined were taken from the 1989 PIR database and consisted of 1,792 "super-family" proteins selected to have little sequence identity, 623 E. coli sequences, and 398 human sequences. The length distributions of the proteins could be described with high significance by either of two closely related probability density functions: The gamma distribution with parameter 2 or the distribution for the sum of two exponential random independent variables. A simple theory for the distributions was developed which assumes that (1) protoprotein sequences had exponentially distributed random independent lengths, (2) the length dependence of protein stability determined which of these protoproteins could fold into compact primitive proteins and thereby attain the potential for biochemical activity, (3) the useful protein sequences were preserved by the primitive genome, and (4) the resulting distribution of sequence lengths is reflected by modern proteins. The theory successfully predicts the two observed distributions which can be distinguished by the functional form of the dependence of protein stability on length. The theory leads to three interesting conclusions. First, it predicts that a tetra-nucleotide was the signal for primitive translation termination. This prediction is

  6. A Comparison of mRNA Sequencing with Random Primed and 3'-Directed Libraries.

    Science.gov (United States)

    Xiong, Yuguang; Soumillon, Magali; Wu, Jie; Hansen, Jens; Hu, Bin; van Hasselt, Johan G C; Jayaraman, Gomathi; Lim, Ryan; Bouhaddou, Mehdi; Ornelas, Loren; Bochicchio, Jim; Lenaeus, Lindsay; Stocksdale, Jennifer; Shim, Jaehee; Gomez, Emilda; Sareen, Dhruv; Svendsen, Clive; Thompson, Leslie M; Mahajan, Milind; Iyengar, Ravi; Sobie, Eric A; Azeloglu, Evren U; Birtwistle, Marc R

    2017-11-07

    Creating a cDNA library for deep mRNA sequencing (mRNAseq) is generally done by random priming, creating multiple sequencing fragments along each transcript. A 3'-end-focused library approach cannot detect differential splicing, but has potentially higher throughput at a lower cost, along with the ability to improve quantification by using transcript molecule counting with unique molecular identifiers (UMI) that correct PCR bias. Here, we compare an implementation of such a 3'-digital gene expression (3'-DGE) approach with "conventional" random primed mRNAseq. Given our particular datasets on cultured human cardiomyocyte cell lines, we find that, while conventional mRNAseq detects ~15% more genes and needs ~500,000 fewer reads per sample for equivalent statistical power, the resulting differentially expressed genes, biological conclusions, and gene signatures are highly concordant between two techniques. We also find good quantitative agreement at the level of individual genes between two techniques for both read counts and fold changes between given conditions. We conclude that, for high-throughput applications, the potential cost savings associated with 3'-DGE approach are likely a reasonable tradeoff for modest reduction in sensitivity and inability to observe alternative splicing, and should enable many larger scale studies focusing on not only differential expression analysis, but also quantitative transcriptome profiling.

  7. RSARF: Prediction of residue solvent accessibility from protein sequence using random forest method

    KAUST Repository

    Ganesan, Pugalenthi

    2012-01-01

    Prediction of protein structure from its amino acid sequence is still a challenging problem. The complete physicochemical understanding of protein folding is essential for the accurate structure prediction. Knowledge of residue solvent accessibility gives useful insights into protein structure prediction and function prediction. In this work, we propose a random forest method, RSARF, to predict residue accessible surface area from protein sequence information. The training and testing was performed using 120 proteins containing 22006 residues. For each residue, buried and exposed state was computed using five thresholds (0%, 5%, 10%, 25%, and 50%). The prediction accuracy for 0%, 5%, 10%, 25%, and 50% thresholds are 72.9%, 78.25%, 78.12%, 77.57% and 72.07% respectively. Further, comparison of RSARF with other methods using a benchmark dataset containing 20 proteins shows that our approach is useful for prediction of residue solvent accessibility from protein sequence without using structural information. The RSARF program, datasets and supplementary data are available at http://caps.ncbs.res.in/download/pugal/RSARF/. - See more at: http://www.eurekaselect.com/89216/article#sthash.pwVGFUjq.dpuf

  8. Rapid selection of accessible and cleavable sites in RNA by Escherichia coli RNase P and random external guide sequences

    OpenAIRE

    Lundblad, Eirik W.; Xiao, Gaoping; Ko, Jae-hyeong; Altman, Sidney

    2008-01-01

    A method of inhibiting the expression of particular genes by using external guide sequences (EGSs) has been improved in its rapidity and specificity. Random EGSs that have 14-nt random sequences are used in the selection procedure for an EGS that attacks the mRNA for a gene in a particular location. A mixture of the random EGSs, the particular target RNA, and RNase P is used in the diagnostic procedure, which, after completion, is analyzed in a gel with suitable control lanes. Within a few ho...

  9. Pseudo-random-bit-sequence phase modulation for reduced errors in a fiber optic gyroscope.

    Science.gov (United States)

    Chamoun, Jacob; Digonnet, Michel J F

    2016-12-15

    Low noise and drift in a laser-driven fiber optic gyroscope (FOG) are demonstrated by interrogating the sensor with a low-coherence laser. The laser coherence was reduced by broadening its optical spectrum using an external electro-optic phase modulator driven by either a sinusoidal or a pseudo-random bit sequence (PRBS) waveform. The noise reduction measured in a FOG driven by a modulated laser agrees with the calculations based on the broadened laser spectrum. Using PRBS modulation, the linewidth of a laser was broadened from 10 MHz to more than 10 GHz, leading to a measured FOG noise of only 0.00073  deg/√h and a drift of 0.023  deg/h. To the best of our knowledge, these are the lowest noise and drift reported in a laser-driven FOG, and this noise is below the requirement for the inertial navigation of aircraft.

  10. LigandRFs: random forest ensemble to identify ligand-binding residues from sequence information alone

    KAUST Repository

    Chen, Peng

    2014-12-03

    Background Protein-ligand binding is important for some proteins to perform their functions. Protein-ligand binding sites are the residues of proteins that physically bind to ligands. Despite of the recent advances in computational prediction for protein-ligand binding sites, the state-of-the-art methods search for similar, known structures of the query and predict the binding sites based on the solved structures. However, such structural information is not commonly available. Results In this paper, we propose a sequence-based approach to identify protein-ligand binding residues. We propose a combination technique to reduce the effects of different sliding residue windows in the process of encoding input feature vectors. Moreover, due to the highly imbalanced samples between the ligand-binding sites and non ligand-binding sites, we construct several balanced data sets, for each of which a random forest (RF)-based classifier is trained. The ensemble of these RF classifiers forms a sequence-based protein-ligand binding site predictor. Conclusions Experimental results on CASP9 and CASP8 data sets demonstrate that our method compares favorably with the state-of-the-art protein-ligand binding site prediction methods.

  11. AQUa: An Adaptive Framework for Compression of Sequencing Quality Scores with Random Access Functionality.

    Science.gov (United States)

    Paridaens, Tom; Van Wallendael, Glenn; De Neve, Wesley; Lambert, Peter

    2017-09-25

    The past decade has seen the introduction of new technologies that significantly lowered the cost of genome sequencing. As a result, the amount of genomic data that must be stored and transmitted is increasing exponentially. To mitigate storage and transmission issues, we introduce a framework for lossless compression of quality scores. This paper proposes AQUa, an adaptive framework for lossless compression of quality scores. To compress these quality scores, AQUa makes use of a configurable set of coding tools, extended with a Context-Adaptive Binary Arithmetic Coding scheme (CABAC). When benchmarking AQUa against generic single-pass compressors, file sizes are reduced by up to 38.49% when comparing with GNU Gzip and by up to 6.48% when comparing with 7-Zip at the Ultra Setting, while still providing support for random access. When comparing AQUa with the purpose-built, single-pass, and state-of-the-art compressor SCALCE, which does not support random access, file sizes are reduced by up to 21.14%. When comparing AQUa with the purpose-built, dual-pass, and state-of-the-art compressor QVZ, which does not support random access, file sizes are larger by 6.42% to 33.47%. However, for one test file, the file size is 0.38% smaller, illustrating the strength of our single-pass compression framework. This work has been spurred by the current activity on genomic information representation (MPEG-G) within the ISO/IEC SC29/WG11 technical committee. The software is available on Github: https://github.com/tparidae/AQUa. Tom Paridaens (tom.paridaens@ugent.be).

  12. Rapid selection of accessible and cleavable sites in RNA by Escherichia coli RNase P and random external guide sequences.

    Science.gov (United States)

    Lundblad, Eirik W; Xiao, Gaoping; Ko, Jae-Hyeong; Altman, Sidney

    2008-02-19

    A method of inhibiting the expression of particular genes by using external guide sequences (EGSs) has been improved in its rapidity and specificity. Random EGSs that have 14-nt random sequences are used in the selection procedure for an EGS that attacks the mRNA for a gene in a particular location. A mixture of the random EGSs, the particular target RNA, and RNase P is used in the diagnostic procedure, which, after completion, is analyzed in a gel with suitable control lanes. Within a few hours, the procedure is complete. The action of EGSs designed by an older method is compared with EGSs designed by the random EGS method on mRNAs from two bacterial pathogens.

  13. Fully Automatic Myocardial Segmentation of Contrast Echocardiography Sequence Using Random Forests Guided by Shape Model.

    Science.gov (United States)

    Li, Yuanwei; Ho, Chin Pang; Toulemonde, Matthieu; Chahal, Navtej; Senior, Roxy; Tang, Meng-Xing

    2017-09-26

    Myocardial contrast echocardiography (MCE) is an imaging technique that assesses left ventricle function and myocardial perfusion for the detection of coronary artery diseases. Automatic MCE perfusion quantification is challenging and requires accurate segmentation of the myocardium from noisy and time-varying images. Random forests (RF) have been successfully applied to many medical image segmentation tasks. However, the pixel-wise RF classifier ignores contextual relationships between label outputs of individual pixels. RF which only utilizes local appearance features is also susceptible to data suffering from large intensity variations. In this paper, we demonstrate how to overcome the above limitations of classic RF by presenting a fully automatic segmentation pipeline for myocardial segmentation in full-cycle 2D MCE data. Specifically, a statistical shape model is used to provide shape prior information that guide the RF segmentation in two ways. First, a novel shape model (SM) feature is incorporated into the RF framework to generate a more accurate RF probability map. Second, the shape model is fitted to the RF probability map to refine and constrain the final segmentation to plausible myocardial shapes. We further improve the performance by introducing a bounding box detection algorithm as a preprocessing step in the segmentation pipeline. Our approach on 2D image is further extended to 2D+t sequences which ensures temporal consistency in the final sequence segmentations. When evaluated on clinical MCE datasets, our proposed method achieves notable improvement in segmentation accuracy and outperforms other state-of-the-art methods including the classic RF and its variants, active shape model and image registration.

  14. Parametric and non-parametric masking of randomness in sequence alignments can be improved and leads to better resolved trees

    Directory of Open Access Journals (Sweden)

    von Reumont Björn M

    2010-03-01

    Full Text Available Abstract Background Methods of alignment masking, which refers to the technique of excluding alignment blocks prior to tree reconstructions, have been successful in improving the signal-to-noise ratio in sequence alignments. However, the lack of formally well defined methods to identify randomness in sequence alignments has prevented a routine application of alignment masking. In this study, we compared the effects on tree reconstructions of the most commonly used profiling method (GBLOCKS which uses a predefined set of rules in combination with alignment masking, with a new profiling approach (ALISCORE based on Monte Carlo resampling within a sliding window, using different data sets and alignment methods. While the GBLOCKS approach excludes variable sections above a certain threshold which choice is left arbitrary, the ALISCORE algorithm is free of a priori rating of parameter space and therefore more objective. Results ALISCORE was successfully extended to amino acids using a proportional model and empirical substitution matrices to score randomness in multiple sequence alignments. A complex bootstrap resampling leads to an even distribution of scores of randomly similar sequences to assess randomness of the observed sequence similarity. Testing performance on real data, both masking methods, GBLOCKS and ALISCORE, helped to improve tree resolution. The sliding window approach was less sensitive to different alignments of identical data sets and performed equally well on all data sets. Concurrently, ALISCORE is capable of dealing with different substitution patterns and heterogeneous base composition. ALISCORE and the most relaxed GBLOCKS gap parameter setting performed best on all data sets. Correspondingly, Neighbor-Net analyses showed the most decrease in conflict. Conclusions Alignment masking improves signal-to-noise ratio in multiple sequence alignments prior to phylogenetic reconstruction. Given the robust performance of alignment

  15. Least squares deconvolution for leak detection with a pseudo random binary sequence excitation

    Science.gov (United States)

    Nguyen, Si Tran Nguyen; Gong, Jinzhe; Lambert, Martin F.; Zecchin, Aaron C.; Simpson, Angus R.

    2018-01-01

    Leak detection and localisation is critical for water distribution system pipelines. This paper examines the use of the time-domain impulse response function (IRF) for leak detection and localisation in a pressurised water pipeline with a pseudo random binary sequence (PRBS) signal excitation. Compared to the conventional step wave generated using a single fast operation of a valve closure, a PRBS signal offers advantageous correlation properties, in that the signal has very low autocorrelation for lags different from zero and low cross correlation with other signals including noise and other interference. These properties result in a significant improvement in the IRF signal to noise ratio (SNR), leading to more accurate leak localisation. In this paper, the estimation of the system IRF is formulated as an optimisation problem in which the l2 norm of the IRF is minimised to suppress the impact of noise and interference sources. Both numerical and experimental data are used to verify the proposed technique. The resultant estimated IRF provides not only accurate leak location estimation, but also good sensitivity to small leak sizes due to the improved SNR.

  16. Controlled random sequences: methods of convex analysis and problems with functional constraints

    Science.gov (United States)

    Piunovskii, A. B.

    1998-12-01

    ContentsIntroduction § 1. Controlled random sequences: main definitions and traditional approaches § 1.1. Description of the mathematical model § 1.2. Models with integral functionals § 1.3. Homogeneous Markov decision processes with average cost criteria § 2. Application of methods of convex analysis § 2.1. Properties of the space \\mathcal D § 2.2. Existence of optimal policies § 2.3. Sufficiency of selectors § 2.4. Preliminary results. The notion of an occupation measure § 2.5. Markov decision processes with total cost criteria and occupation measures § 2.6. Discounted costs and the corresponding occupation measures § 2.7. Average costs and ergodic occupation measures § 3. Problems with functional constraints § 3.1. General results § 3.2. Preliminary conclusions § 3.3. Markov decision processes with total cost criteria § 3.4. Homogeneous Markov decision processes with discounting § 3.5. Homogeneous Markov decision processes with average cost criteria § 3.6. Other constrained problems, related topics, and future prospectsConclusionAppendix. Elements of convex analysis and measure theory Bibliography

  17. Two-Level Adaptive Algebraic Multigrid for a Sequence of Problems with Slowly Varying Random Coefficients [Adaptive Algebraic Multigrid for Sequence of Problems with Slowly Varying Random Coefficients

    Energy Technology Data Exchange (ETDEWEB)

    Kalchev, D. [Lawrence Livermore National Lab. (LLNL), Livermore, CA (United States); Ketelsen, C. [Lawrence Livermore National Lab. (LLNL), Livermore, CA (United States); Vassilevski, P. S. [Lawrence Livermore National Lab. (LLNL), Livermore, CA (United States)

    2013-11-07

    Our paper proposes an adaptive strategy for reusing a previously constructed coarse space by algebraic multigrid to construct a two-level solver for a problem with nearby characteristics. Furthermore, a main target application is the solution of the linear problems that appear throughout a sequence of Markov chain Monte Carlo simulations of subsurface flow with uncertain permeability field. We demonstrate the efficacy of the method with extensive set of numerical experiments.

  18. Development and evaluation of a non-ribosomal random PCR and next-generation sequencing based assay for detection and sequencing of hand, foot and mouth disease pathogens.

    Science.gov (United States)

    Nguyen, Anh To; Tran, Thanh Tan; Hoang, Van Minh Tu; Nghiem, Ngoc My; Le, Nhu Nguyen Truc; Le, Thanh Thi My; Phan, Qui Tu; Truong, Khanh Huu; Le, Nhan Nguyen Thanh; Ho, Viet Lu; Do, Viet Chau; Ha, Tuan Manh; Nguyen, Hung Thanh; Nguyen, Chau Van Vinh; Thwaites, Guy; van Doorn, H Rogier; Le, Tan Van

    2016-07-07

    Hand, foot and mouth disease (HFMD) has become a major public health problem across the Asia-Pacific region, and is commonly caused by enterovirus A71 (EV-A71) and coxsackievirus A6 (CV-A6), CV-A10 and CV-A16. Generating pathogen whole-genome sequences is essential for understanding their evolutionary biology. The frequent replacements among EV serotypes and a limited numbers of available whole-genome sequences hinder the development of overlapping PCRs for whole-genome sequencing. We developed and evaluated a non-ribosomal random PCR (rPCR) and next-generation sequencing based assay for sequence-independent whole-genome amplification and sequencing of HFMD pathogens. A total of 16 EV-A71/CV-A6/CV-A10/CV-A16 PCR positive rectal/throat swabs (Cp values: 20.9-33.3) were used for assay evaluation. Our assay evidently outperformed the conventional rPCR in terms of the total number of EV-A71 reads and the percentage of EV-A71 reads: 2.6 % (1275/50,000 reads) vs. 0.1 % (31/50,000) and 6 % (3008/50,000) vs. 0.9 % (433/50,000) for two samples with Cp values of 30 and 26, respectively. Additionally the assay could generate genome sequences with the percentages of coverage of 94-100 % of 4 different enterovirus serotypes in 73 % of the tested samples, representing the first whole-genome sequences of CV-A6/10/16 from Vietnam, and could assign correctly serotyping results in 100 % of 24 tested specimens. In all but three the obtained consensuses of two replicates from the same sample were 100 % identical, suggesting that our assay is highly reproducible. In conclusion, we have successfully developed a non-ribosomal rPCR and next-generation sequencing based assay for sensitive detection and direct whole-genome sequencing of HFMD pathogens from clinical samples.

  19. 13 CFR 134.715 - Can a Judge reconsider his decision?

    Science.gov (United States)

    2010-01-01

    ... 13 Business Credit and Assistance 1 2010-01-01 2010-01-01 false Can a Judge reconsider his....715 Can a Judge reconsider his decision? (a) The Judge may reconsider an appeal decision within 20... also reconsider a decision on his or her own initiative. (b) The Judge may remand a proceeding to the D...

  20. Protein Ordered Sequences are Formed by Random Joining of Amino Acids in Protein 0th-Order Structure, Followed by Evolutionary Process

    Science.gov (United States)

    Ikehara, Kenji

    2014-12-01

    Only random processes should occur on the primitive Earth. In contrast, many ordered sequences are synthesized according to genetic information on the present Earth. In this communication, I have proposed an idea that protein 0th-order structures or specific amino acid compositions would mediate the transfer from random process to formation of ordered sequences, after formation of double-stranded genes.

  1. Quasi-Coherent Noise Jamming to LFM Radar Based on Pseudo-random Sequence Phase-modulation

    Directory of Open Access Journals (Sweden)

    N. Tai

    2015-12-01

    Full Text Available A novel quasi-coherent noise jamming method is proposed against linear frequency modulation (LFM signal and pulse compression radar. Based on the structure of digital radio frequency memory (DRFM, the jamming signal is acquired by the pseudo-random sequence phase-modulation of sampled radar signal. The characteristic of jamming signal in time domain and frequency domain is analyzed in detail. Results of ambiguity function indicate that the blanket jamming effect along the range direction will be formed when jamming signal passes through the matched filter. By flexible controlling the parameters of interrupted-sampling pulse and pseudo-random sequence, different covering distances and jamming effects will be achieved. When the jamming power is equivalent, this jamming obtains higher process gain compared with non-coherent jamming. The jamming signal enhances the detection threshold and the real target avoids being detected. Simulation results and circuit engineering implementation validate that the jamming signal covers real target effectively.

  2. Cryptographic pseudo-random sequences from the chaotic Hénon ...

    Indian Academy of Sciences (India)

    dimensional discrete-time Hénon map is proposed. Properties of the proposed sequences pertaining to linear complexity, linear complexity profile, correlation and auto-correlation are investigated. All these properties of the sequences suggest a ...

  3. A novel whole genome amplification method using type IIS restriction enzymes to create overhangs with random sequences.

    Science.gov (United States)

    Pan, Xiaoming; Wan, Baihui; Li, Chunchuan; Liu, Yu; Wang, Jing; Mou, Haijin; Liang, Xingguo

    2014-08-20

    Ligation-mediated polymerase chain reaction (LM-PCR) is a whole genome amplification (WGA) method, for which genomic DNA is cleaved into numerous fragments and then all of the fragments are amplified by PCR after attaching a universal end sequence. However, the self-ligation of these fragments could happen and may cause biased amplification and restriction of its application. To decrease the self-ligation probability, here we use type IIS restriction enzymes to digest genomic DNA into fragments with 4-5nt long overhangs with random sequences. After ligation to an adapter with random end sequences to above fragments, PCR is carried out and almost all present DNA sequences are amplified. In this study, whole genome of Vibrio parahaemolyticus was amplified and the amplification efficiency was evaluated by quantitative PCR. The results suggested that our approach could provide sufficient genomic DNA with good quality to meet requirements of various genetic analyses. Copyright © 2014. Published by Elsevier B.V.

  4. Time to Reconsider Stem Cell Induction Strategies

    Directory of Open Access Journals (Sweden)

    Hans-Werner Denker

    2012-12-01

    Full Text Available Recent developments in stem cell research suggest that it may be time to reconsider the current focus of stem cell induction strategies. During the previous five years, approximately, the induction of pluripotency in somatic cells, i.e., the generation of so-called ‘induced pluripotent stem cells’ (iPSCs, has become the focus of ongoing research in many stem cell laboratories, because this technology promises to overcome limitations (both technical and ethical seen in the production and use of embryonic stem cells (ESCs. A rapidly increasing number of publications suggest, however, that it is now possible to choose instead other, alternative ways of generating stem and progenitor cells bypassing pluripotency. These new strategies may offer important advantages with respect to ethics, as well as to safety considerations. The present communication discusses why these strategies may provide possibilities for an escape from the dilemma presented by pluripotent stem cells (self-organization potential, cloning by tetraploid complementation, patenting problems and tumor formation risk.

  5. A Method for Large-Scale Screening of Random Sequence Libraries to Determine the Function of Unstructured Regions from Essential Proteins.

    Science.gov (United States)

    Millau, Jean-François; Guillemette, Benoit; Gaudreau, Luc

    2017-01-01

    In this chapter we present a method allowing the screening of random sequences to discover essential aspects of unstructured protein regions in yeast. The approach can be applied to any protein with unstructured peptide sequences for which functions are difficult to decipher, for example the N-terminal tails of histones. The protocol first describes the building and preparation of a large library of random peptides in fusion with a protein of interest. Recent technical advances in oligonucleotide synthesis allow the construction of long random sequences up to 35 residues long. The protocol details the screening of the library in yeast for sequences that can functionally replace an unstructured domain in an essential protein in vivo. Our method typically identifies sequences that, while being totally different from the wild type, retain essential features allowing yeast to live. This collection of proteins with functional synthetic sequences can subsequently be used in phenotypic tests or genetic screens in order to discover genetic interaction.

  6. Random Tagging Genotyping by Sequencing (rtGBS, an Unbiased Approach to Locate Restriction Enzyme Sites across the Target Genome.

    Directory of Open Access Journals (Sweden)

    Elena Hilario

    Full Text Available Genotyping by sequencing (GBS is a restriction enzyme based targeted approach developed to reduce the genome complexity and discover genetic markers when a priori sequence information is unavailable. Sufficient coverage at each locus is essential to distinguish heterozygous from homozygous sites accurately. The number of GBS samples able to be pooled in one sequencing lane is limited by the number of restriction sites present in the genome and the read depth required at each site per sample for accurate calling of single-nucleotide polymorphisms. Loci bias was observed using a slight modification of the Elshire et al.some restriction enzyme sites were represented in higher proportions while others were poorly represented or absent. This bias could be due to the quality of genomic DNA, the endonuclease and ligase reaction efficiency, the distance between restriction sites, the preferential amplification of small library restriction fragments, or bias towards cluster formation of small amplicons during the sequencing process. To overcome these issues, we have developed a GBS method based on randomly tagging genomic DNA (rtGBS. By randomly landing on the genome, we can, with less bias, find restriction sites that are far apart, and undetected by the standard GBS (stdGBS method. The study comprises two types of biological replicates: six different kiwifruit plants and two independent DNA extractions per plant; and three types of technical replicates: four samples of each DNA extraction, stdGBS vs. rtGBS methods, and two independent library amplifications, each sequenced in separate lanes. A statistically significant unbiased distribution of restriction fragment size by rtGBS showed that this method targeted 49% (39,145 of BamH I sites shared with the reference genome, compared to only 14% (11,513 by stdGBS.

  7. KinMutRF: a random forest classifier of sequence variants in the human protein kinase superfamily

    DEFF Research Database (Denmark)

    Pons, Tirso; Vazquez, Miguel; Matey-Hernandez, María Luisa

    2016-01-01

    remains challenging: cells tolerate most genomic alterations and only a minor fraction disrupt molecular function sufficiently and drive disease. Results: KinMutRF is a novel random-forest method to automatically identify pathogenic variants in human kinases. Twenty six decision trees implemented......Background: The association between aberrant signal processing by protein kinases and human diseases such as cancer was established long time ago. However, understanding the link between sequence variants in the protein kinase superfamily and the mechanistic complex traits at the molecular level...... as a random forest ponder a battery of features that characterize the variants: a) at the gene level, including membership to a Kinbase group and Gene Ontology terms; b) at the PFAM domain level; and c) at the residue level, the types of amino acids involved, changes in biochemical properties, functional...

  8. A specific brushing sequence and plaque removal efficacy : a randomized split-mouth design

    NARCIS (Netherlands)

    van der Sluijs, E.; Slot, D.E.; Hennequin-Hoenderdos, N.L.; van der Weijden, G.A.

    2018-01-01

    Aim: It has been propagated by the dental care professionals to start toothbrushing the lingual aspect of teeth first. In general, it is assumed that these surfaces of teeth are more difficult to clean. The evidence to support this recommendation is sparse. Method: In this randomized controlled

  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)

    2010-01-01

    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 multiple sequences, as well

  11. Genetic alterations of hepatocellular carcinoma by random amplified polymorphic DNA analysis and cloning sequencing of tumor differential DNA fragment

    Science.gov (United States)

    Xian, Zhi-Hong; Cong, Wen-Ming; Zhang, Shu-Hui; Wu, Meng-Chao

    2005-01-01

    AIM: To study the genetic alterations and their association with clinicopathological characteristics of hepatocellular carcinoma (HCC), and to find the tumor related DNA fragments. METHODS: DNA isolated from tumors and corresponding noncancerous liver tissues of 56 HCC patients was amplified by random amplified polymorphic DNA (RAPD) with 10 random 10-mer arbitrary primers. The RAPD bands showing obvious differences in tumor tissue DNA corresponding to that of normal tissue were separated, purified, cloned and sequenced. DNA sequences were analyzed and compared with GenBank data. RESULTS: A total of 56 cases of HCC were demonstrated to have genetic alterations, which were detected by at least one primer. The detestability of genetic alterations ranged from 20% to 70% in each case, and 17.9% to 50% in each primer. Serum HBV infection, tumor size, histological grade, tumor capsule, as well as tumor intrahepatic metastasis, might be correlated with genetic alterations on certain primers. A band with a higher intensity of 480 bp or so amplified fragments in tumor DNA relative to normal DNA could be seen in 27 of 56 tumor samples using primer 4. Sequence analysis of these fragments showed 91% homology with Homo sapiens double homeobox protein DUX10 gene. CONCLUSION: Genetic alterations are a frequent event in HCC, and tumor related DNA fragments have been found in this study, which may be associated with hepatocarcin-ogenesis. RAPD is an effective method for the identification and analysis of genetic alterations in HCC, and may provide new information for further evaluating the molecular mechanism of hepatocarcinogenesis. PMID:15996039

  12. Reconsidering the Role of Stephen Foster in the Music Classroom

    Science.gov (United States)

    Forness, Jennifer

    2016-01-01

    The place of Stephen Foster and the music of American minstrelsy should be reconsidered for the music classroom. Some of this repertoire can be offensive because of its historical context and racially insensitive language. Critical theory can provide a framework for choosing repertoire that creates dialogue about racial structures in music. The…

  13. Reconsidering the Social and Economic Purposes of Higher Education

    Science.gov (United States)

    McArthur, Jan

    2011-01-01

    In this article I seek to reconsider the social and economic purposes of higher education. It begins with the premise that there appears to be a general trend towards governments positioning higher education primarily in terms of the economic role that it can fulfil. Such a trend, however, has attracted considerable criticism. In this article I…

  14. Good reasons to reconsider the copper intrauterine device for ...

    African Journals Online (AJOL)

    DOWNLOAD FULL TEXT Open Access DOWNLOAD FULL TEXT Subscription or Fee Access. Good reasons to reconsider the copper intrauterine device for contraception. ME Moss. Abstract. Modern Copper Intrauterine Devices [Cu IUDs] are extremely safe, highly effective, long acting yet rapidly reversible contraceptives.

  15. Genotypic detection of rifampicin and isoniazid resistant Mycobacterium tuberculosis strains by DNA sequencing: a randomized trial

    Directory of Open Access Journals (Sweden)

    El mashad Noha

    2009-01-01

    Full Text Available Abstract Background Tuberculosis is a growing international health concern. It is the biggest killer among the infectious diseases in the world today. Early detection of drug resistance allows starting of an appropriate treatment. Resistance to drugs is due to particular genomic mutations in specific genes of Mycobacterium tuberculosis(MTB. The aim of this study was to identify the presence of Isoniazid (INH and Rifampicin(RIF drug resistance in new and previously treated tuberculosis (TB cases using DNA sequencing. Methods This study was carried out on 153 tuberculous patients with positive Bactec 460 culture for acid fast bacilli. Results Of the 153 patients, 105 (68.6% were new cases and 48 (31.4% were previously treated cases. Drug susceptibility testing on Bactec revealed 50 resistant cases for one or more of the first line antituberculous. Genotypic analysis was done only for rifampicin resistant specimens (23 cases and INH resistant specimens (26 cases to detect mutations responsible for drug resistance by PCR amplification of rpoB gene for rifampicin resistant cases and KatG gene for isoniazid resistant cases. Finally, DNA sequencing was done for detection of mutation within rpoB and KatG genes. Genotypic analysis of RIF resistant cases revealed that 20/23 cases (86.9% of RIF resistance were having rpoB gene mutation versus 3 cases (13.1% having no mutation with a high statistical significant difference between them (P Conclusion We can conclude that rifampicin resistance could be used as a useful surrogate marker for estimation of multidrug resistance. In addition, Genotypic method was superior to that of the traditional phenotypic method which is time-consuming taking several weeks or longer.

  16. Folded Proteins Occur Frequently in Libraries of Random Amino Acid Sequences

    Science.gov (United States)

    Davidson, Alan R.; Sauer, Robert T.

    1994-03-01

    A library of synthetic genes encoding 80- to 100-residue proteins composed mainly of random combinations of glutamine (Q), leucine (L), and arginine (R) has been expressed in Escherichia coli. These genes also encode an epitope tag and six carboxyl-terminal histidines. Screening of this library by immunoblotting showed that 5% of these QLR proteins are expressed at readily detectable levels. Three well-expressed QLR proteins were purified and characterized. Each of these proteins has significant α-helical content, is largely resistant to degradation by Pronase, and has a distinct oligomeric structure. In addition, one protein unfolds in a highly cooperative manner. These properties of the QLR proteins demonstrate that they possess folded structures with some native-like properties. The QLR proteins differ from most natural proteins, however, in being remarkably resistant to denaturant-induced and thermal-induced unfolding and in being relatively insoluble in the absence of denaturants.

  17. Fire detection system using random forest classification for image sequences of complex background

    Science.gov (United States)

    Kim, Onecue; Kang, Dong-Joong

    2013-06-01

    We present a fire alarm system based on image processing that detects fire accidents in various environments. To reduce false alarms that frequently appeared in earlier systems, we combined image features including color, motion, and blinking information. We specifically define the color conditions of fires in hue, saturation and value, and RGB color space. Fire features are represented as intensity variation, color mean and variance, motion, and image differences. Moreover, blinking fire features are modeled by using crossing patches. We propose an algorithm that classifies patches into fire or nonfire areas by using random forest supervised learning. We design an embedded surveillance device made with acrylonitrile butadiene styrene housing for stable fire detection in outdoor environments. The experimental results show that our algorithm works robustly in complex environments and is able to detect fires in real time.

  18. The sequencing of adverbial clauses of time in academic English: Random forest modelling

    Directory of Open Access Journals (Sweden)

    Abbas Ali Rezaee

    2016-12-01

    Full Text Available Adverbial clauses of time are positioned either before or after their associated main clauses. This study aims to assess the importance of discourse-pragmatics and processing-related constraints on the positioning of adverbial clauses of time in research articles of applied linguistics written by authors for whom English is considered a native language. Previous research has revealed that the ordering is co-determined by various factors from the domains of semantics and discourse-pragmatics (bridging, iconicity, and subordinator and language processing (deranking, length, and complexity. This research conducts a multifactorial analysis on the motivators of the positioning of adverbial clauses of time in 100 research articles of applied linguistics. The study will use a random forest of conditional inference trees as the statistical technique to measure the weights of the aforementioned variables. It was found that iconicity and bridging, which are factors associated with discourse and semantics, are the two most salient predictors of clause ordering.

  19. Probability distribution of intersymbol distances in random symbolic sequences: Applications to improving detection of keywords in texts and of amino acid clustering in proteins.

    Science.gov (United States)

    Carpena, Pedro; Bernaola-Galván, Pedro A; Carretero-Campos, Concepción; Coronado, Ana V

    2016-11-01

    Symbolic sequences have been extensively investigated in the past few years within the framework of statistical physics. Paradigmatic examples of such sequences are written texts, and deoxyribonucleic acid (DNA) and protein sequences. In these examples, the spatial distribution of a given symbol (a word, a DNA motif, an amino acid) is a key property usually related to the symbol importance in the sequence: The more uneven and far from random the symbol distribution, the higher the relevance of the symbol to the sequence. Thus, many techniques of analysis measure in some way the deviation of the symbol spatial distribution with respect to the random expectation. The problem is then to know the spatial distribution corresponding to randomness, which is typically considered to be either the geometric or the exponential distribution. However, these distributions are only valid for very large symbolic sequences and for many occurrences of the analyzed symbol. Here, we obtain analytically the exact, randomly expected spatial distribution valid for any sequence length and any symbol frequency, and we study its main properties. The knowledge of the distribution allows us to define a measure able to properly quantify the deviation from randomness of the symbol distribution, especially for short sequences and low symbol frequency. We apply the measure to the problem of keyword detection in written texts and to study amino acid clustering in protein sequences. In texts, we show how the results improve with respect to previous methods when short texts are analyzed. In proteins, which are typically short, we show how the measure quantifies unambiguously the amino acid clustering and characterize its spatial distribution.

  20. Trichoderma asperellum reconsidered: two cryptic species

    Science.gov (United States)

    Analysis of a world-wide collection of strains of Trichoderma asperellum using multilocus genealogies of four genomic regions (tef1, rbp2, act, ITS1, 2, 5.8s), sequence polymorphism-derived (SPD) markers, matrix-assisted laser desorption/ionisation–time of flight mass spectrometry (MALDI-TOF MS) of ...

  1. Molecular Analysis of Date Palm Genetic Diversity Using Random Amplified Polymorphic DNA (RAPD) and Inter-Simple Sequence Repeats (ISSRs).

    Science.gov (United States)

    El Sharabasy, Sherif F; Soliman, Khaled A

    2017-01-01

    The date palm is an ancient domesticated plant with great diversity and has been cultivated in the Middle East and North Africa for at last 5000 years. Date palm cultivars are classified based on the fruit moisture content, as dry, semidry, and soft dates. There are a number of biochemical and molecular techniques available for characterization of the date palm variation. This chapter focuses on the DNA-based markers random amplified polymorphic DNA (RAPD) and inter-simple sequence repeats (ISSR) techniques, in addition to biochemical markers based on isozyme analysis. These techniques coupled with appropriate statistical tools proved useful for determining phylogenetic relationships among date palm cultivars and provide information resources for date palm gene banks.

  2. Cooperation of deterministic dynamics and random noise in production of complex syntactical avian song sequences: a neural network model

    Directory of Open Access Journals (Sweden)

    Yuichi eYamashita

    2011-04-01

    Full Text Available How the brain learns and generates temporal sequences is a fundamental issue in neuroscience. The production of birdsongs, a process which involves complex learned sequences, provides researchers with an excellent biological model for this topic. The Bengalese finch in particular learns a highly complex song with syntactical structure. The nucleus HVC (HVC, a premotor nucleus within the avian song system, plays a key role in generating the temporal structures of their songs. From lesion studies, the nucleus interfacialis (NIf projecting to the HVC is considered one of the essential regions that contribute to the complexity of their songs. However, the types of interaction between the HVC and the NIf that can produce complex syntactical songs remain unclear. In order to investigate the function of interactions between the HVC and NIf, we have proposed a neural network model based on previous biological evidence. The HVC is modeled by a recurrent neural network (RNN that learns to generate temporal patterns of songs. The NIf is modeled as a mechanism that provides auditory feedback to the HVC and generates random noise that feeds into the HVC. The model showed that complex syntactical songs can be replicated by simple interactions between deterministic dynamics of the RNN and random noise. In the current study, the plausibility of the model is tested by the comparison between the changes in the songs of actual birds induced by pharmacological inhibition of the NIf and the changes in the songs produced by the model resulting from modification of parameters representing NIf functions. The efficacy of the model demonstrates that the changes of songs induced by pharmacological inhibition of the NIf can be interpreted as a trade-off between the effects of noise and the effects of feedback on the dynamics of the RNN of the HVC. These facts suggest that the current model provides a convincing hypothesis for the functional role of NIf-HVC interaction.

  3. The space transformation in the simulation of multidimensional random fields

    Science.gov (United States)

    Christakos, G.

    1987-01-01

    Space transformations are proposed as a mathematically meaningful and practically comprehensive approach to simulate multidimensional random fields. Within this context the turning bands method of simulation is reconsidered and improved in both the space and frequency domains. ?? 1987.

  4. Sequence-Based Prediction of RNA-Binding Proteins Using Random Forest with Minimum Redundancy Maximum Relevance Feature Selection

    Directory of Open Access Journals (Sweden)

    Xin Ma

    2015-01-01

    Full Text Available The prediction of RNA-binding proteins is one of the most challenging problems in computation biology. Although some studies have investigated this problem, the accuracy of prediction is still not sufficient. In this study, a highly accurate method was developed to predict RNA-binding proteins from amino acid sequences using random forests with the minimum redundancy maximum relevance (mRMR method, followed by incremental feature selection (IFS. We incorporated features of conjoint triad features and three novel features: binding propensity (BP, nonbinding propensity (NBP, and evolutionary information combined with physicochemical properties (EIPP. The results showed that these novel features have important roles in improving the performance of the predictor. Using the mRMR-IFS method, our predictor achieved the best performance (86.62% accuracy and 0.737 Matthews correlation coefficient. High prediction accuracy and successful prediction performance suggested that our method can be a useful approach to identify RNA-binding proteins from sequence information.

  5. Automatic sequences

    CERN Document Server

    Haeseler, Friedrich

    2003-01-01

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

  6. Difference in muscle activation patterns during high-speed versus standard-speed yoga: A randomized sequence crossover study.

    Science.gov (United States)

    Potiaumpai, Melanie; Martins, Maria Carolina Massoni; Wong, Claudia; Desai, Trusha; Rodriguez, Roberto; Mooney, Kiersten; Signorile, Joseph F

    2017-02-01

    To compare the difference in muscle activation between high-speed yoga and standard-speed yoga and to compare muscle activation of the transitions between poses and the held phases of a yoga pose. Randomized sequence crossover trial SETTING: A laboratory of neuromuscular research and active aging Interventions: Eight minutes of continuous Sun Salutation B was performed, at a high speed versus a standard-speed, separately. Electromyography was used to quantify normalized muscle activation patterns of eight upper and lower body muscles (pectoralis major, medial deltoids, lateral head of the triceps, middle fibers of the trapezius, vastus medialis, medial gastrocnemius, thoracic extensor spinae, and external obliques) during the high-speed and standard-speed yoga protocols. Difference in normalized muscle activation between high-speed yoga and standard-speed yoga. Normalized muscle activity signals were significantly higher in all eight muscles during the transition phases of poses compared to the held phases (pyoga across the entire session. Our results show that transitions from one held phase of a pose to another produces higher normalized muscle activity than the held phases of the poses and that overall activity is greater during highspeed yoga than standard-speed yoga. Therefore, the transition speed and associated number of poses should be considered when targeting specific improvements in performance. Copyright © 2016 Elsevier Ltd. All rights reserved.

  7. Analysis of heart rate and oxygen uptake kinetics studied by two different pseudo-random binary sequence work rate amplitudes.

    Science.gov (United States)

    Drescher, U; Koschate, J; Schiffer, T; Schneider, S; Hoffmann, U

    2017-06-01

    The aim of the study was to compare the kinetics responses of heart rate (HR), pulmonary (V˙O2pulm) and predicted muscular (V˙O2musc) oxygen uptake between two different pseudo-random binary sequence (PRBS) work rate (WR) amplitudes both below anaerobic threshold. Eight healthy individuals performed two PRBS WR protocols implying changes between 30W and 80W and between 30W and 110W. HR and V˙O2pulm were measured beat-to-beat and breath-by-breath, respectively. V˙O2musc was estimated applying the approach of Hoffmann et al. (Eur J Appl Physiol 113: 1745-1754, 2013) considering a circulatory model for venous return and cross-correlation functions (CCF) for the kinetics analysis. HR and V˙O2musc kinetics seem to be independent of WR intensity (p>0.05). V˙O2pulm kinetics show prominent differences in the lag of the CCF maximum (39±9s; 31±4s; pkinetics remain unchanged. Copyright © 2017 Elsevier B.V. All rights reserved.

  8. KinMutRF: a random forest classifier of sequence variants in the human protein kinase superfamily.

    Science.gov (United States)

    Pons, Tirso; Vazquez, Miguel; Matey-Hernandez, María Luisa; Brunak, Søren; Valencia, Alfonso; Izarzugaza, Jose Mg

    2016-06-23

    The association between aberrant signal processing by protein kinases and human diseases such as cancer was established long time ago. However, understanding the link between sequence variants in the protein kinase superfamily and the mechanistic complex traits at the molecular level remains challenging: cells tolerate most genomic alterations and only a minor fraction disrupt molecular function sufficiently and drive disease. KinMutRF is a novel random-forest method to automatically identify pathogenic variants in human kinases. Twenty six decision trees implemented as a random forest ponder a battery of features that characterize the variants: a) at the gene level, including membership to a Kinbase group and Gene Ontology terms; b) at the PFAM domain level; and c) at the residue level, the types of amino acids involved, changes in biochemical properties, functional annotations from UniProt, Phospho.ELM and FireDB. KinMutRF identifies disease-associated variants satisfactorily (Acc: 0.88, Prec:0.82, Rec:0.75, F-score:0.78, MCC:0.68) when trained and cross-validated with the 3689 human kinase variants from UniProt that have been annotated as neutral or pathogenic. All unclassified variants were excluded from the training set. Furthermore, KinMutRF is discussed with respect to two independent kinase-specific sets of mutations no included in the training and testing, Kin-Driver (643 variants) and Pon-BTK (1495 variants). Moreover, we provide predictions for the 848 protein kinase variants in UniProt that remained unclassified. A public implementation of KinMutRF, including documentation and examples, is available online ( http://kinmut2.bioinfo.cnio.es ). The source code for local installation is released under a GPL version 3 license, and can be downloaded from https://github.com/Rbbt-Workflows/KinMut2 . KinMutRF is capable of classifying kinase variation with good performance. Predictions by KinMutRF compare favorably in a benchmark with other state

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

    Science.gov (United States)

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

    2018-01-22

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

  10. The optimal sequence for bronchial brushing and forceps biopsy in lung cancer diagnosis: a random control study.

    Science.gov (United States)

    Hou, Gang; Miao, Yuan; Hu, Xue-Jun; Wang, Wei; Wang, Qiu-Yue; Wu, Guang-Ping; Wang, En-Hua; Kang, Jian

    2016-03-01

    Optimizing basic techniques in diagnostic bronchoscopy is important for improving medical services in developing countries. In this study, the optimal sequence of bronchial brushing relative to bronchial biopsy for lung cancer diagnosis was evaluated. A total of 420 patients with visible endobronchial tumors were prospectively and randomly enrolled in two groups: a pre-biopsy brushing group, receiving two brushings before biopsy; two brushings which performed afterwards; were set as self-control and compared with the pre-biopsy brushings as the intra-group comparison; and a post-biopsy brushing group, only receiving two brushings after biopsy, which were compared with the pre-biopsy brushings as the inter-group comparison. Diagnostic yield of brushing was compared before and after biopsy, and as well as for different tumor pathologies and bronchoscopic morphologies. The occurrence of treated bleeding which defined as bleeding needed further intervention with argon plasma coagulation and/or anti-coagulation drugs in two groups was also compared. Only patients with a definitive cytological or histological diagnosis of lung cancer based on bronchoscopy or other confirmatory techniques were included. Patients were excluded if they had submucosal lesions, extrinsic compressions, pulmonary metastasis of extrapulmonary malignancies or uncommon non-small cell lung carcinoma (NSCLC). A total of 362 patients who met the inclusion criteria were analyzed. Diagnostic yield for pre-biopsy brushing (49.2%, 88/179) was significantly higher than for post-biopsy brushing within the same pre-biopsy brushing group (31.8%, 57/179) (P=0.007) as the intra-group comparison, and significantly higher than for post-biopsy brushing in the post group (30.6%, 56/183) (Pcancer. In cases of endobronchial exophytic tumors, pre-biopsy brushing appears to be superior to post-biopsy brushing.

  11. 20 CFR 410.672 - Reopening initial, revised or reconsidered determinations of the Administration and decisions of...

    Science.gov (United States)

    2010-04-01

    ... Representation of Parties § 410.672 Reopening initial, revised or reconsidered determinations of the... location or identification of his or her body; or (5) Such initial, revised, or reconsidered determination...

  12. Social Scholarship: Reconsidering Scholarly Practices in the Age of Social Media

    Science.gov (United States)

    Greenhow, Christine; Gleason, Benjamin

    2014-01-01

    This conceptual exploration inquires, what is scholarship reconsidered in the age of social media? How ought we to conceptualize "social scholarship"--a new set of practices being discussed in various disciplines? The paper offers a critical examination of the practical and policy implications of reconsidering scholarship in light of…

  13. Anomalous stress diffusion, Omori's law and Continuous Time Random Walk in the 2010 Efpalion aftershock sequence (Corinth rift, Greece)

    Science.gov (United States)

    Michas, Georgios; Vallianatos, Filippos; Karakostas, Vassilios; Papadimitriou, Eleftheria; Sammonds, Peter

    2014-05-01

    Efpalion aftershock sequence occurred in January 2010, when an M=5.5 earthquake was followed four days later by another strong event (M=5.4) and numerous aftershocks (Karakostas et al., 2012). This activity interrupted a 15 years period of low to moderate earthquake occurrence in Corinth rift, where the last major event was the 1995 Aigion earthquake (M=6.2). Coulomb stress analysis performed in previous studies (Karakostas et al., 2012; Sokos et al., 2012; Ganas et al., 2013) indicated that the second major event and most of the aftershocks were triggered due to stress transfer. The aftershocks production rate decays as a power-law with time according to the modified Omori law (Utsu et al., 1995) with an exponent larger than one for the first four days, while after the occurrence of the second strong event the exponent turns to unity. We consider the earthquake sequence as a point process in time and space and study its spatiotemporal evolution considering a Continuous Time Random Walk (CTRW) model with a joint probability density function of inter-event times and jumps between the successive earthquakes (Metzler and Klafter, 2000). Jump length distribution exhibits finite variance, whereas inter-event times scale as a q-generalized gamma distribution (Michas et al., 2013) with a long power-law tail. These properties are indicative of a subdiffusive process in terms of CTRW. Additionally, the mean square displacement of aftershocks is constant with time after the occurrence of the first event, while it changes to a power-law with exponent close to 0.15 after the second major event, illustrating a slow diffusive process. During the first four days aftershocks cluster around the epicentral area of the second major event, while after that and taking as a reference the second event, the aftershock zone is migrating slowly with time to the west near the epicentral area of the first event. This process is much slower from what would be expected from normal diffusion, a

  14. Use of molecular diversity of Mycoplasma gallisepticum by gene-targeted sequencing (GTS) and random amplified polymorphic DNA (RAPD) analysis for epidemiological studies.

    Science.gov (United States)

    Ferguson, Naola M; Hepp, Diego; Sun, Shulei; Ikuta, Nilo; Levisohn, Sharon; Kleven, Stanley H; García, Maricarmen

    2005-06-01

    A total of 67 Mycoplasma gallisepticum field isolates from the USA, Israel and Australia, and 10 reference strains, were characterized by gene-targeted sequencing (GTS) analysis of portions of the putative cytadhesin pvpA gene, the cytadhesin gapA gene, the cytadhesin mgc2 gene, and an uncharacterized hypothetical surface lipoprotein-encoding gene designated genome coding DNA sequence (CDS) MGA_0319. The regions of the surface-protein-encoding genes targeted in this analysis were found to be stable within a strain, after sequencing different in vitro passages of M. gallisepticum reference strains. Gene sequences were first analysed on the basis of gene size polymorphism. The pvpA and mgc2 genes are characterized by the presence of different nucleotide insertions/deletions. However, differentiation of isolates based solely on pvpA/mgc2 PCR size polymorphism was not found to be a reliable method to differentiate among M. gallisepticum isolates. On the other hand, GTS analysis based on the nucleotide sequence identities of individual and multiple genes correlated with epidemiologically linked isolates and with random amplified polymorphic DNA (RAPD) analysis. GTS analysis of individual genes, gapA, MGA_0319, mgc2 and pvpA, identified 17, 16, 20 and 22 sequence types, respectively. GTS analysis using multiple gene sequences mgc2/pvpa and gapA/MGA_0319/mgc2/pvpA identified 38 and 40 sequence types, respectively. GTS of multiple surface-protein-encoding genes showed better discriminatory power than RAPD analysis, which identified 36 pattern types from the same panel of M. gallisepticum strains. These results are believed to provide the first evidence that typing of M. gallisepticum isolates by GTS analysis of surface-protein genes is a sensitive and reproducible typing method and will allow rapid global comparisons between laboratories.

  15. DS/LPI autocorrelation detection in noise plus random-tone interference. [Direct Sequence Low-Probabilty of Intercept

    Science.gov (United States)

    Hinedi, S.; Polydoros, A.

    1988-01-01

    The authors present and analyze a frequency-noncoherent two-lag autocorrelation statistic for the wideband detection of random BPSK signals in noise-plus-random-multitone interference. It is shown that this detector is quite robust to the presence or absence of interference and its specific parameter values, contrary to the case of an energy detector. The rule assumes knowledge of the data rate and the active scenario under H0. It is concluded that the real-time autocorrelation domain and its samples (lags) are a viable approach for detecting random signals in dense environments.

  16. Quantum theory at the crossroads reconsidering the 1927 Solvay conference

    CERN Document Server

    Bacciagaluppi, Guido

    2009-01-01

    We reconsider the crucial 1927 Solvay conference in the context of current research in the foundations of quantum theory. Contrary to folklore, the interpretation question was not settled at this conference and no consensus was reached; instead, a range of sharply conflicting views were presented and extensively discussed. Today, there is no longer an established or dominant interpretation of quantum theory, so it is important to re-evaluate the historical sources and keep the interpretation debate open. In this spirit, we provide a complete English translation of the original proceedings (lectures and discussions), and give background essays on the three main interpretations presented: de Broglie's pilot-wave theory, Born and Heisenberg's quantum mechanics, and Schroedinger's wave mechanics. We provide an extensive analysis of the lectures and discussions that took place, in the light of current debates about the meaning of quantum theory. The proceedings contain much unexpected material, including extensive...

  17. Histamine in diabetes: Is it time to reconsider?

    Science.gov (United States)

    Pini, Alessandro; Obara, Ilona; Battell, Emma; Chazot, Paul L; Rosa, Arianna Carolina

    2016-09-01

    The first studies of histamine and diabetes date back to the 1950s. Since that time the involvement of histamine in diabetes was related to its well known vasoactive properties and permeability leakage effects. In particular, the first evidence for a correlation between histamine and diabetes arose in 1989 when an increase in plasma and leucocyte histamine content was observed. Limited independent evidence followed in the subsequent two decades, focusing on both histamine glyceamic control and macro- and microvascular complications of diabetes. However, recent observations have sparked the question whether it is time to reconsider the functional contribution of histamine in diabetes. We reveal an interesting upsurge in the field which provides scope for new insights into the role of histamine in diabetes. Copyright © 2016 Elsevier Ltd. All rights reserved.

  18. Reconsidering Data Logging in Light of Digital Forensics

    Science.gov (United States)

    Chou, Bin-Hui; Takahashi, Kenichi; Hori, Yoshiaki; Sakurai, Kouichi

    Logs record the events that have happened within in a system so they are considered the history of system activities. They are one of the objects that digital forensic investigators would like to examine when a security incident happens. However, logs were initially created for trouble shooting, and are not purposefully designed for digital forensics. Thus, enormous and redundant log data make analysis tasks complicated and time-consuming to find valuable information, and make logging-related techniques difficult utilized in some systems such as embedded systems. In this paper, we reconsider a data logging mechanism in terms of forensics and consequently, we propose purpose-based forensic logging. In purpose-based forensic logging, we only collect the required logs according to a specific purpose, which could decrease the space that logs occupy and may mitigate the analysis tasks during forensic investigations.

  19. Drying of latex films and coatings: Reconsidering the fundamental mechanisms

    DEFF Research Database (Denmark)

    Kiil, Søren

    2006-01-01

    The two existing theories describing drying of latex films or coatings are reconsidered. Subsequently, a novel mathematical drying model is presented, the simulations of which can match and explain experimental drying rate data of two previous investigations with latex films. In contrast...... to previous model studies, but in agreement with observations, simulations suggest that during the falling rate period of the drying process of a latex film, a porous skin of partly coalesced latex particles is indeed formed, which limits transport of water vapour from the receding air-liquid interphase......), latex particle size (500-600 nm), initial polymer volume concentration (19-47 vol.%), and molecular weight of latex polymer (not quantified). Simulations also demonstrate that the transition from a constant to a falling drying rate in all cases takes place when the polymer volume concentration...

  20. Sequence correction of random coil chemical shifts: correlation between neighbor correction factors and changes in the Ramachandran distribution

    DEFF Research Database (Denmark)

    Kjærgaard, Magnus; Poulsen, Flemming Martin

    2011-01-01

    . The contributions from the neighboring residues are typically removed by using neighbor correction factors determined based on each residue's effect on glycine chemical shifts. Due to its unusual conformational freedom, glycine may be particularly unrepresentative for the remaining residue types. In this study, we......Random coil chemical shifts are necessary for secondary chemical shift analysis, which is the main NMR method for identification of secondary structure in proteins. One of the largest challenges in the determination of random coil chemical shifts is accounting for the effect of neighboring residues...... use random coil peptides containing glutamine instead of glycine to determine the random coil chemical shifts and the neighbor correction factors. The resulting correction factors correlate to changes in the populations of the major wells in the Ramachandran plot, which demonstrates that changes...

  1. Random-effects linear modeling and sample size tables for two special crossover designs of average bioequivalence studies: the four-period, two-sequence, two-formulation and six-period, three-sequence, three-formulation designs.

    Science.gov (United States)

    Diaz, Francisco J; Berg, Michel J; Krebill, Ron; Welty, Timothy; Gidal, Barry E; Alloway, Rita; Privitera, Michael

    2013-12-01

    Due to concern and debate in the epilepsy medical community and to the current interest of the US Food and Drug Administration (FDA) in revising approaches to the approval of generic drugs, the FDA is currently supporting ongoing bioequivalence studies of antiepileptic drugs, the EQUIGEN studies. During the design of these crossover studies, the researchers could not find commercial or non-commercial statistical software that quickly allowed computation of sample sizes for their designs, particularly software implementing the FDA requirement of using random-effects linear models for the analyses of bioequivalence studies. This article presents tables for sample-size evaluations of average bioequivalence studies based on the two crossover designs used in the EQUIGEN studies: the four-period, two-sequence, two-formulation design, and the six-period, three-sequence, three-formulation design. Sample-size computations assume that random-effects linear models are used in bioequivalence analyses with crossover designs. Random-effects linear models have been traditionally viewed by many pharmacologists and clinical researchers as just mathematical devices to analyze repeated-measures data. In contrast, a modern view of these models attributes an important mathematical role in theoretical formulations in personalized medicine to them, because these models not only have parameters that represent average patients, but also have parameters that represent individual patients. Moreover, the notation and language of random-effects linear models have evolved over the years. Thus, another goal of this article is to provide a presentation of the statistical modeling of data from bioequivalence studies that highlights the modern view of these models, with special emphasis on power analyses and sample-size computations.

  2. Development and comparison of algorithms for generating a scan sequence for a random access scanner. [ZAP (and flow charts for ZIP and SCAN), in FORTRAN for DEC-10

    Energy Technology Data Exchange (ETDEWEB)

    Eason, R. O.

    1980-09-01

    Many data acquisition systems incorporate high-speed scanners to convert analog signals into digital format for further processing. Some systems multiplex many channels into a single scanner. A random access scanner whose scan sequence is specified by a table in random access memory will permit different scan rates on different channels. Generation of this scan table can be a tedious manual task when there are many channels (e.g. 50), when there are more than a few scan rates (e.g. 5), and/or when the ratio of the highest scan rate to the lowest scan rate becomes large (e.g. 100:1). An algorithm is developed which will generate these scan sequences for the random access scanner and implements the algorithm on a digital computer. Application of number theory to the mathematical statement of the problem led to development of several algorithms which were implemented in FORTRAN. The most efficient of these algorithms operates by partitioning the problem into a set of subproblems. Through recursion they solve each subproblem by partitioning it repeatedly into even smaller parts, continuing until a set of simple problems is created. From this process, a pictorial representation or wheel diagram of the problem can be constructed. From the wheel diagram and a description of the original problem, a scan table can be constructed. In addition, the wheel diagram can be used as a method of storing the scan sequence in a smaller amount of memory. The most efficient partitioning algorithm solved most scan table problems in less than a second of CPU time. Some types of problems, however, required as much as a few minutes of CPU time. 26 figures, 2 tables.

  3. Design of Long Period Pseudo-Random Sequences from the Addition of m -Sequences over 𝔽 p

    OpenAIRE

    Ren Jian

    2004-01-01

    Pseudo-random sequence with good correlation property and large linear span is widely used in code division multiple access (CDMA) communication systems and cryptology for reliable and secure information transmission. In this paper, sequences with long period, large complexity, balance statistics, and low cross-correlation property are constructed from the addition of m -sequences with pairwise-prime linear spans (AMPLS). Using m -sequences as building blocks, the proposed method proved to...

  4. Determining Phylogenetic Relationships Among Date Palm Cultivars Using Random Amplified Polymorphic DNA (RAPD) and Inter-Simple Sequence Repeat (ISSR) Markers.

    Science.gov (United States)

    Haider, Nadia

    2017-01-01

    Investigation of genetic variation and phylogenetic relationships among date palm (Phoenix dactylifera L.) cultivars is useful for their conservation and genetic improvement. Various molecular markers such as restriction fragment length polymorphisms (RFLPs), simple sequence repeat (SSR), representational difference analysis (RDA), and amplified fragment length polymorphism (AFLP) have been developed to molecularly characterize date palm cultivars. PCR-based markers random amplified polymorphic DNA (RAPD) and inter-simple sequence repeat (ISSR) are powerful tools to determine the relatedness of date palm cultivars that are difficult to distinguish morphologically. In this chapter, the principles, materials, and methods of RAPD and ISSR techniques are presented. Analysis of data generated from these two techniques and the use of these data to reveal phylogenetic relationships among date palm cultivars are also discussed.

  5. 42 CFR 426.563 - Future new or revised or reconsidered NCDs.

    Science.gov (United States)

    2010-10-01

    ... DETERMINATIONS Review of an NCD § 426.563 Future new or revised or reconsidered NCDs. CMS may not reinstate an NCD provision(s) found to be unreasonable unless CMS has a different basis (such as additional...

  6. Evolution towards ergodic behavior of stationary fractal random processes with memory: application to the study of long-range correlations of nucleotide sequences in DNA

    Science.gov (United States)

    Vlad, Marcel Ovidiu; Schönfisch, Birgitt; Mackey, Michael C.

    1996-02-01

    The possible occurrence of ergodic behavior for large times is investigated in the case of stationary random processes with memory. It is shown that for finite times the time average of a state function is generally a random variable and thus two types of cumulants can be introduced: for the time average and for the statistical ensemble, respectively. In the limit of infinite time a transition from the random to the deterministic behavior of the time average may occur, resulting in an ergodic behavior. The conditions of occurrence of this transition are investigated by analyzing the scaling behavior of the cumulants of the time average. A general approach for the computation of these cumulants is developed; explicit computations are presented both for short and long memory in the particular case of separable stationary processes for which the cumulants of a statistical ensemble can be factorized into products of functions depending on binary time differences. In both cases the ergodic behavior emerges for large times provided that the cumulants of a statistical ensemble decrease to zero as the time differences increase to infinity. The analysis leads to the surprising conclusion that the scaling behavior of the cumulants of the time average is relatively insensitive to the type of memory considered: both for short and long memory the cumulants of the time average obey inverse different from zero for large time differences, then the time averaage is random even as the length of the total time interval tends to infinity and the ergodic behavior no longer holds. The theory is applied to the study of long range correlations of nucleotide sequences in DNA; in this case the length t of a sequence of nucleotides plays the role of the time variable. A proportionality relationship is established between the cumulants of the pyrimidine excess in a sequence of length t and the cumulants of the time (length) average of the probability of occurrence of a pyrimidine. It is shown

  7. Periodic mass extinctions and the Planet X model reconsidered

    Science.gov (United States)

    Whitmire, Daniel P.

    2016-01-01

    The 27 Myr period in the fossil extinction record has been confirmed in modern data bases dating back 500 Myr, which is twice the time interval of the original analysis from 30 years ago. The surprising regularity of this period has been used to reject the Nemesis model. A second model based on the Sun's vertical Galactic oscillations has been challenged on the basis of an inconsistency in period and phasing. The third astronomical model originally proposed to explain the periodicity is the Planet X model in which the period is associated with the perihelion precession of the inclined orbit of a trans-Neptunian planet. Recently, and unrelated to mass extinctions, a trans-Neptunian super-Earth planet has been proposed to explain the observation that the inner Oort cloud objects Sedna and 2012VP113 have perihelia that lie near the ecliptic plane. In this Letter, we reconsider the Planet X model in light of the confluence of the modern palaeontological and outer Solar system dynamical evidence.

  8. Flight into sanity. Jones's allegation of Ferenczi's mental deterioration reconsidered.

    Science.gov (United States)

    Bonomi, C

    1999-06-01

    In 'The Life and Work of Sigmund Freud', Volume III, Ernest Jones explained Ferenczi's final contributions as the product of a mental deterioration based on a progressive psychosis. Erich Fromm collected various testimonies by witnesses of Ferenczi's last years, all contrasting with Jones's assertions, and challenged Jones's manner of writing history. However, since Fromm was himself a dissident, and his witnesses were pupils, relatives or friends of Ferenczi's, they were discarded as 'partisans'. The present study aims at reconsidering the question of Ferenczi's insanity on the basis of many unpublished documents. The consulted documents do not support Jones's allegation of Ferenczi's insanity. At the same time, they show that Jones's allegation was not a one-man fabrication, but reflected a shared belief, eliciting many questions about the nature of this belief, the lack of scrutiny that characterised its spreading, and its possible function within the psychoanalytic community. It is suggested that Ferenczi's personality and teaching, especially his emphasis on the need to accept the patient's criticism, contrasted with the dominant conception of psychoanalysis, based on the analyst's infallibility.

  9. Assessing the amount of quadruplex structures present within G₂-tract synthetic random-sequence DNA libraries.

    Directory of Open Access Journals (Sweden)

    Simon A McManus

    Full Text Available The process of in vitro selection has led to the discovery of many aptamers with potential to be developed into inhibitors and biosensors, but problems in isolating aptamers against certain targets with desired affinity and specificity still remain. One possible improvement is to use libraries enhanced for motifs repeatedly isolated in aptamer molecules. One such frequently observed motif is the two-tiered guanine quadruplex. In this study we investigated whether DNA libraries could be designed to contain a large fraction of molecules capable of folding into two-tiered guanine quadruplexes. Using comprehensive circular dichroism analysis, we found that DNA libraries could be designed to contain a large proportion of sequences that adopt guanine quadruplex structures. Analysis of individual sequences from a small library revealed a mixture of quadruplexes of different topologies providing the diversity desired for an in vitro selection. We also found that primer-binding sites are detrimental to quadruplex formation and devised a method for post-selection amplification of primer-less quadruplex libraries. With the development of guanine quadruplex enriched DNA libraries, it should be possible to improve the chances of isolating aptamers that utilize a quadruplex scaffold and enhance the success of in vitro selection experiments.

  10. Theoretical study of polymeric mixtures with different sequence statistics. II. Brazovskii class: Linear random copolymers with diblock copolymers

    Energy Technology Data Exchange (ETDEWEB)

    Qi, Shuyan [Department of Chemical Engineering, Department of Chemistry, and Materials Science Division, Lawrence Berkeley National Laboratory, University of California, Berkeley, California 94720 (United States); Chakraborty, Arup K. [Department of Chemical Engineering, Department of Chemistry, and Materials Science Division, Lawrence Berkeley National Laboratory, University of California, Berkeley, California 94720 (United States)

    2000-01-15

    We use a Landau theory to study the instability of the homogeneous state of a mixture of linear random copolymers and diblock copolymers. Interesting features of the calculated structure factors for different components of the mixture are found, which can be directly compared with scattering experiments with selectively deuterated samples. We also investigate the least stable concentration fluctuations and find four different types of segregation modes at the spinodal depending upon the characteristics of the mixture (e.g., average compositions, statistical correlation lengths and volume fractions). The different segregation modes are also indicative of the kinetic pathways leading to the formation of ordered microstructures. Experiments probing these pathways are suggested. (c) 2000 American Institute of Physics.

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

    Science.gov (United States)

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

    2005-02-01

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

  12. Reconsidering the one leptoquark solution: flavor anomalies and neutrino mass

    Science.gov (United States)

    Cai, Yi; Gargalionis, John; Schmidt, Michael A.; Volkas, Raymond R.

    2017-10-01

    We reconsider a model introducing a scalar leptoquark ϕ ˜ ( 3 , 1 , -1 /3) to explain recent deviations from the standard model in semileptonic B decays. The leptoquark can accommodate the persistent tension in the decays \\overline{B}\\to {D}^{(\\ast )}τ \\overline{ν} as long as its mass is lower than approximately 10 TeV, and we show that a sizeable Yukawa coupling to the right-chiral tau lepton is necessary for an acceptable explanation. A characteristic prediction of this scenario is a value of {R}_{D^{*}} slightly smaller than the current world average. Agreement with the measured \\overline{B}\\to {D}^{(\\ast )}τ \\overline{ν} rates is mildly compromised for parameter choices addressing the tensions in b → sμμ, where the model can significantly reduce the discrepancies in angular observables, branching ratios and the lepton-flavor-universality observables R K and {R}_{K^{*}} . The leptoquark can also reconcile the predicted and measured value of the anomalous magnetic moment of the muon and appears naturally in models of radiative neutrino mass derived from lepton-number violating effective operators. As a representative example, we incorporate the particle into an existing two-loop neutrino mass scenario derived from a dimension-nine operator. In this specific model, the structure of the neutrino mass matrix provides enough freedom to explain the small masses of the neutrinos in the region of parameter space dictated by agreement with the anomalies in \\overline{B}\\to {D}^{(\\ast )}τ \\overline{ν} , but not the b → s transition. This is achieved without excessive fine-tuning in the parameters important for neutrino mass.

  13. Analysis of genetic diversity of Sclerotinia sclerotiorum from eggplant by mycelial compatibility, random amplification of polymorphic DNA (RAPD and simple sequence repeat (SSR analyses

    Directory of Open Access Journals (Sweden)

    Fatih Mehmet Tok

    2016-09-01

    Full Text Available The genetic diversity and pathogenicity/virulence among 60 eggplant Sclerotinia sclerotiorum isolates collected from six different geographic regions of Turkey were analysed using mycelial compatibility groupings (MCGs, random amplified polymorphic DNA (RAPD and simple sequence repeat (SSR polymorphism. By MCG tests, the isolates were classified into 22 groups. Out of 22 MCGs, 36% were represented each by a single isolate. The isolates showed great variability for virulence regardless of MCG and geographic origin. Based on the results of RAPD and SSR analyses, 60 S. sclerotiorum isolates representing 22 MCGs were grouped in 2 and 3 distinct clusters, respectively. Analyses using RAPD and SSR markers illustrated that cluster groupings or genetic distance of S. sclerotiorum populations from eggplant were not distinctly relative to the MCG, geographical origin and virulence diversity. The patterns obtained revealed a high heterogeneity of genetic composition and suggested the occurrence of clonal and sexual reproduction of S. sclerotiorum on eggplant in the areas surveyed.

  14. Reconsidering low-dose aspirin therapy for cardiovascular disease: a study protocol for physician and patient behavioral change

    Directory of Open Access Journals (Sweden)

    Staton Elizabeth W

    2011-06-01

    Full Text Available Abstract Background There are often disparities between current evidence and current practice. Decreasing the gap between desired practice outcomes and observed practice outcomes in the healthcare system is not always easy. Stopping previously recommended or variably recommended interventions may be even harder to achieve than increasing the use of a desired but under-performed activity. For over a decade, aspirin has been prescribed for primary prevention of cardiovascular disease and for patients with the coronary artery disease risk equivalents; yet, there is no substantial evidence of an appropriate risk-benefit ratio to support this practice. This paper describes the protocol of a randomized trial being conducted in six primary care practices in the Denver metropolitan area to examine the effectiveness of three interventional strategies to change physician behavior regarding prescription of low-dose aspirin. Methods All practices received academic detailing, one arm received clinician reminders to reconsider aspirin, a second arm received both clinician and patient messages to reconsider aspirin. The intervention will run for 15 to 18 months. Data collected at baseline and for outcomes from an electronic health record will be used to assess pre- and post-interventional prescribing, as well as to explore any inappropriate decrease in aspirin use by patients with known cardiovascular disease. Discussion This study was designed to investigate effective methods of changing physician behavior to decrease the use of aspirin for primary cardiovascular disease prevention. The results of this study will contribute to the small pool of knowledge currently available on the topic of ceasing previously supported practices. Trial Registration ClinicalTrials.gov: NCT01247454

  15. Fast and cost-effective single nucleotide polymorphism (SNP) detection in the absence of a reference genome using semideep next-generation Random Amplicon Sequencing (RAMseq).

    Science.gov (United States)

    Bayerl, Helmut; Kraus, Robert H S; Nowak, Carsten; Foerster, Daniel W; Fickel, Joerns; Kuehn, Ralph

    2017-09-15

    Biodiversity has suffered a dramatic global decline during the past decades, and monitoring tools are urgently needed providing data for the development and evaluation of conservation efforts both on a species and on a genetic level. However, in wild species, the assessment of genetic diversity is often hampered by the lack of suitable genetic markers. In this article, we present Random Amplicon Sequencing (RAMseq), a novel approach for fast and cost-effective detection of single nucleotide polymorphisms (SNPs) in nonmodel species by semideep sequencing of random amplicons. By applying RAMseq to the Eurasian otter (Lutra lutra), we identified 238 putative SNPs after quality filtering of all candidate loci and were able to validate 32 of 77 loci tested. In a second step, we evaluated the genotyping performance of these SNP loci in noninvasive samples, one of the most challenging genotyping applications, by comparing it with genotyping results of the same faecal samples at microsatellite markers. We compared (i) polymerase chain reaction (PCR) success rate, (ii) genotyping errors and (iii) Mendelian inheritance (population parameters). SNPs produced a significantly higher PCR success rate (75.5% vs. 65.1%) and lower mean allelic error rate (8.8% vs. 13.3%) than microsatellites, but showed a higher allelic dropout rate (29.7% vs. 19.8%). Genotyping results showed no deviations from Mendelian inheritance in any of the SNP loci. Hence, RAMseq appears to be a valuable tool for the detection of genetic markers in nonmodel species, which is a common challenge in conservation genetic studies. © 2017 John Wiley & Sons Ltd.

  16. A Developmental and Sequenced One-to-One Educational Intervention (DS1-EI for autism spectrum disorder: a randomized single-blind controlled trial.

    Directory of Open Access Journals (Sweden)

    TANET Antoine

    2016-09-01

    Full Text Available Introduction: Individuals with Autism Spectrum Disorder (ASD who also exhibit severe to moderate ranges of intellectual disability (ID still face many challenges (i.e. less evidence-based trials, less inclusion in school with peers.Methods: We implemented a novel model called the Developmental and Sequenced One-to-One Educational Intervention (DS1-EI in 5-9-year-old children with co-occurring ASD and ID. The treatment protocol was adapted for school implementation by designing it using an educational agenda. The intervention was based on intensity, regular assessments, updating objectives, encouraging spontaneous communication, promoting skills through play with peers, supporting positive behaviours, providing supervision, capitalizing on teachers’ unique skills, and providing developmental and sequenced learning. Developmental learning implies that the focus of training is what is close to the developmental expectations given a child’s development in a specific domain. Sequenced learning means that the teacher changes the learning activities every 10-15 minutes to maintain the child’s attention in the context of an anticipated time agenda.We selected 11 French institutions in which we implemented the model in small classrooms. Each institution recruited participants per dyads matched by age, sex and developmental quotient. Patients from each dyad were then randomized to a DS1-EI group or a Treatment as usual (TAU group for 36 months. The primary variables – the Childhood Autism Rating scale (CARS and the psychoeducational profile (PEP-3 – will be blindly assessed by independent raters at the 18-month and 36-month follow-up.Discussion and baseline description: We enrolled 75 participants: 38 were randomized to the DS1-EI and 37 to the TAU groups. At enrolment, we found no significant differences in participants’ characteristics between groups. As expected, exposure to school was the only significant difference (9.4 (±4.1 h/week in

  17. Seeing the trees through the forest : sequence-based homo- and heteromeric protein-protein interaction sites prediction using random forest

    NARCIS (Netherlands)

    Hou, Qingzhen; De Geest, Paul F.G.; Vranken, Wim F.; Heringa, Jaap; Feenstra, K. Anton

    2017-01-01

    Motivation: Genome sequencing is producing an ever-increasing amount of associated protein sequences. Few of these sequences have experimentally validated annotations, however, and computational predictions are becoming increasingly successful in producing such annotations. One key challenge remains

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

    Energy Technology Data Exchange (ETDEWEB)

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

    2016-07-15

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

  19. Reconsidering the concept of 'dual-use' in the context of neuroscience research

    Directory of Open Access Journals (Sweden)

    Voarino, Nathalie

    2014-11-01

    Full Text Available The concept of ‘dual-use’ research usually refers to research with both civilian (e.g., therapeutic and military applications. I argue here that this dichotomy can and should be reconsidered and thus that the concept of dual-use can be helpful in examining other potential misuses, such as neuroenhancement or neuromarketing.

  20. 'Cut in two', Part 2: Reconsidering the redaction of Q 12:42−46

    African Journals Online (AJOL)

    2015-06-24

    Jun 24, 2015 ... 'Cut in two', Part 2: Reconsidering the redaction of Q 12:42−46. In his influential 1987 ... Q people, while Q 12:39–59 breaches the boundaries of the Q people, threatening everyone with apocalyptic judgement. .... spirit of grace or benefaction (Oakman 1986:151–152; 2008:95,. 105, 138; cf. Lk 11:11).

  1. Navy and Coast Guard Shipbuilding: Navy Should Reconsider Approach to Warranties for Correcting Construction Defects

    Science.gov (United States)

    2016-03-01

    NAVY AND COAST GUARD SHIPBUILDING Navy Should Reconsider Approach to Warranties for Correcting Construction...Accountability Office Highlights of GAO-16-71, a report to congressional committees March 2016 NAVY AND COAST GUARD SHIPBUILDING Navy Should...guarantees are both mechanisms to fix defects for which shipbuilders are responsible. • Warranties give the government a contractual right to

  2. To Lift the Leaden-Eyed: The Historical Roots of Ernest L. Boyer's "Scholarship Reconsidered"

    Science.gov (United States)

    Moser, Drew

    2014-01-01

    This article focuses on the historical roots of Ernest Boyer's most popular work, "Scholarship Reconsidered: Priorities of the Professoriate" (1990). Seeking to transcend the traditional view of scholarship as simply that which is published, Boyer expanded scholarship to include four domains: discovery, application, integration, and…

  3. Reconsidering "Ubuntu": On the Educational Potential of a Particular Ethic of Care

    Science.gov (United States)

    Waghid, Yusef; Smeyers, Paul

    2012-01-01

    In this article we argue that "ubuntu" (human interdependence) is not some form of essentialist notion that unfolds in exactly the same way as some critics of "ubuntu" might want to suggest. Rather, we offer a philosophical position that (re)considers the situation of the self in relation to others. The article starts from the general issues at…

  4. Chaotic attractors, chaotic saddles, and fractal basin boundaries : Goodwin's nonlinear accelerator model reconsidered

    NARCIS (Netherlands)

    Lorenz, HW; Nusse, HE

    Goodwin's nonlinear accelerator model with periodic investment outlays is reconsidered and used as an economic example of the emergence of complex motion in nonlinear dynamical systems. In addition to chaotic attractors, the model can possess coexisting attracting periodic orbits or simple

  5. (Re)Considering Foucault for Science Education Research: Considerations of Truth, Power and Governance

    Science.gov (United States)

    Bazzul, Jesse; Carter, Lyn

    2017-01-01

    This article is a response to Anna Danielsonn, Maria Berge, and Malena Lidar's paper, "Knowledge and power in the technology classroom: a framework for studying teachers and students in action," and an appeal to science educators of all epistemological orientations to (re)consider the work of Michel Foucault for research in science…

  6. 20 CFR 416.1417 - Disability hearing-disability hearing officer's reconsidered determination.

    Science.gov (United States)

    2010-04-01

    ... 20 Employees' Benefits 2 2010-04-01 2010-04-01 false Disability hearing-disability hearing officer... Review Process, and Reopening of Determinations and Decisions Reconsideration § 416.1417 Disability hearing—disability hearing officer's reconsidered determination. (a) General. The disability hearing...

  7. Intrafamilial, Preferentially Mother-to-Child and Intraspousal, Helicobacter pylori Infection in Japan Determined by Mutilocus Sequence Typing and Random Amplified Polymorphic DNA Fingerprinting.

    Science.gov (United States)

    Yokota, Shin-ichi; Konno, Mutsuko; Fujiwara, Shin-ichi; Toita, Nariaki; Takahashi, Michiko; Yamamoto, Soh; Ogasawara, Noriko; Shiraishi, Tsukasa

    2015-10-01

    The infection route of Helicobacter pylori has been recognized to be mainly intrafamilial, preferentially mother-to-child, especially in developed countries. To determine the transmission route, we examined whether multilocus sequence typing (MLST) was useful for analysis of intrafamilial infection. The possibility of intraspousal infection was also evaluated. Clonal relationships between strains derived from 35 index Japanese pediatric patients, and their family members were analyzed by two genetic typing procedures, MLST and random amplified polymorphic DNA (RAPD) fingerprinting. Mostly coincident results were obtained by MLST and RAPD. By MLST, the allele of loci in the isolates mostly matched between the index child and both the father and mother for 9 (25.7%) of the 35 patients, between the index child and the mother for 25 (60.0%) of the 35 patients. MLST is useful for analyzing the infection route of H. pylori as a highly reproducible method. Intrafamilial, especially mother-to-children and sibling, infection is the dominant transmission route. Intraspousal infection is also thought to occur in about a quarter in the Japanese families. © 2015 John Wiley & Sons Ltd.

  8. Dynamical system modeling to simulate donor T cell response to whole exome sequencing-derived recipient peptides: Understanding randomness in alloreactivity incidence following stem cell transplantation.

    Directory of Open Access Journals (Sweden)

    Vishal Koparde

    Full Text Available Quantitative relationship between the magnitude of variation in minor histocompatibility antigens (mHA and graft versus host disease (GVHD pathophysiology in stem cell transplant (SCT donor-recipient pairs (DRP is not established. In order to elucidate this relationship, whole exome sequencing (WES was performed on 27 HLA matched related (MRD, & 50 unrelated donors (URD, to identify nonsynonymous single nucleotide polymorphisms (SNPs. An average 2,463 SNPs were identified in MRD, and 4,287 in URD DRP (p<0.01; resulting peptide antigens that may be presented on HLA class I molecules in each DRP were derived in silico (NetMHCpan ver2.0 and the tissue expression of proteins these were derived from determined (GTex. MRD DRP had an average 3,670 HLA-binding-alloreactive peptides, putative mHA (pmHA with an IC50 of <500 nM, and URD, had 5,386 (p<0.01. To simulate an alloreactive donor cytotoxic T cell response, the array of pmHA in each patient was considered as an operator matrix modifying a hypothetical cytotoxic T cell clonal vector matrix; each responding T cell clone's proliferation was determined by the logistic equation of growth, accounting for HLA binding affinity and tissue expression of each alloreactive peptide. The resulting simulated organ-specific alloreactive T cell clonal growth revealed marked variability, with the T cell count differences spanning orders of magnitude between different DRP. Despite an estimated, uniform set of constants used in the model for all DRP, and a heterogeneously treated group of patients, higher total and organ-specific T cell counts were associated with cumulative incidence of moderate to severe GVHD in recipients. In conclusion, exome wide sequence differences and the variable alloreactive peptide binding to HLA in each DRP yields a large range of possible alloreactive donor T cell responses. Our findings also help understand the apparent randomness observed in the development of alloimmune responses.

  9. The Impact of Whole-Genome Sequencing on the Primary Care and Outcomes of Healthy Adult Patients: A Pilot Randomized Trial.

    Science.gov (United States)

    Vassy, Jason L; Christensen, Kurt D; Schonman, Erica F; Blout, Carrie L; Robinson, Jill O; Krier, Joel B; Diamond, Pamela M; Lebo, Matthew; Machini, Kalotina; Azzariti, Danielle R; Dukhovny, Dmitry; Bates, David W; MacRae, Calum A; Murray, Michael F; Rehm, Heidi L; McGuire, Amy L; Green, Robert C

    2017-06-27

    Whole-genome sequencing (WGS) in asymptomatic adults might prevent disease but increase health care use without clinical value. To describe the effect on clinical care and outcomes of adding WGS to standardized family history assessment in primary care. Pilot randomized trial. (ClinicalTrials.gov: NCT01736566). Academic primary care practices. 9 primary care physicians (PCPs) and 100 generally healthy patients recruited at ages 40 to 65 years. Patients were randomly assigned to receive a family history report alone (FH group) or in combination with an interpreted WGS report (FH + WGS group), which included monogenic disease risk (MDR) results (associated with Mendelian disorders), carrier variants, pharmacogenomic associations, and polygenic risk estimates for cardiometabolic traits. Each patient met with his or her PCP to discuss the report. Clinical outcomes and health care use through 6 months were obtained from medical records and audio-recorded discussions between PCPs and patients. Patients' health behavior changes were surveyed 6 months after receiving results. A panel of clinician-geneticists rated the appropriateness of how PCPs managed MDR results. Mean age was 55 years; 58% of patients were female. Eleven FH + WGS patients (22% [95% CI, 12% to 36%]) had new MDR results. Only 2 (4% [CI, 0.01% to 15%]) had evidence of the phenotypes predicted by an MDR result (fundus albipunctatus due to RDH5 and variegate porphyria due to PPOX). Primary care physicians recommended new clinical actions for 16% (CI, 8% to 30%) of FH patients and 34% (CI, 22% to 49%) of FH + WGS patients. Thirty percent (CI, 17% to 45%) and 41% (CI, 27% to 56%) of FH and FH + WGS patients, respectively, reported making a health behavior change after 6 months. Geneticists rated PCP management of 8 MDR results (73% [CI, 39% to 99%]) as appropriate and 2 results (18% [CI, 3% to 52%]) as inappropriate. Limited sample size and ancestral and socioeconomic diversity. Adding WGS to primary care

  10. Reconsidering the classification of tick-borne encephalitis virus within the Siberian subtype gives new insights into its evolutionary history.

    Science.gov (United States)

    Kovalev, S Y; Mukhacheva, T A

    2017-11-01

    Tick-borne encephalitis is widespread in Eurasia and transmitted by Ixodes ticks. Classification of its causative agent, tick-borne encephalitis virus (TBEV), includes three subtypes, namely Far-Eastern, European, and Siberian (TBEV-Sib), as well as a group of 886-84-like strains with uncertain taxonomic status. TBEV-Sib is subdivided into three phylogenetic lineages: Baltic, Asian, and South-Siberian. A reason to reconsider TBEV-Sib classification was the analysis of 186 nucleotide sequences of an E gene fragment submitted to GenBank during the last two years. Within the South-Siberian lineage, we have identified a distinct group with prototype strains Aina and Vasilchenko as an individual lineage named East-Siberian. The analysis of reclassified lineages has promoted a new model of the evolutionary history of TBEV-Sib lineages and TBEV-Sib as a whole. Moreover, we present arguments supporting separation of 886-84-like strains into an individual TBEV subtype, which we propose to name Baikalian (TBEV-Bkl). Copyright © 2017 Elsevier B.V. All rights reserved.

  11. Development of a new method for detection and identification of Oenococcus oeni bacteriophages based on endolysin gene sequence and randomly amplified polymorphic DNA.

    Science.gov (United States)

    Doria, Francesca; Napoli, Chiara; Costantini, Antonella; Berta, Graziella; Saiz, Juan-Carlos; Garcia-Moruno, Emilia

    2013-08-01

    Malolactic fermentation (MLF) is a biochemical transformation conducted by lactic acid bacteria (LAB) that occurs in wine at the end of alcoholic fermentation. Oenococcus oeni is the main species responsible for MLF in most wines. As in other fermented foods, where bacteriophages represent a potential risk for the fermentative process, O. oeni bacteriophages have been reported to be a possible cause of unsuccessful MLF in wine. Thus, preparation of commercial starters that take into account the different sensitivities of O. oeni strains to different phages would be advisable. However, currently, no methods have been described to identify phages infecting O. oeni. In this study, two factors are addressed: detection and typing of bacteriophages. First, a simple PCR method was devised targeting a conserved region of the endolysin (lys) gene to detect temperate O. oeni bacteriophages. For this purpose, 37 O. oeni strains isolated from Italian wines during different phases of the vinification process were analyzed by PCR for the presence of the lys gene, and 25 strains gave a band of the expected size (1,160 bp). This is the first method to be developed that allows identification of lysogenic O. oeni strains without the need for time-consuming phage bacterial-lysis induction methods. Moreover, a phylogenetic analysis was conducted to type bacteriophages. After the treatment of bacteria with UV light, lysis was obtained for 15 strains, and the 15 phage DNAs isolated were subjected to two randomly amplified polymorphic DNA (RAPD)-PCRs. By combining the RAPD profiles and lys sequences, 12 different O. oeni phages were clearly distinguished.

  12. Re-considering the Concept of Peace-building from Strategic Perspectives on International Peace Operations

    OpenAIRE

    篠田, 英朗

    2002-01-01

    This essay aims to reconsider and refine the concept of peace building in light ofpractical and strategic interests of international peace operations. Peace-buildinggenerally refers to activities to solidify structures for stable peace in conflict riddensociety. As it is understood to include so many divergent activities conducted byinternational organizations, governments, NGOs and so on, it tends to lack coherentperspectives. As a result, the contents of peace-building remain ambiguous. The...

  13. Bioequivalence of generic lamotrigine 100-mg tablets in healthy Thai male volunteers: a randomized, single-dose, two-period, two-sequence crossover study.

    Science.gov (United States)

    Srichaiya, Arunee; Longchoopol, Chaowanee; Oo-Puthinan, Sarawut; Sayasathid, Jarun; Sripalakit, Pattana; Viyoch, Jarupa

    2008-10-01

    Lamotrigine is an antiepileptic drug which has been used in the treatment of epilepsy and bipolar disorder. A search of the literature did not find previously published bioequivalence and pharmacokinetic evaluations of lamotrigine in healthy Thai male volunteers. The aim of this study was to compare the pharmacokinetic parameters between 2 brands of lamotrigine in healthy Thai male volunteers. A randomized, single-dose, 2-period, 2-sequence, crossover study design with a 2-week washout period was conducted in healthy Thai males. Subjects were randomized to receive either the test or reference formulation in the first period. All subjects were required to be nonsmokers and without a history of alcohol or drug abuse. Plasma samples were collected over a 120-hour period after 100-mg lamotrigine administration in each period. A validated high-performance liquid chromatography ultraviolet method was used to analyze lamotrigine concentration in plasma. Pharmacokinetic parameters were determined using a noncompartmental method. Bioequivalence between the test and reference products, as defined by the US Food and Drug Administration (FDA), is determined when the ratio for the 90% CIs of the difference in the means of the log-transformed AUC(0-t), AUC(0-infinity), and C(max) of the 2 products are within 0.80 and 1.25. Adverse events were determined by measuring vital signs after dosing. Subjects were also asked if they suffered from undesirable effects such as nausea, vomiting, dizziness, and headache. This bioequivalence study was performed in 24 healthy Thai males (mean [SD] age, 20.5 [1.3] years; range, 19-24 years; weight, 62.5 [7.4] kg; height, 172.8 [6.9] cm; body mass index, 20.9 [2.0] kg/m(2)). The mean (SD) C(max) and T(max) of the test formulation of lamotrigine were 1.7 (0.3) microg/mL and 1.2 (0.9) hours, respectively. The mean (SD) C(max) and T(max) of the reference formulation of lamotrigine were 1.7 (0.3) microg/mL and 1.4 (1.0) hours, respectively. The mean

  14. Sequence based prediction of DNA-binding proteins based on hybrid feature selection using random forest and Gaussian naïve Bayes.

    Directory of Open Access Journals (Sweden)

    Wangchao Lou

    Full Text Available Developing an efficient method for determination of the DNA-binding proteins, due to their vital roles in gene regulation, is becoming highly desired since it would be invaluable to advance our understanding of protein functions. In this study, we proposed a new method for the prediction of the DNA-binding proteins, by performing the feature rank using random forest and the wrapper-based feature selection using forward best-first search strategy. The features comprise information from primary sequence, predicted secondary structure, predicted relative solvent accessibility, and position specific scoring matrix. The proposed method, called DBPPred, used Gaussian naïve Bayes as the underlying classifier since it outperformed five other classifiers, including decision tree, logistic regression, k-nearest neighbor, support vector machine with polynomial kernel, and support vector machine with radial basis function. As a result, the proposed DBPPred yields the highest average accuracy of 0.791 and average MCC of 0.583 according to the five-fold cross validation with ten runs on the training benchmark dataset PDB594. Subsequently, blind tests on the independent dataset PDB186 by the proposed model trained on the entire PDB594 dataset and by other five existing methods (including iDNA-Prot, DNA-Prot, DNAbinder, DNABIND and DBD-Threader were performed, resulting in that the proposed DBPPred yielded the highest accuracy of 0.769, MCC of 0.538, and AUC of 0.790. The independent tests performed by the proposed DBPPred on completely a large non-DNA binding protein dataset and two RNA binding protein datasets also showed improved or comparable quality when compared with the relevant prediction methods. Moreover, we observed that majority of the selected features by the proposed method are statistically significantly different between the mean feature values of the DNA-binding and the non DNA-binding proteins. All of the experimental results indicate that

  15. Bioequivalence of two tablet formulations of clopidogrel in healthy Argentinian volunteers: a single-dose, randomized-sequence, open-label crossover study.

    Science.gov (United States)

    Di Girolamo, Guillermo; Czerniuk, Paola; Bertuola, Roberto; Keller, Guillermo A

    2010-01-01

    Platelet activation is a major component in the pathogenesis of coronary thrombosis and myocardial infarction. Thienopyridines, particularly clopidogrel, are highly effective in reducing in-stent thrombosis and functional inhibition of adenosine diphosphate-induced platelet activation. The aim of this study was to evaluate the bioequivalence of a new generic formulation of clopidogrel 75-mg tablets (test) and the available branded formulation (reference) to meet regulatory criteria for marketing the test product in Argentina. This was a randomized-sequence, open-label, 2-period crossover study conducted in healthy white volunteers in the fasted state. A single oral dose of the test or reference formulation was followed by a 7-day washout period, after which subjects received the alternative formulation. Blood samples were collected at baseline and at 0.25, 0.5, 0.75, 1, 1.25, 1.5, 2, 2.5, 3, 4, 6, 8, and 12 hours after dosing. Clopidogrel concentrations were determined using an LC-MS/MS method. The formulations were considered bioequivalent if the 90% CI of the geometric mean ratios (test:reference) for C(max) and AUC(0-last) were within the range from 80% to 125%. Adverse events were monitored throughout the study based on clinical parameters and patient reports. Twenty-four volunteers (13 male, 11 female; mean [SD] age, 33.7 [5.2] years [range, 21-42 years]; weight, 72.4 [6.83] kg [range, 59-82 kg]) were enrolled in and completed the study. The geometric mean C(max) for the test and reference formulations was 877.76 and 913.49 pg/mL, respectively. The geometric mean AUC(0-t) was 1911.53 and 2053.09 pg . h/mL, and the geometric mean AUC(0-infinity)) was 2021.33 and 2188.25 pg . h/mL. The geometric mean ratios (test:reference) for C(max), AUC(0-t), and AUC(0-infinity)) were 96.09% (90% CI, 90.71-101.78), 93.10% (90% CI, 85.57-101.3), and 92.37% (90% CI, 85.06-100.31), respectively. There were no significant differences in pharmacokinetic parameters between groups

  16. Relative bioavailability of levodropropizine 60 mg capsule and syrup formulations in healthy male Korean volunteers: a singledose, randomized-sequence, open-label, two-way crossover study.

    Science.gov (United States)

    Jang, Jae-Won; Seo, Ji-Hyung; Jo, Min-Ho; Lee, Young-Joo; Cho, Young-Wuk; Yim, Sung-Vin; Lee, Kyung-Tae

    2013-02-01

    Levodropropizine is an oral non-opioid anti-tussive drug used in treatment of cough. A new generic 60 mg capsule formulation of levodropropizine has recently been developed. The aim of this study was to assess the pharmacokinetics and bioequivalence of the test (capsule) formulation and reference (syrup) formulation of levodropropizine (60 mg) in healthy, fasted, male Korean volunteers. This was a single-dose, randomized sequence, open-label, 2-period crossover study conducted in healthy male Korean volunteers in the fasted state at Kyung Hee University Medical Center (Seoul, Republic of Korea). A single oral dose of the test or reference formulation was followed by a 1-week washout period, after which subjects received the alternative formulation. Blood samples were collected at 0 (predose), 0.17, 0.33, 0.5, 0.75, 1, 1.5, 2, 3, 4, 6, 8, and 12 hours after study drug administration. Plasma concentration of levodropropizine was determined using a validated liquid chromatography tandem mass spectrometry (LCMS/ MS) method. The formulations were considered bioequivalent if the 90% CIs for C(max), AUC(0-12h) and AUC(0-∞) were within the predetermined bioequivalence range (80 - 125%, according to the guidelines of the Korea Food and Drug Administration (Korea FDA)). Tolerability was evaluated throughout the study based on vital sign measurements, laboratory analysis (blood biochemistry, hematology, hepatic function and urinalysis) and subject interviews concerning adverse events (AEs). A total of 36 male Korean subjects (mean (SD) age, 23.9 (2.4) years (range 19 - 30 years); height, 176.2 (6.1) cm (range 161 - 190 cm); weight, 69.8 (9.1) kg (range 54.0 - 92.2 kg); body mass index, 22.4 (2.1) kg/m2 (range 19.1 - 28.3 kg/m2)) was enrolled and completed the study. The mean values for C(max), t(max), AUC(0-12h), and AUC(0-∞) with the test formulation of levodropropizine were 331.51 ng/ml, 0.60 hours, 784.32 ng×h/ml, and 825.82 ng×h/ml, respectively; for the reference

  17. The roots of success: industrial growth in Italy reconsidered, 1911-1951

    OpenAIRE

    Emanuele Felice; Albert Carreras

    2012-01-01

    This article reconsiders the growth of Italian industry from the First World War to the eve of the economic miracle, with the aid of sector-specific new value-added series, at three different price-bases. The new estimates reduce growth during the First World War, making the Italian case comparable to the other belligerent countries, while improving the performance of the 1920s. The 1929 crisis looks more profound than before, while the recovery after 1933 is now stronger. During the 1920s an...

  18. The roots of success : industrial growth in Italy reconsidered, 1911- 1951

    OpenAIRE

    Felice, Emanuele

    2012-01-01

    This article reconsiders the growth of Italian industry from the First World War to the eve of the economic miracle, with the aid of sector-specific new value-added series, at three different price-bases. The new estimates reduce growth during the First World War, making the Italian case comparable to the other belligerent countries, while improving the performance of the 1920s. The 1929 crisis looks more profound than before, while the recovery after 1933 is now stronger. During the 1920s an...

  19. Characterization of constitutive and putative differentially expressed mRNAs by means of expressed sequence tags, differential display reverse transcriptase-PCR and randomly amplified polymorphic DNA-PCR from the sand fly vector Lutzomyia longipalpis

    Directory of Open Access Journals (Sweden)

    JM Ramalho-Ortigão

    2001-01-01

    Full Text Available Molecular studies of insect disease vectors are of paramount importance for understanding parasite-vector relationship. Advances in this area have led to important findings regarding changes in vectors' physiology upon blood feeding and parasite infection. Mechanisms for interfering with the vectorial capacity of insects responsible for the transmission of diseases such as malaria, Chagas disease and dengue fever are being devised with the ultimate goal of developing transgenic insects. A primary necessity for this goal is information on gene expression and control in the target insect. Our group is investigating molecular aspects of the interaction between Leishmania parasites and Lutzomyia sand flies. As an initial step in our studies we have used random sequencing of cDNA clones from two expression libraries made from head/thorax and abdomen of sugar fed L. longipalpis for the identification of expressed sequence tags (EST. We applied differential display reverse transcriptase-PCR and randomly amplified polymorphic DNA-PCR to characterize differentially expressed mRNA from sugar and blood fed insects, and, in one case, from a L. (V. braziliensis-infected L. longipalpis. We identified 37 cDNAs that have shown homology to known sequences from GeneBank. Of these, 32 cDNAs code for constitutive proteins such as zinc finger protein, glutamine synthetase, G binding protein, ubiquitin conjugating enzyme. Three are putative differentially expressed cDNAs from blood fed and Leishmania-infected midgut, a chitinase, a V-ATPase and a MAP kinase. Finally, two sequences are homologous to Drosophila melanogaster gene products recently discovered through the Drosophila genome initiative.

  20. Cerebral activation related to skills practice in a double serial reaction time task : striatal involvement in random-order sequence learning

    NARCIS (Netherlands)

    van der Graaf, FHCE; de Jong, BM; Maguire, RP; Meiners, LC; Leenders, KL

    We used functional Magnetic Resonance Imaging (fMRI) to examine the distribution of cerebral activation related to prolonged skill practice. In a bimanual variant of the Serial Reaction Time Task (SRT), simultaneous finger movements of the two hands were made in response to randomly ordered pairs of

  1. Reconsidering Innovation

    DEFF Research Database (Denmark)

    Vaaben, Nana Katrine

    Innovation and reforms seem to be on the agenda everywhere, not least in political attempts to reorganize the public sector in ways that are supposed to enable our welfare societies to survive economic turmoil and sinister future prognosis. This paper examines how classical anthropological theories...... and debates about change, myths, and othering can help us rethink theoretical approaches to innovation in organizational studies, and the concern is especially to consider the implications that our “innovation myths” can have for public employees and the valuation their work. The argument in the paper...... is that innovation is better understood as a perspective (a prism) than as a product or a process, and that this perspective tends to “other” people who’s work is not visible as a positive asset in a budget, but may be visible as a positive contribution in people’s lives. The way in which that point is made...

  2. Reconsidering Innovation

    DEFF Research Database (Denmark)

    Vaaben, Nana Katrine

    2014-01-01

    is that innovation is better understood as a perspective (a prism) than as a product or a process, and that this perspective tends to “other” people who’s work is not visible as a positive asset in a budget, but may be visible as a positive contribution in people’s lives. The way in which that point is made......Innovation and reforms seem to be on the agenda everywhere, not least in political attempts to reorganize the public sector in ways that are supposed to enable our welfare societies to survive economic turmoil and sinister future prognosis. This paper examines how classical anthropological theories...... and debates about change, myths, and othering can help us rethink theoretical approaches to innovation in organizational studies, and the concern is especially to consider the implications that our “innovation myths” can have for public employees and the valuation their work. The argument in the paper...

  3. Reconsidering Facebook

    Directory of Open Access Journals (Sweden)

    Hilary Davis

    2011-01-01

    Full Text Available Last year there was a revolt against Facebook. Lots of people were weighing the pros and cons of becoming a Facebook dropout, including librarians. For many of these detractors and potential detractors of Facebook, the disjunct structure of personal and professional identity was no longer holding up under the pressure of Facebook’s urgings to reveal [...

  4. Nemesis reconsidered

    Science.gov (United States)

    Melott, Adrian L.; Bambach, Richard K.

    2010-09-01

    The hypothesis of a companion object (Nemesis) orbiting the Sun was motivated by the claim of a terrestrial extinction periodicity, thought to be mediated by comet showers. The orbit of a distant companion to the Sun is expected to be perturbed by the Galactic tidal field and encounters with passing stars, which will induce variation in the period. We examine the evidence for the previously proposed periodicity, using two modern, greatly improved paleontological data sets of fossil biodiversity. We find that there is a narrow peak at 27 Myr in the cross-spectrum of extinction intensity time series between these independent data sets. This periodicity extends over a time period nearly twice that for which it was originally noted. An excess of extinction events is associated with this periodicity at 99 per cent confidence. In this sense we confirm the originally noted feature in the time series for extinction. However, we find that it displays extremely regular timing for about 0.5 Gyr. The regularity of the timing compared with earlier calculations of orbital perturbation would seem to exclude the Nemesis hypothesis as a causal factor.

  5. Reconsidering Innovation

    DEFF Research Database (Denmark)

    Vaaben, Nana Katrine

    2014-01-01

    Innovation og reformer er på dagsordenen allevegne, ikke mindst i politiske forsøg på at reorganisere den offentlige sektor for at få velfærdssamfundet til at kunne overleve økonomisk tumult og dystre fremtidsprognoser. Dette papir undersøger, hvordan klassiske antropologiske teorier og debatter om...... forandring og myter kan hjælpe os med at genoverveje teoretiske forståelser af innovation i organisatoriske studier. I særlig grad sættes der fokus på de implikationer som vores "innovationsmyte" kan have for offentligt ansatte og værdsættelsen af deres arbejde. Analysens argument er, at innovation ikke skal...

  6. Reconsidering Teamwork

    Science.gov (United States)

    Barker, Dean

    2007-01-01

    Teamwork is often seen as an inseparable part of sport. Other than work done by sport psychologists, however, the topic has received scant attention. The broad aim of this article is to stimulate discussion on the topic. Specifically, I examine how we can think about and "do" teamwork in an alternative way to that presented in current…

  7. 42 CFR 426.520 - Withdrawing an NCD under review or issuing a revised or reconsidered NCD.

    Science.gov (United States)

    2010-10-01

    ... 42 Public Health 3 2010-10-01 2010-10-01 false Withdrawing an NCD under review or issuing a revised or reconsidered NCD. 426.520 Section 426.520 Public Health CENTERS FOR MEDICARE & MEDICAID... DETERMINATIONS AND LOCAL COVERAGE DETERMINATIONS Review of an NCD § 426.520 Withdrawing an NCD under review or...

  8. Reconsidering educational theory and practice from the point of view of emotions

    Directory of Open Access Journals (Sweden)

    Père DARDER

    2009-11-01

    Full Text Available The aim of the work presented is to highlight the new scientific approach to emotional dimensions and their functions for personal and social development, as well as the new theoretical and practical consideration of education that this approach requires. The absence of structured and continuous training of emotions in the current educational system reduces the scope of integral education, which is proposed as an objective. The integration of thought, emotion and action is an essentially human characteristic, and must therefore be the basis of the educational act. The paradigm of emotional intelligence, through the theory of multiple intelligences, the contributions of neuroscience and the cognitive and humanistic tradition, has deep pedagogical implications and is highly important to guide educational renovation. Emphasizing this change, which we consider fundamental for education, it is indispensable to reconsider teacher training.

  9. Reconsidering The Minimum Competency Test Strategy In No Child Left Behind: An Agenda For Reform

    Directory of Open Access Journals (Sweden)

    Danielle Beth Kuper

    2006-01-01

    Full Text Available The minimum competency test (MCT strategy used in the No Child Left Behind Act of 2001 (NCLB requires schools, in return for federal funding, to bring their students up to the level of proficiency (the minimum standard in mathematics and reading/language arts by school year 2013-2014. This strategy involves both students (who have to reach the minimum level of achievement and schools (who suffer the high stakes if students don't achieve the minimum. Reconsidering NCLB's MCT strategy suggests comparing it with other MCTs on the basic issues all MCTs must address: what achievement, what performance standards, and what consequences. Doing so suggests possible reforms to improve NCLB.

  10. The hot (invisible? hand: can time sequence patterns of success/failure in sports be modeled as repeated random independent trials?

    Directory of Open Access Journals (Sweden)

    Gur Yaari

    Full Text Available The long lasting debate initiated by Gilovich, Vallone and Tversky in [Formula: see text] is revisited: does a "hot hand" phenomenon exist in sports? Hereby we come back to one of the cases analyzed by the original study, but with a much larger data set: all free throws taken during five regular seasons ([Formula: see text] of the National Basketball Association (NBA. Evidence supporting the existence of the "hot hand" phenomenon is provided. However, while statistical traces of this phenomenon are observed in the data, an open question still remains: are these non random patterns a result of "success breeds success" and "failure breeds failure" mechanisms or simply "better" and "worse" periods? Although free throws data is not adequate to answer this question in a definite way, we speculate based on it, that the latter is the dominant cause behind the appearance of the "hot hand" phenomenon in the data.

  11. Reconsidering the use of rankings in the valuation of health states: a model for estimating cardinal values from ordinal data

    Directory of Open Access Journals (Sweden)

    Salomon Joshua A

    2003-12-01

    Full Text Available Abstract Background In survey studies on health-state valuations, ordinal ranking exercises often are used as precursors to other elicitation methods such as the time trade-off (TTO or standard gamble, but the ranking data have not been used in deriving cardinal valuations. This study reconsiders the role of ordinal ranks in valuing health and introduces a new approach to estimate interval-scaled valuations based on aggregate ranking data. Methods Analyses were undertaken on data from a previously published general population survey study in the United Kingdom that included rankings and TTO values for hypothetical states described using the EQ-5D classification system. The EQ-5D includes five domains (mobility, self-care, usual activities, pain/discomfort and anxiety/depression with three possible levels on each. Rank data were analysed using a random utility model, operationalized through conditional logit regression. In the statistical model, probabilities of observed rankings were related to the latent utilities of different health states, modeled as a linear function of EQ-5D domain scores, as in previously reported EQ-5D valuation functions. Predicted valuations based on the conditional logit model were compared to observed TTO values for the 42 states in the study and to predictions based on a model estimated directly from the TTO values. Models were evaluated using the intraclass correlation coefficient (ICC between predictions and mean observations, and the root mean squared error of predictions at the individual level. Results Agreement between predicted valuations from the rank model and observed TTO values was very high, with an ICC of 0.97, only marginally lower than for predictions based on the model estimated directly from TTO values (ICC = 0.99. Individual-level errors were also comparable in the two models, with root mean squared errors of 0.503 and 0.496 for the rank-based and TTO-based predictions, respectively. Conclusions

  12. Complete mtDNA sequences of two millipedes suggest a new model for mitochondrial gene rearrangements: Duplication and non-random loss

    Energy Technology Data Exchange (ETDEWEB)

    Lavrov, Dennis V.; Boore, Jeffrey L.; Brown, Wesley M.

    2001-11-08

    We determined the complete mtDNA sequences of the millipedes Narceus annularus and Thyropygus sp. (Arthropoda: Diplopoda) and identified in both genomes all 37 genes typical for metazoan mtDNA. The arrangement of these genes is identical in the two millipedes, but differs from that inferred to be ancestral for arthropods by the location of four genes/gene clusters. This novel gene arrangement is unusual for animal mtDNA, in that genes with opposite transcriptional polarities are clustered in the genome and the two clusters are separated by two non-coding regions. The only exception to this pattern is the gene for cysteine tRNA, which is located in the part of the genome that otherwise contains all genes with the opposite transcriptional polarity. We suggest that a mechanism involving complete mtDNA duplication followed by the loss of genes, predetermined by their transcriptional polarity and location in the genome, could generate this gene arrangement from the one ancestral for arthropods. The proposed mechanism has important implications for phylogenetic inferences that are drawn on the basis of gene arrangement comparisons.

  13. Information Theory of DNA Sequencing

    CERN Document Server

    Motahari, Abolfazl; Tse, David

    2012-01-01

    DNA sequencing is the basic workhorse of modern day biology and medicine. Shotgun sequencing is the dominant technique used: many randomly located short fragments called reads are extracted from the DNA sequence, and these reads are assembled to reconstruct the original sequence. By drawing an analogy between the DNA sequencing problem and the classic communication problem, we define an information theoretic notion of sequencing capacity. This is the maximum number of DNA base pairs that can be resolved reliably per read, and provides a fundamental limit to the performance that can be achieved by any assembly algorithm. We compute the sequencing capacity explicitly for a simple statistical model of the DNA sequence and the read process. Using this framework, we also study the impact of noise in the read process on the sequencing capacity.

  14. Reconsidering Sequential Double Running Suture Removal After Penetrating Keratoplasty: A Prospective Randomized Study Comparing Excimer Laser and Motor Trephination.

    Science.gov (United States)

    Seitz, Berthold; Hager, Tobias; Langenbucher, Achim; Naumann, Gottfried O H

    2017-12-14

    We assessed the impact of sequential double running suture removal on corneal curvature after penetrating keratoplasty (PK), comparing mechanical and nonmechanical excimer laser trephination. PK was performed in 134 patients (mean age 51 ± 18 yrs) using either the excimer laser [excimer, n = 60 (37 keratoconus and 23 Fuchs dystrophy)] or motor trephination [control, n = 74 (44 keratoconus and 30 Fuchs dystrophy)] and a double running cross-stitch suture. Refractometry, Zeiss keratometry, and Tomey corneal topography were performed before removal of the first suture (15.2 ± 4.2 mo) and immediately before and at least 6 weeks after removal of the second suture (21.4 ± 5.6 mo). Keratometry before removal of the first (-1.7 ± 2.3 D vs. -3.1 ± 2.8 D) and second (-2.3 ± 2.6 D vs. -3.8 ± 2.8 D) sutures showed that the change in the corneal base curve was significantly smaller in the excimer group than the control group (P control groups, respectively, resulting in significantly lower astigmatism in the excimer (3.1 ± 2.1 D) group compared with the control group (6.2 ± 2.9 D) with "all-sutures-out" (P vector-corrected astigmatism (Jaffe) was significantly smaller in the excimer group (4.3 ± 3.5 D) than in the control group (6.9 ± 4.5 D; P motor trephination.

  15. a randomized controlled trial.

    African Journals Online (AJOL)

    milk, only an estimated one -fourth of neonates in India were breastfed within ... standard of care in India and mothers are informed about. 6 months of ... weeks postpartum. A random number sequence was generated using a com- puter program. Block randomization was used with a fixed block size of four. Concealment of ...

  16. Neoadjuvant sunitinib for surgically complex advanced renal cell cancer of doubtful resectability: initial experience with downsizing to reconsider cytoreductive surgery.

    Science.gov (United States)

    Bex, Axel; van der Veldt, Astrid A M; Blank, Christian; van den Eertwegh, Alfons J M; Boven, Epie; Horenblas, Simon; Haanen, John

    2009-08-01

    To evaluate neoadjuvant sunitinib in patients with synchronous metastatic renal cell cancer (mRCC) to downsize surgically complex tumours and reconsider cytoreductive surgery. Retrospective analysis of ten consecutive mRCC patients treated with sunitinib in an expanded access program who presented with surgically complex primary tumours or bulky locoregional metastases. Surgery-limiting tumour sites (SLTSs) were defined as primary or retroperitoneal lesions with direct invasion of adjacent organs or encasement of vital structures on imaging. Patients received sunitinib 50 mg/day for 4 weeks on and 2 weeks off to be followed by cytoreductive surgery after downsizing and individual reassessment. Response was measured according to Response Evaluation Criteria in Solid Tumours (RECIST). Six out of ten SLTSs revealed a reduction of tumour size with a median of 14% according to RECIST. None of the ten SLTSs had a partial response (PR), whilst at distant metastatic sites one complete remission and two PRs occurred. Downsizing of SLTSs appeared most prominent in the first 2-4 months, which resulted in reconsidering cytoreductive nephrectomy in three patients. These three tumours invaded the liver on imaging and were reduced by 11, 18 and 20%. In this patient group with mRCC and surgically complex primary tumours or locoregional metastases, downsizing of SLTSs by neoadjuvant sunitinib was limited. Cytoreductive surgery was reconsidered in three patients. Given the overall reduction in tumour burden by sunitinib alone, further investigation to define the role of cytoreductive surgery is warranted.

  17. Reconsidering "inattention" in attention-deficit hyperactivity disorder: implications for neuropsychological assessment and intervention.

    Science.gov (United States)

    Carmichael, Jessica A; Kubas, Hanna A; Carlson, Helen L; Fitzer, Kim R; Wilcox, Gabrielle; Lemay, Jean-François; Bray, Signe; MacMaster, Frank P; Hale, James B

    2015-01-01

    Attention-deficit hyperactivity disorder (ADHD) does not exist. This explicit statement needs elucidation of course given ADHD is a common neurodevelopmental disorder, but it provides the reader with the impetus to reconsider long-held beliefs about this condition and its treatment. Surely, there is a disorder called ADHD from which this thesis is framed, but primary attention and hyperactivity-impulsivity problems are mediated by different albeit interrelated brain systems. Like many neurodevelopmental disorders (e.g., learning disabilities, autism spectrum disorder), the medical and psychological professions have used a single, large inclusive ADHD diagnostic category to represent children with different etiologies for their overt symptoms. Despite neurobiological differences among children diagnosed with ADHD, the clinical position that attention-deficit or primary attention problems are sufficient for ADHD identification undermines clinical practice. This commonly accepted dubious position not only undermines the diagnostic utility of our neuropsychological measures, but it attenuates treatment effects as well. Supported with evidence from our ongoing ADHD research program, this data-based review will support these contentions and provide implications for diagnosis and treatment of children with attention problems.

  18. (Re)considering Foucault for science education research: considerations of truth, power and governance

    Science.gov (United States)

    Bazzul, Jesse; Carter, Lyn

    2017-06-01

    This article is a response to Anna Danielsonn, Maria Berge, and Malena Lidar's paper, "Knowledge and power in the technology classroom: a framework for studying teachers and students in action", and an appeal to science educators of all epistemological orientations to (re)consider the work of Michel Foucault for research in science education. Although this essay does not come close to outlining the importance of Foucault's work for science education, it does present a lesser-known side of Foucault as an anti-polemical, realist, modern philosopher interested in the way objective knowledge is entangled with governance in modernity. This latter point is important for science educators, as it is the intersection of objective knowledge and institutional imperatives that characterizes the field(s) of science education. Considering the lack of engagement with philosophy and social theory in science education, this paper offers one of many possible readings of Foucault (we as authors have also published different readings of Foucault) in order to engage crucial questions related to truth, power, governance, discourse, ethics and education.

  19. Reconsidering the evolution of brain, cognition and behaviour in birds and mammals

    Directory of Open Access Journals (Sweden)

    Romain eWillemet

    2013-07-01

    Full Text Available Despite decades of research, some of the most basic issues concerning the extraordinarily complex brains and behaviour of birds and mammals, such as the factors responsible for the diversity of brain size and composition, are still unclear. This is partly due to a number of conceptual and methodological issues. Determining species and group differences in brain composition requires accounting for the presence of taxon-cerebrotypes and the use of precise statistical methods. The role of allometry in determining brain variables should be revised. In particular, bird and mammalian brains appear to have evolved in response to a variety of selective pressures influencing both brain size and composition. Brain and cognition are indeed meta-variables, made up of the variables that are ecologically relevant and evolutionarily selected. External indicators of species differences in cognition and behaviour are limited by the complexity of these differences. Indeed, behavioural differences between species and individuals are caused by cognitive and affective components. Although intra-species variability forms the basis of species evolution, some of the mechanisms underlying individual differences in brain and behaviour appear to differ from those between species. While many issues have persisted over the years because of a lack of appropriate data or methods to test them; several fallacies, particularly those related to the human brain, reflect scientists’ preconceptions. The theoretical framework on the evolution of brain, cognition and behaviour in birds and mammals should be reconsidered with these biases in mind.

  20. Methodological and ethical aspects of randomized controlled clinical trials in minors with malignant diseases.

    Science.gov (United States)

    Rothenberger, Lillian G; Henschel, Andreas Dirk; Schrey, Dominik; Becker, Andreas; Boos, Joachim

    2011-10-01

    Due to the new European regulations for pediatric medications, future clinical trials will include an increasing number of minors. It is therefore important to reconsider and evaluate recent methodological and ethical aspects of clinical trials in minors. The following questions were investigated: How are randomized controlled clinical trials (RCTs) performed in practice? Do investigators take into consideration biomedical ethical principles, explicated for example by Beauchamp and Childress, when planning and conducting a trial? The study was conducted in a descriptive manner. A systematic, algorithm-guided search focusing on RCTs in minors with malignant diseases was carried out in PubMed. One-thousand-nine-hundred-sixty-two publications from 2001 to 2005 were randomized in sequence. The first 1,000 publications were screened according to a priori defined inclusion criteria. One hundred seventy-five publications met the criteria and were reviewed using the SIGN methodological checklist (2004), the CONSORT Statement (2001, section Methods, items 3-12) and indicators for ethical aspects. Seventeen publications were checked by two raters. Information on randomization and blinding was often equivocal. The publications were mainly rated positive for the criteria of the SIGN checklist, and mostly rated negative for the additional items of the CONSORT Statement. Regarding the ethical principles, only few contributions were found in the publications. Inter-rater reliability was good. In the publications analyzed, we found only limited information concerning methods and reflections on ethical principles of the trials. Improvements are thus necessary and possible. We suggest how such trials and their respective publications can be optimized for these aspects. Copyright © 2011 Wiley-Liss, Inc.

  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 plays an important role in processing the information generated by these methods. Here, we provide a comprehensive overview of the current publicly available sequence assembly programs. We describe the basic principles of computational assembly along with the main concerns, such as repetitive sequences...... 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. Mapping sequences by parts

    Directory of Open Access Journals (Sweden)

    Guziolowski Carito

    2007-09-01

    Full Text Available Abstract Background: We present the N-map method, a pairwise and asymmetrical approach which allows us to compare sequences by taking into account evolutionary events that produce shuffled, reversed or repeated elements. Basically, the optimal N-map of a sequence s over a sequence t is the best way of partitioning the first sequence into N parts and placing them, possibly complementary reversed, over the second sequence in order to maximize the sum of their gapless alignment scores. Results: We introduce an algorithm computing an optimal N-map with time complexity O (|s| × |t| × N using O (|s| × |t| × N memory space. Among all the numbers of parts taken in a reasonable range, we select the value N for which the optimal N-map has the most significant score. To evaluate this significance, we study the empirical distributions of the scores of optimal N-maps and show that they can be approximated by normal distributions with a reasonable accuracy. We test the functionality of the approach over random sequences on which we apply artificial evolutionary events. Practical Application: The method is illustrated with four case studies of pairs of sequences involving non-standard evolutionary events.

  3. Pharmacokinetic and bioequivalence comparison of a single 100-mg dose of cefteram pivoxil powder suspension and tablet formulations: a randomized-sequence, open-label, two-period crossover study in healthy Chinese adult male volunteers.

    Science.gov (United States)

    Zou, Jianjun; Di, Bin; Wu, Chun Yong; Hu, Qin; Li, Jian Hua; Zhu, Yubing; Fan, Hongwei; Xiao, DaWei; Wang, Guang Ji

    2008-04-01

    Cefteram pivoxil (CFTM-PI) is an oral antibiotic available in powder suspension and tablet formulations indicated in China for the treatment of bacterial infections. Although these 2 formulations are marketed in China, published information regarding their pharmacokinetics and bioequivalence in the Chinese population is not available. The aim of this study was to compare the pharmacokinetics and bioequivalence of the powder suspension (test) and tablet (reference) formulations of CFTM-PI 100 mg available in China. This single-dose, randomized-sequence, open-label, 2-period crossover study was performed at the Nanjing First Hospital of Nanjing Medical University. Eligible subjects were healthy male volunteers who were randomly assigned at a 1:1 ratio to receive a single 100-mg dose of the test or reference formulation, followed by a 1-week washout period and administration of the alternate formulation. The study drugs were administered after a 12-hour overnight fast. Plasma was assayed using a high-performance liquid chromatography method. For analysis of pharmacokinetic properties, including C(max), AUC from time 0 (baseline) to 6 hours (AUC(0-6)), and AUC from baseline to infinity (AUC(0-infinity)), blood samples were obtained at intervals over the 6-hour period after study drug administration. The formulations were considered bioequivalent if the log-transformed ratios of C(max) and AUC were within the predetermined equivalence range (80%-125%) as established by the US Food and Drug Administration (FDA). Tolerability was assessed by monitoring vital signs and laboratory tests (hematology, blood biochemistry, hepatic function, and urinalysis), and by questioning subjects about adverse events (AEs). Twenty-four Chinese male subjects (mean [range] age,24.2 [23-32] years;weight,64.3 [58-67] kg; height, 172 [167-185] cm) enrolled; all completed the study. No period or sequence effect was observed. The 90% CIs for the log-transformed ratios of C(max), AUC(0-6;), and

  4. Bioequivalence of two formulations of glucosamine sulfate 500-mg capsules in healthy male Chinese volunteers: an open-label, randomized-sequence, single-dose, fasting, two-way crossover study.

    Science.gov (United States)

    Zhu, YuBing; Zou, JianJun; Xiao, DaWei; Fan, HongWei; Yu, CuiXia; Zhang, JingJing; Yang, Jing; Guo, DaQing

    2009-07-01

    Glucosamine sulfate is used for the treatment of arthrosis, especially osteoarthritis of the knee joint. The available evidence suggests differences in its pharmacokinetics in Chinese subjects compared with non-Chinese subjects. The aim of this study was to compare the pharmacokinetics and relative bioavailability of a test and reference formulation of glucosamine sulfate 500 mg after single oral administration in healthy Chinese volunteers. This open-label, randomized-sequence, single-dose, 2-way crossover study was performed at the First Hospital of Nanjing Medical University, Nanjing, China. Eligible subjects were healthy male volunteers who were randomly assigned at a 1:1 ratio to receive a single 500-mg dose of the test or reference capsule formulation, followed by a 1-week washout period and administration of the alternate formulation. The study drugs were administered after a 12-hour overnight fast. Glucosamine sulfate was assayed using a liquid-chromatography tandem mass spectrometry method. For analysis of pharmacokinetic properties, including C(max), AUC(0-t), and AUC(0-infinity)), blood samples were obtained at intervals over a 14-hour period after study drug administration. The formulations were considered bioequivalent if the log-transformed ratios of C(max) and AUC were within the predetermined equivalence range (70%-143% for C(max) and 80%-125% for AUC) as established by the State Food and Drug Administration (SFDA) of China. Tolerability was assessed by monitoring vital signs and laboratory tests (hematology, blood biochemistry, hepatic function, and urinalysis), and by questioning subjects about adverse events (AEs). Twenty-two healthy male Chinese subjects were enrolled (mean [range] age, 24 [22-26] years; weight, 63.9 [58.5-69.3] kg; height, 172 [167-177] cm); all completed the study. No period or sequence effect was observed. The 90% CIs for the log-transformed ratios of C(max), AUC(0-t), and AUC(0-infinity)) were 93.4 to 127.3, 92.4 to 114

  5. Genome Sequencing

    DEFF Research Database (Denmark)

    Sato, Shusei; Andersen, Stig Uggerhøj

    2014-01-01

    The current Lotus japonicus reference genome sequence is based on a hybrid assembly of Sanger TAC/BAC, Sanger shotgun and Illumina shotgun sequencing data generated from the Miyakojima-MG20 accession. It covers nearly all expressed L. japonicus genes and has been annotated mainly based...... on transcriptional evidence. Analysis of repetitive sequences suggests that they are underrepresented in the reference assembly, reflecting an enrichment of gene-rich regions in the current assembly. Characterization of Lotus natural variation by resequencing of L. japonicus accessions and diploid Lotus species...... is currently ongoing, facilitated by the MG20 reference sequence...

  6. Novel Bacteriocinogenic Lactobacillus plantarum Strains and Their Differentiation by Sequence Analysis of 16S rDNA, 16S-23S and 23S-5S Intergenic Spacer Regions and Randomly Amplified Polymorphic DNA Analysis

    Directory of Open Access Journals (Sweden)

    Morteza Shojaei Moghadam

    2010-01-01

    Full Text Available Six strains of bacteriocinogenic Lactobacillus plantarum (TL1, RG11, RS5, UL4, RG14 and RI11 isolated from Malaysian foods were investigated for their structural bacteriocin genes. A new combination of plantaricin EF and plantaricin W bacteriocin structural genes was successfully amplified from all studied strains, suggesting that they were novel bacteriocin-producing L. plantarum strains. A four-base pair variable region was detected in the short 16S-23S intergenic spacer regions of the studied strains by a comparative analysis with 17 L. plantarum strains deposited in the GenBank, implying they were new genotypes. The studied L. plantarum strains were subsequently differentiated into four groups on the basis of the detected four-base pair variable region of the short 16S-23S intergenic spacer region. Further analysis of the DNA sequence of 23S-5S intergenic spacer region revealed only one type of 23S-5S intergenic spacer region present in the studied strains, indicating it was highly conserved among the studied L. plantarum strains. Three randomly amplified polymorphic DNA experiments using three different combinations of arbitrary primers successfully differentiated the studied L. plantarum strains from each other, confirming they were different strains. In conclusion, the studied L. plantarum strains were shown to be novel bacteriocin producers and high level of strain discrimination could be achieved with a combination of randomly amplified polymorphic DNA analysis and the analysis of the variable region of short 16S-23S intergenic spacer region present in L. plantarum strains.

  7. Transposon facilitated DNA sequencing

    Energy Technology Data Exchange (ETDEWEB)

    Berg, D.E.; Berg, C.M.; Huang, H.V.

    1990-01-01

    The purpose of this research is to investigate and develop methods that exploit the power of bacterial transposable elements for large scale DNA sequencing: Our premise is that the use of transposons to put primer binding sites randomly in target DNAs should provide access to all portions of large DNA fragments, without the inefficiencies of methods involving random subcloning and attendant repetitive sequencing, or of sequential synthesis of many oligonucleotide primers that are used to match systematically along a DNA molecule. Two unrelated bacterial transposons, Tn5 and {gamma}{delta}, are being used because they have both proven useful for molecular analyses, and because they differ sufficiently in mechanism and specificity of transposition to merit parallel development.

  8. What's Next? Judging Sequences of Binary Events

    Science.gov (United States)

    Oskarsson, An T.; Van Boven, Leaf; McClelland, Gary H.; Hastie, Reid

    2009-01-01

    The authors review research on judgments of random and nonrandom sequences involving binary events with a focus on studies documenting gambler's fallacy and hot hand beliefs. The domains of judgment include random devices, births, lotteries, sports performances, stock prices, and others. After discussing existing theories of sequence judgments,…

  9. Scholarship reconsidered: implications for reward and recognition of academic staff in schools of nursing and beyond.

    Science.gov (United States)

    Smith, Kylie M; Crookes, Patrick A; Else, Fabienne; Crookes, Ellie

    2012-03-01

    This paper discusses the issues facing the nursing academic workforce and the development of a project at the University of Wollongong in Australia which attempts to address this problem. The project draws on Boyer's work around 'scholarship reconsidered' to enable new ways of thinking about the nature of 'research' and how the work of a diversifying workforce can be recognized and rewarded within institutions. We conducted a series of interviews with senior university staff to identify key issues around academic promotion processes. Feedback from these interviews, along with extensive internal and external consultation and benchmarking, will be used to redraft promotion documentation that includes discipline-specific performance expectations. Interviews revealed a number of perceived and actual barriers to promotion of academic staff who did not conform to a 'traditional' view of research expectations. It was widely felt that unspoken expectations about research performance were being used to judge applications for promotion, and that this disadvantaged people from practice or professional backgrounds, or people who had heavy administrative or clinical roles. Internal university processes need to reflect the reality of a diversified workforce. Practice and professional disciplines have responsibilities beyond meeting traditional research output measurements. More flexible and transparent expectation guidelines and career development pathways are needed to build holistic schools and faculty and enable maximum staff productivity. By redefining scholarship, schools and faculties are able to meet the multiple demands of the government, the institution, individual staff, students and the profession. Not everyone can do traditional research all the time, and staff involved in other scholarly work should be able to rewarded and promoted. By taking the lead in this issue, nursing as a discipline can set its own agenda, and pave the way for other disciplines. It can also

  10. Reconsidering evidence-based practice in prosthetic rehabilitation: a shared enterprise.

    Science.gov (United States)

    van Twillert, Sacha; Geertzen, Jan; Hemminga, Titia; Postema, Klaas; Lettinga, Ant

    2013-06-01

    A divide is experienced between producers and users of evidence in prosthetic rehabilitation. To discuss the complexity inherent in establishing evidence-based practice in a prosthetic rehabilitation team illustrated by the case of prosthetic prescription for elderly dysvascular transfemoral amputee patients. A qualitative research design was used, in which data from multiple sources was triangulated to extract themes for discussion. This discussion paper draws on empirical material gathered by individual and focus-group interviews with members of a prosthetic rehabilitation team, information on technological advancements presented on websites of orthopaedic industry, guidelines and literature study. A prosthetic rehabilitation team needs to deal with lack of evidence, contradictory results, various classification systems, diverging interests of different stakeholders and many modifying factors, and all of this in a continuous technological changing environment. Integrating research designs with different strengths but not sharing the same biases may help researchers to deal with the multimorbidity and multifaceted disability of the target group. Articulating clinical knowledge, patients' needs and values in a systematic way provides depth, detail, nuance and context for evidence-based practice issues in prosthetic rehabilitation. Reconsidering the relationship between evidence, technology and rehabilitation practice is an imperative shared enterprise for clinicians and researchers. Scientific, clinical and patient-related knowledge are seen as important knowledge practices that should inform and strengthen each other. This discussion paper puts the academic clinical debate on evidence-based practice in prosthetics and orthotics in another light. By demonstrating the complexities surrounding evidence-based practice, it is argued and illustrated how both researchers and clinicians can contribute to optimal patient care in which evidence, technology and

  11. Autonomous Byte Stream Randomizer

    Science.gov (United States)

    Paloulian, George K.; Woo, Simon S.; Chow, Edward T.

    2013-01-01

    Net-centric networking environments are often faced with limited resources and must utilize bandwidth as efficiently as possible. In networking environments that span wide areas, the data transmission has to be efficient without any redundant or exuberant metadata. The Autonomous Byte Stream Randomizer software provides an extra level of security on top of existing data encryption methods. Randomizing the data s byte stream adds an extra layer to existing data protection methods, thus making it harder for an attacker to decrypt protected data. Based on a generated crypto-graphically secure random seed, a random sequence of numbers is used to intelligently and efficiently swap the organization of bytes in data using the unbiased and memory-efficient in-place Fisher-Yates shuffle method. Swapping bytes and reorganizing the crucial structure of the byte data renders the data file unreadable and leaves the data in a deconstructed state. This deconstruction adds an extra level of security requiring the byte stream to be reconstructed with the random seed in order to be readable. Once the data byte stream has been randomized, the software enables the data to be distributed to N nodes in an environment. Each piece of the data in randomized and distributed form is a separate entity unreadable on its own right, but when combined with all N pieces, is able to be reconstructed back to one. Reconstruction requires possession of the key used for randomizing the bytes, leading to the generation of the same cryptographically secure random sequence of numbers used to randomize the data. This software is a cornerstone capability possessing the ability to generate the same cryptographically secure sequence on different machines and time intervals, thus allowing this software to be used more heavily in net-centric environments where data transfer bandwidth is limited.

  12. Bioequivalence and pharmacokinetic comparison of a single 200-mg dose of meclofenoxate hydrochloride capsule and tablet formulations in healthy Chinese adult male volunteers: a randomized sequence, open-label, two-period crossover study.

    Science.gov (United States)

    Zou, Jian-Jun; Ji, Hong-Jian; Wu, Ding-Wei; Yao, Jing; Hu, Qin; Xiao, Da-Wei; Wang, Guang-Ji

    2008-09-01

    Meclofenoxate hydrochloride is a psychostimulant in the nootropic agent group available in capsule and tablet formulations approved for traumatic cataphora, alcoholic poisoning, anoxia neonatorum, and children's enuresis in China. Although these 2 generic formulations are marketed in China, information regarding their pharmacokinetics and bioequivalence in humans has not been published. The aim of this study was to compare the pharmacokinetic properties and bioequivalence of the capsule (test) and tablet (reference) formulations of meclofenoxate hydrochloride 200 mg in healthy Chinese volunteers. This single-dose, randomized-sequence, open-label, 2-period crossover study was performed at the Nanjing First Hospital of Nanjing Medical University, Nanjing, China. Eligible subjects were healthy male volunteers who were randomly assigned at a 1:1 ratio to receive a single 200-mg dose of the test or reference formulation, followed by a 1-week washout period and administration of the alternate formulation. The study drugs were administered after a 12-hour overnight fast. As a prodrug, meclofenoxate is hydrolyzed into 4-chlorophenoxyacetic acid and is not detected in plasma. The active metabolite of meclofenoxate, chlorophenoxyacetic acid, was assayed using a high-performance liquid chromatography method. For analysis of pharmacokinetic properties, including Cmax, AUC0-24, and AUC0-infinity, blood samples were obtained at 0.33, 0.67, 1, 1.5, 2, 2.5, 3, 4, 6, 8, 10, 14, and 24 hours after administration. The formulations were considered bioequivalent if the log-transformed ratios of Cmax and AUC were within the predetermined equivalence range (80%-125%) as established by the US Food and Drug Administration (FDA). Subjects were interviewed concerning the occurrence of adverse events including excitement, insomnia, lassitude, and headache. Tolerability was assessed at baseline (before administration) and at 1, 2, 6, and 12 hours after administration by monitoring vital signs

  13. Influence of Ginkgo biloba extract on the pharmacodynamic effects and pharmacokinetic properties of ticlopidine: an open-label, randomized, two-period, two-treatment, two-sequence, single-dose crossover study in healthy Korean male volunteers.

    Science.gov (United States)

    Kim, Bo-Hyung; Kim, Kyu-Pyo; Lim, Kyoung Soo; Kim, Jung-Ryul; Yoon, Seo Hyun; Cho, Joo-Youn; Lee, Yong-Oh; Lee, Kyung-Hee; Jang, In-Jin; Shin, Sang-Goo; Yu, Kyung-Sang

    2010-02-01

    Ginkgo biloba extract is an herbal medicine used in the treatment of vascular disorders that may be coadministered with antiplatelet agents such as ticlopidine. Regulatory authorities requested evaluation of the pharmacodynamic and pharmacokinetic interactions between these entities, according to the drug-development guidance for fixed-dose combination formulations in Korea. This study was performed to evaluate the potential pharmacodynamic and pharmacokinetic interactions between ticlopidine and Ginkgo biloba extract. An open-label, randomized, 2-period, 2-treatment, 2-sequence, single-dose crossover study was conducted in healthy Korean male volunteers. All volunteers were randomly assigned to a sequence group for the 2 treatments, which consisted of ticlopidine 250 mg alone and ticlopidine 250 mg with Ginkgo biloba extract 80 mg, separated by a 1-week washout period between the treatments. Bleeding time was determined just before dosing and at 5, 12, and 48 hours after dosing. Platelet aggregation was evaluated before dosing and at 4, 8, 26, and 48 hours after dosing. Blood samples (8 mL) from each of the volunteers were collected from an indwelling intravenous cannula inserted into a forearm vein before dosing and at 0.5, 1, 1.5, 2, 2.5, 3, 4, 6, 8, 12, 24, and 48 hours after dosing. Ticlopidine concentrations were determined by a validated method using HPLC and ultraviolet detection. Adverse events were identified using general health-related questions, vital signs, physical examinations, ECGs, and laboratory tests. A total of 24 healthy men participated in the study (mean [SD] age, 24.1 [4.3] years; weight, 66.6 [7.4] kg; height, 174.7 [5.0] cm). The baseline corrected bleeding times were not significantly different between the ticlopidine-alone and ticlopidine/ Ginkgo biloba groups, and changes in platelet aggregation were not significantly different between the groups. Likewise, the pharmacokinetic parameters of ticlopidine were not significantly different

  14. Pharmacokinetic properties and bioequivalence of two formulations of arbidol: an open-label, single-dose, randomized-sequence, two-period crossover study in healthy Chinese male volunteers.

    Science.gov (United States)

    Liu, Ming-Yan; Wang, Shuang; Yao, Wei-Fan; Wu, Hui-zhe; Meng, Sheng-Nan; Wei, Min-Jie

    2009-04-01

    Arbidol is an antiviral drug indicated for the prevention and treatment of all types of influenza infection and some other kinds of acute respiratory infections, specifically against influenza groups A and B, and severe acute respiratory syndrome. It is used to help prevent influenza infection as long as necessary with little risk for influenza mutation rendering it less effective. The aim of this study was to compare the pharmacokinetic properties and tolerability, and to determine bioequivalence, of a newly developed generic dispersible tablet formulation (test) and a branded capsule formulation (reference) of arbidol 200 mg in healthy Chinese fasted male volunteers. This open-label, single-dose, randomized-sequence, 2-period crossover study was conducted in healthy native Chinese male volunteers. Eligible subjects were randomly assigned in a 1:1 ratio to receive a single 200-mg dose of the test or reference formulation, followed by a 1-week washout period and administration of the alternate formulation. The study drugs were administered after a 12-hour overnight fast. After the study drug administration, serial blood samples were collected for 72 hours after administration. Plasma drug concentrations were determined using high-performance liquid chromatography coupled with tandem mass spectrometry. Several pharmacokinetic pararameters, including C(max), T(max), t((1/2)), AUC(0-t), and AUC(0-infinity), were determined from the plasma concentrations of the 2 formulations of arbidol using noncompartmental analysis. The formulations were to be considered bioequivalent if the log-transformed ratios of C(max) and AUC were within the predetermined bioequivalence range of 80% to 125% established by the State Food and Drug Administration (SFDA) of the People's Republic of China. Tolerability was assessed by monitoring vital signs (blood pressure, heart rate, temperature, and electrocardiography), laboratory analysis (hematology, blood biochemistry, hepatic function, and

  15. Relative bioavailability of generic and branded acetylcysteine effervescent tablets: A single-dose, open-label, randomized-sequence, two-period crossover study in fasting healthy Chinese male volunteers.

    Science.gov (United States)

    Liu, Yan-Mei; Liu, Yun; Lu, Chuan; Jia, Jing-Ying; Liu, Gang-Yi; Weng, Li-Ping; Wang, Jia-Yan; Li, Guo-Xiu; Wang, Wei; Li, Shui-Jun; Yu, Chen

    2010-11-01

    Acetylcysteine may be used as a muco- lytic agent for the treatment of chronic bronchitis, chronic obstructive pulmonary disease, and other pulmonary diseases complicated by the production of viscous mucus. However, little is known of its pharmacokinetic properties when given orally in healthy volunteers, particularly in a Chinese Han population. This study was conducted to provide support for the marketing of a generic product in China. The purpose of this study was to compare the pharmacokinetics and relative bioavailability of a generic test formulation and a branded reference formulation of acetylcysteine in fasting healthy Chinese male volunteers. A single-dose, open-label, randomized-sequence, 2-period crossover design with a 7-day washout period between doses was used in this study. Healthy Chinese male nonsmokers aged 18 to 40 years with a body mass index (BMI) of 19 to 25 kg/m(2) were selected. Eligible volunteers were randomly assigned to receive acetylcysteine 600 mg PO as either the test formulation (3 tablets of 200 mg each) or reference formulation (1 tablet of 600 mg) under fasting conditions. A total of 15 serial blood samples were collected over a 24-hour interval, and total plasma acetylcysteine concentrations were analyzed by a validated liquid chromatography-isotopic dilution mass spectrometry method. Pharmacokinetic parameters (C(max), T(max), t(½) AUC(0-t), and AUC(0-∞) were calculated and analyzed statistically. The 2 formulations were considered bioequivalent if the 90% CIs of the log-transformed ratios (test/reference) of C(max) and AUC were within the predetermined bioequivalence ranges (70%-143% for C(max); 80%-125% for AUC), as established by the State Food and Drug Administration of China. Tolerability was determined by vital signs, clinical laboratory tests, 12-lead ECGs, physical examinations, and interviews with the subjects about adverse events (AEs). A total of 24 healthy Chinese Han male volunteers were enrolled in and

  16. Reconsidering the Meaning of Home in the Rehabilitation - Towards a Sustainable Historical Town

    Directory of Open Access Journals (Sweden)

    Qasem Awad, S.

    2011-10-01

    Full Text Available Despite the significant literature about the meaning of home and the scholars’ research concerning the home environment, the concept of home didn’t filter into the rehabilitation process. The conservation theory and the rehabilitation methodology are still concentrating on the material aspects of the built environment and ignoring the immaterial aspects and meanings. In view of that the dwellings are not only artifacts but they are a livable example of the social structure and behavioral patterns. Understanding the dwellers relationship with their dwellings will be helpful in establishing a connection between the rehabilitation of the historical domestic architecture and the concept of home. This requires reconsidering the theoretical frame work of the rehabilitation process so as to be able to recognize the change in the historical house’s spatial structure and order and to link them to the social structure and pattern of use.

    A pesar de la gran cantidad de literatura sobre el significado del hogar y las investigaciones hechas por académicos sobre el ambiente del hogar, el concepto de hogar no se filtró en el proceso de rehabilitación. La teoría de la conservación y la metodología de rehabilitación siguen concentrándose en los aspectos materiales del ambiente construido e ignoran los aspectos inmateriales. Tomando en cuenta que las viviendas no son sólo objetos, sino ejemplos de estructuras sociales, y patrones de conducta, el entendimiento de la relación entre habitantes y sus viviendas será de utilidad para establecer una conexión entre la rehabilitación de la arquitectura doméstica histórica y el concepto del hogar. Para ello es necesario reconsiderar el marco de trabajo teórico del proceso de rehabilitación con el fin de ser capaz de reconocer el cambio en la estructura espacial del hogar histórico y el orden, y vincularlos a la estructura social.

  17. Randomization tests

    CERN Document Server

    Edgington, Eugene

    2007-01-01

    Statistical Tests That Do Not Require Random Sampling Randomization Tests Numerical Examples Randomization Tests and Nonrandom Samples The Prevalence of Nonrandom Samples in Experiments The Irrelevance of Random Samples for the Typical Experiment Generalizing from Nonrandom Samples Intelligibility Respect for the Validity of Randomization Tests Versatility Practicality Precursors of Randomization Tests Other Applications of Permutation Tests Questions and Exercises Notes References Randomized Experiments Unique Benefits of Experiments Experimentation without Mani

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

    Energy Technology Data Exchange (ETDEWEB)

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

    2007-02-21

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

  19. Evaluating Letrozole and Tamoxifen Alone and in Sequence for Postmenopausal Women with Steroid Hormone Receptor-Positive Breast Cancer: the BIG 1-98 Randomized Clinical Trial at 8.1 years Median Follow-Up

    Science.gov (United States)

    Regan, Meredith M.; Neven, Patrick; Giobbie-Hurder, Anita; Goldhirsch, Aron; Ejlertsen, Bent; Mauriac, Louis; Forbes, John F.; Smith, Ian; Láng, István; Wardley, Andrew; Rabaglio, Manuela; Price, Karen N.; Gelber, Richard D.; Coates, Alan S.; Thürlimann, Beat

    2011-01-01

    clinicaltrials.gov NCT00004205. Findings At a median follow-up of 8.7 years from randomization (range 0–12.4), letrozole monotherapy is significantly better than tamoxifen, whether using IPCW or intention-to-treat (ITT) analysis [IPCW: DFS HR 0.82 (95% CI 0.74–0.92), OS HR 0.79 (0.69–0.900, DRFI HR 0.79 (0.68–0.92), BCFI HR 0.80 (0.70–0.92); ITT: DFS HR 0.86 (0.78–0.96), OS HR 0.87 (0.77–0.999), DRFI HR 0.86 (0.74–0.998), BCFI HR 0.86 (0.76–0.98)]. At a median follow-up of 8.0 years from randomization (range 0–11.2), there were no statistically significant differences in any of the four endpoints for either sequence compared with letrozole monotherapy. Eight-year ITT estimates [each with SE ≤ 1.1%] for letrozole monotherapy, letrozole followed by tamoxifen, and tamoxifen followed by letrozole were 78.6%, 77.8%, 77.3% for DFS; 87.5%, 87.7%, 85.9% for OS; 89.9%, 88.7%, 88.1% for DRFI; and 86.1%, 85.3%, 84.3% for BCFI. Interpretation For postmenopausal women with endocrine-responsive early breast cancer, a reduction in breast cancer recurrence and mortality is obtained by letrozole monotherapy when compared to tamoxifen. Sequential treatments involving tamoxifen and letrozole do not improve outcome compared with letrozole monotherapy, but may represent useful strategies considering individual patient’s risk of recurrence and treatment tolerability: more thromboembolic events, vaginal bleeding, hot flushes and night sweats with tamoxifen, while more vaginal dryness, bone fractures, osteoporosis, arthralgia/myalgia, and higher grade cardiac events with letrozole. Funding Novartis, United States National Cancer Institute, International Breast Cancer Study Group. PMID:22018631

  20. Pseudo-random number generator based on asymptotic deterministic randomness

    Energy Technology Data Exchange (ETDEWEB)

    Wang Kai [Department of Radio Engineering, Southeast University, Nanjing (China)], E-mail: kaiwang@seu.edu.cn; Pei Wenjiang; Xia Haishan [Department of Radio Engineering, Southeast University, Nanjing (China); Cheung Yiuming [Department of Computer Science, Hong Kong Baptist University, Hong Kong (China)

    2008-06-09

    A novel approach to generate the pseudorandom-bit sequence from the asymptotic deterministic randomness system is proposed in this Letter. We study the characteristic of multi-value correspondence of the asymptotic deterministic randomness constructed by the piecewise linear map and the noninvertible nonlinearity transform, and then give the discretized systems in the finite digitized state space. The statistic characteristics of the asymptotic deterministic randomness are investigated numerically, such as stationary probability density function and random-like behavior. Furthermore, we analyze the dynamics of the symbolic sequence. Both theoretical and experimental results show that the symbolic sequence of the asymptotic deterministic randomness possesses very good cryptographic properties, which improve the security of chaos based PRBGs and increase the resistance against entropy attacks and symbolic dynamics attacks.

  1. Main: Sequences [KOME

    Lifescience Database Archive (English)

    Full Text Available Sequences Nucleotide Sequence Nucleotide sequence of full length cDNA (trimmed sequence) kome_ine_full_se...quence_db.fasta.zip kome_ine_full_sequence_db.zip kome_ine_full_sequence_db ...

  2. Single-dose bioequivalence assessment of two formulations of polysaccharide iron complex capsules in healthy adult male Chinese volunteers: A sequence-randomized, double-blind, two-way crossover study.

    Science.gov (United States)

    Zhang, Yuan-Yuan; Liu, Jun-Hong; Su, Feng; Lui, Ying-Tao; Li, Jun-Feng

    2009-04-01

    Iron deficiency anemia (IDA) is a common nutritional disease worldwide. Iron supplementation is an efficient method for treating patients with IDA. Polysaccharide iron complex is an oral iron supplement that is associated with generally good tolerability and good bioavailability. The aim of this study was to evaluate the bioequivalence of 2 branded formulations of polysaccharide iron complex in healthy adult male Chinese volunteers by determining the pharmacokinetic parameters after single-dose oral admi ni strati on. This sequence-randomized, double-blind, 2-way crossover study was carried out in the Affiliated Hospital, Institute of Medical Sciences of Qingdao University, Qingdao, China. Healthy adult male Chinese volunteers were enrolled and evenly randomized to receive 1 of 2 formulations on day 1. Subjects received an oral dose of 150 mg (1 capsule) of polysaccharide iron complex with 150 mL of warm water in the morning. Capsules were of similar size, shape, and color to ensure blinding. Four hours after administration, the subjects were given standardized meals. After a 1-week washout period, the subjects were crossed over to receive the other formulation in a similar manner. The serum iron concentration 12 hours after study drug administration was determined using atomic-absorption spectrometry. The pharmacokinetic parameters Cmax, Tmax, AUC0-t, and AUC0-∞ were obtained and analyzed using the Schuir mann 2 one-sided t test. The 2 formulations were considered bioequi valent if the test/reference ratios of Cmax, AUC0-t, and their 90% CIs were within the range of 70% to 143% for Cmax and within 80% to 125% for AUC0-t. Tolerability was monitored by inquiring whether the subjects had experienced adverse events (AEs), with a focus on gastrointestinal AEs, during the clinic visits during the 24-hour period after drag administration and subsequently via telephone throughout the study. Thirty adult male Chinese volunteers were assessed for inclusion. Twenty healthy

  3. Pharmacokinetics and bioavailability comparison of generic and branded citalopram 20 mg tablets: an open-label, randomized-sequence, two-period crossover study in healthy Chinese CYP2C19 extensive metabolizers.

    Science.gov (United States)

    Jiang, Tao; Rong, Zhengxing; Xu, Yiping; Chen, Bing; Xie, Yifan; Chen, Congying; Lu, Yang; Shen, Yifeng; Li, Huafang; Sun, Jing; Chen, Hongzhuan

    2013-01-01

    Citalopram is a selective serotonin reuptake inhibitor (SSRI) mainly prescribed to treat major depression. The aim of this study was to compare the pharmacokinetic characteristics of a new and a branded citalopram 20 mg formulation to support the marketing authorization of the test formulation in China. A single-dose, open-label, randomized-sequence, two-period crossover design was used in this study. Healthy Chinese male cytochrome P450 (CYP) 2C19 extensive metabolizers, aged 18-40 years, were eligible to participate. CYP2C19 poor metabolizers were excluded, based on genotyping of genomic DNA from blood samples. Twenty-four subjects were randomly assigned to receive the test formulation followed by the reference formulation, and then vice versa. A 2-week washout occurred between study periods. Blood samples were collected for up to 144 h post-dose. Quantification was carried out using a validated high-performance liquid chromatography-tandem mass spectrometry (HPLC-MS/MS) method. Pharmacokinetic parameters were calculated and analysed statistically. The two formulations were considered pharmacokinetically equivalent if the 90 % confidence intervals (CIs) of the log-transformed ratios (test/reference) of the maximum plasma concentration (C(max)), area under the plasma concentration-time curve from time zero to the last measurable concentration (AUC(last)), and area under the plasma concentration-time curve from time zero to infinity (AUC(∞)) were within the predetermined acceptance range (70-143 % for C(max); 80-125 % for AUC(last) and AUC(∞)) according to China State Food and Drug Administration bioequivalence guidelines. Tolerability was monitored by clinical assessment, vital signs, laboratory analysis and interviews with participants about adverse events. A total of 24 participants, with a mean (SD) age of 26 (3) years (range 22-32 years), body weight of 65.2 (5.0) kg (range 53-73 kg), and height of 172.7 (4.9) cm (range 159-182 cm), were enrolled in this

  4. Comparisons of the pharmacokinetics and tolerability of fixed-dose combinations of amlodipine besylate/losartan and amlodipine camsylate/losartan in healthy subjects: a randomized, open-label, single-dose, two-period, two-sequence crossover study.

    Science.gov (United States)

    Choi, YoonJung; Lee, SeungHwan; Cho, Sang-Min; Kang, Won-Ho; Nam, Kyu-Yeol; Jang, In-Jin; Yu, Kyung-Sang

    2016-01-01

    A fixed-dose combination (FDC) of amlodipine and losartan has been used to reduce blood pressure in patients whose hypertension is not sufficiently controlled with either drug alone. The aim of this study was to evaluate the pharmacokinetic (PK) characteristics and tolerability of an FDC of 6.94 mg amlodipine besylate (5 mg as amlodipine)/50 mg losartan potassium compared to an FDC of 5 mg amlodipine camsylate/50 mg losartan potassium in healthy subjects. A randomized, open-label, single-dose, two-period, two-sequence crossover study was conducted on 46 healthy male subjects. Blood concentrations were measured by liquid chromatography-tandem mass spectrometry. Blood samples were collected up to 144 hours post dose for each period. PK parameters were calculated in each treatment group using a noncompartmental method. The 90% confidence intervals (CIs) of the geometric mean ratios of the two treatments for the maximum plasma concentration (Cmax) and the area under the concentration curve from time zero to the last quantifiable time point (AUC0-t) were estimated. Tolerability assessments were performed for all subjects who received the drug at least once. The PK profiles of the two treatments were similar. For amlodipine, the geometric mean ratios (90% CIs) of amlodipine besylate to amlodipine camsylate for the Cmax and AUC0-t were 0.98 (0.94-1.01) and 0.97 (0.93-1.01), respectively. The corresponding values for losartan were 0.91 (0.81-1.02) and 1.05 (0.98-1.12), respectively. The incidence of adverse events was not significantly different between the two treatments, and both were well tolerated. An FDC of 6.94 mg amlodipine besylate (5 mg as amlodipine)/50 mg losartan potassium produced similar results to an FDC of 5 mg amlodipine camsylate/50 mg losartan potassium treatment with respect to the PK parameters of amlodipine and losartan based on Cmax and AUC0-t values. The amlodipine besylate/losartan potassium combination was well tolerated by healthy male subjects.

  5. 49 CFR 1503.659 - Petition to reconsider or modify a final decision and order of the TSA decision maker on appeal.

    Science.gov (United States)

    2010-10-01

    ... and order of the TSA decision maker on appeal. 1503.659 Section 1503.659 Transportation Other... Practice in TSA Civil Penalty Actions § 1503.659 Petition to reconsider or modify a final decision and order of the TSA decision maker on appeal. (a) General. Any party may petition the TSA decision maker to...

  6. Chunking in task sequences modulates task inhibition.

    Science.gov (United States)

    Koch, Iring; Philipp, Andrea M; Gade, Miriam

    2006-04-01

    In a study of the formation of representations of task sequences and its influence on task inhibition, participants first performed tasks in a predictable sequence (e.g., ABACBC) and then performed the tasks in a random sequence. Half of the participants were explicitly instructed about the predictable sequence, whereas the other participants did not receive these instructions. Task-sequence learning was inferred from shorter reaction times (RTs) in predictable relative to random sequences. Persisting inhibition of competing tasks was indicated by increased RTs in n- 2 task repetitions (e.g., ABA) compared with n- 2 nonrepetitions (e.g., CBA). The results show task-sequence learning for both groups. However, task inhibition was reduced in predictable relative to random sequences among instructed-learning participants who formed an explicit representation of the task sequence, whereas sequence learning and task inhibition were independent in the noninstructed group. We hypothesize that the explicit instructions led to chunking of the task sequence, and that n- 2 repetitions served as chunk points (ABA-CBC), so that within-chunk facilitation modulated the inhibition effect.

  7. Pharmacokinetics and bioequivalence evaluation of two different atorvastatin calcium 10-mg tablets: A single-dose, randomized-sequence, open-label, two-period crossover study in healthy fasted Chinese adult males.

    Science.gov (United States)

    Liu, Yan-Mei; Pu, Hua-Hua; Liu, Gang-Yi; Jia, Jing-Ying; Weng, Li-Ping; Xu, Rong-Jing; Li, Guo-Xiu; Wang, Wei; Zhang, Meng-Qi; Lu, Chuan; Yu, Chen

    2010-07-01

    Atorvastatin calcium is a 3-hydroxy-3-methylglutaryl-coenzyme A reductase inhibitor indicated for the prevention of cardiovascular disease and for the treatment of dyslipidemia. Information on the pharmacokinetics of atorvastatin in a Chinese population is lacking, and regulatory requirements necessitate a bioequivalence study for the marketing of a generic product in China. The aim of the present study was to assess the pharmacokinetics and bioequivalence of a test and branded reference formulation of atorvastatin calcium 10-mg tablets in healthy fasted Chinese male volunteers. This was a single-dose, randomized-sequence, open-label, 2-period crossover study with a 2-week washout period between doses. Healthy Chinese males were randomly assigned to receive 20 mg of either the test or reference formulation, and 13 blood samples were obtained over a 48-hour interval. Plasma concentrations of parent atorvastatin and ortho-hydroxy-atorvastatin (primary active metabolite) were simultaneously determined using a validated liquid chromatography-isotopic dilution mass spectrometry method. Pharmacokinetic parameters, including C(max), T(max), t((1/2)), AUC(0-t), and AUC(0-infinity)), were calculated. The 2 formulations were to be considered bioequivalent if 90% CIs for the log transformed ratios of AUC and C(max) of atorvastatin were within the predetermined bioequivalence range (0.80-1.25 for AUC and 0.70-1.43 for C(max)) as established by the State Food and Drug Administration of China. Tolerability was evaluated throughout the study by vital signs monitoring, physical examinations, 12-lead ECGs, and subject interviews on adverse events (AEs). A total of 66 subjects were assessed for inclusion; 20 were excluded prior to study initiation. Of the 46 healthy subjects (mean [SD] age, 24.1 [2.5] years; height, 170.8 [5.1] cm; weight, 64.6 [6.4] kg; body mass index (BMI), 22.1 [1.7] kg/m(2)) who completed the study, 45 subjects (mean [SD] age, 24.1 [2.5] years; height, 171.1 [4

  8. Pharmacokinetic properties and bioequivalence of two compound formulations of 1500 mg ampicillin (1167 mg)/probenecid (333 mg): a randomized-sequence, single-dose, open-label, two-period crossover study in healthy Chinese male volunteers.

    Science.gov (United States)

    Wu, Huizhe; Liu, Mingyan; Wang, Shuang; Feng, Wanyu; Yao, Weifan; Zhao, Haishan; Wei, Minjie

    2010-03-01

    Ampicillin/probenecid is an antimicrobial formulation indicated for the treatment of respiratory, urinary tract, and gastrointestinal infections. Ampicillin sodium is the active antimicrobial ingredient that can act on the phase of bacterial breeding and inhibit the biosynthesis of bacterial mucopeptide in the cell wall. Probenecid acts synergistically by competitively inhibiting an organic anion transporter in renal tubules, increasing the plasma concentrations, and thus extending the plasma elimination t(1/2). The aim of this study was to assess and compare the pharmacokinetic (PK) properties, bioavailability, and bioequivalence of a newly developed dispersible tablet formulation (test) of ampicillin/ probenecid with those of an established branded capsule formulation (reference) in healthy Chinese male volunteers. A randomized-sequence, single-dose, open-label, 2-period crossover study was conducted in fasted healthy Chinese male volunteers. Eligible participants were randomly assigned in a 1:1 ratio to receive 6 dispersible tablets (test) or branded capsules (reference) (1500 mg total; 250 mg each containing ampicillin 194.5 mg and probenecid 55.5 mg), followed by a 7-day washout period and administration of the alternate formulation. Plasma samples were collected over a 24-hour period following administration and analyzed for ampicillin and probenecid content by HPLC. PK parameters such as C(max), AUC(0-t), and AUC(0-infinity) were also determined. The formulations were considered bioequivalent if the geometric mean ratios of the log-transformed C(max) and AUC values were within the equivalence range (80%-125%) predetermined by the State Food and Drug Administration (SFDA) of the People's Republic of China. Tolerability was based on the observation of adverse events (AEs), monitoring of vital signs (blood pressure, heart rate, temperature, electrocardiography) and laboratory tests (hematology, blood biochemistry, hepatic function, urinalysis), and subject

  9. Disclosure of individual genetic data to research participants: the debate reconsidered

    NARCIS (Netherlands)

    Bredenoord, A.L.; Kroes, H.Y.; Cuppen, E.; Parker, M.; van Delden, J.J.M.

    2010-01-01

    Despite extensive debate, there is no consensus on whether individual genetic data should be disclosed to research participants. The emergence of whole-genome sequencing methods is increasingly generating unequalled amounts of genetic data, making the need for a clear feedback policy even more

  10. Comparisons of the pharmacokinetics and tolerability of fixed-dose combinations of amlodipine besylate/losartan and amlodipine camsylate/losartan in healthy subjects: a randomized, open-label, single-dose, two-period, two-sequence crossover study

    Directory of Open Access Journals (Sweden)

    Choi Y

    2016-09-01

    Full Text Available YoonJung Choi,1 SeungHwan Lee,2 Sang-Min Cho,3 Won-Ho Kang,3 Kyu-Yeol Nam,4 In-Jin Jang,1 Kyung-Sang Yu1 1Department of Clinical Pharmacology and Therapeutics, Seoul National University College of Medicine, 2Clinical Trials Center, Seoul National University Hospital, 3Research Institute, 4Global R&D, Korea United Pharm Inc., Seoul, Republic of Korea Background: A fixed-dose combination (FDC of amlodipine and losartan has been used to reduce blood pressure in patients whose hypertension is not sufficiently controlled with either drug alone. The aim of this study was to evaluate the pharmacokinetic (PK characteristics and tolerability of an FDC of 6.94 mg amlodipine besylate (5 mg as amlodipine/50 mg losartan potassium compared to an FDC of 5 mg amlodipine camsylate/50 mg losartan potassium in healthy subjects. Subjects and methods: A randomized, open-label, single-dose, two-period, two-sequence crossover study was conducted on 46 healthy male subjects. Blood concentrations were measured by liquid chromatography–tandem mass spectrometry. Blood samples were collected up to 144 hours post dose for each period. PK parameters were calculated in each treatment group using a noncompartmental method. The 90% confidence intervals (CIs of the geometric mean ratios of the two treatments for the maximum plasma concentration (Cmax and the area under the concentration curve from time zero to the last quantifiable time point (AUC0–t were estimated. Tolerability assessments were performed for all subjects who received the drug at least once. Results: The PK profiles of the two treatments were similar. For amlodipine, the geometric mean ratios (90% CIs of amlodipine besylate to amlodipine camsylate for the Cmax and AUC0–t were 0.98 (0.94-1.01 and 0.97 (0.93-1.01, respectively. The corresponding values for losartan were 0.91 (0.81-1.02 and 1.05 (0.98-1.12, respectively. The incidence of adverse events was not significantly different between the two

  11. QUASI-RANDOM TESTING OF COMPUTER SYSTEMS

    Directory of Open Access Journals (Sweden)

    S. V. Yarmolik

    2013-01-01

    Full Text Available Various modified random testing approaches have been proposed for computer system testing in the black box environment. Their effectiveness has been evaluated on the typical failure patterns by employing three measures, namely, P-measure, E-measure and F-measure. A quasi-random testing, being a modified version of the random testing, has been proposed and analyzed. The quasi-random Sobol sequences and modified Sobol sequences are used as the test patterns. Some new methods for Sobol sequence generation have been proposed and analyzed.

  12. Bioequivalence and pharmacokinetic comparison of two mycophenolate mofetil formulations in healthy Chinese male volunteers: an open-label, randomized-sequence, single-dose, two-way crossover study.

    Science.gov (United States)

    Zhang, Qian; Tao, Yifu; Zhu, Yubing; Zhu, Dingchun

    2010-01-01

    Mycophenolate mofetil (MMF) is an ester prodrug of mycophenolic acid (MPA), so clinical studies measure the circulating plasma MPA concentration instead of MMF. MPA is extensively glucuronidated by several uridine diphosphate glycosyltransferases into an inactive 7-O-glucuronide and a pharmacologically active acylglucuronide. Considering the effect of racial differences and genetic factors on the pharmacokinetic (PK) properties of drugs, it is necessary to study them in Chinese populations. The aim of this study was to compare the clinical bioequivalence and PK properties of a test (dispersible tablets) and reference (capsules) formulation of MMF 1.0 g in healthy Chinese volunteers. We also established a validated HPLC method for the determination and quantification of MPA in human plasma. The study was required to obtain Chinese regulatory approval for the test formulation. This open-label, randomized-sequence, single-dose, 2-way crossover study was conducted at the First Hospital of Nanjing Medical University, Nanjing, China. Eligible subjects were healthy male volunteers who were randomly assigned at a 1:1 ratio to receive a single 1.0-g dose of the test or reference formulation, followed by a 1-week washout period and administration of the alternate formulation. The plasma concentration of MPA, which is the active metabolite of MMF, was determined using a validated HPLC method. For analysis of PK properties, blood samples were collected at 0, 10, 20, 30, and 45 minutes, and 1, 1.5, 3, 5, 8, 11, 18, 36, and 48 hour(s). The PK parameters, including C(max), T(max), t((1/2)), AUC(0-48), and AUC(0-infinity), were determined from the plasma concentrations of the 2 formulations by noncompartmental analysis. Tolerability was assessed at baseline (be- fore administration) and at 30 minutes and 1, 5, 18, and 48 hours after administration by monitoring vital signs. Laboratory tests (hematology, blood biochemistry, hepatic function, and urinalysis) were performed for the

  13. Blocked Randomization with Randomly Selected Block Sizes

    Directory of Open Access Journals (Sweden)

    Jimmy Efird

    2010-12-01

    Full Text Available When planning a randomized clinical trial, careful consideration must be given to how participants are selected for various arms of a study. Selection and accidental bias may occur when participants are not assigned to study groups with equal probability. A simple random allocation scheme is a process by which each participant has equal likelihood of being assigned to treatment versus referent groups. However, by chance an unequal number of individuals may be assigned to each arm of the study and thus decrease the power to detect statistically significant differences between groups. Block randomization is a commonly used technique in clinical trial design to reduce bias and achieve balance in the allocation of participants to treatment arms, especially when the sample size is small. This method increases the probability that each arm will contain an equal number of individuals by sequencing participant assignments by block. Yet still, the allocation process may be predictable, for example, when the investigator is not blind and the block size is fixed. This paper provides an overview of blocked randomization and illustrates how to avoid selection bias by using random block sizes.

  14. Blocked randomization with randomly selected block sizes.

    Science.gov (United States)

    Efird, Jimmy

    2011-01-01

    When planning a randomized clinical trial, careful consideration must be given to how participants are selected for various arms of a study. Selection and accidental bias may occur when participants are not assigned to study groups with equal probability. A simple random allocation scheme is a process by which each participant has equal likelihood of being assigned to treatment versus referent groups. However, by chance an unequal number of individuals may be assigned to each arm of the study and thus decrease the power to detect statistically significant differences between groups. Block randomization is a commonly used technique in clinical trial design to reduce bias and achieve balance in the allocation of participants to treatment arms, especially when the sample size is small. This method increases the probability that each arm will contain an equal number of individuals by sequencing participant assignments by block. Yet still, the allocation process may be predictable, for example, when the investigator is not blind and the block size is fixed. This paper provides an overview of blocked randomization and illustrates how to avoid selection bias by using random block sizes.

  15. IDENTIFICATION OF AVIAN-SPECIFIC FECAL METAGENOMIC SEQUENCES USING GENOME FRAGMENT ENRICHMENTS

    Science.gov (United States)

    Sequence analysis of microbial genomes has provided biologists the opportunity to compare genetic differences between closely related microorganisms. While random sequencing has also been used to study natural microbial communities, metagenomic comparisons via sequencing analysis...

  16. Reconsidering great ape imitation and pantomime. Comment on "Towards a Computational Comparative Neuroprimatology: framing the language-ready brain" by Michael A. Arbib

    Science.gov (United States)

    Russon, Anne E.

    2016-03-01

    Like previous commentators, I see Arbib's reconstruction of the mirror neuron system's contribution to language evolution [1] as valuable but in need of revision [2,3]. My concerns focus on his proposed behavioral pathway to language - complex imitation to pantomime to protosign - as it concerns great apes. Arbib portrays these abilities as unique to the human lineage, despite evidence that great apes are capable of all three. I suggest great ape findings worth reconsidering.

  17. Disclosure of individual genetic data to research participants: the debate reconsidered.

    Science.gov (United States)

    Bredenoord, Annelien L; Kroes, Hester Y; Cuppen, Edwin; Parker, Michael; van Delden, Johannes J M

    2011-02-01

    Despite extensive debate, there is no consensus on whether individual genetic data should be disclosed to research participants. The emergence of whole-genome sequencing methods is increasingly generating unequalled amounts of genetic data, making the need for a clear feedback policy even more urgent. In this debate two positions can be broadly discerned: a restrictive disclosure policy ('no feedback except life-saving data') and an intermediate policy of qualified disclosure ('feedback if the results meet certain conditions'). We explain both positions and present the principal underlying arguments. We suggest that the debate should no longer address whether genetic research results should be returned, but instead how best to make an appropriate selection and how to strike a balance between the possible benefits of disclosure and the harms of unduly hindering biomedical research. Copyright © 2010 Elsevier Ltd. All rights reserved.

  18. On Beyond Lidocaine: Reconsidering Local Anesthetics in Tumescent Liposuction-A Critical Review.

    Science.gov (United States)

    Hsia, Henry C

    2016-02-01

    The use of tumescent solution in liposuction is now considered standard of care; however, much debate still exists regarding its ideal components, especially surrounding the inclusion of local anesthetics. This article reviews the discussion regarding the use of local anesthetics in tumescent liposuction and how it may evolve in the future. The need for local anesthetic additives in tumescent liposuction has been questioned, and the use of longer-acting agents discouraged; however, increasing number of reports in recent years have described the increasingly widespread use of tumescent anesthesia where a wetting solution is infiltrated to achieve anesthesia in an operative field for procedures other than liposuction. More high-level evidence, such as randomized controlled clinical trials, will be required; however, it should be possible to develop a useful standardized algorithm that can guide surgeons to optimize patient safety as well as patient experience.

  19. Locomotor sequence learning in visually guided walking

    DEFF Research Database (Denmark)

    Choi, Julia T; Jensen, Peter; Nielsen, Jens Bo

    2016-01-01

    walking. In addition, we determined how age (i.e., healthy young adults vs. children) and biomechanical factors (i.e., walking speed) affected the rate and magnitude of locomotor sequence learning. The results showed that healthy young adults (age 24 ± 5 years, N = 20) could learn a specific sequence...... of step lengths over 300 training steps. Younger children (age 6-10 years, N = 8) have lower baseline performance, but their magnitude and rate of sequence learning was the same compared to older children (11-16 years, N = 10) and healthy adults. In addition, learning capacity may be more limited...... to modify step length from one trial to the next. Our sequence learning paradigm is derived from the serial reaction-time (SRT) task that has been used in upper limb studies. Both random and ordered sequences of step lengths were used to measure sequence-specific and sequence non-specific learning during...

  20. Reconsidering plant memory: Intersections between stress recovery, RNA turnover, and epigenetics.

    Science.gov (United States)

    Crisp, Peter A; Ganguly, Diep; Eichten, Steven R; Borevitz, Justin O; Pogson, Barry J

    2016-02-01

    Plants grow in dynamic environments where they can be exposed to a multitude of stressful factors, all of which affect their development, yield, and, ultimately, reproductive success. Plants are adept at rapidly acclimating to stressful conditions and are able to further fortify their defenses by retaining memories of stress to enable stronger or more rapid responses should an environmental perturbation recur. Indeed, one mechanism that is often evoked regarding environmental memories is epigenetics. Yet, there are relatively few examples of such memories; neither is there a clear understanding of their duration, considering the plethora of stresses in nature. We propose that this field would benefit from investigations into the processes and mechanisms enabling recovery from stress. An understanding of stress recovery could provide fresh insights into when, how, and why environmental memories are created and regulated. Stress memories may be maladaptive, hindering recovery and affecting development and potential yield. In some circumstances, it may be advantageous for plants to learn to forget. Accordingly, the recovery process entails a balancing act between resetting and memory formation. During recovery, RNA metabolism, posttranscriptional gene silencing, and RNA-directed DNA methylation have the potential to play key roles in resetting the epigenome and transcriptome and in altering memory. Exploration of this emerging area of research is becoming ever more tractable with advances in genomics, phenomics, and high-throughput sequencing methodology that will enable unprecedented profiling of high-resolution stress recovery time series experiments and sampling of large natural populations.

  1. A measurement of disorder in binary sequences

    Science.gov (United States)

    Gong, Longyan; Wang, Haihong; Cheng, Weiwen; Zhao, Shengmei

    2015-03-01

    We propose a complex quantity, AL, to characterize the degree of disorder of L-length binary symbolic sequences. As examples, we respectively apply it to typical random and deterministic sequences. One kind of random sequences is generated from a periodic binary sequence and the other is generated from the logistic map. The deterministic sequences are the Fibonacci and Thue-Morse sequences. In these analyzed sequences, we find that the modulus of AL, denoted by |AL | , is a (statistically) equivalent quantity to the Boltzmann entropy, the metric entropy, the conditional block entropy and/or other quantities, so it is a useful quantitative measure of disorder. It can be as a fruitful index to discern which sequence is more disordered. Moreover, there is one and only one value of |AL | for the overall disorder characteristics. It needs extremely low computational costs. It can be easily experimentally realized. From all these mentioned, we believe that the proposed measure of disorder is a valuable complement to existing ones in symbolic sequences.

  2. Main: Sequences [KOME

    Lifescience Database Archive (English)

    Full Text Available Sequences Amino Acid Sequence Amino Acid sequence of full length cDNA (Longest ORF) kome_ine_full_se...quence_amino_db.fasta.zip kome_ine_full_sequence_amino_db.zip kome_ine_full_sequence_amino_db ...

  3. The sequence of sequencers: The history of sequencing DNA

    Science.gov (United States)

    Heather, James M.; Chain, Benjamin

    2016-01-01

    Determining the order of nucleic acid residues in biological samples is an integral component of a wide variety of research applications. Over the last fifty years large numbers of researchers have applied themselves to the production of techniques and technologies to facilitate this feat, sequencing DNA and RNA molecules. This time-scale has witnessed tremendous changes, moving from sequencing short oligonucleotides to millions of bases, from struggling towards the deduction of the coding sequence of a single gene to rapid and widely available whole genome sequencing. This article traverses those years, iterating through the different generations of sequencing technology, highlighting some of the key discoveries, researchers, and sequences along the way. PMID:26554401

  4. Are we operating too late? Mortality Analysis and Stochastic Simulation of Costs Associated with Bariatric Surgery: Reconsidering the BMI Threshold.

    Science.gov (United States)

    Sinha, Ashish C; Singh, Preet Mohinder; Bhat, Suneel

    2016-01-01

    Present guidelines recommend bariatric surgery at BMI ≥ 40 kg/m2 or BMI ≥ 35 kg/m2 with obesity-related morbidity. Evidence for cost and mortality/morbidity risk of bariatric surgery and obesity-related diseases was evaluated determining equivalency point of absolute incremental mortality risk by BMI and risks associated with bariatric surgery. A stochastic model was developed evaluating costs related to surgical procedure at a given BMI. Bariatric surgery produces significant lifetime cost savings associated with diabetes, gallstones, hypertension, high cholesterol, colon cancer, heart disease, and stroke in men at BMI 30 kg/m2 for laparoscopic gastric bypass. For women, laparoscopic gastric bypass saves cost at BMI 32 kg/m2 and laparoscopic gastric banding at BMI 37 kg/m2. In white men, relative to single-year mortality risks by BMI, surgical intervention becomes risk-beneficial at BMI 25 kg/m2 for laparoscopic gastric banding, BMI 27 kg/m2 for laparoscopic gastric bypass procedure and open gastric banding, and BMI 37 kg/m2 for open gastric bypass. Risk benefit for African-American men by procedure occurs at BMI Risk benefit for black women by procedure occurs at BMI 27.5 kg/m2, BMI 33.5 kg/m2, and BMI 50+ kg/m2, respectively. Risk and cost benefit suggest surgical guidelines should be reconsidered. Threshold for bariatric surgery should be redefined to BMI 35 kg/m2 or BMI 30 kg/m2 with comorbidities.

  5. Whole Genome Sequencing

    Science.gov (United States)

    ... you want to learn. Search form Search Whole Genome Sequencing You are here Home Testing & Services Testing ... the full story, click here . What is whole genome sequencing? Whole genome sequencing is the mapping out ...

  6. Sequence Read Archive (SRA)

    Data.gov (United States)

    U.S. Department of Health & Human Services — The Sequence Read Archive (SRA) stores raw sequencing data from the next generation of sequencing platforms including Roche 454 GS System®, Illumina Genome...

  7. Coordinate cytokine regulatory sequences

    Science.gov (United States)

    Frazer, Kelly A.; Rubin, Edward M.; Loots, Gabriela G.

    2005-05-10

    The present invention provides CNS sequences that regulate the cytokine gene expression, expression cassettes and vectors comprising or lacking the CNS sequences, host cells and non-human transgenic animals comprising the CNS sequences or lacking the CNS sequences. The present invention also provides methods for identifying compounds that modulate the functions of CNS sequences as well as methods for diagnosing defects in the CNS sequences of patients.

  8. Random thoughts

    Science.gov (United States)

    ajansen; kwhitefoot; panteltje1; edprochak; sudhakar, the

    2014-07-01

    In reply to the physicsworld.com news story “How to make a quantum random-number generator from a mobile phone” (16 May, http://ow.ly/xFiYc, see also p5), which describes a way of delivering random numbers by counting the number of photons that impinge on each of the individual pixels in the camera of a Nokia N9 smartphone.

  9. Identifying driver mutations in sequenced cancer genomes

    DEFF Research Database (Denmark)

    Raphael, Benjamin J; Dobson, Jason R; Oesper, Layla

    2014-01-01

    High-throughput DNA sequencing is revolutionizing the study of cancer and enabling the measurement of the somatic mutations that drive cancer development. However, the resulting sequencing datasets are large and complex, obscuring the clinically important mutations in a background of errors, noise......, and random mutations. Here, we review computational approaches to identify somatic mutations in cancer genome sequences and to distinguish the driver mutations that are responsible for cancer from random, passenger mutations. First, we describe approaches to detect somatic mutations from high-throughput DNA...... sequencing data, particularly for tumor samples that comprise heterogeneous populations of cells. Next, we review computational approaches that aim to predict driver mutations according to their frequency of occurrence in a cohort of samples, or according to their predicted functional impact on protein...

  10. Review of: Carol M. Richardson, Kim W. Woods and Michael W. Franklin (eds, Renaissance Art Reconsidered: An Anthology of Primar y Sources,

    Directory of Open Access Journals (Sweden)

    Eugenia Drakopoulou

    2017-02-01

    Full Text Available The title of this volume refers to the course of the Open University entitled Renaissance Art Reconsidered and more particularly to its three course books, which reflect three reference fields in the modern history of art: the method and arduous work of making works of art; the centres of art production, the trade networks and the relations between artists and clients; and the means of viewing art, whether in the context of religious practice, theory or patronage, during the fifteenth and early sixteenth centuries.

  11. Targeted ultra-deep sequencing unveils a lack of driver-gene mutations linking non-hereditary gastrointestinal stromal tumors and highly prevalent second primary malignancies: random or nonrandom, that is the question.

    Science.gov (United States)

    Lai, Bo-Ru; Wu, Yu-Tung; Kuo, Yung-Chia; Hsu, Hung-Chih; Chen, Jen-Shi; Chen, Tse-Ching; Wu, Ren-Chin; Chiu, Cheng-Tang; Yeh, Chun-Nan; Yeh, Ta-Sen

    2016-12-13

    The association of non-hereditary (sporadic) gastrointestinal stromal tumors (GISTs) and second primary malignancies is known to be nonrandom, although the underlying molecular mechanisms remain unknown. In this study, 136 of 749 (18.1%) patients with sporadic GISTs were found to have additional associated cancers, with gastrointestinal and genitourinary/gynecologic/breast cancers being the most prevalent. Gene mutations in GISTs and their associated colorectal cancers (CRCs) (n=9) were analyzed using a panel of 409 cancer-related genes, while a separate group of 40 sporadic CRCs not associated with GISTs served as controls. All 9 of the GISTs had either KIT (8 of 9) or PDGFRA (1 of 9) mutations that were not present in their associated CRCs. Conversely, all but one of the 9 GIST-associated CRCs exhibited an APC mutation, a TP53 mutation or both, while none of their corresponding GISTs harbored either APC or TP53 mutations. The genetic profile of CRCs with and without associated GISTs did not differ. Although population-based studies and case series worldwide, including ours, have unanimously indicated that the GIST-CRC association is nonrandom, our targeted ultra-deep sequencing unveiled a lack of driver-gene mutations linking sporadic GISTs to highly prevalent second primaries. Further studies are needed to elucidate other genetic alterations that may be responsible for this puzzling contradiction.

  12. Evaluation of Genome Sequencing Quality in Selected Plant Species Using Expressed Sequence Tags

    Science.gov (United States)

    Shangguan, Lingfei; Han, Jian; Kayesh, Emrul; Sun, Xin; Zhang, Changqing; Pervaiz, Tariq; Wen, Xicheng; Fang, Jinggui

    2013-01-01

    Background With the completion of genome sequencing projects for more than 30 plant species, large volumes of genome sequences have been produced and stored in online databases. Advancements in sequencing technologies have reduced the cost and time of whole genome sequencing enabling more and more plants to be subjected to genome sequencing. Despite this, genome sequence qualities of multiple plants have not been evaluated. Methodology/Principal Finding Integrity and accuracy were calculated to evaluate the genome sequence quality of 32 plants. The integrity of a genome sequence is presented by the ratio of chromosome size and genome size (or between scaffold size and genome size), which ranged from 55.31% to nearly 100%. The accuracy of genome sequence was presented by the ratio between matched EST and selected ESTs where 52.93% ∼ 98.28% and 89.02% ∼ 98.85% of the randomly selected clean ESTs could be mapped to chromosome and scaffold sequences, respectively. According to the integrity, accuracy and other analysis of each plant species, thirteen plant species were divided into four levels. Arabidopsis thaliana, Oryza sativa and Zea mays had the highest quality, followed by Brachypodium distachyon, Populus trichocarpa, Vitis vinifera and Glycine max, Sorghum bicolor, Solanum lycopersicum and Fragaria vesca, and Lotus japonicus, Medicago truncatula and Malus × domestica in that order. Assembling the scaffold sequences into chromosome sequences should be the primary task for the remaining nineteen species. Low GC content and repeat DNA influences genome sequence assembly. Conclusion The quality of plant genome sequences was found to be lower than envisaged and thus the rapid development of genome sequencing projects as well as research on bioinformatics tools and the algorithms of genome sequence assembly should provide increased processing and correction of genome sequences that have already been published. PMID:23922843

  13. Evaluation of genome sequencing quality in selected plant species using expressed sequence tags.

    Directory of Open Access Journals (Sweden)

    Lingfei Shangguan

    Full Text Available BACKGROUND: With the completion of genome sequencing projects for more than 30 plant species, large volumes of genome sequences have been produced and stored in online databases. Advancements in sequencing technologies have reduced the cost and time of whole genome sequencing enabling more and more plants to be subjected to genome sequencing. Despite this, genome sequence qualities of multiple plants have not been evaluated. METHODOLOGY/PRINCIPAL FINDING: Integrity and accuracy were calculated to evaluate the genome sequence quality of 32 plants. The integrity of a genome sequence is presented by the ratio of chromosome size and genome size (or between scaffold size and genome size, which ranged from 55.31% to nearly 100%. The accuracy of genome sequence was presented by the ratio between matched EST and selected ESTs where 52.93% ∼ 98.28% and 89.02% ∼ 98.85% of the randomly selected clean ESTs could be mapped to chromosome and scaffold sequences, respectively. According to the integrity, accuracy and other analysis of each plant species, thirteen plant species were divided into four levels. Arabidopsis thaliana, Oryza sativa and Zea mays had the highest quality, followed by Brachypodium distachyon, Populus trichocarpa, Vitis vinifera and Glycine max, Sorghum bicolor, Solanum lycopersicum and Fragaria vesca, and Lotus japonicus, Medicago truncatula and Malus × domestica in that order. Assembling the scaffold sequences into chromosome sequences should be the primary task for the remaining nineteen species. Low GC content and repeat DNA influences genome sequence assembly. CONCLUSION: The quality of plant genome sequences was found to be lower than envisaged and thus the rapid development of genome sequencing projects as well as research on bioinformatics tools and the algorithms of genome sequence assembly should provide increased processing and correction of genome sequences that have already been published.

  14. Universal randomness

    Energy Technology Data Exchange (ETDEWEB)

    Dotsenko, Viktor S [Landau Institute for Theoretical Physics, Russian Academy of Sciences, Moscow (Russian Federation)

    2011-03-31

    In the last two decades, it has been established that a single universal probability distribution function, known as the Tracy-Widom (TW) distribution, in many cases provides a macroscopic-level description of the statistical properties of microscopically different systems, including both purely mathematical ones, such as increasing subsequences in random permutations, and quite physical ones, such as directed polymers in random media or polynuclear crystal growth. In the first part of this review, we use a number of models to examine this phenomenon at a simple qualitative level and then consider the exact solution for one-dimensional directed polymers in a random environment, showing that free energy fluctuations in such a system are described by the universal TW distribution. The second part provides detailed appendix material containing the necessary mathematical background for the first part. (reviews of topical problems)

  15. Random triangles

    OpenAIRE

    Matula, Dominik

    2013-01-01

    The author summarizes some previous results concerning random triangles. He describes the Gaussian triangle and random triangles whose vertices lie in a unit n-dimensional ball, in a rectangle or in a general bounded convex set. In the second part, the author deals with an inscribed triangle in a triangle - let ABC be an equilateral triangle and let M, N, O be three points, each laying on one side of the ABC. We call MNO inscribed triangle (in an equi- laterral triangle). The median triangle ...

  16. Random matrices

    CERN Document Server

    Mehta, Madan Lal

    1990-01-01

    Since the publication of Random Matrices (Academic Press, 1967) so many new results have emerged both in theory and in applications, that this edition is almost completely revised to reflect the developments. For example, the theory of matrices with quaternion elements was developed to compute certain multiple integrals, and the inverse scattering theory was used to derive asymptotic results. The discovery of Selberg's 1944 paper on a multiple integral also gave rise to hundreds of recent publications. This book presents a coherent and detailed analytical treatment of random matrices, leading

  17. Aspects of insertion in random trees

    NARCIS (Netherlands)

    Bagchi, Arunabha; Reingold, E.M.

    1982-01-01

    A method formulated by Yao and used by Brown has yielded bounds on the fraction of nodes with specified properties in trees bult by a sequence of random internal nodes in a random tree built by binary search and insertion, and show that in such a tree about bounds better than those now known. We

  18. Individual Differences Methods for Randomized Experiments

    Science.gov (United States)

    Tucker-Drob, Elliot M.

    2011-01-01

    Experiments allow researchers to randomly vary the key manipulation, the instruments of measurement, and the sequences of the measurements and manipulations across participants. To date, however, the advantages of randomized experiments to manipulate both the aspects of interest and the aspects that threaten internal validity have been primarily…

  19. Polynomially Bounded Sequences and Polynomial Sequences

    Directory of Open Access Journals (Sweden)

    Okazaki Hiroyuki

    2015-09-01

    Full Text Available In this article, we formalize polynomially bounded sequences that plays an important role in computational complexity theory. Class P is a fundamental computational complexity class that contains all polynomial-time decision problems [11], [12]. It takes polynomially bounded amount of computation time to solve polynomial-time decision problems by the deterministic Turing machine. Moreover we formalize polynomial sequences [5].

  20. Metagenomics using next-generation sequencing.

    Science.gov (United States)

    Bragg, Lauren; Tyson, Gene W

    2014-01-01

    Traditionally, microbial genome sequencing has been restricted to the small number of species that can be grown in pure culture. The progressive development of culture-independent methods over the last 15 years now allows researchers to sequence microbial communities directly from environmental samples. This approach is commonly referred to as "metagenomics" or "community genomics". However, the term metagenomics is applied liberally in the literature to describe any culture-independent analysis of microbial communities. Here, we define metagenomics as shotgun ("random") sequencing of the genomic DNA of a sample taken directly from the environment. The metagenome can be thought of as a sampling of the collective genome of the microbial community. We outline the considerations and analyses that should be undertaken to ensure the success of a metagenomic sequencing project, including the choice of sequencing platform and methods for assembly, binning, annotation, and comparative analysis.

  1. Reconsidering the Neighborhood Effect

    DEFF Research Database (Denmark)

    Bisgaard, Martin; Dinesen, Peter Thisted; Sønderskov, Kim Mannemar

    2016-01-01

    The state of the national economy often directs voting. But how do citizens form perceptions of a complex and abstract macroeconomy? This study examines whether exposure to unemployment in citizens’ immediate residential surroundings shapes their perceptions of the national economy. Using novel...... microcontexts when forming perceptions of the national economy. Furthermore, we provide evidence that measures of unemployment in more aggregate contexts are not only poor reflections of what individuals are likely to experience in their immediate neighborhood but also seem to capture a different mechanism...... related to local media exposure....

  2. Climate engineering reconsidered

    Science.gov (United States)

    Barrett, Scott; Lenton, Timothy M.; Millner, Antony; Tavoni, Alessandro; Carpenter, Stephen; Anderies, John M.; Chapin, F. Stuart; Crépin, Anne-Sophie; Daily, Gretchen; Ehrlich, Paul; Folke, Carl; Galaz, Victor; Hughes, Terry; Kautsky, Nils; Lambin, Eric F.; Naylor, Rosamond; Nyborg, Karine; Polasky, Stephen; Scheffer, Marten; Wilen, James; Xepapadeas, Anastasios; de Zeeuw, Aart

    2014-07-01

    Stratospheric injection of sulphate aerosols has been advocated as an emergency geoengineering measure to tackle dangerous climate change, or as a stop-gap until atmospheric carbon dioxide levels are reduced. But it may not prove to be the game-changer that some imagine.

  3. RECONSIDERING COMPETITIVE ADVANTAGES

    Directory of Open Access Journals (Sweden)

    Valentina Zaharia

    2011-12-01

    Full Text Available Development of the competitive advantage involves a considerable effort from any organization. In particular, those organizations involved in a strong competitive market require the development of strategies to allocate long-term strategic marketing resources, efficiently and with easily quantifiable results. Faced with a multitude of phenomena and processes sometimes contradictory on different markets of consumption, contemporarily marketing has the mission to develop as creative as possible the business strategy of the organizations, their capacity of interacting with customers and other categories of audience. Such concepts as strategic positioning, relational marketing, management of the relationship with the consumer, marketing integrated research, a.s.o. are only a few of the tools with the help of which the marketing managers will implement successful operational strategies. All these developments are creating a real new paradigm of Marketing aimed to better explain the new types of complex market relationship in which the 21st Century organization is .

  4. Communicative Competence Reconsidered.

    Science.gov (United States)

    Doushaq, Mufeeq

    A discussion of points raised by Dell Hymes in his article "On Communicative Competence" leads to a proposal for a clearer and more comprehensive theory of communicative competence based on two models, a matrix of discourse analysis and a model of communication interaction. Pedagogical implications of the theory are considered, including the…

  5. RECONSIDERING ECONOMIC PRODUCTIVITY

    Directory of Open Access Journals (Sweden)

    RIS A. MIHAI

    2014-12-01

    Full Text Available Economy has changed significantly over the past century, in part due to the scientific discoveries, due to the industrial revolution, to the research, development and innovation, but maybe the most important contributor to the economic development is the human resource. We have witnessed significant changes enhancing the levels of productivity, both labor and capital. This paper analyzes productivity in relation to its social and sustainability dimension. The paper follows a previous study, highlighting the most important findings identified and reinterpreting them on the basis of the most recent research papers produced by the scholars in the field. The analysis is focused on the most unsustainable economies worldwide, respectively, the United Arab Emirates, Qatar, Belgium, Kuwait, Singapore, Netherlands, Republic of Korea, Israel, Saudi Arabia, Macedonia, Japan and the United States of America – selected by considering their per capita ecological deficit. The research uses statistical data provided by the United Nations Development Program, the World Bank and the Global Footprint Network. The research combines economical, development and environmental indexes in our attempt to evaluate productivity and to adjust it so that it considers the ecological deficit of the nations. The research hypothesis that generated the study is: the levels of economic productivity obtained by countries are not limited by their biocapacities. The empirical analysis will verify the research question advocating for the need to consider the limited capacity of the planet, in term of natural resources, when promoting economic and social development.

  6. Reconsidering written language

    CERN Document Server

    Sarma, Gopal

    2013-01-01

    In a previous essay, I argued that European schools of thought on memory and memorization were critical in enabling widespread adoption of the scientific method. Here, as a way of understanding the peculiar relationship the memory arts had to 17th century philosophy and intellectual culture, I propose a historical thought experiment, and examine whether these developments might have occurred several thousand years earlier when the adoption of written language accelerated. I suggest that strong cultural norms discouraging the use of written language may have precipitated a scientific revolution at a much earlier stage in human history. I close by arguing for the value of counter-factual scientific histories in attempting to separate scientific principles from the particular historical circumstances in which they arose.

  7. Literary Celebrity Reconsidered

    OpenAIRE

    Ohlsson, Anders; Forslid, Torbjörn; Steiner, Ann

    2014-01-01

    The ongoing celebritisation of society not only comprises ‘celebrity sectors’ such as entertainment and sports, but also literature. As in other cultural fields, the commodities to be sold – books – are marketed using the ‘personalities’ directly connected to them by authors appearing on television shows or being selected for feature articles. The aim of the article is to point out limitations to the theoretical framework used in the study of literary celebrity. We argue for a differentiation...

  8. eLearning reconsidered

    DEFF Research Database (Denmark)

    Bang, Jørgen

    2006-01-01

    Looking back, the integration of the WWW in the Internet has been a success within almost every area of society: news distribution, public information, self-service, public relations, advertising, etc. Similar high expectations were also related to the introduction of e-learning in the educational...

  9. Reconsidering the Grenada revolution

    Directory of Open Access Journals (Sweden)

    Jay R. Mandle

    1995-01-01

    Full Text Available [First paragraph] Caribbean Revolutions and Revolutionary Theory: An Assessment of Cuba, Nicaragua and Grenada. BRIAN MEEKS. London: Macmillan Caribbean, 1993. ix + 210 pp. (Paper n.p. The Grenada Invasion: Politics, Law, and Foreign Policy Decisionmaking. ROBERT J. BECK. Boulder: Westview, 1993. xiv + 263 pp. (Cloth US$ 49.95 The Gorrión Tree: Cuba and the Grenada Revolution. JOHN WALTON COTMAN. New York: Peter Lang, 1993. xvi + 272 pp. (Cloth US$ 48.95 These three books might be thought of as a second generation of studies concerned with the rise, rule, and destruction of the People's Revolutionary Government (PRG in Grenada. The circumstances surrounding the accession to power in 1979 of the government led by Maurice Bishop, the nature of its rule, and its violent demise in 1983 resulted in the appearance during the mid-1980s of an extensive literature on the Grenada Revolution. Some of these works were scholarly, others polemical. But what they all had in common was the desire to examine, either critically or otherwise, something which was unique in the historical experience of the English-speaking Caribbean. Never, before the rule of the New JEWEL Movement (NJM in Grenada, had a Leninist party come to power; never had a violent coup initiated a new political regime; never had a Caribbean government so explicitly rejected U.S. hegemony in the area; and never, before October 1983, had a government experienced quite so dramatic a crisis as that in Grenada, one which resulted in the killing of the Prime Minister and numerous others of his supporters.

  10. The frequency polygon reconsidered.

    NARCIS (Netherlands)

    van Casteren, P.H.F.M.

    1997-01-01

    The frequency polygon is not compatible with the given frequency distribution in the sense that the areas within the classes are not proportional to the frequencies. As a consequence, the polygon is too flat. Therefore, an alternative polygon is constructed as a continuous version of the histogram

  11. Hate crime legislation reconsidered

    National Research Council Canada - National Science Library

    Bill Dixon; David Gadd

    2012-01-01

    ....8 Finally they reserve judgement on how best to achieve the objective of punishing hate crimes more severely either by creating new substantive offences or providing for evidence of the presence...

  12. Reconsidering Division Cavalry Squadrons

    Science.gov (United States)

    2017-05-25

    control number. PLEASE DO NOT RETURN YOUR FORM TO THE ABOVE ADDRESS. 1. REPORT DATE (DD-MM-YYYY) 25-05-2017 2. REPORT TYPE Monograph 3. DATES ...The Big Red One, demonstrate how specific squadrons maintained enduring relationships with parent divisions over time.9 Veteran military officers...Army, 1978); Stephen Bourque, Jayhawk: The VII Corps in the Persian Gulf War (Washington, DC: Department of the Army, 2002); James Wheeler, The Big Red

  13. Perfect pitch reconsidered.

    Science.gov (United States)

    Moulton, Calum

    2014-10-01

    Perfect pitch, or absolute pitch (AP), is defined as the ability to identify or produce the pitch of a sound without need for a reference pitch, and is generally regarded as a valuable asset to the musician. However, there has been no recent review of the literature examining its aetiology and its utility taking into account emerging scientific advances in AP research, notably in functional imaging. This review analyses the key empirical research on AP, focusing on genetic and neuroimaging studies. The review concludes that: AP probably has a genetic predisposition, although this is based on limited evidence; early musical training is almost certainly essential for AP acquisition; and, although there is evidence that it may be relevant to speech processing, AP can interfere with relative pitch, an ability on which humans rely to communicate effectively. The review calls into question the value of AP to musicians and non-musicians alike. © 2014 Royal College of Physicians.

  14. Reconsidering Schwarzschild's original solution

    OpenAIRE

    Antoci, S; Liebscher, D. -E.

    2001-01-01

    We analyse the Schwarzschild solution in the context of the historical development of its present use, and explain the invariant definition of a singular surface at the Schwarzschild's radius, that can be applied to the Kerr-Newman solution too.

  15. Game Over? Reconsidering Eschatology

    OpenAIRE

    Chalamet, Christophe; Dettwiler, Andréas; Mazzocco, Mariel; Waterlot, Ghislain

    2017-01-01

    Modern science informs us about the end of the universe: "game over" is the message which lies ahead of our world. Christian theology, on the other hand, sees in the end not the cessation of all life, but rather an invitation to play again, in God's presence. Is there a way to articulate together such vastly different claims? Eschatology is a theological topic which merits being considered from several different angles. This book seeks to do this by gathering contributions from esteemed and f...

  16. Reconsidering the unreliable narrator

    DEFF Research Database (Denmark)

    Hansen, Per Krogh

    2007-01-01

    The concept of the unreliable narrator is among the most discussed in current narratology. From being considered a text-internal matter between the personified narrator and the implied author by Booth, or the implied reader by Chatman, cognitive and constructivist narrative theorists like A...

  17. Reconsidering the "Good Divorce"

    Science.gov (United States)

    Amato, Paul R.; Kane, Jennifer B.; James, Spencer

    2011-01-01

    This study attempted to assess the notion that a "good divorce" protects children from the potential negative consequences of marital dissolution. A cluster analysis of data on postdivorce parenting from 944 families resulted in three groups: cooperative coparenting, parallel parenting, and single parenting. Children in the cooperative coparenting…

  18. Reconsidering Water Electrolysis

    DEFF Research Database (Denmark)

    Xue, Song; Watzele, Sebastian; Čolić, Viktor

    2017-01-01

    Electrocatalysis for the oxygen evolution reaction (OER) is of great interest for improving the effectiveness of water splitting devices. Decreasing the anodic overpotential and simultaneously changing the anodic reaction selectively to produce valuable chemicals instead of O2 would be a major...

  19. Rapid Prototyping Reconsidered

    Science.gov (United States)

    Desrosier, James

    2011-01-01

    Continuing educators need additional strategies for developing new programming that can both reduce the time to market and lower the cost of development. Rapid prototyping, a time-compression technique adapted from the high technology industry, represents one such strategy that merits renewed evaluation. Although in higher education rapid…

  20. Interdisciplinary Art Education Reconsidered.

    Science.gov (United States)

    Ulbricht, J.

    1998-01-01

    Highlights the different forms of interdisciplinary teaching methods (integrated, related-arts, and correlated education) in order to provide a historical perspective of interdisciplinary education to art educators. Provides eight guidelines for future interdisciplinary programs in art education. Intends to prepare art educators for the…

  1. Genome Sequence Databases (Overview): Sequencing and Assembly

    Energy Technology Data Exchange (ETDEWEB)

    Lapidus, Alla L.

    2009-01-01

    From the date its role in heredity was discovered, DNA has been generating interest among scientists from different fields of knowledge: physicists have studied the three dimensional structure of the DNA molecule, biologists tried to decode the secrets of life hidden within these long molecules, and technologists invent and improve methods of DNA analysis. The analysis of the nucleotide sequence of DNA occupies a special place among the methods developed. Thanks to the variety of sequencing technologies available, the process of decoding the sequence of genomic DNA (or whole genome sequencing) has become robust and inexpensive. Meanwhile the assembly of whole genome sequences remains a challenging task. In addition to the need to assemble millions of DNA fragments of different length (from 35 bp (Solexa) to 800 bp (Sanger)), great interest in analysis of microbial communities (metagenomes) of different complexities raises new problems and pushes some new requirements for sequence assembly tools to the forefront. The genome assembly process can be divided into two steps: draft assembly and assembly improvement (finishing). Despite the fact that automatically performed assembly (or draft assembly) is capable of covering up to 98% of the genome, in most cases, it still contains incorrectly assembled reads. The error rate of the consensus sequence produced at this stage is about 1/2000 bp. A finished genome represents the genome assembly of much higher accuracy (with no gaps or incorrectly assembled areas) and quality ({approx}1 error/10,000 bp), validated through a number of computer and laboratory experiments.

  2. Deep sequencing to identify the causes of viral encephalitis.

    Directory of Open Access Journals (Sweden)

    Benjamin K Chan

    Full Text Available Deep sequencing allows for a rapid, accurate characterization of microbial DNA and RNA sequences in many types of samples. Deep sequencing (also called next generation sequencing or NGS is being developed to assist with the diagnosis of a wide variety of infectious diseases. In this study, seven frozen brain samples from deceased subjects with recent encephalitis were investigated. RNA from each sample was extracted, randomly reverse transcribed and sequenced. The sequence analysis was performed in a blinded fashion and confirmed with pathogen-specific PCR. This analysis successfully identified measles virus sequences in two brain samples and herpes simplex virus type-1 sequences in three brain samples. No pathogen was identified in the other two brain specimens. These results were concordant with pathogen-specific PCR and partially concordant with prior neuropathological examinations, demonstrating that deep sequencing can accurately identify viral infections in frozen brain tissue.

  3. Automated DNA Sequencing System

    Energy Technology Data Exchange (ETDEWEB)

    Armstrong, G.A.; Ekkebus, C.P.; Hauser, L.J.; Kress, R.L.; Mural, R.J.

    1999-04-25

    Oak Ridge National Laboratory (ORNL) is developing a core DNA sequencing facility to support biological research endeavors at ORNL and to conduct basic sequencing automation research. This facility is novel because its development is based on existing standard biology laboratory equipment; thus, the development process is of interest to the many small laboratories trying to use automation to control costs and increase throughput. Before automation, biology Laboratory personnel purified DNA, completed cycle sequencing, and prepared 96-well sample plates with commercially available hardware designed specifically for each step in the process. Following purification and thermal cycling, an automated sequencing machine was used for the sequencing. A technician handled all movement of the 96-well sample plates between machines. To automate the process, ORNL is adding a CRS Robotics A- 465 arm, ABI 377 sequencing machine, automated centrifuge, automated refrigerator, and possibly an automated SpeedVac. The entire system will be integrated with one central controller that will direct each machine and the robot. The goal of this system is to completely automate the sequencing procedure from bacterial cell samples through ready-to-be-sequenced DNA and ultimately to completed sequence. The system will be flexible and will accommodate different chemistries than existing automated sequencing lines. The system will be expanded in the future to include colony picking and/or actual sequencing. This discrete event, DNA sequencing system will demonstrate that smaller sequencing labs can achieve cost-effective the laboratory grow.

  4. Law of iterated logarithm for NA sequences with non-identical ...

    Indian Academy of Sciences (India)

    Based on a law of the iterated logarithm for independent random variables sequences, an iterated logarithm theorem for NA sequences with non-identical distributions is obtained. The proof is based on a Kolmogrov-type exponential inequality.

  5. The LHC Sequencer

    CERN Document Server

    Alemany-Fernandez, Reyes; Gorbonosov, Roman; Khasbulatov, Denis; Lamont, Mike; Le Roux, Pascal; Roderick, Chris

    2011-01-01

    The Large Hadron Collider (LHC) at CERN is a highly complex system made of many different sub-systems whose operation implies the execution of many tasks with stringent constraints on the order and duration of the execution. To be able to operate such a system in the most efficient and reliable way, the operators in the CERN control room use a high level control system: the LHC Sequencer. The LHC Sequencer system is composed of several components, including an Oracle database where operational sequences are configured, a core server that orchestrates the execution of the sequences, and two graphical user interfaces: one for sequence edition, and another for sequence execution. This paper describes the architecture of the LHC Sequencer system, and how the sequences are prepared and used for LHC operation.

  6. Anomaly Detection in Sequences

    Data.gov (United States)

    National Aeronautics and Space Administration — We present a set of novel algorithms which we call sequenceMiner, that detect and characterize anomalies in large sets of high-dimensional symbol sequences that...

  7. Roles of repetitive sequences

    Energy Technology Data Exchange (ETDEWEB)

    Bell, G.I.

    1991-12-31

    The DNA of higher eukaryotes contains many repetitive sequences. The study of repetitive sequences is important, not only because many have important biological function, but also because they provide information on genome organization, evolution and dynamics. In this paper, I will first discuss some generic effects that repetitive sequences will have upon genome dynamics and evolution. In particular, it will be shown that repetitive sequences foster recombination among, and turnover of, the elements of a genome. I will then consider some examples of repetitive sequences, notably minisatellite sequences and telomere sequences as examples of tandem repeats, without and with respectively known function, and Alu sequences as an example of interspersed repeats. Some other examples will also be considered in less detail.

  8. sequenceMiner algorithm

    Data.gov (United States)

    National Aeronautics and Space Administration — Detecting and describing anomalies in large repositories of discrete symbol sequences. sequenceMiner has been open-sourced! Download the file below to try it out....

  9. DNA sequencing conference, 2

    Energy Technology Data Exchange (ETDEWEB)

    Cook-Deegan, R.M. [Georgetown Univ., Kennedy Inst. of Ethics, Washington, DC (United States); Venter, J.C. [National Inst. of Neurological Disorders and Strokes, Bethesda, MD (United States); Gilbert, W. [Harvard Univ., Cambridge, MA (United States); Mulligan, J. [Stanford Univ., CA (United States); Mansfield, B.K. [Oak Ridge National Lab., TN (United States)

    1991-06-19

    This conference focused on DNA sequencing, genetic linkage mapping, physical mapping, informatics and bioethics. Several were used to study this sequencing and mapping. This article also discusses computer hardware and software aiding in the mapping of genes.

  10. Randomness in retrospect: exploring the interactions between memory and randomness cognition.

    Science.gov (United States)

    Olivola, Christopher Y; Oppenheimer, Daniel M

    2008-10-01

    People tend to believe that sequences of random events produce fewer and shorter streaks than is actually the case. Although this error has been demonstrated repeatedly and in many forms, nearly all studies of randomness cognition have focused on how people think about random events occurring in the present or future. This article examines how our biased beliefs about randomness interact with properties of memory to influence our judgments about and memory for past random events. We explore this interaction by examining how beliefs about randomness affect our memory for random events and how certain properties of memory alter our tendency to categorize events as random. Across three experiments, we demonstrate an interaction between randomness cognition and three well-established but distinct properties of memory: (1) the reconstructive nature of memory, (2) primacy and recency effects, and (3) duration neglect. Theoretical and practical implications are discussed.

  11. Ultra-fast sequence clustering from similarity networks with SiLiX

    Directory of Open Access Journals (Sweden)

    Duret Laurent

    2011-04-01

    Full Text Available Abstract Background The number of gene sequences that are available for comparative genomics approaches is increasing extremely quickly. A current challenge is to be able to handle this huge amount of sequences in order to build families of homologous sequences in a reasonable time. Results We present the software package SiLiX that implements a novel method which reconsiders single linkage clustering with a graph theoretical approach. A parallel version of the algorithms is also presented. As a demonstration of the ability of our software, we clustered more than 3 millions sequences from about 2 billion BLAST hits in 7 minutes, with a high clustering quality, both in terms of sensitivity and specificity. Conclusions Comparing state-of-the-art software, SiLiX presents the best up-to-date capabilities to face the problem of clustering large collections of sequences. SiLiX is freely available at http://lbbe.univ-lyon1.fr/SiLiX.

  12. Algebraic polynomials with random coefficients

    Directory of Open Access Journals (Sweden)

    K. Farahmand

    2002-01-01

    Full Text Available This paper provides an asymptotic value for the mathematical expected number of points of inflections of a random polynomial of the form a0(ω+a1(ω(n11/2x+a2(ω(n21/2x2+…an(ω(nn1/2xn when n is large. The coefficients {aj(w}j=0n, w∈Ω are assumed to be a sequence of independent normally distributed random variables with means zero and variance one, each defined on a fixed probability space (A,Ω,Pr. A special case of dependent coefficients is also studied.

  13. Random walks in a random environment

    Indian Academy of Sciences (India)

    R. Narasimhan (Krishtel eMaging) 1461 1996 Oct 15 13:05:22

    Abstract. Random walks as well as diffusions in random media are considered. Methods are developed that allow one to establish large deviation results for both the 'quenched' and the 'averaged' case. Keywords. Large deviations; random walks in a random environment. 1. Introduction. A random walk on Zd is a stochastic ...

  14. Universality for distances in power-law random graphs

    NARCIS (Netherlands)

    Van der Hofstad, R.; Hooghiemstra, G.

    2008-01-01

    We survey the recent work on phase transition and distances in various random graph models with general degree sequences. We focus on inhomogeneous random graphs, the configuration model, and affine preferential attachment models, and pay special attention to the setting where these random graphs

  15. 32 CFR 1624.1 - Random selection procedures for induction.

    Science.gov (United States)

    2010-07-01

    ... 32 National Defense 6 2010-07-01 2010-07-01 false Random selection procedures for induction. 1624... SYSTEM INDUCTIONS § 1624.1 Random selection procedures for induction. (a) The Director of Selective Service shall from time to time establish a random selection sequence for induction by a drawing to be...

  16. Metaheuristic approaches to order sequencing on a unidirectional ...

    African Journals Online (AJOL)

    In this paper the sequencing of orders on a unidirectional picking line is considered. The aim of the order sequencing is to minimise the number of cycles travelled by a picker within the picking line to complete all orders. A tabu search, simulated annealing, genetic algorithm, generalised extremal optimisation and a random ...

  17. Mining olive genome through library sequencing and bioinformatics ...

    African Journals Online (AJOL)

    As one of the initial steps of olive (Olea europaea L.) genome analysis, a small insert genomic DNA library was constructed (digesting olive genomic DNA with SmaI and cloning the digestion products into pUC19 vector) and randomly picked 83 colonies were sequenced. Analysis of the insert sequences revealed 12 clones ...

  18. Evolution of random catalytic networks

    Energy Technology Data Exchange (ETDEWEB)

    Fraser, S.M. [Santa Fe Inst., NM (United States); Reidys, C.M. [Santa Fe Inst., NM (United States)]|[Los Alamos National Lab., NM (United States)

    1997-06-01

    In this paper the authors investigate the evolution of populations of sequences on a random catalytic network. Sequences are mapped into structures, between which are catalytic interactions that determine their instantaneous fitness. The catalytic network is constructed as a random directed graph. They prove that at certain parameter values, the probability of some relevant subgraphs of this graph, for example cycles without outgoing edges, is maximized. Populations evolving under point mutations realize a comparatively small induced subgraph of the complete catalytic network. They present results which show that populations reliably discover and persist on directed cycles in the catalytic graph, though these may be lost because of stochastic effects, and study the effect of population size on this behavior.

  19. Automated Testing with Targeted Event Sequence Generation

    DEFF Research Database (Denmark)

    Jensen, Casper Svenning; Prasad, Mukul R.; Møller, Anders

    2013-01-01

    Automated software testing aims to detect errors by producing test inputs that cover as much of the application source code as possible. Applications for mobile devices are typically event-driven, which raises the challenge of automatically producing event sequences that result in high coverage....... Some existing approaches use random or model-based testing that largely treats the application as a black box. Other approaches use symbolic execution, either starting from the entry points of the applications or on specific event sequences. A common limitation of the existing approaches...... is that they often fail to reach the parts of the application code that require more complex event sequences. We propose a two-phase technique for automatically finding event sequences that reach a given target line in the application code. The first phase performs concolic execution to build summaries...

  20. Random tensors

    CERN Document Server

    Gurau, Razvan

    2017-01-01

    Written by the creator of the modern theory of random tensors, this book is the first self-contained introductory text to this rapidly developing theory. Starting from notions familiar to the average researcher or PhD student in mathematical or theoretical physics, the book presents in detail the theory and its applications to physics. The recent detections of the Higgs boson at the LHC and gravitational waves at LIGO mark new milestones in Physics confirming long standing predictions of Quantum Field Theory and General Relativity. These two experimental results only reinforce today the need to find an underlying common framework of the two: the elusive theory of Quantum Gravity. Over the past thirty years, several alternatives have been proposed as theories of Quantum Gravity, chief among them String Theory. While these theories are yet to be tested experimentally, key lessons have already been learned. Whatever the theory of Quantum Gravity may be, it must incorporate random geometry in one form or another....

  1. Random functions and turbulence

    CERN Document Server

    Panchev, S

    1971-01-01

    International Series of Monographs in Natural Philosophy, Volume 32: Random Functions and Turbulence focuses on the use of random functions as mathematical methods. The manuscript first offers information on the elements of the theory of random functions. Topics include determination of statistical moments by characteristic functions; functional transformations of random variables; multidimensional random variables with spherical symmetry; and random variables and distribution functions. The book then discusses random processes and random fields, including stationarity and ergodicity of random

  2. DNA Sequences of RAPD Fragments in the Egyptian cotton ...

    African Journals Online (AJOL)

    Random Amplified Polymorphic DNAs (RAPDs) is a DNA polymorphism assay based on the amplification of random DNA segments with single primers of arbitrary nucleotide sequence. Despite the fact that the RAPD technique has become a very powerful tool and has found use in numerous applications, yet, the nature of ...

  3. Probabilistic Motor Sequence Yields Greater Offline and Less Online Learning than Fixed Sequence.

    Science.gov (United States)

    Du, Yue; Prashad, Shikha; Schoenbrun, Ilana; Clark, Jane E

    2016-01-01

    It is well acknowledged that motor sequences can be learned quickly through online learning. Subsequently, the initial acquisition of a motor sequence is boosted or consolidated by offline learning. However, little is known whether offline learning can drive the fast learning of motor sequences (i.e., initial sequence learning in the first training session). To examine offline learning in the fast learning stage, we asked four groups of young adults to perform the serial reaction time (SRT) task with either a fixed or probabilistic sequence and with or without preliminary knowledge (PK) of the presence of a sequence. The sequence and PK were manipulated to emphasize either procedural (probabilistic sequence; no preliminary knowledge (NPK)) or declarative (fixed sequence; with PK) memory that were found to either facilitate or inhibit offline learning. In the SRT task, there were six learning blocks with a 2 min break between each consecutive block. Throughout the session, stimuli followed the same fixed or probabilistic pattern except in Block 5, in which stimuli appeared in a random order. We found that PK facilitated the learning of a fixed sequence, but not a probabilistic sequence. In addition to overall learning measured by the mean reaction time (RT), we examined the progressive changes in RT within and between blocks (i.e., online and offline learning, respectively). It was found that the two groups who performed the fixed sequence, regardless of PK, showed greater online learning than the other two groups who performed the probabilistic sequence. The groups who performed the probabilistic sequence, regardless of PK, did not display online learning, as indicated by a decline in performance within the learning blocks. However, they did demonstrate remarkably greater offline improvement in RT, which suggests that they are learning the probabilistic sequence offline. These results suggest that in the SRT task, the fast acquisition of a motor sequence is driven

  4. Detection of M-Sequences from Spike Sequence in Neuronal Networks

    Directory of Open Access Journals (Sweden)

    Yoshi Nishitani

    2012-01-01

    Full Text Available In circuit theory, it is well known that a linear feedback shift register (LFSR circuit generates pseudorandom bit sequences (PRBS, including an M-sequence with the maximum period of length. In this study, we tried to detect M-sequences known as a pseudorandom sequence generated by the LFSR circuit from time series patterns of stimulated action potentials. Stimulated action potentials were recorded from dissociated cultures of hippocampal neurons grown on a multielectrode array. We could find several M-sequences from a 3-stage LFSR circuit (M3. These results show the possibility of assembling LFSR circuits or its equivalent ones in a neuronal network. However, since the M3 pattern was composed of only four spike intervals, the possibility of an accidental detection was not zero. Then, we detected M-sequences from random spike sequences which were not generated from an LFSR circuit and compare the result with the number of M-sequences from the originally observed raster data. As a result, a significant difference was confirmed: a greater number of “0–1” reversed the 3-stage M-sequences occurred than would have accidentally be detected. This result suggests that some LFSR equivalent circuits are assembled in neuronal networks.

  5. Double sequence core theorems

    Directory of Open Access Journals (Sweden)

    Richard F. Patterson

    1999-01-01

    Full Text Available In 1900, Pringsheim gave a definition of the convergence of double sequences. In this paper, that notion is extended by presenting definitions for the limit inferior and limit superior of double sequences. Also the core of a double sequence is defined. By using these definitions and the notion of regularity for 4-dimensional matrices, extensions, and variations of the Knopp Core theorem are proved.

  6. Efficient probability sequence

    OpenAIRE

    Regnier, Eva

    2014-01-01

    A probability sequence is an ordered set of probability forecasts for the same event. Although single-period probabilistic forecasts and methods for evaluating them have been extensively analyzed, we are not aware of any prior work on evaluating probability sequences. This paper proposes an efficiency condition for probability sequences and shows properties of efficient forecasting systems, including memorylessness and increasing discrimination. These results suggest tests for efficiency and ...

  7. Efficient probability sequences

    OpenAIRE

    Regnier, Eva

    2014-01-01

    DRMI working paper A probability sequence is an ordered set of probability forecasts for the same event. Although single-period probabilistic forecasts and methods for evaluating them have been extensively analyzed, we are not aware of any prior work on evaluating probability sequences. This paper proposes an efficiency condition for probability sequences and shows properties of efficiency forecasting systems, including memorylessness and increasing discrimination. These res...

  8. Classification of periodic, chaotic and random sequences using ...

    Indian Academy of Sciences (India)

    2015-02-19

    Feb 19, 2015 ... 'Complexity' has several definitions in diverse fields. These measures are indicators of some aspects of ... Silpa S Nair1 Nithin Nagaraj1. Department of Electronics and Communication Engineering, Amrita School of Engineering, Amrita Vishwa Vidyapeetham, Amritapuri Campus, Clappana 690 525, India ...

  9. Random amplified polymorphic DNA (RAPD) and simple sequence ...

    African Journals Online (AJOL)

    To compare these two methods, genetic parameters were computed such as the number of polymorphic bands, average number of alleles per locus, effective number of alleles per locus, expected heterozygosity, effectiveness index of analysis and polymorphism information content (PIC). Better results were provided by ...

  10. Random amplified polymorphic DNA (RAPD) and simple sequence ...

    African Journals Online (AJOL)

    Administrator

    2011-06-06

    Jun 6, 2011 ... of polymorphic bands, average number of alleles per locus, effective .... Materials for DNA isolation were obtained from a set of 5 to 7 plants ..... Among factors that might have contributed to ... Inheritance of RAPDs in F1 hybrids of corn. ... by using cluster analysis of RAPD molecular marker, phenotype and.

  11. Long-range correlations and charge transport properties of DNA sequences

    Science.gov (United States)

    Liu, Xiao-liang; Ren, Yi; Xie, Qiong-tao; Deng, Chao-sheng; Xu, Hui

    2010-04-01

    By using Hurst's analysis and transfer approach, the rescaled range functions and Hurst exponents of human chromosome 22 and enterobacteria phage lambda DNA sequences are investigated and the transmission coefficients, Landauer resistances and Lyapunov coefficients of finite segments based on above genomic DNA sequences are calculated. In a comparison with quasiperiodic and random artificial DNA sequences, we find that λ-DNA exhibits anticorrelation behavior characterized by a Hurst exponent 0.5sequence displays a transition from correlation behavior to anticorrelation behavior. The resonant peaks of the transmission coefficient in genomic sequences can survive in longer sequence length than in random sequences but in shorter sequence length than in quasiperiodic sequences. It is shown that the genomic sequences have long-range correlation properties to some extent but the correlations are not strong enough to maintain the scale invariance properties.

  12. Long-range correlations and charge transport properties of DNA sequences

    Energy Technology Data Exchange (ETDEWEB)

    Liu Xiaoliang, E-mail: xlliucsu@yahoo.com.c [College of Physical Science and Technology and College of Metallurgical Science and Engineering, Central South University, Changsha 410083 (China); Ren, Yi [College of Physical Science and Technology and College of Metallurgical Science and Engineering, Central South University, Changsha 410083 (China); Xie, Qiong-tao [Key Laboratory of Low Dimensional Quantum Structures and Quantum Control of Ministry of Education (Hunan Normal University), Changsha 410081 (China); Deng, Chao-sheng; Xu, Hui [College of Physical Science and Technology and College of Metallurgical Science and Engineering, Central South University, Changsha 410083 (China)

    2010-04-26

    By using Hurst's analysis and transfer approach, the rescaled range functions and Hurst exponents of human chromosome 22 and enterobacteria phage lambda DNA sequences are investigated and the transmission coefficients, Landauer resistances and Lyapunov coefficients of finite segments based on above genomic DNA sequences are calculated. In a comparison with quasiperiodic and random artificial DNA sequences, we find that lambda-DNA exhibits anticorrelation behavior characterized by a Hurst exponent 0.5sequence displays a transition from correlation behavior to anticorrelation behavior. The resonant peaks of the transmission coefficient in genomic sequences can survive in longer sequence length than in random sequences but in shorter sequence length than in quasiperiodic sequences. It is shown that the genomic sequences have long-range correlation properties to some extent but the correlations are not strong enough to maintain the scale invariance properties.

  13. Triangulation in Random Refractive Distortions.

    Science.gov (United States)

    Alterman, Marina; Schechner, Yoav Y; Swirski, Yohay

    2017-03-01

    Random refraction occurs in turbulence and through a wavy water-air interface. It creates distortion that changes in space, time and with viewpoint. Localizing objects in three dimensions (3D) despite this random distortion is important to some predators and also to submariners avoiding the salient use of periscopes. We take a multiview approach to this task. Refracted distortion statistics induce a probabilistic relation between any pixel location and a line of sight in space. Measurements of an object's random projection from multiple views and times lead to a likelihood function of the object's 3D location. The likelihood leads to estimates of the 3D location and its uncertainty. Furthermore, multiview images acquired simultaneously in a wide stereo baseline have uncorrelated distortions. This helps reduce the acquisition time needed for localization. The method is demonstrated in stereoscopic video sequences, both in a lab and a swimming pool.

  14. The resistance of randomly grown trees

    Science.gov (United States)

    Colman, E. R.; Rodgers, G. J.

    2011-12-01

    An electrical network with the structure of a random tree is considered: starting from a root vertex, in one iteration each leaf (a vertex with zero or one adjacent edges) of the tree is extended by either a single edge with probability p or two edges with probability 1 - p. With each edge having a resistance equal to 1Ω, the total resistance Rn between the root vertex and a busbar connecting all the vertices at the nth level is considered. A dynamical system is presented which approximates Rn, it is shown that the mean value for this system approaches (1 + p)/(1 - p) as n → ∞, the distribution of Rn at large n is also examined. Additionally, a random sequence construction akin to a random Fibonacci sequence is used to approximate Rn; this sequence is shown to be related to the Legendre polynomials and its mean is shown to converge with | - (1 + p)/(1 - p)| ˜ n-1/2.

  15. Random-walk enzymes

    Science.gov (United States)

    Mak, Chi H.; Pham, Phuong; Afif, Samir A.; Goodman, Myron F.

    2015-09-01

    Enzymes that rely on random walk to search for substrate targets in a heterogeneously dispersed medium can leave behind complex spatial profiles of their catalyzed conversions. The catalytic signatures of these random-walk enzymes are the result of two coupled stochastic processes: scanning and catalysis. Here we develop analytical models to understand the conversion profiles produced by these enzymes, comparing an intrusive model, in which scanning and catalysis are tightly coupled, against a loosely coupled passive model. Diagrammatic theory and path-integral solutions of these models revealed clearly distinct predictions. Comparison to experimental data from catalyzed deaminations deposited on single-stranded DNA by the enzyme activation-induced deoxycytidine deaminase (AID) demonstrates that catalysis and diffusion are strongly intertwined, where the chemical conversions give rise to new stochastic trajectories that were absent if the substrate DNA was homogeneous. The C →U deamination profiles in both analytical predictions and experiments exhibit a strong contextual dependence, where the conversion rate of each target site is strongly contingent on the identities of other surrounding targets, with the intrusive model showing an excellent fit to the data. These methods can be applied to deduce sequence-dependent catalytic signatures of other DNA modification enzymes, with potential applications to cancer, gene regulation, and epigenetics.

  16. Coverage statistics for sequence census methods

    Directory of Open Access Journals (Sweden)

    Evans Steven N

    2010-08-01

    Full Text Available Abstract Background We study the statistical properties of fragment coverage in genome sequencing experiments. In an extension of the classic Lander-Waterman model, we consider the effect of the length distribution of fragments. We also introduce a coding of the shape of the coverage depth function as a tree and explain how this can be used to detect regions with anomalous coverage. This modeling perspective is especially germane to current high-throughput sequencing experiments, where both sample preparation protocols and sequencing technology particulars can affect fragment length distributions. Results Under the mild assumptions that fragment start sites are Poisson distributed and successive fragment lengths are independent and identically distributed, we observe that, regardless of fragment length distribution, the fragments produced in a sequencing experiment can be viewed as resulting from a two-dimensional spatial Poisson process. We then study the successive jumps of the coverage function, and show that they can be encoded as a random tree that is approximately a Galton-Watson tree with generation-dependent geometric offspring distributions whose parameters can be computed. Conclusions We extend standard analyses of shotgun sequencing that focus on coverage statistics at individual sites, and provide a null model for detecting deviations from random coverage in high-throughput sequence census based experiments. Our approach leads to explicit determinations of the null distributions of certain test statistics, while for others it greatly simplifies the approximation of their null distributions by simulation. Our focus on fragments also leads to a new approach to visualizing sequencing data that is of independent interest.

  17. Pierre Robin sequence

    Science.gov (United States)

    Pierre Robin sequence (or syndrome) is a condition in which an infant has a smaller than normal lower jaw, a tongue ... The exact causes of Pierre Robin sequence are unknown. It may be ... jaw develops slowly before birth, but may grow faster during ...

  18. Cosmetology: Scope and Sequence.

    Science.gov (United States)

    Nashville - Davidson County Metropolitan Public Schools, TN.

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

  19. sequences in Chickpea

    African Journals Online (AJOL)

    Milena

    Author(s) retain the copyright of this article http://www.academicjournals.org/AJB. African Journal of Biotechnology. Full Length Research Paper. Evaluation of genetic divergence and phylogenetic relationship using sequence-tagged microsatellite. (STMS) sequences in Chickpea (Cicer arietinum L.) genotypes. Himanshu ...

  20. Sequences, Series, and Mathematica.

    Science.gov (United States)

    Mathews, John H.

    1992-01-01

    Describes how the computer algebra system Mathematica can be used to enhance the teaching of the topics of sequences and series. Examines its capabilities to find exact, approximate, and graphically generated approximate solutions to problems from these topics and to understand proofs about sequences. (MDH)

  1. Random fixed points and random differential inclusions

    Directory of Open Access Journals (Sweden)

    Nikolaos S. Papageorgiou

    1988-01-01

    Full Text Available In this paper, first, we study random best approximations to random sets, using fixed point techniques, obtaining this way stochastic analogues of earlier deterministic results by Browder-Petryshyn, KyFan and Reich. Then we prove two fixed point theorems for random multifunctions with stochastic domain that satisfy certain tangential conditions. Finally we consider a random differential inclusion with upper semicontinuous orientor field and establish the existence of random solutions.

  2. Nanotechnology and Nanopore Sequencing.

    Science.gov (United States)

    Abedini-Nassab, Roozbeh

    2017-01-01

    DNA sequencing is one of the crucially important tasks in the fields of genetics and cellular biology, which is benefiting from nanotechnology. DNA carries genetic information and sequencing it in a quick way helps researchers in achieving essential goals, including personalized medicine. Solid state nanopores potentially can offer more durability, in sequencing biomolecules, over the proteinbased nanopores. In recent years, various ideas are introduced towards the goal of fast and low cost sequencing. In this review article recent advances presented in journal articles as well as patents in this field, including sequencing methods, membrane materials and their fabrication techniques, drilling methods, and biomolecule translocation speed control ideas are investigated. Copyright© Bentham Science Publishers; For any queries, please email at epub@benthamscience.org.

  3. Compressive Sensing with Tent Chaotic Sequence

    Directory of Open Access Journals (Sweden)

    Li Liu

    2014-02-01

    Full Text Available Compressive sensing is a new sampling theory to capture signals at sub-Nyquist rate. To guarantee exact recovery from sparse measurements, specific sensing matrix, which satisfies the Restricted Isometry Property, should be well chosen. Random matrix has been proved to meet the property with high probability; however, the practical implementation is expensive in hardware design. Chaotic matrices which generated by Logistic sequence, Chua and Lorenz dynamical systems have been verified to be Toeplitz-structured and sufficient to satisfy the property. In this paper, we propose that another chaotic sequence - Tent map can also be used to construct the sensing matrix. By numerical performance, we show that, the proposed Tent chaotic sensing matrix has similar performance to random matrix or Logistic chaotic matrix for exact reconstructing compressible signals and images from fewer measurements.

  4. Locomotor sequence learning in visually guided walking.

    Science.gov (United States)

    Choi, Julia T; Jensen, Peter; Nielsen, Jens Bo

    2016-04-01

    Voluntary limb modifications must be integrated with basic walking patterns during visually guided walking. In this study we tested whether voluntary gait modifications can become more automatic with practice. We challenged walking control by presenting visual stepping targets that instructed subjects to modify step length from one trial to the next. Our sequence learning paradigm is derived from the serial reaction-time (SRT) task that has been used in upper limb studies. Both random and ordered sequences of step lengths were used to measure sequence-specific and sequence-nonspecific learning during walking. In addition, we determined how age (i.e., healthy young adults vs. children) and biomechanical factors (i.e., walking speed) affected the rate and magnitude of locomotor sequence learning. The results showed that healthy young adults (age 24 ± 5 yr,n= 20) could learn a specific sequence of step lengths over 300 training steps. Younger children (age 6-10 yr,n= 8) had lower baseline performance, but their magnitude and rate of sequence learning were the same compared with those of older children (11-16 yr,n= 10) and healthy adults. In addition, learning capacity may be more limited at faster walking speeds. To our knowledge, this is the first study to demonstrate that spatial sequence learning can be integrated with a highly automatic task such as walking. These findings suggest that adults and children use implicit knowledge about the sequence to plan and execute leg movement during visually guided walking. Copyright © 2016 the American Physiological Society.

  5. Law of iterated logarithm for NA sequences with non-identical ...

    Indian Academy of Sciences (India)

    There are many results about law of iterated logarithm for independent random variables sequences. ... As for negatively associated (NA) random variables, Joag [2] gave the following defi- nition. DEFINITION [2] ... Recently, some authors focused on the problem of limiting behavior of partial sums of. NA sequences. Su et al ...

  6. HIV Sequence Compendium 2015

    Energy Technology Data Exchange (ETDEWEB)

    Foley, Brian Thomas [Los Alamos National Lab. (LANL), Los Alamos, NM (United States); Leitner, Thomas Kenneth [Los Alamos National Lab. (LANL), Los Alamos, NM (United States); Apetrei, Cristian [Univ. of Pittsburgh, PA (United States); Hahn, Beatrice [Univ. of Pennsylvania, Philadelphia, PA (United States); Mizrachi, Ilene [National Center for Biotechnology Information, Bethesda, MD (United States); Mullins, James [Univ. of Washington, Seattle, WA (United States); Rambaut, Andrew [Univ. of Edinburgh, Scotland (United Kingdom); Wolinsky, Steven [Northwestern Univ., Evanston, IL (United States); Korber, Bette Tina Marie [Los Alamos National Lab. (LANL), Los Alamos, NM (United States)

    2015-10-05

    This compendium is an annual printed summary of the data contained in the HIV sequence database. We try to present a judicious selection of the data in such a way that it is of maximum utility to HIV researchers. Each of the alignments attempts to display the genetic variability within the different species, groups and subtypes of the virus. This compendium contains sequences published before January 1, 2015. Hence, though it is published in 2015 and called the 2015 Compendium, its contents correspond to the 2014 curated alignments on our website. The number of sequences in the HIV database is still increasing. In total, at the end of 2014, there were 624,121 sequences in the HIV Sequence Database, an increase of 7% since the previous year. This is the first year that the number of new sequences added to the database has decreased compared to the previous year. The number of near complete genomes (>7000 nucleotides) increased to 5834 by end of 2014. However, as in previous years, the compendium alignments contain only a fraction of these. A more complete version of all alignments is available on our website, http://www.hiv.lanl.gov/ content/sequence/NEWALIGN/align.html As always, we are open to complaints and suggestions for improvement. Inquiries and comments regarding the compendium should be addressed to seq-info@lanl.gov.

  7. Evolution of DNA sequencing.

    Science.gov (United States)

    Tipu, Hamid Nawaz; Shabbir, Ambreen

    2015-03-01

    Sanger and coworkers introduced DNA sequencing in 1970s for the first time. It principally relied on termination of growing nucleotide chain when a dideoxythymidine triphosphate (ddTTP) was inserted in it. Detection of terminated sequences was done radiographically on Polyacrylamide Gel Electrophoresis (PAGE). Improvements that have evolved over time in original Sanger sequencing include replacement of radiography with fluorescence, use of separate fluorescent markers for each nucleotide, use of capillary electrophoresis instead of polyacrylamide gel electrophoresis and then introduction of capillary array electrophoresis. However, this technique suffered from few inherent limitations like decreased sensitivity for low level mutant alleles, complexities in analyzing highly polymorphic regions like Major Histocompatibility Complex (MHC) and high DNA concentrations required. Several Next Generation Sequencing (NGS) technologies have been introduced by Roche, Illumina and other commercial manufacturers that tend to overcome Sanger sequencing limitations and have been reviewed. Introduction of NGS in clinical research and medical diagnostics is expected to change entire diagnostic approach. These include study of cancer variants, detection of minimal residual disease, exome sequencing, detection of Single Nucleotide Polymorphisms (SNPs) and their disease association, epigenetic regulation of gene expression and sequencing of microorganisms genome.

  8. Bias of purine stretches in sequenced chromosomes

    DEFF Research Database (Denmark)

    Ussery, David; Soumpasis, Dikeos Mario; Brunak, Søren

    2002-01-01

    We examined more than 700 DNA sequences (full length chromosomes and plasmids) for stretches of purines (R) or pyrimidines (Y) and alternating YR stretches; such regions will likely adopt structures which are different from the canonical B-form. Since one turn of the DNA helix is roughly 10 bp, we...... to contain 1.0% of purine tracts and also 1.0% of the alternating pyr/pur tracts. In the vast majority of cases, there are more purine tracts than would be expected from a random sequence, with an average of 3.5%, significantly larger than the expectation value. The fraction of the chromosomes containing pyr......, in eukaryotes there is an abundance of long stretches of purines or alternating purine/pyrimidine tracts, which cannot be explained in this way; these sequences are likely to play an important role in eukaryotic chromosome organisation....

  9. Sublinear Time Motif Discovery from Multiple Sequences

    Directory of Open Access Journals (Sweden)

    Yunhui Fu

    2013-10-01

    Full Text Available In this paper, a natural probabilistic model for motif discovery has been used to experimentally test the quality of motif discovery programs. In this model, there are k background sequences, and each character in a background sequence is a random character from an alphabet, Σ. A motif G = g1g2 ... gm is a string of m characters. In each background sequence is implanted a probabilistically-generated approximate copy of G. For a probabilistically-generated approximate copy b1b2 ... bm of G, every character, bi, is probabilistically generated, such that the probability for bi ≠ gi is at most α. We develop two new randomized algorithms and one new deterministic algorithm. They make advancements in the following aspects: (1 The algorithms are much faster than those before. Our algorithms can even run in sublinear time. (2 They can handle any motif pattern. (3 The restriction for the alphabet size is a lower bound of four. This gives them potential applications in practical problems, since gene sequences have an alphabet size of four. (4 All algorithms have rigorous proofs about their performances. The methods developed in this paper have been used in the software implementation. We observed some encouraging results that show improved performance for motif detection compared with other software.

  10. Delayed Sequence Intubation

    DEFF Research Database (Denmark)

    Weingart, Scott D; Trueger, N Seth; Wong, Nelson

    2015-01-01

    , patients were paralyzed and intubated. The primary outcome of this study was the difference in oxygen saturations after maximal attempts at preoxygenation before delayed sequence intubation compared with saturations just before intubation. Predetermined secondary outcomes and complications were also...... assessed. RESULTS: A total of 62 patients were enrolled: 19 patients required delayed sequence intubation to allow nonrebreather mask, 39 patients required it to allow NIPPV, and 4 patients required it for nasogastric tube placement. Saturations increased from a mean of 89.9% before delayed sequence...... intubation to 98.8% afterward, with an increase of 8.9% (95% confidence interval 6.4% to 10.9%). Thirty-two patients were in a predetermined group with high potential for critical desaturation (pre-delayed sequence intubation saturations ≤93%). All of these patients increased their saturations post...

  11. Gomphid DNA sequence data

    Data.gov (United States)

    U.S. Environmental Protection Agency — DNA sequence data for several genetic loci. This dataset is not publicly accessible because: It's already publicly available on GenBank. It can be accessed through...

  12. HIV Sequence Compendium 2010

    Energy Technology Data Exchange (ETDEWEB)

    Kuiken, Carla [Los Alamos National Lab. (LANL), Los Alamos, NM (United States); Foley, Brian [Los Alamos National Lab. (LANL), Los Alamos, NM (United States); Leitner, Thomas [Los Alamos National Lab. (LANL), Los Alamos, NM (United States); Apetrei, Christian [Univ. of Pittsburgh, PA (United States); Hahn, Beatrice [Univ. of Alabama, Tuscaloosa, AL (United States); Mizrachi, Ilene [National Center for Biotechnology Information, Bethesda, MD (United States); Mullins, James [Univ. of Washington, Seattle, WA (United States); Rambaut, Andrew [Univ. of Edinburgh, Scotland (United Kingdom); Wolinsky, Steven [Northwestern Univ., Evanston, IL (United States); Korber, Bette [Los Alamos National Lab. (LANL), Los Alamos, NM (United States)

    2010-12-31

    This compendium is an annual printed summary of the data contained in the HIV sequence database. In these compendia we try to present a judicious selection of the data in such a way that it is of maximum utility to HIV researchers. Each of the alignments attempts to display the genetic variability within the different species, groups and subtypes of the virus. This compendium contains sequences published before January 1, 2010. Hence, though it is called the 2010 Compendium, its contents correspond to the 2009 curated alignments on our website. The number of sequences in the HIV database is still increasing exponentially. In total, at the time of printing, there were 339,306 sequences in the HIV Sequence Database, an increase of 45% since last year. The number of near complete genomes (>7000 nucleotides) increased to 2576 by end of 2009, reflecting a smaller increase than in previous years. However, as in previous years, the compendium alignments contain only a small fraction of these. Included in the alignments are a small number of sequences representing each of the subtypes and the more prevalent circulating recombinant forms (CRFs) such as 01 and 02, as well as a few outgroup sequences (group O and N and SIV-CPZ). Of the rarer CRFs we included one representative each. A more complete version of all alignments is available on our website, http://www.hiv.lanl.gov/content/sequence/NEWALIGN/align.html. Reprints are available from our website in the form of both HTML and PDF files. As always, we are open to complaints and suggestions for improvement. Inquiries and comments regarding the compendium should be addressed to seq-info@lanl.gov.

  13. What's Decidable About Sequences?

    OpenAIRE

    Furia, Carlo A.

    2010-01-01

    We present a first-order theory of sequences with integer elements, Presburger arithmetic, and regular constraints, which can model significant properties of data structures such as arrays and lists. We give a decision procedure for the quantifier-free fragment, based on an encoding into the first-order theory of concatenation; the procedure has PSPACE complexity. The quantifier-free fragment of the theory of sequences can express properties such as sortedness and injectivity, as well as Bool...

  14. F-specific RNA bacteriophages, especially members of subgroup II, should be reconsidered as good indicators of viral pollution of oysters.

    Science.gov (United States)

    Hartard, C; Leclerc, M; Rivet, R; Maul, A; Loutreul, J; Banas, S; Boudaud, N; Gantzer, C

    2017-10-27

    Norovirus (NoV) is the leading cause of gastroenteritis outbreaks linked to oyster consumption. In this study, we investigated the potential of F-specific RNA bacteriophages (FRNAPH) as indicators of viral contamination in oysters, by focusing especially on the subgroup FRNAPH-II. These viral indicators have been neglected because of their sometimes different behavior from that of NoV in shellfish, especially during the depuration processes usually performed before marketing. However, a significant bias needs to be taken into account which is that, in the absence of routine culture methods, NoV is targeted by genome detection while FRNAPH presence is usually investigated by isolation of infectious particles. In this study, by targeting both viruses using genome detection, a significant correlation was observed between FRNAPH-II and NoV in shellfish collected from various European harvesting areas impacted by fecal pollution. Moreover, during their depuration, while high persistence of NoV was confirmed, similar or even greater persistence was observed for FRNAPH-II genome over 30 days. Such striking genome persistence calls into question the relevance of molecular methods in assessing viral hazard. Targeting the same virus (i.e. FRNAPH-II) by culture and genome detection in specimens coming from harvesting areas as well as during depuration, we concluded that the presence of genomes in shellfish does not provide any information on the presence of the corresponding infectious particles. In view of these results, infectious FRNAPH detection should be reconsidered as a valuable indicator in oysters and its potential for assessing viral hazard needs to be investigated.IMPORTANCE This work brings new data about the behavior of viruses in shellfish, as well as concerning the relevance of molecular methods to detect them and evaluate the viral hazard. Firstly, a high correlation has been observed between F-specific RNA bacteriophages of subgroup II (FRNAPH-II) and

  15. Sequence Classification: 889154 [

    Lifescience Database Archive (English)

    Full Text Available n involved in bud-site selection; diploid mutants display a random budding pattern instead of the wild-type bipolar pattern; Bud23p || http://www.ncbi.nlm.nih.gov/protein/6319895 ...

  16. Sequence Classification: 891457 [

    Lifescience Database Archive (English)

    Full Text Available n involved in bud-site selection; diploid mutants display a random budding pattern instead of the wild-type bipolar pattern; Bud32p || http://www.ncbi.nlm.nih.gov/protein/6321701 ...

  17. Sequence Classification: 892481 [

    Lifescience Database Archive (English)

    Full Text Available n involved in bud-site selection; diploid mutants display a random budding pattern instead of the wild-type bipolar pattern; Bud20p || http://www.ncbi.nlm.nih.gov/protein/6323103 ...

  18. Sequence Classification: 891700 [

    Lifescience Database Archive (English)

    Full Text Available in involved in bud-site selection; diploid mutants display a random budding pattern instead of the wild-type bipolar pattern; Bud25p || http://www.ncbi.nlm.nih.gov/protein/13112038 ...

  19. Sequence Classification: 889164 [

    Lifescience Database Archive (English)

    Full Text Available n involved in bud-site selection; diploid mutants display a random budding pattern instead of the wild-type bipolar pattern; Bud31p || http://www.ncbi.nlm.nih.gov/protein/6319908 ...

  20. Conversion of the random amplified polymorphic DNA (RAPD ...

    African Journals Online (AJOL)

    Conversion of the random amplified polymorphic DNA (RAPD) marker UBC#116 linked to Fusarium crown and root rot resistance gene (Frl) into a co-dominant sequence characterized amplified region (SCAR) marker for marker-assisted selection of tomato.

  1. Motor sequence chunking is impaired by basal ganglia stroke.

    Science.gov (United States)

    Boyd, L A; Edwards, J D; Siengsukon, C S; Vidoni, E D; Wessel, B D; Linsdell, M A

    2009-07-01

    Our main aim was to determine whether individuals with stroke that affected the basal ganglia, organized movement sequences into chunks in the same fashion as neurologically intact individuals. To address this question, we compared motor response times during the performance of repeated sequences that were learned, and thus may be planned in advance, with random sequences where there is minimal if any advance preparation or organization of responses. The pattern of responses illustrated that, after basal ganglia stroke, individuals do not chunk elements of the repeated sequence into functional sub-sequences of movement to the same extent as neurologically intact age-matched people. Limited chunking of learned movements after stroke may explain past findings that show overall slower responses even when sequences of action are learned by this population. Further, our data in combination with other work, suggest that chunking may be a function of the basal ganglia.

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

    CSIR Research Space (South Africa)

    Vlok, JD

    2014-06-01

    Full Text Available system is a BPSK DSSS system, both c and d are sequences with values ±1. The noise sequence is assumed to be a realisation of a standard normal random variable (RV) represented by w ∼ N (0, 1) which contains independent and identically distributed (i... receiver must be equipped with powerful tech- niques to detect the signals and estimate their parameter values at very low SNR levels. The BER that can be tolerated in a system depends on the application; it has been reported that in wireless multimedia...

  3. Adaptive Processing for Sequence Alignment

    KAUST Repository

    Zidan, Mohammed A.

    2012-01-26

    Disclosed are various embodiments for adaptive processing for sequence alignment. In one embodiment, among others, a method includes obtaining a query sequence and a plurality of database sequences. A first portion of the plurality of database sequences is distributed to a central processing unit (CPU) and a second portion of the plurality of database sequences is distributed to a graphical processing unit (GPU) based upon a predetermined splitting ratio associated with the plurality of database sequences, where the database sequences of the first portion are shorter than the database sequences of the second portion. A first alignment score for the query sequence is determined with the CPU based upon the first portion of the plurality of database sequences and a second alignment score for the query sequence is determined with the GPU based upon the second portion of the plurality of database sequences.

  4. Improving randomness characterization through Bayesian model selection.

    Science.gov (United States)

    Díaz Hernández Rojas, Rafael; Solís, Aldo; Angulo Martínez, Alí M; U'Ren, Alfred B; Hirsch, Jorge G; Marsili, Matteo; Pérez Castillo, Isaac

    2017-06-08

    Random number generation plays an essential role in technology with important applications in areas ranging from cryptography to Monte Carlo methods, and other probabilistic algorithms. All such applications require high-quality sources of random numbers, yet effective methods for assessing whether a source produce truly random sequences are still missing. Current methods either do not rely on a formal description of randomness (NIST test suite) on the one hand, or are inapplicable in principle (the characterization derived from the Algorithmic Theory of Information), on the other, for they require testing all the possible computer programs that could produce the sequence to be analysed. Here we present a rigorous method that overcomes these problems based on Bayesian model selection. We derive analytic expressions for a model's likelihood which is then used to compute its posterior distribution. Our method proves to be more rigorous than NIST's suite and Borel-Normality criterion and its implementation is straightforward. We applied our method to an experimental device based on the process of spontaneous parametric downconversion to confirm it behaves as a genuine quantum random number generator. As our approach relies on Bayesian inference our scheme transcends individual sequence analysis, leading to a characterization of the source itself.

  5. Program Synthesizes UML Sequence Diagrams

    Science.gov (United States)

    Barry, Matthew R.; Osborne, Richard N.

    2006-01-01

    A computer program called "Rational Sequence" generates Universal Modeling Language (UML) sequence diagrams of a target Java program running on a Java virtual machine (JVM). Rational Sequence thereby performs a reverse engineering function that aids in the design documentation of the target Java program. Whereas previously, the construction of sequence diagrams was a tedious manual process, Rational Sequence generates UML sequence diagrams automatically from the running Java code.

  6. Sequence determinants in human polyadenylation site selection

    Directory of Open Access Journals (Sweden)

    Gautheret Daniel

    2003-02-01

    Full Text Available Abstract Background Differential polyadenylation is a widespread mechanism in higher eukaryotes producing mRNAs with different 3' ends in different contexts. This involves several alternative polyadenylation sites in the 3' UTR, each with its specific strength. Here, we analyze the vicinity of human polyadenylation signals in search of patterns that would help discriminate strong and weak polyadenylation sites, or true sites from randomly occurring signals. Results We used human genomic sequences to retrieve the region downstream of polyadenylation signals, usually absent from cDNA or mRNA databases. Analyzing 4956 EST-validated polyadenylation sites and their -300/+300 nt flanking regions, we clearly visualized the upstream (USE and downstream (DSE sequence elements, both characterized by U-rich (not GU-rich segments. The presence of a USE and a DSE is the main feature distinguishing true polyadenylation sites from randomly occurring A(A/UUAAA hexamers. While USEs are indifferently associated with strong and weak poly(A sites, DSEs are more conspicuous near strong poly(A sites. We then used the region encompassing the hexamer and DSE as a training set for poly(A site identification by the ERPIN program and achieved a prediction specificity of 69 to 85% for a sensitivity of 56%. Conclusion The availability of complete genomes and large EST sequence databases now permit large-scale observation of polyadenylation sites. Both U-rich sequences flanking both sides of poly(A signals contribute to the definition of "true" sites. However, the downstream U-rich sequences may also play an enhancing role. Based on this information, poly(A site prediction accuracy was moderately but consistently improved compared to the best previously available algorithm.

  7. Next-generation sequencing

    DEFF Research Database (Denmark)

    Rieneck, Klaus; Bak, Mads; Jønson, Lars

    2013-01-01

    information obtained allows well for statistical analysis of the data. This general approach can be integrated into current laboratory practice and has numerous applications. Besides DNA-based predictions of blood group phenotypes, platelet phenotypes, or sickle cell anemia, and the determination of zygosity......, Illumina); several millions of PCR sequences were analyzed. RESULTS: The results demonstrated the feasibility of diagnosing the fetal KEL1 or KEL2 blood group from cell-free DNA purified from maternal plasma. CONCLUSION: This method requires only one primer pair, and the large amount of sequence...

  8. Some limit theorems for negatively associated random variables

    Indian Academy of Sciences (India)

    Abstract. Let {Xn,n ≥ 1} be a sequence of negatively associated random vari- ables. The aim of this paper is to establish some limit theorems of negatively associated sequence, which include the Lp-convergence theorem and Marcinkiewicz–Zygmund strong law of large numbers. Furthermore, we consider the strong law of ...

  9. A Bayesian approach on molecules and behavior: reconsidering phylogenetic and evolutionary patterns of the Salamandridae with emphasis on Triturus newts.

    Science.gov (United States)

    Steinfartz, Sebastian; Vicario, Saverio; Arntzen, J W; Caccone, Adalgisa

    2007-03-15

    The monophyly of European newts of the genus Triturus within the family Salamandridae has for decades rested on presumably homologous behavioral and morphological characters. Molecular data challenge this hypothesis, but the phylogenetic position of Triturus within the Salamandridae has not yet been convincingly resolved. We addressed this issue and the temporal divergence of Triturus within the Salamandridae with novel Bayesian approaches applied to DNA sequence data from three mitochondrial genes (12S, 16S and cytb). We included 38 salamandrid species comprising all 13 recognized species of Triturus and 16 out of 17 salamandrid genera. A clade comprising all the "Newts" can be separated from the "True Salamanders" and Salamandrina clades. Within the "Newts" well-supported clades are: Tylototriton-Pleurodeles, the "New World Newts" (Notophthalmus-Taricha), and the "Modern Eurasian Newts" (Cynops, Pachytriton, Paramesotriton=together the "Modern Asian Newts", Calotriton, Euproctus, Neurergus and Triturus species). We found that Triturus is a non-monophyletic species assemblage, which includes four groups that are themselves monophyletic: (i) the "Large-Bodied Triturus" (six species), (ii) the "Small-Bodied Triturus" (five species), (iii) T. alpestris and (iv) T. vittatus. We estimated that the last common ancestor of Triturus existed around 64 million years ago (mya) while the root of the Salamandridae dates back to 95 mya. This was estimated using a fossil-based molecular dating approach and an explicit framework to select calibration points that least underestimated their corresponding nodes. Using the molecular phylogeny we mapped the evolution of life history and courtship traits in Triturus and found that several Triturus-specific courtship traits evolved independently. (c) 2006 Wiley-Liss, Inc.

  10. Random broadcast on random geometric graphs

    Energy Technology Data Exchange (ETDEWEB)

    Bradonjic, Milan [Los Alamos National Laboratory; Elsasser, Robert [UNIV OF PADERBORN; Friedrich, Tobias [ICSI/BERKELEY; Sauerwald, Tomas [ICSI/BERKELEY

    2009-01-01

    In this work, we consider the random broadcast time on random geometric graphs (RGGs). The classic random broadcast model, also known as push algorithm, is defined as: starting with one informed node, in each succeeding round every informed node chooses one of its neighbors uniformly at random and informs it. We consider the random broadcast time on RGGs, when with high probability: (i) RGG is connected, (ii) when there exists the giant component in RGG. We show that the random broadcast time is bounded by {Omicron}({radical} n + diam(component)), where diam(component) is a diameter of the entire graph, or the giant component, for the regimes (i), or (ii), respectively. In other words, for both regimes, we derive the broadcast time to be {Theta}(diam(G)), which is asymptotically optimal.

  11. Twin anemia polycythemia sequence

    NARCIS (Netherlands)

    Slaghekke, Femke

    2014-01-01

    In this thesis we describe that Twin Anemia Polycythemia Sequence (TAPS) is a form of chronic feto-fetal transfusion in monochorionic (identical) twins based on a small amount of blood transfusion through very small anastomoses. For the antenatal diagnosis of TAPS, Middle Cerebral Artery – Peak

  12. Sequence Classification: 893720 [

    Lifescience Database Archive (English)

    Full Text Available ial ribosomal protein of the large subunit; MRP51 exhibits genetic interactions with mutations in the COX2 and COX3 mRNA 5'-untransla...ted leader sequences; Mrp51p || http://www.ncbi.nlm.nih.gov/protein/6325139 ...

  13. Goldbach Partitions and Sequences

    Indian Academy of Sciences (India)

    Home; Journals; Resonance – Journal of Science Education; Volume 19; Issue 11. Goldbach Partitions and Sequences. Subhash Kak. General Article Volume 19 Issue 11 November 2014 pp 1028-1037. Fulltext. Click here to view fulltext PDF. Permanent link: http://www.ias.ac.in/article/fulltext/reso/019/11/1028-1037 ...

  14. The Compliment Sequence.

    Science.gov (United States)

    Sims, Anntarie L.

    1989-01-01

    Describes and examines 150 tape-recorded compliment sequences. Reports that the course and outcome of compliments and compliment responses are affected by: (1) the way a compliment is worded; (2) the type of statement that precedes or follows the compliment; and (3) the status and sex of the compliment participants. (RAE)

  15. Biological sequence analysis

    DEFF Research Database (Denmark)

    Durbin, Richard; Eddy, Sean; Krogh, Anders Stærmose

    This book provides an up-to-date and tutorial-level overview of sequence analysis methods, with particular emphasis on probabilistic modelling. Discussed methods include pairwise alignment, hidden Markov models, multiple alignment, profile searches, RNA secondary structure analysis, and phylogene...

  16. Cognitive processing in new and practiced discrete keying sequences

    Directory of Open Access Journals (Sweden)

    Willem B Verwey

    2010-07-01

    Full Text Available This study addresses the role of cognitive control in the initiation and execution of familiar and unfamiliar movement sequences. To become familiar with two movement sequences participants first practiced two discrete key press sequences by responding to two fixed series of 6 key specific stimuli. In the ensuing test phase they executed these two familiar and also two unfamiliar keying sequences while there was a two-third chance a tone was presented together with one randomly selected key specific stimulus in each sequence. In the counting condition of the test phase participants counted the low pitched (i.e., target tones. By and large the results support the dual processor model in which the prime role of the cognitive processor shifts from executing to initiating sequences while the gradual development of motor chunks allows a motor processor to execute the sequences. Yet, the results extend this simple model by suggesting that with little practice sequence execution is based also on some non-cognitive (perhaps associative learning mechanism and, for some participants, on the use of explicit sequence knowledge. Also, after extensive practice the cognitive processor appears to still contribute to slower responses. The occurrence of long interkey intervals was replicated suggesting that fixed 6-key sequences include several motor chunks. Yet, no indication was found that the cognitive processor is responsible for concatenating these chunks.

  17. Determination of the recognition sequence of Mycobacterium smegmatis topoisomerase I on mycobacterial genomic sequences

    OpenAIRE

    Sikder, Devanjan; Nagaraja, Valakunja

    2000-01-01

    Mycobacterium smegmatis topoisomerase I has several distinctive features. The absence of the zinc finger motif found in other prokaryotic type I topoisomerases and the ability of the enzyme to recognise single-stranded and duplex DNA are unique characteristics of the enzyme. We have mapped the strong topoisomerase sites of the enzyme on genomic DNA sequences from Mycobacterium tuberculosis and M.smegmatis. The enzyme does not nick DNA in random fashion and DNA cleavage occurred at a few speci...

  18. Ergodicity of Random Walks on Random DFA

    OpenAIRE

    Balle, Borja

    2013-01-01

    Given a DFA we consider the random walk that starts at the initial state and at each time step moves to a new state by taking a random transition from the current state. This paper shows that for typical DFA this random walk induces an ergodic Markov chain. The notion of typical DFA is formalized by showing that ergodicity holds with high probability when a DFA is sampled uniformly at random from the set of all automata with a fixed number of states. We also show the same result applies to DF...

  19. Sequence Classification: 894257 [

    Lifescience Database Archive (English)

    Full Text Available mutant that displays a random budding pattern; Bud21p || http://www.ncbi.nlm.nih.gov/protein/6324652 ... ...mall ribosomal subunit (SSU) processosome that contains U3 snoRNA; originally isolated as bud-site selection

  20. Sequence Classification: 890642 [

    Lifescience Database Archive (English)

    Full Text Available tern instead of the wild-type bipolar pattern; Bud14p || http://www.ncbi.nlm.nih.gov/protein/41629669 ... ...in bud-site selection, Bud14p-Glc7p complex functions as a cortical regulator of dynein; diploid mutants display a random budding pat

  1. Sequence Classification: 893197 [

    Lifescience Database Archive (English)

    Full Text Available Non-TMB Non-TMH Non-TMB Non-TMB Non-TMB TMB >gi|6324354|ref|NP_014424.1| Protein involved in bud-site select...ion; diploid mutants display a random budding pattern instead of the wild-type bipolar pattern; Bud17p || http://www.ncbi.nlm.nih.gov/protein/6324354 ...

  2. Sequence Classification: 891658 [

    Lifescience Database Archive (English)

    Full Text Available n involved in bud-site selection; diploid mutants display a random budding pattern instead of the wild-type ...Non-TMB Non-TMH Non-TMB Non-TMB Non-TMB Non-TMB >gi|6320806|ref|NP_010885.1| Protei

  3. Random fractional Fourier transform.

    Science.gov (United States)

    Liu, Zhengjun; Liu, Shutian

    2007-08-01

    We propose a novel random fractional Fourier transform by randomizing the transform kernel function of the conventional fractional Fourier transform. The random fractional Fourier transform inherits the excellent mathematical properties from the fractional Fourier transform and can be easily implemented in optics. As a primary application the random fractional Fourier transform can be directly used in optical image encryption and decryption. The double phase encoding image encryption schemes can thus be modeled with cascaded random fractional Fourier transformers.

  4. Targeted sequencing of plant genomes

    Science.gov (United States)

    Mark D. Huynh

    2014-01-01

    Next-generation sequencing (NGS) has revolutionized the field of genetics by providing a means for fast and relatively affordable sequencing. With the advancement of NGS, wholegenome sequencing (WGS) has become more commonplace. However, sequencing an entire genome is still not cost effective or even beneficial in all cases. In studies that do not require a whole-...

  5. Swaps in protein sequences.

    Science.gov (United States)

    Fliess, Amit; Motro, Benny; Unger, Ron

    2002-08-01

    An important question in protein evolution is to what extent proteins may have undergone swaps (switches of domain or fragment order) during evolution. Such events might have occurred in several forms: Swaps of short fragments, swaps of structural and functional motifs, or recombination of domains in multidomain proteins. This question is important for the theoretical understanding of the evolution of proteins, and has practical implications for using swaps as a design tool in protein engineering. In order to analyze the question systematically, we conducted a large scale survey of possible swaps and permutations among all pairs of protein from the Swissport database. A swap is defined as a specific kind of sequence mutation between two proteins in which two fragments that appear in both sequences have different relative order in the two sequences. For example, aXbYc and dYeXf are defined as a swap, where X and Y represent sequence fragments that switched their order. Identifying such swaps is difficult using standard sequence comparison packages. One of the main problems in the analysis stems from the fact that many sequences contain repeats, which may be identified as false-positive swaps. We have used two different approaches to detect pairs of proteins with swaps. The first approach is based on the predefined list of domains in Pfam. We identified all the proteins that share at least two domains and analyzed their relative order, looking for pairs in which the order of these domains was switched. We designed an algorithm to distinguish between real swaps and duplications. In the second approach, we used Blast to detect pairs of proteins that share several fragments. Then, we used an automatic procedure to select pairs that are likely to contain swaps. Those pairs were analyzed visually, using a graphical tool, to eliminate duplications. Combining these approaches, about 140 different cases of swaps in the Swissprot database were found (after eliminating

  6. Scaling behaviors of CG clusters in coding and noncoding DNA sequences

    Energy Technology Data Exchange (ETDEWEB)

    Zhang Linxi [Department of Physics, Wenzhou Normal College, Wenzhou 325027 (China)]. E-mail: lxzhang@hzcnc.com; Chen Jin [Department of Physics, Wenzhou Normal College, Wenzhou 325027 (China)

    2005-04-01

    In this paper the statistical properties of CG clusters in coding and non-coding DNA sequences are investigated through calculating the cluster-size distribution of CG clusters P(S) and the breadth of the distribution of the root-mean-square size of CG clusters {sigma}{sub m} in consecutive, non-overlapping blocks of m bases. There do exist some differences between coding and non-coding sequences. The cluster-size distribution of CG clusters P(S) for both coding and noncoding sequences follows an exponential decay of P(S){proportional_to}e{sup -{alpha}}{sup S}, and the value of {alpha} depends on the percentage of C-G content for coding sequences. It can fit into a linear line regularly but the case is contrary for noncoding sequences. We find that {xi}(m)={sigma}mm of CG clusters all obeys the good power-law decay of {xi}(m){proportional_to}m{sup -{gamma}} in both coding and non-coding sequences, and the value of {gamma} is 0.949+/-0.014 and 0.826+/-0.011 for coding and noncoding sequences, respectively. Therefore, we can distinguish between coding and non-coding sequences on the basis of the value of {gamma}. At the meantime, we also discuss the power-law of {xi}(m){proportional_to}m{sup -{gamma}} for random sequence, and find that the value of {gamma} for random sequence is very close to 1.00. So we can know that the value of {gamma} for coding sequences is more close to the random sequence, and obtain the conclusion that the behavior of coding sequence trends to random sequence more similarly. This investigation can provide some insights into DNA sequences.

  7. Sequence-Dependent Persistence Lengths of DNA.

    Science.gov (United States)

    Mitchell, Jonathan S; Glowacki, Jaroslaw; Grandchamp, Alexandre E; Manning, Robert S; Maddocks, John H

    2017-04-11

    A Monte Carlo code applied to the cgDNA coarse-grain rigid-base model of B-form double-stranded DNA is used to predict a sequence-averaged persistence length of l F = 53.5 nm in the sense of Flory, and of l p = 160 bp or 53.5 nm in the sense of apparent tangent-tangent correlation decay. These estimates are slightly higher than the consensus experimental values of 150 bp or 50 nm, but we believe the agreement to be good given that the cgDNA model is itself parametrized from molecular dynamics simulations of short fragments of length 10-20 bp, with no explicit fit to persistence length. Our Monte Carlo simulations further predict that there can be substantial dependence of persistence lengths on the specific sequence [Formula: see text] of a fragment. We propose, and confirm the numerical accuracy of, a simple factorization that separates the part of the apparent tangent-tangent correlation decay [Formula: see text] attributable to intrinsic shape, from a part [Formula: see text] attributable purely to stiffness, i.e., a sequence-dependent version of what has been called sequence-averaged dynamic persistence length l̅ d (=58.8 nm within the cgDNA model). For ensembles of both random and λ-phage fragments, the apparent persistence length [Formula: see text] has a standard deviation of 4 nm over sequence, whereas our dynamic persistence length [Formula: see text] has a standard deviation of only 1 nm. However, there are notable dynamic persistence length outliers, including poly(A) (exceptionally straight and stiff), poly(TA) (tightly coiled and exceptionally soft), and phased A-tract sequence motifs (exceptionally bent and stiff). The results of our numerical simulations agree reasonably well with both molecular dynamics simulation and diverse experimental data including minicircle cyclization rates and stereo cryo-electron microscopy images.

  8. Exome sequencing reveals a potential mutational trajectory and treatments for a specific pancreatic cancer patient

    Directory of Open Access Journals (Sweden)

    Cotterell J

    2014-05-01

    Full Text Available James Cotterell1,21Center for Genomic Regulation, Barcelona, Spain; 2Garvan Institute for Medical Research, Sydney, NSW, AustraliaAbstract: Pancreatic cancer is the fourth biggest killer, and has one of the worst prognoses, of any cancer type. Approximately 95% of patients diagnosed with pancreatic cancer will not survive beyond 5 years post diagnosis, and these statistics have barely improved in over 40 years. Here, genomic changes in one particular patient with stage IV metastatic pancreatic cancer were explored to suggest a potential personalized treatment. In particular, exome sequencing of genomic DNA extracted from blood and the cancer biopsy was utilized with the aim of identifying mutational drivers of the cancer. This analysis revealed a splice site mutation in RBCK1 as the most promising driver of the cancer and a therapy based on a pan-cyclin-dependent kinase (pan-CDK inhibitor, flavopiridol. This study suggests that drugs whose effectiveness is unclear for general populations of cancer sufferers should possibly be reconsidered for specific patients where the drug could be rationally argued to improve outcome.Keyword: personalized medicine, driver mutation identification, next generation sequencing

  9. Shaking the Tree: Multi-locus Sequence Typing Usurps Current Onchocercid (Filarial Nematode) Phylogeny

    Science.gov (United States)

    Lefoulon, Emilie; Bourret, Jérôme; Junker, Kerstin; Guerrero, Ricardo; Cañizales, Israel; Kuzmin, Yuriy; Satoto, Tri Baskoro T.; Cardenas-Callirgos, Jorge Manuel; de Souza Lima, Sueli; Raccurt, Christian; Mutafchiev, Yasen; Gavotte, Laurent; Martin, Coralie

    2015-01-01

    During the past twenty years, a number of molecular analyses have been performed to determine the evolutionary relationships of Onchocercidae, a family of filarial nematodes encompassing several species of medical or veterinary importance. However, opportunities for broad taxonomic sampling have been scarce, and analyses were based mainly on 12S rDNA and coxI gene sequences. While being suitable for species differentiation, these mitochondrial genes cannot be used to infer phylogenetic hypotheses at higher taxonomic levels. In the present study, 48 species, representing seven of eight subfamilies within the Onchocercidae, were sampled and sequences of seven gene loci (nuclear and mitochondrial) analysed, resulting in the hitherto largest molecular phylogenetic investigation into this family. Although our data support the current hypothesis that the Oswaldofilariinae, Waltonellinae and Icosiellinae subfamilies separated early from the remaining onchocercids, Setariinae was recovered as a well separated clade. Dirofilaria, Loxodontofilaria and Onchocerca constituted a strongly supported clade despite belonging to different subfamilies (Onchocercinae and Dirofilariinae). Finally, the separation between Splendidofilariinae, Dirofilariinae and Onchocercinae will have to be reconsidered. PMID:26588229

  10. L’accès aux ressources en création d’entreprise: vers une reconsidération des facteurs sociaux

    Directory of Open Access Journals (Sweden)

    Amina Omrane

    2015-03-01

    Full Text Available Les travaux de recherche en entrepreneuriat ont largement mis en valeur le capital relationnel d’un porteur de projet et sa contribution à l’acquisition des moyens financiers, des informations et du support social. Ceci revient à ce que l’entrepreneur, dès qu’il se trouve emporté par le désir d’assurer la survie et le rayonnement de son projet, il se trouve le plus souvent confronté à un handicap de financier mitigé à un manque d’informations et de support social en provenance de ses collaborateurs. Or, toujours est-il que le capital social entrepreneurial en soi suscite une polémique et une interrogation sur les facteurs qui propulsent son développement. Dans cette perspective, nous proposons de centrer notre réflexion sur les compétences sociales afin d’apporter un éclairage à la manière dont se forme le capital relationnel du porteur d’un projet. Dans le même sillage d’idées, nous soulignons les influences que ces habiletés sont susceptibles d’exercer autant sur la mobilisation des moyens nécessaires que sur l’extension du capital relationnel de l’entrepreneur. Une investigation qualitative conduite sur une dizaine de porteurs de projets tunisiens a été effectuée pour tester ces propos, via une reconsidération des catégories d’aptitudes socio-relationnelles les plus saillantes.

  11. Random walks in a random environment

    Indian Academy of Sciences (India)

    Home; Journals; Proceedings – Mathematical Sciences; Volume 114; Issue 4. Random Walks in a Random Environment. S R S Varadhan. Invited Articles Volume 114 Issue ... Author Affiliations. S R S Varadhan1. Department of Mathematics, Courant Institute of Mathematical Sciences, New York University, NY 10012, USA ...

  12. New Design of Crypto-Based Pseudo random number generator (CBPRNG) using BLOW FISH cipher

    OpenAIRE

    T.Chalama Reddy; Dr.R.Seshadri

    2013-01-01

    Random Number Generators (RNGs) are an important building block for algorithms and protocols in cryptography. Random number generation is used in a wide variety of cryptographic operations, such as key generation and challenge/response protocols. A random number generator outputs a sequence of 0s and 1s such that at any position, the next bit cannot be expected on the previous bits. However, true random number produces non- deterministic output since if the same random generator is run twice,...

  13. Yeast genome sequencing:

    DEFF Research Database (Denmark)

    Piskur, Jure; Langkjær, Rikke Breinhold

    2004-01-01

    they are short and degenerate and occupy different positions. Comparative genomics helps to understand the origin of yeasts and points out crucial molecular events in yeast evolutionary history, such as whole-genome duplication and horizontal gene transfer(s). In addition, the accumulating sequence data provide...... that the minimum number of genes from each species that need to be compared to produce a reliable phylogeny is about 20. Yeast has also become an attractive model to study speciation in eukaryotes, especially to understand molecular mechanisms behind the establishment of reproductive isolation. Comparison...... of closely related species helps in gene annotation and to answer how many genes there really are within the genomes. Analysis of non-coding regions among closely related species has provided an example of how to determine novel gene regulatory sequences, which were previously difficult to analyse because...

  14. Moebius syndrome (moebius sequence)

    OpenAIRE

    A.A. Desai; Bansal, Sandeep

    1999-01-01

    Moebius Syndrome is one of the rare disorder amongst the oromandibular limb hypogenesis. It is of a unknown atiology with sporadic occurrence in which there is congenital bilateral facial palsy,-bilateral involvement of abducent nerve along with other cranial nerves like III, V, IX, X, Xllth and the patient having masklike expressionless face. We are reporting a case of Moebius Sequence who presented to us in the department of ENT and Head and Neck Surgery, Baroda.

  15. Moebius syndrome (moebius sequence).

    Science.gov (United States)

    Desai, A A; Bansal, S

    1999-10-01

    Moebius Syndrome is one of the rare disorder amongst the oromandibular limb hypogenesis. It is of a unknown atiology with sporadic occurrence in which there is congenital bilateral facial palsy,-bilateral involvement of abducent nerve along with other cranial nerves like III, V, IX, X, Xllth and the patient having masklike expressionless face. We are reporting a case of Moebius Sequence who presented to us in the department of ENT and Head and Neck Surgery, Baroda.

  16. Random walks on random Koch curves

    Energy Technology Data Exchange (ETDEWEB)

    Seeger, S; Hoffmann, K H [Institut fuer Physik, Technische Universitaet, D-09107 Chemnitz (Germany); Essex, C [Department of Applied Mathematics, University of Western Ontario, London, ON N6A 5B7 (Canada)

    2009-06-05

    Diffusion processes in porous materials are often modeled as random walks on fractals. In order to capture the randomness of the materials random fractals are employed, which no longer show the deterministic self-similarity of regular fractals. Finding a continuum differential equation describing the diffusion on such fractals has been a long-standing goal, and we address the question of whether the concepts developed for regular fractals are still applicable. We use the random Koch curve as a convenient example as it provides certain technical advantages by its separation of time and space features. While some of the concepts developed for regular fractals can be used unaltered, others have to be modified. Based on the concept of fibers, we introduce ensemble-averaged density functions which produce a differentiable estimate of probability explicitly and compare it to random walk data.

  17. Evolutionary optimization of biopolymers and sequence structure maps

    Energy Technology Data Exchange (ETDEWEB)

    Reidys, C.M.; Kopp, S.; Schuster, P. [Institut fuer Molekulare Biotechnologie, Jena (Germany)

    1996-06-01

    Searching for biopolymers having a predefined function is a core problem of biotechnology, biochemistry and pharmacy. On the level of RNA sequences and their corresponding secondary structures we show that this problem can be analyzed mathematically. The strategy will be to study the properties of the RNA sequence to secondary structure mapping that is essential for the understanding of the search process. We show that to each secondary structure s there exists a neutral network consisting of all sequences folding into s. This network can be modeled as a random graph and has the following generic properties: it is dense and has a giant component within the graph of compatible sequences. The neutral network percolates sequence space and any two neutral nets come close in terms of Hamming distance. We investigate the distribution of the orders of neutral nets and show that above a certain threshold the topology of neutral nets allows to find practically all frequent secondary structures.

  18. Interpolation of missing data in image sequences.

    Science.gov (United States)

    Kokaram, A C; Morris, R D; Fitzgerald, W J; Rayner, P W

    1995-01-01

    This paper presents a number of model based interpolation schemes tailored to the problem of interpolating missing regions in image sequences. These missing regions may be of arbitrary size and of random, but known, location. This problem occurs regularly with archived film material. The film is abraded or obscured in patches, giving rise to bright and dark flashes, known as "dirt and sparkle" in the motion picture industry. Both 3-D autoregressive models and 3-D Markov random fields are considered in the formulation of the different reconstruction processes. The models act along motion directions estimated using a multiresolution block matching scheme. It is possible to address this sort of impulsive noise suppression problem with median filters, and comparisons with earlier work using multilevel median filters are performed. These comparisons demonstrate the higher reconstruction fidelity of the new interpolators.

  19. Sequencing BPS spectra

    Energy Technology Data Exchange (ETDEWEB)

    Gukov, Sergei [Walter Burke Institute for Theoretical Physics, California Institute of Technology,1200 E California Blvd, Pasadena, CA 91125 (United States); Max-Planck-Institut für Mathematik,Vivatsgasse 7, D-53111 Bonn (Germany); Nawata, Satoshi [Walter Burke Institute for Theoretical Physics, California Institute of Technology,1200 E California Blvd, Pasadena, CA 91125 (United States); Centre for Quantum Geometry of Moduli Spaces, University of Aarhus,Nordre Ringgade 1, DK-8000 (Denmark); Saberi, Ingmar [Walter Burke Institute for Theoretical Physics, California Institute of Technology,1200 E California Blvd, Pasadena, CA 91125 (United States); Stošić, Marko [CAMGSD, Departamento de Matemática, Instituto Superior Técnico,Av. Rovisco Pais, 1049-001 Lisbon (Portugal); Mathematical Institute SANU,Knez Mihajlova 36, 11000 Belgrade (Serbia); Sułkowski, Piotr [Walter Burke Institute for Theoretical Physics, California Institute of Technology,1200 E California Blvd, Pasadena, CA 91125 (United States); Faculty of Physics, University of Warsaw,ul. Pasteura 5, 02-093 Warsaw (Poland)

    2016-03-02

    This paper provides both a detailed study of color-dependence of link homologies, as realized in physics as certain spaces of BPS states, and a broad study of the behavior of BPS states in general. We consider how the spectrum of BPS states varies as continuous parameters of a theory are perturbed. This question can be posed in a wide variety of physical contexts, and we answer it by proposing that the relationship between unperturbed and perturbed BPS spectra is described by a spectral sequence. These general considerations unify previous applications of spectral sequence techniques to physics, and explain from a physical standpoint the appearance of many spectral sequences relating various link homology theories to one another. We also study structural properties of colored HOMFLY homology for links and evaluate Poincaré polynomials in numerous examples. Among these structural properties is a novel “sliding” property, which can be explained by using (refined) modular S-matrix. This leads to the identification of modular transformations in Chern-Simons theory and 3d N=2 theory via the 3d/3d correspondence. Lastly, we introduce the notion of associated varieties as classical limits of recursion relations of colored superpolynomials of links, and study their properties.

  20. Image sequence analysis

    CERN Document Server

    1981-01-01

    The processing of image sequences has a broad spectrum of important applica­ tions including target tracking, robot navigation, bandwidth compression of TV conferencing video signals, studying the motion of biological cells using microcinematography, cloud tracking, and highway traffic monitoring. Image sequence processing involves a large amount of data. However, because of the progress in computer, LSI, and VLSI technologies, we have now reached a stage when many useful processing tasks can be done in a reasonable amount of time. As a result, research and development activities in image sequence analysis have recently been growing at a rapid pace. An IEEE Computer Society Workshop on Computer Analysis of Time-Varying Imagery was held in Philadelphia, April 5-6, 1979. A related special issue of the IEEE Transactions on Pattern Anal­ ysis and Machine Intelligence was published in November 1980. The IEEE Com­ puter magazine has also published a special issue on the subject in 1981. The purpose of this book ...

  1. Influence of different copolymer sequences in low band gap polymers on their performance in organic solar cells

    NARCIS (Netherlands)

    Lange, Alexander; Krueger, Hartmut; Ecker, Bernhard; Tunc, Ali Veysel; von Hauff, Elizabeth; Morana, Mauro

    2012-01-01

    The chemical design of a polymer can be tailored by a random or a block sequence of the comonomers in order to influence the properties of the final material. In this work, two sequences, PCPDTBT and F8BT (F8), were polymerized to form a block or a random copolymer. Differences between the various

  2. Whistle sequences in wild killer whales (Orcinus orca).

    Science.gov (United States)

    Riesch, Rüdiger; Ford, John K B; Thomsen, Frank

    2008-09-01

    Combining different stereotyped vocal signals into specific sequences increases the range of information that can be transferred between individuals. The temporal emission pattern and the behavioral context of vocal sequences have been described in detail for a variety of birds and mammals. Yet, in cetaceans, the study of vocal sequences is just in its infancy. Here, we provide a detailed analysis of sequences of stereotyped whistles in killer whales off Vancouver Island, British Columbia. A total of 1140 whistle transitions in 192 whistle sequences recorded from resident killer whales were analyzed using common spectrographic analysis techniques. In addition to the stereotyped whistles described by Riesch et al., [(2006). "Stability and group specificity of stereotyped whistles in resident killer whales, Orcinus orca, off British Columbia," Anim. Behav. 71, 79-91.] We found a new and rare stereotyped whistle (W7) as well as two whistle elements, which are closely linked to whistle sequences: (1) stammers and (2) bridge elements. Furthermore, the frequency of occurrence of 12 different stereotyped whistle types within the sequences was not randomly distributed and the transition patterns between whistles were also nonrandom. Finally, whistle sequences were closely tied to close-range behavioral interactions (in particular among males). Hence, we conclude that whistle sequences in wild killer whales are complex signal series and propose that they are most likely emitted by single individuals.

  3. Sequence signatures of nucleosome positioning in Caenorhabditis elegans.

    Science.gov (United States)

    Chen, Kaifu; Wang, Lei; Yang, Meng; Liu, Jiucheng; Xin, Chengqi; Hu, Songnian; Yu, Jun

    2010-06-01

    Our recent investigation in the protist Trichomonas vaginalis suggested a DNA sequence periodicity with a unit length of 120.9 nt, which represents a sequence signature for nucleosome positioning. We now extended our observation in higher eukaryotes and identified a similar periodicity of 175 nt in length in Caenorhabditis elegans. In the process of defining the sequence compositional characteristics, we found that the 10.5-nt periodicity, the sequence signature of DNA double helix, may not be sufficient for cross-nucleosome positioning but provides essential guiding rails to facilitate positioning. We further dissected nucleosome-protected sequences and identified a strong positive purine (AG) gradient from the 5'-end to the 3'-end, and also learnt that the nucleosome-enriched regions are GC-rich as compared to the nucleosome-free sequences as purine content is positively correlated with GC content. Sequence characterization allowed us to develop a hidden Markov model (HMM) algorithm for decoding nucleosome positioning computationally, and based on a set of training data from the fifth chromosome of C. elegans, our algorithm predicted 60%-70% of the well-positioned nucleosomes, which is 15%-20% higher than random positioning. We concluded that nucleosomes are not randomly positioned on DNA sequences and yet bind to different genome regions with variable stability, well-positioned nucleosomes leave sequence signatures on DNA, and statistical positioning of nucleosomes across genome can be decoded computationally based on these sequence signatures. Copyright 2010 Beijing Genomics Institute. Published by Elsevier Ltd. All rights reserved.

  4. Plant DNA sequencing for phylogenetic analyses: from plants to sequences.

    Science.gov (United States)

    Neves, Susana S; Forrest, Laura L

    2011-01-01

    DNA sequences are important sources of data for phylogenetic analysis. Nowadays, DNA sequencing is a routine technique in molecular biology laboratories. However, there are specific questions associated with project design and sequencing of plant samples for phylogenetic analysis, which may not be familiar to researchers starting in the field. This chapter gives an overview of methods and protocols involved in the sequencing of plant samples, including general recommendations on the selection of species/taxa and DNA regions to be sequenced, and field collection of plant samples. Protocols of plant sample preparation, DNA extraction, PCR and cloning, which are critical to the success of molecular phylogenetic projects, are described in detail. Common problems of sequencing (using the Sanger method) are also addressed. Possible applications of second-generation sequencing techniques in plant phylogenetics are briefly discussed. Finally, orientation on the preparation of sequence data for phylogenetic analyses and submission to public databases is also given.

  5. Sequence analysis of mitochondrial 16S ribosomal RNA gene ...

    Indian Academy of Sciences (India)

    Unknown

    restriction fragment length polymorphism; RAPD, random amplified polymorphic DNA; An. step, Anopheles stephensi; An. quad,. Anopheles ... interesting feature of the sequences was a stretch of Ts that distinguished between Aedes and Culex on the one hand, and ... genome structure and complexity of mosquito species.

  6. Comparative effectiveness of inter-simple sequence repeat and ...

    African Journals Online (AJOL)

    iisr

    2013-10-10

    Oct 10, 2013 ... whereas RAPD markers showed segregation based on geographical location as well as species based. Key words: Garcinia, genetic diversity, inter-simple sequence repeats, randomly amplified polymorphic DNA, principal component analysis. INTRODUCTION. Garcinia is a large genus with 240 species ...

  7. Flanking region sequence information to refine microRNA target ...

    Indian Academy of Sciences (India)

    Prakash

    block of four bases or more could be required by the target sites to find suitable interactions with the targeting ... end, and (ii) randomized target UTRs retaining the same nucleotide composition, in order to avoid any ... analysis were the complete target region of 70-base flanking sequences around the microRNA target site.

  8. Psychoacoustic Properties of Fibonacci Sequences

    Directory of Open Access Journals (Sweden)

    J. Sokoll

    2008-01-01

    Full Text Available 1202, Fibonacci set up one of the most interesting sequences in number theory. This sequence can be represented by so-called Fibonacci Numbers, and by a binary sequence of zeros and ones. If such a binary Fibonacci Sequence is played back as an audio file, a very dissonant sound results. This is caused by the “almost-periodic”, “self-similar” property of the binary sequence. The ratio of zeros and ones converges to the golden ratio, as do the primary and secondary spectral components intheir frequencies and amplitudes. These Fibonacci Sequences will be characterized using listening tests and psychoacoustic analyses. 

  9. Randomized Prediction Games for Adversarial Machine Learning.

    Science.gov (United States)

    Rota Bulo, Samuel; Biggio, Battista; Pillai, Ignazio; Pelillo, Marcello; Roli, Fabio

    In spam and malware detection, attackers exploit randomization to obfuscate malicious data and increase their chances of evading detection at test time, e.g., malware code is typically obfuscated using random strings or byte sequences to hide known exploits. Interestingly, randomization has also been proposed to improve security of learning algorithms against evasion attacks, as it results in hiding information about the classifier to the attacker. Recent work has proposed game-theoretical formulations to learn secure classifiers, by simulating different evasion attacks and modifying the classification function accordingly. However, both the classification function and the simulated data manipulations have been modeled in a deterministic manner, without accounting for any form of randomization. In this paper, we overcome this limitation by proposing a randomized prediction game, namely, a noncooperative game-theoretic formulation in which the classifier and the attacker make randomized strategy selections according to some probability distribution defined over the respective strategy set. We show that our approach allows one to improve the tradeoff between attack detection and false alarms with respect to the state-of-the-art secure classifiers, even against attacks that are different from those hypothesized during design, on application examples including handwritten digit recognition, spam, and malware detection.In spam and malware detection, attackers exploit randomization to obfuscate malicious data and increase their chances of evading detection at test time, e.g., malware code is typically obfuscated using random strings or byte sequences to hide known exploits. Interestingly, randomization has also been proposed to improve security of learning algorithms against evasion attacks, as it results in hiding information about the classifier to the attacker. Recent work has proposed game-theoretical formulations to learn secure classifiers, by simulating different

  10. ERP Indices of Stimulus Prediction in Letter Sequences

    Directory of Open Access Journals (Sweden)

    Edith Kaan

    2014-10-01

    Full Text Available Given the current focus on anticipation in perception, action and cognition, including language processing, there is a need for a method to tap into predictive processing in situations in which cue and feedback stimuli are not explicitly marked as such. To this aim, event related potentials (ERPs were obtained while participants viewed alphabetic letter sequences (“A”, “B”, “C”, “D”, “E”, …, in which the letters were highly predictable, and random sequences (“S”, “B”, “A”, “I”, “F”, “M”, …, without feedback. Occasionally, the presentation of a letter in a sequence was delayed by 300 ms. During this delay period, an increased negativity was observed for predictive versus random sequences. In addition, the early positivity following the delay was larger for predictive compared with random sequences. These results suggest that expectation-sensitive ERP modulations can be elicited in anticipation of stimuli that are not explicit targets, rewards, feedback or instructions, and that a delay can strengthen the prediction for a particular stimulus. Applications to language processing will be discussed.

  11. Novel expressed sequence tag- simple sequence repeats (EST-SSR)

    African Journals Online (AJOL)

    Using different bioinformatic criteria, the SUCEST database was used to mine for simple sequence repeat (SSR) markers. Among 42,189 clusters, 1,425 expressed sequence tag- simple sequence repeats (EST-SSRs) were identified in silico. Trinucleotide repeats were the most abundant SSRs detected. Of 212 primer pairs ...

  12. Explicit motor sequence learning with the paretic arm after stroke.

    Science.gov (United States)

    Fleming, Melanie K; Newham, Di J; Rothwell, John C

    2018-02-01

    Motor sequence learning is important for stroke recovery, but experimental tasks require dexterous movements, which are impossible for people with upper limb impairment. This makes it difficult to draw conclusions about the impact of stroke on learning motor sequences. We aimed to test a paradigm requiring gross arm movements to determine whether stroke survivors with upper limb impairment were capable of learning a movement sequence as effectively as age-matched controls. In this case-control study, 12 stroke survivors (10-138 months post-stroke, mean age 64 years) attempted the task once using their affected arm. Ten healthy controls (mean 66 years) used their non-dominant arm. A sequence of 10 movements was repeated 25 times. The variables were: time from target illumination until the cursor left the central square (onset time; OT), accuracy (path length), and movement speed. OT reduced with training (p  0.1). We quantified learning as the OT difference between the end of training and a random sequence; this was smaller for stroke survivors than controls (p = 0.015). Stroke survivors can learn a movement sequence with their paretic arm, but demonstrate impairments in sequence specific learning. Implications for Rehabilitation Motor sequence learning is important for recovery of movement after stroke. Stroke survivors were found to be capable of learning a movement sequence with their paretic arm, supporting the concept of repetitive task training for recovery of movement. Stroke survivors showed impaired sequence specific learning in comparison with age-matched controls, indicating that they may need more repetitions of a sequence in order to re-learn movements. Further research is required into the effect of lesion location, time since stroke, hand dominance and gender on learning of motor sequences after stroke.

  13. Random matrices, random processes and integrable systems

    CERN Document Server

    2011-01-01

    This book explores the remarkable connections between two domains that, a priori, seem unrelated: Random matrices (together with associated random processes) and integrable systems. The relations between random matrix models and the theory of classical integrable systems have long been studied. These appear mainly in the deformation theory, when parameters characterizing the measures or the domain of localization of the eigenvalues are varied. The resulting differential equations determining the partition function and correlation functions are, remarkably, of the same type as certain equations appearing in the theory of integrable systems. They may be analyzed effectively through methods based upon the Riemann-Hilbert problem of analytic function theory and by related approaches to the study of nonlinear asymptotics in the large N limit. Associated with studies of matrix models are certain stochastic processes, the "Dyson processes", and their continuum diffusion limits, which govern the spectrum in random ma...

  14. Tuning of the sequence technique

    OpenAIRE

    Laude, Dominique; Baudrie, Véronique; Elghozi, Jean-Luc

    2009-01-01

    The sequence method was first described in cats, and applied in different species including humans. Up to now, there is no systematic study of the spontaneous baroreflex sensitivity (BRS) estimated by the sequence method to mice.

  15. Time-dependent ARMA modeling of genomic sequences.

    Science.gov (United States)

    Zielinski, Jerzy S; Bouaynaya, Nidhal; Schonfeld, Dan; O'Neill, William

    2008-08-12

    in the nucleotide chain. Specifically, we define a quantitative measure of randomness to assess how far a process deviates from white noise. Our simulation results on various gene sequences show that both the coding and non-coding regions are non-random. However, coding sequences are "whiter" than non-coding sequences as attested by a higher index of randomness. We demonstrate that the proposed TD-ARMA model can be used to provide a stable time series tool for the analysis of non-stationary genomic sequences. The estimated time-varying coefficients are used to define an index of randomness, in order to assess the statistical correlations in coding and non-coding DNA sequences. It turns out that the statistical differences between coding and non-coding sequences are more subtle than previously thought using stationary analysis tools: Both coding and non-coding sequences exhibit statistical correlations, with the coding regions being "whiter" than the non-coding regions. These results corroborate the evolutionary periodogram analysis of genomic sequences and revoke the stationary analysis' conclusion that coding DNA behaves like random sequences.

  16. The complexity of sequences generated by the arc-fractal system.

    Directory of Open Access Journals (Sweden)

    Hoai Nguyen Huynh

    Full Text Available We study properties of the symbolic sequences extracted from the fractals generated by the arc-fractal system introduced earlier by Huynh and Chew. The sequences consist of only a few symbols yet possess several nontrivial properties. First using an operator approach, we show that the sequences are not periodic, even though they are constructed from very simple rules. Second by employing the ϵ-machine approach developed by Crutchfield and Young, we measure the complexity and randomness of the sequences and show that they are indeed complex, i.e. neither periodic nor random, with the value of complexity measure being significant as compared to the known example of logistic map at the edge of chaos. The complexity and randomness of the sequences are then discussed in relation with the properties of associated fractal objects, such as their fractal dimension, symmetry and orientations of the arcs.

  17. The Complexity of Sequences Generated by the Arc-Fractal System

    Science.gov (United States)

    Huynh, Hoai Nguyen; Pradana, Andri; Chew, Lock Yue

    2015-01-01

    We study properties of the symbolic sequences extracted from the fractals generated by the arc-fractal system introduced earlier by Huynh and Chew. The sequences consist of only a few symbols yet possess several nontrivial properties. First using an operator approach, we show that the sequences are not periodic, even though they are constructed from very simple rules. Second by employing the ϵ-machine approach developed by Crutchfield and Young, we measure the complexity and randomness of the sequences and show that they are indeed complex, i.e. neither periodic nor random, with the value of complexity measure being significant as compared to the known example of logistic map at the edge of chaos. The complexity and randomness of the sequences are then discussed in relation with the properties of associated fractal objects, such as their fractal dimension, symmetry and orientations of the arcs. PMID:25700034

  18. Sequence Handling by Sequence Analysis Toolbox v1.0

    DEFF Research Database (Denmark)

    Ingrell, Christian Ravnsborg; Matthiesen, Rune; Jensen, Ole Nørregaard

    2006-01-01

    The fact that mass spectrometry have become a high-throughput method calls for bioinformatic tools for automated sequence handling and prediction. For efficient use of bioinformatic tools, it is important that these tools are integrated or interfaced with each other. The purpose of sequence...... analysis toolbox v1.0 was to have a general purpose sequence analyzing tool that can import sequences obtained by high-throughput sequencing methods. The program includes algorithms for calculation or prediction of isoelectric point, hydropathicity index, transmembrane segments, and glycosylphosphatidyl...

  19. Rapid Polymer Sequencer

    Science.gov (United States)

    Stolc, Viktor (Inventor); Brock, Matthew W (Inventor)

    2013-01-01

    Method and system for rapid and accurate determination of each of a sequence of unknown polymer components, such as nucleic acid components. A self-assembling monolayer of a selected substance is optionally provided on an interior surface of a pipette tip, and the interior surface is immersed in a selected liquid. A selected electrical field is impressed in a longitudinal direction, or in a transverse direction, in the tip region, a polymer sequence is passed through the tip region, and a change in an electrical current signal is measured as each polymer component passes through the tip region. Each of the measured changes in electrical current signals is compared with a database of reference electrical change signals, with each reference signal corresponding to an identified polymer component, to identify the unknown polymer component with a reference polymer component. The nanopore preferably has a pore inner diameter of no more than about 40 nm and is prepared by heating and pulling a very small section of a glass tubing.

  20. Misuse of randomization

    DEFF Research Database (Denmark)

    Liu, Jianping; Kjaergard, Lise Lotte; Gluud, Christian

    2002-01-01

    The quality of randomization of Chinese randomized trials on herbal medicines for hepatitis B was assessed. Search strategy and inclusion criteria were based on the published protocol. One hundred and seventy-six randomized clinical trials (RCTs) involving 20,452 patients with chronic hepatitis B....../150) of the studies were imbalanced at the 0.05 level of probability for the two treatments and 13.3% (20/150) imbalanced at the 0.01 level in the randomization. It is suggested that there may exist misunderstanding of the concept and the misuse of randomization based on the review....

  1. Multiple sequence alignments of partially coding nucleic acid sequences

    Directory of Open Access Journals (Sweden)

    Fried Claudia

    2005-06-01

    Full Text Available Abstract Background High quality sequence alignments of RNA and DNA sequences are an important prerequisite for the comparative analysis of genomic sequence data. Nucleic acid sequences, however, exhibit a much larger sequence heterogeneity compared to their encoded protein sequences due to the redundancy of the genetic code. It is desirable, therefore, to make use of the amino acid sequence when aligning coding nucleic acid sequences. In many cases, however, only a part of the sequence of interest is translated. On the other hand, overlapping reading frames may encode multiple alternative proteins, possibly with intermittent non-coding parts. Examples are, in particular, RNA virus genomes. Results The standard scoring scheme for nucleic acid alignments can be extended to incorporate simultaneously information on translation products in one or more reading frames. Here we present a multiple alignment tool, codaln, that implements a combined nucleic acid plus amino acid scoring model for pairwise and progressive multiple alignments that allows arbitrary weighting for almost all scoring parameters. Resource requirements of codaln are comparable with those of standard tools such as ClustalW. Conclusion We demonstrate the applicability of codaln to various biologically relevant types of sequences (bacteriophage Levivirus and Vertebrate Hox clusters and show that the combination of nucleic acid and amino acid sequence information leads to improved alignments. These, in turn, increase the performance of analysis tools that depend strictly on good input alignments such as methods for detecting conserved RNA secondary structure elements.

  2. Sequence Factorial and Its Applications

    Science.gov (United States)

    Asiru, Muniru A.

    2012-01-01

    In this note, we introduce sequence factorial and use this to study generalized M-bonomial coefficients. For the sequence of natural numbers, the twin concepts of sequence factorial and generalized M-bonomial coefficients, respectively, extend the corresponding concepts of factorial of an integer and binomial coefficients. Some latent properties…

  3. The advantages of SMRT sequencing.

    Science.gov (United States)

    Roberts, Richard J; Carneiro, Mauricio O; Schatz, Michael C

    2013-07-03

    Of the current next-generation sequencing technologies, SMRT sequencing is sometimes overlooked. However, attributes such as long reads, modified base detection and high accuracy make SMRT a useful technology and an ideal approach to the complete sequencing of small genomes.

  4. Blazar Sequence in Fermi Era

    Indian Academy of Sciences (India)

    2016-01-27

    Jan 27, 2016 ... In this paper, we review the latest research results on the topic of blazar sequence. It seems that the blazar sequence is phenomenally ruled out, while the theoretical blazar sequence still holds. We point out that black hole mass is a dominated parameter accounting for high-power-high-synchrotron-peaked ...

  5. Allele Re-sequencing Technologies

    DEFF Research Database (Denmark)

    Byrne, Stephen; Farrell, Jacqueline Danielle; Asp, Torben

    2013-01-01

    The development of next-generation sequencing technologies has made sequencing an affordable approach for detection of genetic variations associated with various traits. However, the cost of whole genome re-sequencing still remains too high to be feasible for many plant species with large and com...

  6. Region segmentation along image sequence

    Energy Technology Data Exchange (ETDEWEB)

    Monchal, L.; Aubry, P.

    1995-12-31

    A method to extract regions in sequence of images is proposed. Regions are not matched from one image to the following one. The result of a region segmentation is used as an initialization to segment the following and image to track the region along the sequence. The image sequence is exploited as a spatio-temporal event. (authors). 12 refs., 8 figs.

  7. Children's discrimination of vowel sequences

    Science.gov (United States)

    Coady, Jeffry A.; Kluender, Keith R.; Evans, Julia

    2003-10-01

    Children's ability to discriminate sequences of steady-state vowels was investigated. Vowels (as in ``beet,'' ``bat,'' ``bought,'' and ``boot'') were synthesized at durations of 40, 80, 160, 320, 640, and 1280 ms. Four different vowel sequences were created by concatenating different orders of vowels for each duration, separated by 10-ms intervening silence. Thus, sequences differed in vowel order and duration (rate). Sequences were 12 s in duration, with amplitude ramped linearly over the first and last 2 s. Sequence pairs included both same (identical sequences) and different trials (sequences with vowels in different orders). Sequences with vowel of equal duration were presented on individual trials. Children aged 7;0 to 10;6 listened to pairs of sequences (with 100 ms between sequences) and responded whether sequences sounded the same or different. Results indicate that children are best able to discriminate sequences of intermediate-duration vowels, typical of conversational speaking rate. Children were less accurate with both shorter and longer vowels. Results are discussed in terms of auditory processing (shortest vowels) and memory (longest vowels). [Research supported by NIDCD DC-05263, DC-04072, and DC-005650.

  8. PREDICTION OF CHROMATIN STATES USING DNA SEQUENCE PROPERTIES

    KAUST Repository

    Bahabri, Rihab R.

    2013-06-01

    Activities of DNA are to a great extent controlled epigenetically through the internal struc- ture of chromatin. This structure is dynamic and is influenced by different modifications of histone proteins. Various combinations of epigenetic modification of histones pinpoint to different functional regions of the DNA determining the so-called chromatin states. How- ever, the characterization of chromatin states by the DNA sequence properties remains largely unknown. In this study we aim to explore whether DNA sequence patterns in the human genome can characterize different chromatin states. Using DNA sequence motifs we built binary classifiers for each chromatic state to eval- uate whether a given genomic sequence is a good candidate for belonging to a particular chromatin state. Of four classification algorithms (C4.5, Naive Bayes, Random Forest, and SVM) used for this purpose, the decision tree based classifiers (C4.5 and Random Forest) yielded best results among those we evaluated. Our results suggest that in general these models lack sufficient predictive power, although for four chromatin states (insulators, het- erochromatin, and two types of copy number variation) we found that presence of certain motifs in DNA sequences does imply an increased probability that such a sequence is one of these chromatin states.

  9. Identifying novel sequence variants of RNA 3D motifs

    Science.gov (United States)

    Zirbel, Craig L.; Roll, James; Sweeney, Blake A.; Petrov, Anton I.; Pirrung, Meg; Leontis, Neocles B.

    2015-01-01

    Predicting RNA 3D structure from sequence is a major challenge in biophysics. An important sub-goal is accurately identifying recurrent 3D motifs from RNA internal and hairpin loop sequences extracted from secondary structure (2D) diagrams. We have developed and validated new probabilistic models for 3D motif sequences based on hybrid Stochastic Context-Free Grammars and Markov Random Fields (SCFG/MRF). The SCFG/MRF models are constructed using atomic-resolution RNA 3D structures. To parameterize each model, we use all instances of each motif found in the RNA 3D Motif Atlas and annotations of pairwise nucleotide interactions generated by the FR3D software. Isostericity relations between non-Watson–Crick basepairs are used in scoring sequence variants. SCFG techniques model nested pairs and insertions, while MRF ideas handle crossing interactions and base triples. We use test sets of randomly-generated sequences to set acceptance and rejection thresholds for each motif group and thus control the false positive rate. Validation was carried out by comparing results for four motif groups to RMDetect. The software developed for sequence scoring (JAR3D) is structured to automatically incorporate new motifs as they accumulate in the RNA 3D Motif Atlas when new structures are solved and is available free for download. PMID:26130723

  10. LINE-1 retrotransposons: from 'parasite' sequences to functional elements.

    Science.gov (United States)

    Paço, Ana; Adega, Filomena; Chaves, Raquel

    2015-02-01

    Long interspersed nuclear elements-1 (LINE-1) are the most abundant and active retrotransposons in the mammalian genomes. Traditionally, the occurrence of LINE-1 sequences in the genome of mammals has been explained by the selfish DNA hypothesis. Nevertheless, recently, it has also been argued that these sequences could play important roles in these genomes, as in the regulation of gene expression, genome modelling and X-chromosome inactivation. The non-random chromosomal distribution is a striking feature of these retroelements that somehow reflects its functionality. In the present study, we have isolated and analysed a fraction of the open reading frame 2 (ORF2) LINE-1 sequence from three rodent species, Cricetus cricetus, Peromyscus eremicus and Praomys tullbergi. Physical mapping of the isolated sequences revealed an interspersed longitudinal AT pattern of distribution along all the chromosomes of the complement in the three genomes. A detailed analysis shows that these sequences are preferentially located in the euchromatic regions, although some signals could be detected in the heterochromatin. In addition, a coincidence between the location of imprinted gene regions (as Xist and Tsix gene regions) and the LINE-1 retroelements was also observed. According to these results, we propose an involvement of LINE-1 sequences in different genomic events as gene imprinting, X-chromosome inactivation and evolution of repetitive sequences located at the heterochromatic regions (e.g. satellite DNA sequences) of the rodents' genomes analysed.

  11. Sequence space and the ongoing expansion of the protein universe.

    Science.gov (United States)

    Povolotskaya, Inna S; Kondrashov, Fyodor A

    2010-06-17

    The need to maintain the structural and functional integrity of an evolving protein severely restricts the repertoire of acceptable amino-acid substitutions. However, it is not known whether these restrictions impose a global limit on how far homologous protein sequences can diverge from each other. Here we explore the limits of protein evolution using sequence divergence data. We formulate a computational approach to study the rate of divergence of distant protein sequences and measure this rate for ancient proteins, those that were present in the last universal common ancestor. We show that ancient proteins are still diverging from each other, indicating an ongoing expansion of the protein sequence universe. The slow rate of this divergence is imposed by the sparseness of functional protein sequences in sequence space and the ruggedness of the protein fitness landscape: approximately 98 per cent of sites cannot accept an amino-acid substitution at any given moment but a vast majority of all sites may eventually be permitted to evolve when other, compensatory, changes occur. Thus, approximately 3.5 x 10(9) yr has not been enough to reach the limit of divergent evolution of proteins, and for most proteins the limit of sequence similarity imposed by common function may not exceed that of random sequences.

  12. Alternation Blindness in the Representation of Binary Sequences.

    Science.gov (United States)

    Yu, Ru Qi; Osherson, Daniel; Zhao, Jiaying

    2017-08-17

    Binary information is prevalent in the environment and contains 2 distinct outcomes. Binary sequences consist of a mixture of alternation and repetition. Understanding how people perceive such sequences would contribute to a general theory of information processing. In this study, we examined how people process alternation and repetition in binary sequences. Across 4 paradigms involving estimation, working memory, change detection, and visual search, we found that the number of alternations is underestimated compared with repetitions (Experiment 1). Moreover, recall for binary sequences deteriorates as the sequence alternates more (Experiment 2). Changes in bits are also harder to detect as the sequence alternates more (Experiment 3). Finally, visual targets superimposed on bits of a binary sequence take longer to process as alternation increases (Experiment 4). Overall, our results indicate that compared with repetition, alternation in a binary sequence is less salient in the sense of requiring more attention for successful encoding. The current study thus reveals the cognitive constraints in the representation of alternation and provides a new explanation for the overalternation bias in randomness perception. (PsycINFO Database Record (c) 2017 APA, all rights reserved).

  13. Brain potentials index executive functions during random number generation.

    Science.gov (United States)

    Joppich, Gregor; Däuper, Jan; Dengler, Reinhard; Johannes, Sönke; Rodriguez-Fornells, Antoni; Münte, Thomas F

    2004-06-01

    The generation of random sequences is considered to tax different executive functions. To explore the involvement of these functions further, brain potentials were recorded in 16 healthy young adults while either engaging in random number generation (RNG) by pressing the number keys on a computer keyboard in a random sequence or in ordered number generation (ONG) necessitating key presses in the canonical order. Key presses were paced by an external auditory stimulus to yield either fast (1 press/800 ms) or slow (1 press/1300 ms) sequences in separate runs. Attentional demands of random and ordered tasks were assessed by the introduction of a secondary task (key-press to a target tone). The P3 amplitude to the target tone of this secondary task was reduced during RNG, reflecting the greater consumption of attentional resources during RNG. Moreover, RNG led to a left frontal negativity peaking 140 ms after the onset of the pacing stimulus, whenever the subjects produced a true random response. This negativity could be attributed to the left dorsolateral prefrontal cortex and was absent when numbers were repeated. This negativity was interpreted as an index for the inhibition of habitual responses. Finally, in response locked ERPs a negative component was apparent peaking about 50 ms after the key-press that was more prominent during RNG. Source localization suggested a medial frontal source. This effect was tentatively interpreted as a reflection of the greater monitoring demands during random sequence generation.

  14. Integrated and Differentiated Sequence Spaces

    Directory of Open Access Journals (Sweden)

    Murat Kirişci

    2015-01-01

    Full Text Available In this paper, we investigate integrated and differentiated sequence spaces which emerge from the concept of the sequence space $\\ell_{1}$. The integrated and differentiated sequence spaces were initiated by Goes and Goes [4]. The main propose of the present paper, we study matrix domains and some properties of the integrated and differentiated sequence spaces. In Section 3, we compute the alpha-, beta- and gamma duals of these spaces. Afterward, we characterize the matrix classes of these spaces with well-known sequence spaces.

  15. Analysis of the genetic polymorphism of Paracoccidioides brasiliensis and Paracoccidioides cerebriformis "Moore" by random amplified polymorphic DNA (RAPD and 28S ribosomal DNA sequencing: Paracoccidioides cerebriformis revisited Análise do polimorfismo genético do Paracoccidioides brasiliensis e Paracoccidioides cerebriformis "Moore" pela técnica de amplificação aleatória do polimorfismo do DNA (RAPD e sequenciamento do DNA ribossomal 28S: Paracoccidioides cerebriformis revisitado

    Directory of Open Access Journals (Sweden)

    Sarah Desirée Barbosa Cavalcanti

    2005-06-01

    Full Text Available Our purpose was to compare the genetic polymorphism of six samples of P. brasiliensis (113, 339, BAT, T1F1, T3B6, T5LN1, with four samples of P. cerebriformis (735, 741, 750, 361 from the Mycological Laboratory of the Instituto de Medicina Tropical de São Paulo, using Random Amplified Polymorphic DNA Analysis (RAPD. RAPD profiles clearly segregated P. brasiliensis and P. cerebriformis isolates. However, the variation on band patterns among P. cerebriformis isolates was high. Sequencing of the 28S rDNA gene showed nucleotide conservancy among P. cerebriformis isolates, providing basis for taxonomical grouping, and disclosing high divergence to P. brasiliensis supporting that they are in fact two distinct species. Moreover, DNA sequence suggests that P. cerebriformis belongs in fact to the Aspergillus genus.Nosso propósito foi comparar o polimorfismo genético de seis amostras de P. brasiliensis (113, 339, BAT, T1F1, T3B6, T5LN1, com quatro amostras de P. cerebriformis (735, 741, 750, 361 do laboratório de micologia do Instituto de Medicina Tropical de São Paulo, utilizando a técnica de Amplificação Aleatória do Polimorfismo de DNA (RAPD. O perfil de bandas do RAPD diferenciou claramente os isolados de P. brasiliensis de P. cerebriformis. Entretanto, ocorreu uma variação significativa no padrão de bandas das amostras de P. cerebriformis. O sequenciamento do gene ribossomal 28S revelou seqüências de nucleotídeos bastante conservadas entre os isolados de P. cerebriformis, fornecendo subsídio para o agrupamento taxonômico destas amostras, diferenciando estas de P. brasiliensis e mostrando que de fato são espécies distintas. A seqüência de DNA sugere que P. cerebriformis pertence ao gênero Aspergillus.

  16. Asteroid Ida Rotation Sequence

    Science.gov (United States)

    1994-01-01

    This montage of 14 images (the time order is right to left, bottom to top) shows Ida as it appeared in the field of view of Galileo's camera on August 28, 1993. Asteroid Ida rotates once every 4 hours, 39 minutes and clockwise when viewed from above the north pole; these images cover about one Ida 'day.' This sequence has been used to create a 3-D model that shows Ida to be almost croissant shaped. The earliest view (lower right) was taken from a range of 240,000 kilometers (150,000 miles), 5.4 hours before closest approach. The asteroid Ida draws its name from mythology, in which the Greek god Zeus was raised by the nymph Ida.

  17. The resistance of randomly grown trees

    Energy Technology Data Exchange (ETDEWEB)

    Colman, E R; Rodgers, G J, E-mail: Ewan.Colman@brunel.ac.uk [Department of Mathematical Sciences, Brunel University, Uxbridge, Middlesex UB8 3PH (United Kingdom)

    2011-12-16

    An electrical network with the structure of a random tree is considered: starting from a root vertex, in one iteration each leaf (a vertex with zero or one adjacent edges) of the tree is extended by either a single edge with probability p or two edges with probability 1 - p. With each edge having a resistance equal to 1{Omega}, the total resistance R{sub n} between the root vertex and a busbar connecting all the vertices at the nth level is considered. A dynamical system is presented which approximates R{sub n}, it is shown that the mean value Left-Pointing-Angle-Bracket R{sub n} Right-Pointing-Angle-Bracket for this system approaches (1 + p)/(1 - p) as n {yields} {infinity}, the distribution of R{sub n} at large n is also examined. Additionally, a random sequence construction akin to a random Fibonacci sequence is used to approximate R{sub n}; this sequence is shown to be related to the Legendre polynomials and its mean is shown to converge with | Left-Pointing-Angle-Bracket R{sub n} Right-Pointing-Angle-Bracket - (1 + p)/(1 - p)| {approx} n{sup -1/2}. (paper)

  18. Solid phase sequencing of biopolymers

    Energy Technology Data Exchange (ETDEWEB)

    Cantor, Charles (Del Mar, CA); Koster, Hubert (La Jolla, CA)

    2010-09-28

    This invention relates to methods for detecting and sequencing target nucleic acid sequences, to mass modified nucleic acid probes and arrays of probes useful in these methods, and to kits and systems which contain these probes. Useful methods involve hybridizing the nucleic acids or nucleic acids which represent complementary or homologous sequences of the target to an array of nucleic acid probes. These probes comprise a single-stranded portion, an optional double-stranded portion and a variable sequence within the single-stranded portion. The molecular weights of the hybridized nucleic acids of the set can be determined by mass spectroscopy, and the sequence of the target determined from the molecular weights of the fragments. Nucleic acids whose sequences can be determined include DNA or RNA in biological samples such as patient biopsies and environmental samples. Probes may be fixed to a solid support such as a hybridization chip to facilitate automated molecular weight analysis and identification of the target sequence.

  19. Weight Distributions for Turbo Codes Using Random and Nonrandom Permutations

    Science.gov (United States)

    Dolinar, S.; Divsalar, D.

    1995-04-01

    This article takes a preliminary look at the weight distributions achievable for turbo codes using random, nonrandom, and semirandom permutations. Due to the recursiveness of the encoders, it is important to distinguish between self-terminating and non-self-terminating input sequences. The non-self-terminating sequences have little effect on decoder performance, because they accumulate high encoded weight until they are artificially terminated at the end of the block. From probabilistic arguments based on selecting the permutations randomly, it is concluded that the self-terminating weight-2 data sequences are the most important consideration in the design of the constituent codes; higher-weight self-terminating sequences have successively decreasing importance. Also, increasing the number of codes and, correspondingly, the number of permutations makes it more and more likely that the bad input sequences will be broken up by one or more of the permuters. It is possible to design nonrandom permutations that ensure that the minimum distance due to weight-2 input sequences grows roughly as p 2N, where N is the block length. However, these nonrandom permutations amplify the bad effects of higher-weight inputs, and as a result they are inferior in performance to randomly selected permutations. But there are "semirandom" permutations that perform nearly as well as the designed nonrandom permutations with respect to weight-2 input sequences and are not as susceptible to being foiled by higher-weight inputs.

  20. Test on the structure of biological sequences via Chaos Game Representation.

    Science.gov (United States)

    Cénac, Peggy

    2005-01-01

    In this paper biological sequences are modelled by stationary ergodic sequences. A new family of statistical tests to characterize the randomness of the inputs is proposed and analyzed. Tests for independence and for the determination of the appropriate order of a Markov chain are constructed with the Chaos Game Representation (CGR), and applied to several genomes.

  1. Assessing the Impact of Sequencing Practicums for Welding in Agricultural Mechanics

    Science.gov (United States)

    Rose, Malcolm; Pate, Michael L.; Lawver, Rebecca G.; Warnick, Brian K.; Dai, Xin

    2015-01-01

    This study examined the impact of sequencing practicums for welding on students' ability to perform a 1F (flat position-fillet lap joint) weld on low-carbon steel. Participants were randomly assigned a specific practice sequence of welding for using gas metal arc welding (GMAW) and shielded metal arc welding (SMAW). A total of 71 participants…

  2. PHARMACOGENETIC TESTING OPPORTUNITIES IN CARDIOLOGY BASED ON EXOME SEQUENCING

    Directory of Open Access Journals (Sweden)

    N. V. Shcherbakova

    2014-01-01

    Full Text Available Aim. To study what cardiac drugs currently have any comments on biomarkers and what information can be obtained by pharmacogenetic testing using data exome sequencing in patients with cardiac diseases.Material and methods. Exome sequencing in random participant of the ATEROGEN IVANOVO study and bioinformatics analysis of the data were performed. Point mutations were annotated using ANNOVAR program, as well as comparison with a number of specialized databases was done on the basis of user protocols.Results. 11 cardiac drugs and 7 genes which variants can influence cardiac drug metabolism were analyzed. According to exome sequencing of the participant we did not reveal allelic variants that require dose regime correction and careful efficacy control.Conclusion. The exome sequencing application is the next step to a wide range of personalized therapy. Future opportunities for improvement of the risk-benefit ratio in each patient are the main purpose of the collection and analysis of pharmacogenetic data.

  3. Rand, Rothbard, and Rights Reconsidered

    OpenAIRE

    Kathleen Touchstone

    2010-01-01

    This paper examines rights and the protection of rights from both the minarchist and the anarchist perspectives. The former relies on Objectivist (and Neo-Objectivist) perspectives and the latter relies primarily on Murray Rothbard’s views. My view is that government protection as put forth by Objectivists is coercive, as are all methods of financing. However, under anarcho-capitalism, children (and those with diminished capacity) who have been killed or abused by their caregivers do not have...

  4. Reconsidering the Management of Marketing

    OpenAIRE

    Murray, John; O'Driscoll, Aidan

    1996-01-01

    The pace and extent of change in marketing landscape over the past decade has left many questioning the worth of marketing and its tenets. For many marketing educators it is a period of doubt and self-searching about the efficacy and role of the discipline. Yet empirical evidence reveals firms that have not only coped with these changing circumstances but have also found new and imaginative ways of winning competitive advantage. Marketing practice is adopting novel shapes and modes. In the fi...

  5. Evidence-based management reconsidered.

    Science.gov (United States)

    Kovner, Anthony R; Rundall, Thomas G

    2006-01-01

    Reports of medical mistakes have splashed across newspapers and magazines in the United States. At the same time, instances of overuse, underuse, and misuse of management tactics and strategies receive far less attention. The sense of urgency associated with improving the quality of medical care does not exist with respect to improving the quality of management decision making. A more evidence-based approach would improve the competence of the decision-makers and their motivation to use more scientific methods when making a decision. The authors of this article consider a study of 68 U.S. health services managers that found a low level of evidence-based management behaviors. From the findings, four strategies are suggested to increase health systems managers' use of research evidence to improve decision making: focusing evidence-based decision making on strategically important issues, developing committees and other structures to diffuse management research throughout the organization, building a management culture that values research, and training managers in the competencies required to apply research evidence to health services management decisions. To aid the manager in understanding and applying an evidenced-based approach to decision making, the article provides practical tools, techniques, and resources for immediate use.

  6. Eucharistic Hospitality : Reconsidering the Terminology

    NARCIS (Netherlands)

    Casadei, Giulia; Wouda, Fokke

    2016-01-01

    Giulia Casadei MA and Fokke Wouda MA work on PhD projects about Eucharistic sharing in ecumenical relations; a pressing, yet controversial topic in Roman Catholic ecumenical engagement. As they both encounter questions concerning the terminology of this field, they decided on writing an article

  7. Rand, Rothbard, and Rights Reconsidered

    Directory of Open Access Journals (Sweden)

    Kathleen Touchstone

    2010-07-01

    Full Text Available This paper examines rights and the protection of rights from both the minarchist and the anarchist perspectives. The former relies on Objectivist (and Neo-Objectivist perspectives and the latter relies primarily on Murray Rothbard’s views. My view is that government protection as put forth by Objectivists is coercive, as are all methods of financing. However, under anarcho-capitalism, children (and those with diminished capacity who have been killed or abused by their caregivers do not have equal (or any protection under the law. The principle of equal protection is one with which both Objectivists and Rothbard agree. A case is made for government protection of rights under those circumstances. In addition, a case is made for positive rights to parental care for children, and also for government protection of those rights if they have been violated by their caregivers. I also argue for government oversight in instances when the rights of children (and those with diminished capacity have been violated and as a consequence the children (and those with diminished capacity have no alternative means of care.

  8. Reconsidering the sedentary behaviour paradigm.

    Directory of Open Access Journals (Sweden)

    Carol Maher

    Full Text Available AIMS: Recent literature has posed sedentary behaviour as an independent entity to physical inactivity. This study investigated whether associations between sedentary behaviour and cardio-metabolic biomarkers remain when analyses are adjusted for total physical activity. METHODS: Cross-sectional analyses were undertaken on 4,618 adults from the 2003/04 and 2005/06 U.S. National Health and Nutrition Examination Survey. Minutes of sedentary behaviour and moderate-to-vigorous physical activity (MVPA, and total physical activity (total daily accelerometer counts minus counts accrued during sedentary minutes were determined from accelerometry. Associations between sedentary behaviour and cardio-metabolic biomarkers were examined using linear regression. RESULTS: Results showed that sedentary behaviour was detrimentally associated with 8/11 cardio-metabolic biomarkers when adjusted for MVPA. However, when adjusted for total physical activity, the associations effectively disappeared, except for C-reactive protein, which showed a very small, favourable association (β = -0.06 and triglycerides, which showed a very small, detrimental association (β = 0.04. Standardised betas suggested that total physical activity was consistently, favourably associated with cardio-metabolic biomarkers (9/11 biomarkers, standardized β = 0.08-0.30 while sedentary behaviour was detrimentally associated with just 1 biomarker (standardized β = 0.12. CONCLUSION: There is virtually no association between sedentary behaviour and cardio-metabolic biomarkers once analyses are adjusted for total physical activity. This suggests that sedentary behaviour may not have health effects independent of physical activity.

  9. Reconsidering Teenage Pregnancy and Parenthood

    Directory of Open Access Journals (Sweden)

    Frank Furstenberg

    2016-11-01

    Full Text Available This paper looks back at the findings reported in Destinies of the Disadvantaged: The Politics of Teenage Parenthood, a decade after its publication in light of recent research. Increasingly, the most methodologically sophisticated research has minimized the “causal impact” of early childbearing on later life events consistent with the findings of the Baltimore Study. I argue in the paper that we must see early childbearing primarily as a marker rather than a cause of economic disadvantage. As such, reducing early childbearing will have a minimal impact on the lives of highly disadvantaged teens unless those teens use the delay in childbearing to improve their education and labor market prospects.

  10. Reconsidering punitive and harsh discipline.

    Science.gov (United States)

    Mohr, Wanda K; Anderson, Jeffrey A

    2002-12-01

    Corporal punishment and other harsh interventions continue to be widespread despite the fact that the leading theories or models of behavioral management do not support their effectiveness. There is overwhelming evidence that harsh interventions are damaging to children, both emotionally and physically. The effects of such trauma may be compounded when a child has preexisting learning difficulties. When schools respond to these challenges using harsh methods, children can be further traumatized. The authors review principles of childhood neurodevelopment, describe a model to understand children in context, and discuss how exposure to certain noxious sensory experiences can affect children's responses to threat or perceived threat. They also describe implications for school nurses.

  11. The Principles of War Reconsidered

    Science.gov (United States)

    2009-06-01

    consist of a checklist of principles of war. There existed the Art of War (not the Science) and the works of ancient, medieval , and nineteenth...third chapter of the thesis presents the transformation of the concept of the principles of war in the twentieth century. The canonizing of Napoleonic...This maelstrom of opinions, lacking in basic principles and clear laws round which they could be crystallized, was bound to be intellectually

  12. Beyond Professionalism: or Professionalism Reconsidered

    Science.gov (United States)

    Moore, Gilbert D.

    1969-01-01

    Questions role of organized counselor educators, suggesting that such role not be limited to school counseling but be widened to open new career patterns for poor by providing opportunity for them to use intuitive skills in helping professions. Speech at ACES luncheon, APGA Convention, Las Vegas, 1969. (CJ)

  13. ECONOMICS OF DISTANCE EDUCATION RECONSIDERED

    Directory of Open Access Journals (Sweden)

    Wolfram LAASER

    2008-07-01

    Full Text Available ABSTRACT According to Gartner a certain hype of e-Learning was followed by a downturn but eLearning will continue to be an important factor in learning scenarios. However the economic viability of e-learning projects will be questioned with more scrutiny than in earlier periods. Therefore it seems to be a good opportunity to see what can be learned from past experience in costing distance learning projects and what aspects are added by current attempts to measure economic efficiency. After reviewing early research about costing distance learning some more recent approaches will be discussed, such as eLearning ROI-calculators and the concept of total cost of ownership. Furthermore some microeconomic effects referring to localization of distance learning courses are outlined. Finally several unsolved issues in costing distance education are summarized.

  14. Bibliotherapy: "Literature as Exploration" Reconsidered

    Science.gov (United States)

    Justman, Stewart

    2010-01-01

    In this article, the author examines Louise Rosenblatt's "Literature as Exploration," a popular textbook used since 1938 (in five successive editions) in high school English classrooms across America. He discusses how the one-time college roommate of Margaret Mead managed to transform teaching literature into a form of student therapy that…

  15. Adolescent Storm and Stress, Reconsidered.

    Science.gov (United States)

    Arnett, Jeffrey Jensen

    1999-01-01

    Explores G. Hall's (1904) view that adolescence is a period of heightened storm and stress in light of contemporary research, focusing on (1) conflict with parents; (2) mood disruptions; and (3) risk behavior. In all these areas, evidence supports a modified storm-and-stress view that takes into account individual differences and cultural…

  16. Reconsidering Constructivism in Qualitative Research

    Science.gov (United States)

    Lee, Cheu-Jey George

    2012-01-01

    This article examines constructivism, a paradigm in qualitative research that has been propagated by Egon Guba, Yvonna Lincoln, and Norman Denzin. A distinction is made between whether the basic presuppositions of constructivism are credible compared to those of a competing paradigm and whether constructivism's beliefs are internally consistent.…

  17. Reconsidering Styles of Regulatory Enforcement

    DEFF Research Database (Denmark)

    May, Peter J.; Winter, Søren

    2000-01-01

    This study addresses enforcement styles of regulatory inspectors, based on an examination of the municipal enforcement of agro-environmental policies in Denmark. Our findings make three contributions to the regulatory literature. One contribution is to add empirical support for theorizing about...

  18. Reconsidering Styles of Regulatory Enforcement

    DEFF Research Database (Denmark)

    J. May, Peter; Winter, Søren

    2007-01-01

    This study addresses enforcement styles of regulatory inspectors based on an examination of the municipal enforcement of agro-environmental policies in Denmark. Our findings make three contributions to the regulatory literature. One contribution is to add empirical support for theorizing about...

  19. Random walks, random fields, and disordered systems

    CERN Document Server

    Černý, Jiří; Kotecký, Roman

    2015-01-01

    Focusing on the mathematics that lies at the intersection of probability theory, statistical physics, combinatorics and computer science, this volume collects together lecture notes on recent developments in the area. The common ground of these subjects is perhaps best described by the three terms in the title: Random Walks, Random Fields and Disordered Systems. The specific topics covered include a study of Branching Brownian Motion from the perspective of disordered (spin-glass) systems, a detailed analysis of weakly self-avoiding random walks in four spatial dimensions via methods of field theory and the renormalization group, a study of phase transitions in disordered discrete structures using a rigorous version of the cavity method, a survey of recent work on interacting polymers in the ballisticity regime and, finally, a treatise on two-dimensional loop-soup models and their connection to conformally invariant systems and the Gaussian Free Field. The notes are aimed at early graduate students with a mod...

  20. Hybridization capture using short PCR products enriches small genomes by capturing flanking sequences (CapFlank.

    Directory of Open Access Journals (Sweden)

    Kyriakos Tsangaras

    Full Text Available Solution hybridization capture methods utilize biotinylated oligonucleotides as baits to enrich homologous sequences from next generation sequencing (NGS libraries. Coupled with NGS, the method generates kilo to gigabases of high confidence consensus targeted sequence. However, in many experiments, a non-negligible fraction of the resulting sequence reads are not homologous to the bait. We demonstrate that during capture, the bait-hybridized library molecules add additional flanking library sequences iteratively, such that baits limited to targeting relatively short regions (e.g. few hundred nucleotides can result in enrichment across entire mitochondrial and bacterial genomes. Our findings suggest that some of the off-target sequences derived in capture experiments are non-randomly enriched, and that CapFlank will facilitate targeted enrichment of large contiguous sequences with minimal prior target sequence information.

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

    Science.gov (United States)

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

    2014-03-01

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

  2. Quantum random number generators

    Science.gov (United States)

    Herrero-Collantes, Miguel; Garcia-Escartin, Juan Carlos

    2017-01-01

    Random numbers are a fundamental resource in science and engineering with important applications in simulation and cryptography. The inherent randomness at the core of quantum mechanics makes quantum systems a perfect source of entropy. Quantum random number generation is one of the most mature quantum technologies with many alternative generation methods. This review discusses the different technologies in quantum random number generation from the early devices based on radioactive decay to the multiple ways to use the quantum states of light to gather entropy from a quantum origin. Randomness extraction and amplification and the notable possibility of generating trusted random numbers even with untrusted hardware using device-independent generation protocols are also discussed.

  3. Integrity of Evidence-Based Practice: Are Providers Modifying Practice Content or Practice Sequencing?

    OpenAIRE

    Park, Alayna L.; Chorpita, Bruce F.; Regan, Jennifer; Weisz, John R

    2014-01-01

    This study examined patterns of evidence-based treatment (EBT) implementation within community settings by evaluating integrity along separate dimensions of practice content (PC; a session included the prescribed procedure) and practice sequencing (a session occurred in the prescribed sequence) within a recent randomized effectiveness trial. We measured whether sessions showed integrity to PC and to flexible or linear practice sequences. Findings revealed that providers tended to incorporate ...

  4. The EMBL Nucleotide Sequence Database.

    Science.gov (United States)

    Kanz, Carola; Aldebert, Philippe; Althorpe, Nicola; Baker, Wendy; Baldwin, Alastair; Bates, Kirsty; Browne, Paul; van den Broek, Alexandra; Castro, Matias; Cochrane, Guy; Duggan, Karyn; Eberhardt, Ruth; Faruque, Nadeem; Gamble, John; Diez, Federico Garcia; Harte, Nicola; Kulikova, Tamara; Lin, Quan; Lombard, Vincent; Lopez, Rodrigo; Mancuso, Renato; McHale, Michelle; Nardone, Francesco; Silventoinen, Ville; Sobhany, Siamak; Stoehr, Peter; Tuli, Mary Ann; Tzouvara, Katerina; Vaughan, Robert; Wu, Dan; Zhu, Weimin; Apweiler, Rolf

    2005-01-01

    The EMBL Nucleotide Sequence Database (http://www.ebi.ac.uk/embl), maintained at the European Bioinformatics Institute (EBI) near Cambridge, UK, is a comprehensive collection of nucleotide sequences and annotation from available public sources. The database is part of an international collaboration with DDBJ (Japan) and GenBank (USA). Data are exchanged daily between the collaborating institutes to achieve swift synchrony. Webin is the preferred tool for individual submissions of nucleotide sequences, including Third Party Annotation (TPA) and alignments. Automated procedures are provided for submissions from large-scale sequencing projects and data from the European Patent Office. New and updated data records are distributed daily and the whole EMBL Nucleotide Sequence Database is released four times a year. Access to the sequence data is provided via ftp and several WWW interfaces. With the web-based Sequence Retrieval System (SRS) it is also possible to link nucleotide data to other specialist molecular biology databases maintained at the EBI. Other tools are available for sequence similarity searching (e.g. FASTA and BLAST). Changes over the past year include the removal of the sequence length limit, the launch of the EMBLCDSs dataset, extension of the Sequence Version Archive functionality and the revision of quality rules for TPA data.

  5. Large-Scale Sequence Comparison.

    Science.gov (United States)

    Lal, Devi; Verma, Mansi

    2017-01-01

    There are millions of sequences deposited in genomic databases, and it is an important task to categorize them according to their structural and functional roles. Sequence comparison is a prerequisite for proper categorization of both DNA and protein sequences, and helps in assigning a putative or hypothetical structure and function to a given sequence. There are various methods available for comparing sequences, alignment being first and foremost for sequences with a small number of base pairs as well as for large-scale genome comparison. Various tools are available for performing pairwise large sequence comparison. The best known tools either perform global alignment or generate local alignments between the two sequences. In this chapter we first provide basic information regarding sequence comparison. This is followed by the description of the PAM and BLOSUM matrices that form the basis of sequence comparison. We also give a practical overview of currently available methods such as BLAST and FASTA, followed by a description and overview of tools available for genome comparison including LAGAN, MumMER, BLASTZ, and AVID.

  6. Random Differential Privacy

    OpenAIRE

    Hall, Rob; Rinaldo, Alessandro; Wasserman, Larry

    2011-01-01

    We propose a relaxed privacy definition called {\\em random differential privacy} (RDP). Differential privacy requires that adding any new observation to a database will have small effect on the output of the data-release procedure. Random differential privacy requires that adding a {\\em randomly drawn new observation} to a database will have small effect on the output. We show an analog of the composition property of differentially private procedures which applies to our new definition. We sh...

  7. A blackberry (Rubus L.) expressed sequence tag library for the development of simple sequence repeat markers.

    Science.gov (United States)

    Lewers, Kim S; Saski, Chris A; Cuthbertson, Brandon J; Henry, David C; Staton, Meg E; Main, Dorrie S; Dhanaraj, Anik L; Rowland, Lisa J; Tomkins, Jeff P

    2008-06-20

    The recent development of novel repeat-fruiting types of blackberry (Rubus L.) cultivars, combined with a long history of morphological marker-assisted selection for thornlessness by blackberry breeders, has given rise to increased interest in using molecular markers to facilitate blackberry breeding. Yet no genetic maps, molecular markers, or even sequences exist specifically for cultivated blackberry. The purpose of this study is to begin development of these tools by generating and annotating the first blackberry expressed sequence tag (EST) library, designing primers from the ESTs to amplify regions containing simple sequence repeats (SSR), and testing the usefulness of a subset of the EST-SSRs with two blackberry cultivars. A cDNA library of 18,432 clones was generated from expanding leaf tissue of the cultivar Merton Thornless, a progenitor of many thornless commercial cultivars. Among the most abundantly expressed of the 3,000 genes annotated were those involved with energy, cell structure, and defense. From individual sequences containing SSRs, 673 primer pairs were designed. Of a randomly chosen set of 33 primer pairs tested with two blackberry cultivars, 10 detected an average of 1.9 polymorphic PCR products. This rate predicts that this library may yield as many as 940 SSR primer pairs detecting 1,786 polymorphisms. This may be sufficient to generate a genetic map that can be used to associate molecular markers with phenotypic traits, making possible molecular marker-assisted breeding to compliment existing morphological marker-assisted breeding in blackberry.

  8. Solid phase sequencing of biopolymers

    Energy Technology Data Exchange (ETDEWEB)

    Cantor, Charles R.; Hubert, Koster

    2014-06-24

    This invention relates to methods for detecting and sequencing target nucleic acid sequences, to mass modified nucleic acid probes and arrays of probes useful in these methods, and to kits and systems which contain these probes. Useful methods involve hybridizing the nucleic acids or nucleic acids which represent complementary or homologous sequences of the target to an array of nucleic acid probes. These probes comprise a single-stranded portion, an optional double-stranded portion and a variable sequence within the single-stranded portion. The molecular weights of the hybridized nucleic acids of the set can be determined by mass spectroscopy, and the sequence of the target determined from the molecular weights of the fragments. Probes may be affixed to a solid support such as a hybridization chip to facilitate automated molecular weight analysis and identification of the target sequence.

  9. Graphene nanodevices for DNA sequencing

    Science.gov (United States)

    Heerema, Stephanie J.; Dekker, Cees

    2016-02-01

    Fast, cheap, and reliable DNA sequencing could be one of the most disruptive innovations of this decade, as it will pave the way for personalized medicine. In pursuit of such technology, a variety of nanotechnology-based approaches have been explored and established, including sequencing with nanopores. Owing to its unique structure and properties, graphene provides interesting opportunities for the development of a new sequencing technology. In recent years, a wide range of creative ideas for graphene sequencers have been theoretically proposed and the first experimental demonstrations have begun to appear. Here, we review the different approaches to using graphene nanodevices for DNA sequencing, which involve DNA passing through graphene nanopores, nanogaps, and nanoribbons, and the physisorption of DNA on graphene nanostructures. We discuss the advantages and problems of each of these key techniques, and provide a perspective on the use of graphene in future DNA sequencing technology.

  10. Random roots and lineage sorting.

    Science.gov (United States)

    Rosenfeld, Jeffrey A; Payne, Ansel; DeSalle, Rob

    2012-07-01

    Lineage sorting has been suggested as a major force in generating incongruent phylogenetic signal when multiple gene partitions are examined. The degree of lineage sorting can be estimated using the coalescent process and simulation studies have also pointed to a major role for incomplete lineage sorting as a factor in phylogenetic inference. Some recent empirical studies point to an extreme role for this phenomenon with up to 50-60% of all informative genes showing incongruence as a result of lineage sorting. Here, we examine seven large multi-partition genome level data sets over a large range of taxonomic representation. We took the approach of examining outgroup choice and its impact on tree topology, by swapping outgroups into analyses with successively larger genetics distances to the ingroup. Our results indicate a linear relationship of outgroup distance with incongruence in the data sets we examined suggesting a strong random rooting effect. In addition, we attempted to estimate the degree of lineage sorting in several large genome level data sets by examining triads of very closely related taxa. This exercise resulted in much lower estimates of incongruent genes that could be the result of lineage sorting, with an overall estimate of around 10% of the total number of genes in a genome showing incongruence as a result of true lineage sorting. Finally we examined the behavior of likelihood and parsimony approaches on the random rooting phenomenon. Likelihood tends to stabilize incongruence as outgroups get further and further away from the ingroup. In one extreme case, likelihood overcompensates for sequence divergence but increases random rooting causing long branch repulsion. Copyright © 2012 Elsevier Inc. All rights reserved.

  11. Folding and Stabilization of Native-Sequence-Reversed Proteins

    CERN Document Server

    Zhang, Yuanzhao; Zhou, Ruhong

    2016-01-01

    Though the problem of sequence-reversed protein folding is largely unexplored, one might speculate that reversed native protein sequences should be significantly more foldable than purely random heteropolymer sequences. In this article, we investigate how the reverse-sequences of native proteins might fold by examining a series of small proteins of increasing structural complexity ({\\alpha}-helix, \\b{eta}-hairpin, {\\alpha}-helix bundle, and {\\alpha}/\\b{eta}-protein). Employing a tandem protein structure prediction algorithmic and molecular dynamics simulation approach, we find that the ability of reverse sequences to adopt native-like folds is strongly in influenced by protein size and the flexibility of the native hydrophobic core. For \\b{eta}-hairpins with reverse-sequences that fail to fold, we employ a simple mutational strategy for guiding stable hairpin formation that involves the insertion of amino acids into the \\b{eta}-turn region. This systematic look at reverse sequence duality sheds new light on t...

  12. Biosensors for DNA sequence detection

    Science.gov (United States)

    Vercoutere, Wenonah; Akeson, Mark

    2002-01-01

    DNA biosensors are being developed as alternatives to conventional DNA microarrays. These devices couple signal transduction directly to sequence recognition. Some of the most sensitive and functional technologies use fibre optics or electrochemical sensors in combination with DNA hybridization. In a shift from sequence recognition by hybridization, two emerging single-molecule techniques read sequence composition using zero-mode waveguides or electrical impedance in nanoscale pores.

  13. Nonlinear analysis of biological sequences

    Energy Technology Data Exchange (ETDEWEB)

    Torney, D.C.; Bruno, W.; Detours, V. [and others

    1998-11-01

    This is the final report of a three-year, Laboratory Directed Research and Development (LDRD) project at the Los Alamos National Laboratory (LANL). The main objectives of this project involved deriving new capabilities for analyzing biological sequences. The authors focused on tabulating the statistical properties exhibited by Human coding DNA sequences and on techniques of inferring the phylogenetic relationships among protein sequences related by descent.

  14. Shaping the spectrum of random-phase radar waveforms

    Science.gov (United States)

    Doerry, Armin W.; Marquette, Brandeis

    2017-05-09

    The various technologies presented herein relate to generation of a desired waveform profile in the form of a spectrum of apparently random noise (e.g., white noise or colored noise), but with precise spectral characteristics. Hence, a waveform profile that could be readily determined (e.g., by a spoofing system) is effectively obscured. Obscuration is achieved by dividing the waveform into a series of chips, each with an assigned frequency, wherein the sequence of chips are subsequently randomized. Randomization can be a function of the application of a key to the chip sequence. During processing of the echo pulse, a copy of the randomized transmitted pulse is recovered or regenerated against which the received echo is correlated. Hence, with the echo energy range-compressed in this manner, it is possible to generate a radar image with precise impulse response.

  15. Assembly sequencing with toleranced parts

    Energy Technology Data Exchange (ETDEWEB)

    Latombe, J.C. [Stanford Univ., CA (United States). Robotics Lab.; Wilson, R.H. [Sandia National Labs., Albuquerque, NM (United States). Intelligent Systems and Robotics Center

    1995-02-21

    The goal of assembly sequencing is to plan a feasible series of operations to construct a product from its individual parts. Previous research has thoroughly investigated assembly sequencing under the assumption that parts have nominal geometry. This paper considers the case where parts have toleranced geometry. Its main contribution is an efficient procedure that decides if a product admits an assembly sequence with infinite translations that is feasible for all possible instances of the components within the specified tolerances. If the product admits one such sequence, the procedure can also generate it. For the cases where there exists no such assembly sequence, another procedure is proposed which generates assembly sequences that are feasible only for some values of the toleranced dimensions. If this procedure produces no such sequence, then no instance of the product is assemblable. Finally, this paper analyzes the relation between assembly and disassembly sequences in the presence of toleranced parts. This work assumes a simple, but non-trivial tolerance language that falls short of capturing all imperfections of a manufacturing process. Hence, it is only one step toward assembly sequencing with toleranced parts.

  16. Fast global sequence alignment technique

    KAUST Repository

    Bonny, Mohamed Talal

    2011-11-01

    Bioinformatics database is growing exponentially in size. Processing these large amount of data may take hours of time even if super computers are used. One of the most important processing tool in Bioinformatics is sequence alignment. We introduce fast alignment algorithm, called \\'Alignment By Scanning\\' (ABS), to provide an approximate alignment of two DNA sequences. We compare our algorithm with the wellknown sequence alignment algorithms, the \\'GAP\\' (which is heuristic) and the \\'Needleman-Wunsch\\' (which is optimal). The proposed algorithm achieves up to 51% enhancement in alignment score when it is compared with the GAP Algorithm. The evaluations are conducted using different lengths of DNA sequences. © 2011 IEEE.

  17. ABS: Sequence alignment by scanning

    KAUST Repository

    Bonny, Mohamed Talal

    2011-08-01

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

  18. Sanger dideoxy sequencing of DNA.

    Science.gov (United States)

    Walker, Sarah E; Lorsch, Jon

    2013-01-01

    While the ease and reduced cost of automated DNA sequencing has largely obviated the need for manual dideoxy sequencing for routine purposes, specific applications require manual DNA sequencing. For instance, in studies of enzymes or proteins that bind or modify DNA, a DNA ladder is often used to map the site at which an enzyme is bound or a modification occurs. In these cases, the Sanger method for dideoxy sequencing provides a rapid and facile method for producing a labeled DNA ladder. Copyright © 2013 Elsevier Inc. All rights reserved.

  19. The ontology of biological sequences

    Directory of Open Access Journals (Sweden)

    Kelso Janet

    2009-11-01

    Full Text Available Abstract Background Biological sequences play a major role in molecular and computational biology. They are studied as information-bearing entities that make up DNA, RNA or proteins. The Sequence Ontology, which is part of the OBO Foundry, contains descriptions and definitions of sequences and their properties. Yet the most basic question about sequences remains unanswered: what kind of entity is a biological sequence? An answer to this question benefits formal ontologies that use the notion of biological sequences and analyses in computational biology alike. Results We provide both an ontological analysis of biological sequences and a formal representation that can be used in knowledge-based applications and other ontologies. We distinguish three distinct kinds of entities that can be referred to as "biological sequence": chains of molecules, syntactic representations such as those in biological databases, and the abstract information-bearing entities. For use in knowledge-based applications and inclusion in biomedical ontologies, we implemented the developed axiom system for use in automated theorem proving. Conclusion Axioms are necessary to achieve the main goal of ontologies: to formally specify the meaning of terms used within a domain. The axiom system for the ontology of biological sequences is the first elaborate axiom system for an OBO Foundry ontology and can serve as starting point for the development of more formal ontologies and ultimately of knowledge-based applications.

  20. SNMR pulse sequence phase cycling

    Science.gov (United States)

    Walsh, David O; Grunewald, Elliot D

    2013-11-12

    Technologies applicable to SNMR pulse sequence phase cycling are disclosed, including SNMR acquisition apparatus and methods, SNMR processing apparatus and methods, and combinations thereof. SNMR acquisition may include transmitting two or more SNMR pulse sequences and applying a phase shift to a pulse in at least one of the pulse sequences, according to any of a variety cycling techniques. SNMR processing may include combining SNMR from a plurality of pulse sequences comprising pulses of different phases, so that desired signals are preserved and indesired signals are canceled.

  1. Quasirandom geometric networks from low-discrepancy sequences

    Science.gov (United States)

    Estrada, Ernesto

    2017-08-01

    We define quasirandom geometric networks using low-discrepancy sequences, such as Halton, Sobol, and Niederreiter. The networks are built in d dimensions by considering the d -tuples of digits generated by these sequences as the coordinates of the vertices of the networks in a d -dimensional Id unit hypercube. Then, two vertices are connected by an edge if they are at a distance smaller than a connection radius. We investigate computationally 11 network-theoretic properties of two-dimensional quasirandom networks and compare them with analogous random geometric networks. We also study their degree distribution and their spectral density distributions. We conclude from this intensive computational study that in terms of the uniformity of the distribution of the vertices in the unit square, the quasirandom networks look more random than the random geometric networks. We include an analysis of potential strategies for generating higher-dimensional quasirandom networks, where it is know that some of the low-discrepancy sequences are highly correlated. In this respect, we conclude that up to dimension 20, the use of scrambling, skipping and leaping strategies generate quasirandom networks with the desired properties of uniformity. Finally, we consider a diffusive process taking place on the nodes and edges of the quasirandom and random geometric graphs. We show that the diffusion time is shorter in the quasirandom graphs as a consequence of their larger structural homogeneity. In the random geometric graphs the diffusion produces clusters of concentration that make the process more slow. Such clusters are a direct consequence of the heterogeneous and irregular distribution of the nodes in the unit square in which the generation of random geometric graphs is based on.

  2. Quasirandom geometric networks from low-discrepancy sequences.

    Science.gov (United States)

    Estrada, Ernesto

    2017-08-01

    We define quasirandom geometric networks using low-discrepancy sequences, such as Halton, Sobol, and Niederreiter. The networks are built in d dimensions by considering the d-tuples of digits generated by these sequences as the coordinates of the vertices of the networks in a d-dimensional I^{d} unit hypercube. Then, two vertices are connected by an edge if they are at a distance smaller than a connection radius. We investigate computationally 11 network-theoretic properties of two-dimensional quasirandom networks and compare them with analogous random geometric networks. We also study their degree distribution and their spectral density distributions. We conclude from this intensive computational study that in terms of the uniformity of the distribution of the vertices in the unit square, the quasirandom networks look more random than the random geometric networks. We include an analysis of potential strategies for generating higher-dimensional quasirandom networks, where it is know that some of the low-discrepancy sequences are highly correlated. In this respect, we conclude that up to dimension 20, the use of scrambling, skipping and leaping strategies generate quasirandom networks with the desired properties of uniformity. Finally, we consider a diffusive process taking place on the nodes and edges of the quasirandom and random geometric graphs. We show that the diffusion time is shorter in the quasirandom graphs as a consequence of their larger structural homogeneity. In the random geometric graphs the diffusion produces clusters of concentration that make the process more slow. Such clusters are a direct consequence of the heterogeneous and irregular distribution of the nodes in the unit square in which the generation of random geometric graphs is based on.

  3. Random errors revisited

    DEFF Research Database (Denmark)

    Jacobsen, Finn

    2000-01-01

    the random errors of estimates of the sound intensity in, say, one-third octave bands from the power and cross power spectra of the signals from an intensity probe determined with a dual channel FFT analyser. This is not very practical, though. In this paper it is demonstrated that one can predict the random...

  4. Hashing, Randomness and Dictionaries

    DEFF Research Database (Denmark)

    Pagh, Rasmus

    time and memory space. To some extent we also consider lower bounds, i.e., we attempt to show limitations on how efficient algorithms are possible. A central theme in the thesis is randomness. Randomized algorithms play an important role, in particular through the key technique of hashing. Additionally...

  5. Predicting tissue-specific expressions based on sequence characteristics

    KAUST Repository

    Paik, Hyojung

    2011-04-30

    In multicellular organisms, including humans, understanding expression specificity at the tissue level is essential for interpreting protein function, such as tissue differentiation. We developed a prediction approach via generated sequence features from overrepresented patterns in housekeeping (HK) and tissue-specific (TS) genes to classify TS expression in humans. Using TS domains and transcriptional factor binding sites (TFBSs), sequence characteristics were used as indices of expressed tissues in a Random Forest algorithm by scoring exclusive patterns considering the biological intuition; TFBSs regulate gene expression, and the domains reflect the functional specificity of a TS gene. Our proposed approach displayed better performance than previous attempts and was validated using computational and experimental methods.

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

    Directory of Open Access Journals (Sweden)

    Kirkness Ewen

    2006-10-01

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

  7. Discrete Painlev\\'e equations and random matrix averages

    OpenAIRE

    Forrester, P. J.; Witte, N. S.

    2003-01-01

    The $\\tau$-function theory of Painlev\\'e systems is used to derive recurrences in the rank $n$ of certain random matrix averages over U(n). These recurrences involve auxilary quantities which satisfy discrete Painlev\\'e equations. The random matrix averages include cases which can be interpreted as eigenvalue distributions at the hard edge and in the bulk of matrix ensembles with unitary symmetry. The recurrences are illustrated by computing the value of a sequence of these distributions as $...

  8. Random Walks and Trees

    Directory of Open Access Journals (Sweden)

    Shi Zhan

    2011-03-01

    Full Text Available These notes provide an elementary and self-contained introduction to branching random walks. Section 1 gives a brief overview of Galton–Watson trees, whereas Section 2 presents the classical law of large numbers for branching random walks. These two short sections are not exactly indispensable, but they introduce the idea of using size-biased trees, thus giving motivations and an avant-goût to the main part, Section 3, where branching random walks are studied from a deeper point of view, and are connected to the model of directed polymers on a tree. Tree-related random processes form a rich and exciting research subject. These notes cover only special topics. For a general account, we refer to the St-Flour lecture notes of Peres [47] and to the forthcoming book of Lyons and Peres [42], as well as to Duquesne and Le Gall [23] and Le Gall [37] for continuous random trees.

  9. Conservation of Shannon's redundancy for proteins. [information theory applied to amino acid sequences

    Science.gov (United States)

    Gatlin, L. L.

    1974-01-01

    Concepts of information theory are applied to examine various proteins in terms of their redundancy in natural originators such as animals and plants. The Monte Carlo method is used to derive information parameters for random protein sequences. Real protein sequence parameters are compared with the standard parameters of protein sequences having a specific length. The tendency of a chain to contain some amino acids more frequently than others and the tendency of a chain to contain certain amino acid pairs more frequently than other pairs are used as randomness measures of individual protein sequences. Non-periodic proteins are generally found to have random Shannon redundancies except in cases of constraints due to short chain length and genetic codes. Redundant characteristics of highly periodic proteins are discussed. A degree of periodicity parameter is derived.

  10. Quantum random number generator based on ‘Fermi–Dirac’ statistics of photocounts of faint laser pulses with a 75 Mbit s‑1 rate

    Science.gov (United States)

    Balygin, K. A.; Zaitsev, V. I.; Klimov, A. N.; Kulik, S. P.; Molotkov, S. N.; Popova, E.; Vinogradov, S.

    2017-12-01

    We implemented experimentally a quantum random number generator, based on the registration of quasi-single-photon light by a silicon photo-multiplier, which allows one to reliably achieve the Poisson statistics of photocounts. The use of the optimal grouping of photocounts and a polynomial-length sequence of the method for extracting the random sequence 0 and 1 made it possible to achieve the output rate of a provably random sequence up to 75 Mbit s-1 .

  11. Random walk centrality for temporal networks

    Science.gov (United States)

    Rocha, Luis E. C.; Masuda, Naoki

    2014-06-01

    Nodes can be ranked according to their relative importance within a network. Ranking algorithms based on random walks are particularly useful because they connect topological and diffusive properties of the network. Previous methods based on random walks, for example the PageRank, have focused on static structures. However, several realistic networks are indeed dynamic, meaning that their structure changes in time. In this paper, we propose a centrality measure for temporal networks based on random walks under periodic boundary conditions that we call TempoRank. It is known that, in static networks, the stationary density of the random walk is proportional to the degree or the strength of a node. In contrast, we find that, in temporal networks, the stationary density is proportional to the in-strength of the so-called effective network, a weighted and directed network explicitly constructed from the original sequence of transition matrices. The stationary density also depends on the sojourn probability q, which regulates the tendency of the walker to stay in the node, and on the temporal resolution of the data. We apply our method to human interaction networks and show that although it is important for a node to be connected to another node with many random walkers (one of the principles of the PageRank) at the right moment, this effect is negligible in practice when the time order of link activation is included.

  12. NAFASS in action: How to control randomness?

    Science.gov (United States)

    Nigmatullin, R. R.; Zhang, Wei

    2013-03-01

    In this paper the original method of transformation of one random function to another one is suggested. The problem of transformation of one random function to another one is based on the NAFASS approach suggested previously by one of the authors (RRN) in paper [1]. The problem can be formulated as follows: is it possible to transform one random function to another one (the functional forms of the both functions are not known) during the fixed segment of time t1? The solution of this problem shown in this paper gives a chance to manage with random functions that describe many complex systems, where the adequate model pretending on their functional or analytical description is not known. This transformation based on the successful solution of the Prony's problem gives unique chances to manage with some chemical processes, technological processes and understand better the general behavior of the different complex systems which cannot be managed by the human being. Besides this solution another solution of this problem related to control of detrended random sequences is considered also.

  13. Hedysarum L. (Fabaceae: Hedysareae Is Not Monophyletic - Evidence from Phylogenetic Analyses Based on Five Nuclear and Five Plastid Sequences.

    Directory of Open Access Journals (Sweden)

    Pei-Liang Liu

    Full Text Available The legume family (Fabaceae exhibits a high level of species diversity and evolutionary success worldwide. Previous phylogenetic studies of the genus Hedysarum L. (Fabaceae: Hedysareae showed that the nuclear and the plastid topologies might be incongruent, and the systematic position of the Hedysarum sect. Stracheya clade was uncertain. In this study, phylogenetic relationships of Hedysarum were investigated based on the nuclear ITS, ETS, PGDH, SQD1, TRPT and the plastid psbA-trnH, trnC-petN, trnL-trnF, trnS-trnG, petN-psbM sequences. Both nuclear and plastid data support two major lineages in Hedysarum: the Hedysarum s.s. clade and the Sartoria clade. In the nuclear tree, Hedysarum is biphyletic with the Hedysarum s.s. clade sister to the Corethrodendron + Eversmannia + Greuteria + Onobrychis clade (the CEGO clade, whereas the Sartoria clade is sister to the genus Taverniera DC. In the plastid tree, Hedysarum is monophyletic and sister to Taverniera. The incongruent position of the Hedysarum s.s. clade between the nuclear and plastid trees may be best explained by a chloroplast capture hypothesis via introgression. The Hedysarum sect. Stracheya clade is resolved as sister to the H. sect. Hedysarum clade in both nuclear and plastid trees, and our analyses support merging Stracheya into Hedysarum. Based on our new evidence from multiple sequences, Hedysarum is not monophyletic, and its generic delimitation needs to be reconsidered.

  14. Chameleon sequences in neurodegenerative diseases.

    Science.gov (United States)

    Bahramali, Golnaz; Goliaei, Bahram; Minuchehr, Zarrin; Salari, Ali

    2016-03-25

    Chameleon sequences can adopt either alpha helix sheet or a coil conformation. Defining chameleon sequences in PDB (Protein Data Bank) may yield to an insight on defining peptides and proteins responsible in neurodegeneration. In this research, we benefitted from the large PDB and performed a sequence analysis on Chameleons, where we developed an algorithm to extract peptide segments with identical sequences, but different structures. In order to find new chameleon sequences, we extracted a set of 8315 non-redundant protein sequences from the PDB with an identity less than 25%. Our data was classified to "helix to strand (HE)", "helix to coil (HC)" and "strand to coil (CE)" alterations. We also analyzed the occurrence of singlet and doublet amino acids and the solvent accessibility in the chameleon sequences; we then sorted out the proteins with the most number of chameleon sequences and named them Chameleon Flexible Proteins (CFPs) in our dataset. Our data revealed that Gly, Val, Ile, Tyr and Phe, are the major amino acids in Chameleons. We also found that there are proteins such as Insulin Degrading Enzyme IDE and GTP-binding nuclear protein Ran (RAN) with the most number of chameleons (640 and 405 respectively). These proteins have known roles in neurodegenerative diseases. Therefore it can be inferred that other CFP's can serve as key proteins in neurodegeneration, and a study on them can shed light on curing and preventing neurodegenerative diseases. Copyright © 2016 Elsevier Inc. All rights reserved.

  15. A criterion for regular sequences

    Indian Academy of Sciences (India)

    R. Narasimhan (Krishtel eMaging) 1461 1996 Oct 15 13:05:22

    D P PATIL1, U STORCH2 and J ST ¨UCKRAD3. 1Department of Mathematics, Indian Institute of Science, Bangalore 560 012, India ... For general notations in com- mutative algebra we also refer to [1]. ... Note that every sequence is a strongly regular as well as regular sequence on the zero module. Further, it is clear that a ...

  16. Chameleon sequences in neurodegenerative diseases

    Energy Technology Data Exchange (ETDEWEB)

    Bahramali, Golnaz [Institute of Biochemistry and Biophysics, University of Tehran, Tehran (Iran, Islamic Republic of); Goliaei, Bahram, E-mail: goliaei@ut.ac.ir [Institute of Biochemistry and Biophysics, University of Tehran, Tehran (Iran, Islamic Republic of); Minuchehr, Zarrin, E-mail: minuchehr@nigeb.ac.ir [Department of Systems Biotechnology, National Institute of Genetic Engineering and Biotechnology, (NIGEB), Tehran (Iran, Islamic Republic of); Salari, Ali [Department of Systems Biotechnology, National Institute of Genetic Engineering and Biotechnology, (NIGEB), Tehran (Iran, Islamic Republic of)

    2016-03-25

    Chameleon sequences can adopt either alpha helix sheet or a coil conformation. Defining chameleon sequences in PDB (Protein Data Bank) may yield to an insight on defining peptides and proteins responsible in neurodegeneration. In this research, we benefitted from the large PDB and performed a sequence analysis on Chameleons, where we developed an algorithm to extract peptide segments with identical sequences, but different structures. In order to find new chameleon sequences, we extracted a set of 8315 non-redundant protein sequences from the PDB with an identity less than 25%. Our data was classified to “helix to strand (HE)”, “helix to coil (HC)” and “strand to coil (CE)” alterations. We also analyzed the occurrence of singlet and doublet amino acids and the solvent accessibility in the chameleon sequences; we then sorted out the proteins with the most number of chameleon sequences and named them Chameleon Flexible Proteins (CFPs) in our dataset. Our data revealed that Gly, Val, Ile, Tyr and Phe, are the major amino acids in Chameleons. We also found that there are proteins such as Insulin Degrading Enzyme IDE and GTP-binding nuclear protein Ran (RAN) with the most number of chameleons (640 and 405 respectively). These proteins have known roles in neurodegenerative diseases. Therefore it can be inferred that other CFP's can serve as key proteins in neurodegeneration, and a study on them can shed light on curing and preventing neurodegenerative diseases.

  17. DNA Sequencing Sensors: An Overview

    Directory of Open Access Journals (Sweden)

    Jose Antonio Garrido-Cardenas

    2017-03-01

    Full Text Available The first sequencing of a complete genome was published forty years ago by the double Nobel Prize in Chemistry winner Frederick Sanger. That corresponded to the small sized genome of a bacteriophage, but since then there have been many complex organisms whose DNA have been sequenced. This was possible thanks to continuous advances in the fields of biochemistry and molecular genetics, but also in other areas such as nanotechnology and computing. Nowadays, sequencing sensors based on genetic material have little to do with those used by Sanger. The emergence of mass sequencing sensors, or new generation sequencing (NGS meant a quantitative leap both in the volume of genetic material that was able to be sequenced in each trial, as well as in the time per run and its cost. One can envisage that incoming technologies, already known as fourth generation sequencing, will continue to cheapen the trials by increasing DNA reading lengths in each run. All of this would be impossible without sensors and detection systems becoming smaller and more precise. This article provides a comprehensive overview on sensors for DNA sequencing developed within the last 40 years.

  18. Diesel Mechanics: Scope and Sequence.

    Science.gov (United States)

    Nashville - Davidson County Metropolitan Public Schools, TN.

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

  19. Graphene nanodevices for DNA sequencing

    NARCIS (Netherlands)

    Heerema, S.J.; Dekker, C.

    2016-01-01

    Fast, cheap, and reliable DNA sequencing could be one of the most disruptive innovations of this decade, as it will pave the way for personalized medicine. In pursuit of such technology, a variety of nanotechnology-based approaches have been explored and established, including sequencing with

  20. AMPLIFICATION OF RIBOSOMAL RNA SEQUENCES

    Science.gov (United States)

    This book chapter offers an overview of the use of ribosomal RNA sequences. A history of the technology traces the evolution of techniques to measure bacterial phylogenetic relationships and recent advances in obtaining rRNA sequence information. The manual also describes procedu...

  1. Combinatorial representations of token sequences

    NARCIS (Netherlands)

    Elzinga, C.H.

    2005-01-01

    This paper presents new representations of token sequences, with and without associated quantities, in Euclidean space. The representations are free of assumptions about the nature of the sequences or the processes that generate them. Algorithms and applications from the domains of structured

  2. Universal Sequencing on a Single Machine

    Science.gov (United States)

    Epstein, Leah; Levin, Asaf; Marchetti-Spaccamela, Alberto; Megow, Nicole; Mestre, Julián; Skutella, Martin; Stougie, Leen

    We consider scheduling on an unreliable machine that may experience unexpected changes in processing speed or even full breakdowns. We aim for a universal solution that performs well without adaptation for any possible machine behavior. For the objective of minimizing the total weighted completion time, we design a polynomial time deterministic algorithm that finds a universal scheduling sequence with a solution value within 4 times the value of an optimal clairvoyant algorithm that knows the disruptions in advance. A randomized version of this algorithm attains in expectation a ratio of e. We also show that both results are best possible among all universal solutions. As a direct consequence of our results, we answer affirmatively the question of whether a constant approximation algorithm exists for the offline version of the problem when machine unavailability periods are known in advance.

  3. Short barcodes for next generation sequencing.

    Directory of Open Access Journals (Sweden)

    Katharina Mir

    Full Text Available We consider the design and evaluation of short barcodes, with a length between six and eight nucleotides, used for parallel sequencing on platforms where substitution errors dominate. Such codes should have not only good error correction properties but also the code words should fulfil certain biological constraints (experimental parameters. We compare published barcodes with codes obtained by two new constructions methods, one based on the currently best known linear codes and a simple randomized construction method. The evaluation done is with respect to the error correction capabilities, barcode size and their experimental parameters and fundamental bounds on the code size and their distance properties. We provide a list of codes for lengths between six and eight nucleotides, where for length eight, two substitution errors can be corrected. In fact, no code with larger minimum distance can exist.

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

    Energy Technology Data Exchange (ETDEWEB)

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

    2013-09-15

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

  5. Exome sequencing covers >98% of mutations identified on targeted next generation sequencing panels.

    Directory of Open Access Journals (Sweden)

    Holly LaDuca

    Full Text Available With the expanded availability of next generation sequencing (NGS-based clinical genetic tests, clinicians seeking to test patients with Mendelian diseases must weigh the superior coverage of targeted gene panels with the greater number of genes included in whole exome sequencing (WES when considering their first-tier testing approach. Here, we use an in silico analysis to predict the analytic sensitivity of WES using pathogenic variants identified on targeted NGS panels as a reference.Corresponding nucleotide positions for 1533 different alterations classified as pathogenic or likely pathogenic identified on targeted NGS multi-gene panel tests in our laboratory were interrogated in data from 100 randomly-selected clinical WES samples to quantify the sequence coverage at each position. Pathogenic variants represented 91 genes implicated in hereditary cancer, X-linked intellectual disability, primary ciliary dyskinesia, Marfan syndrome/aortic aneurysms, cardiomyopathies and arrhythmias.When assessing coverage among 100 individual WES samples for each pathogenic variant (153,300 individual assessments, 99.7% (n = 152,798 would likely have been detected on WES. All pathogenic variants had at least some coverage on exome sequencing, with a total of 97.3% (n = 1491 detectable across all 100 individuals. For the remaining 42 pathogenic variants, the number of WES samples with adequate coverage ranged from 35 to 99. Factors such as location in GC-rich, repetitive, or homologous regions likely explain why some of these alterations were not detected across all samples. To validate study findings, a similar analysis was performed against coverage data from 60,706 exomes available through the Exome Aggregation Consortium (ExAC. Results from this validation confirmed that 98.6% (91,743,296/93,062,298 of pathogenic variants demonstrated adequate depth for detection.Results from this in silico analysis suggest that exome sequencing may achieve a diagnostic

  6. Repeated DNA sequences in fungi

    Energy Technology Data Exchange (ETDEWEB)

    Dutta, S.K.

    1974-11-01

    Several fungal species, representatives of all broad groups like basidiomycetes, ascomycetes and phycomycetes, were examined for the nature of repeated DNA sequences by DNA:DNA reassociation studies using hydroxyapatite chromatography. All of the fungal species tested contained 10 to 20 percent repeated DNA sequences. There are approximately 100 to 110 copies of repeated DNA sequences of approximately 4 x 10/sup 7/ daltons piece size of each. Repeated DNA sequence homoduplexes showed on average 5/sup 0/C difference of T/sub e/50 (temperature at which 50 percent duplexes dissociate) values from the corresponding homoduplexes of unfractionated whole DNA. It is suggested that a part of repetitive sequences in fungi constitutes mitochondrial DNA and a part of it constitutes nuclear DNA. (auth)

  7. Cluster-Based Multipolling Sequencing Algorithm for Collecting RFID Data in Wireless LANs

    Science.gov (United States)

    Choi, Woo-Yong; Chatterjee, Mainak

    2015-03-01

    With the growing use of RFID (Radio Frequency Identification), it is becoming important to devise ways to read RFID tags in real time. Access points (APs) of IEEE 802.11-based wireless Local Area Networks (LANs) are being integrated with RFID networks that can efficiently collect real-time RFID data. Several schemes, such as multipolling methods based on the dynamic search algorithm and random sequencing, have been proposed. However, as the number of RFID readers associated with an AP increases, it becomes difficult for the dynamic search algorithm to derive the multipolling sequence in real time. Though multipolling methods can eliminate the polling overhead, we still need to enhance the performance of the multipolling methods based on random sequencing. To that extent, we propose a real-time cluster-based multipolling sequencing algorithm that drastically eliminates more than 90% of the polling overhead, particularly so when the dynamic search algorithm fails to derive the multipolling sequence in real time.

  8. Random numbers spring from alpha decay

    Energy Technology Data Exchange (ETDEWEB)

    Frigerio, N.A.; Sanathanan, L.P.; Morley, M.; Clark, N.A.; Tyler, S.A.

    1980-05-01

    Congruential random number generators, which are widely used in Monte Carlo simulations, are deficient in that the number they generate are concentrated in a relatively small number of hyperplanes. While this deficiency may not be a limitation in small Monte Carlo studies involving a few variables, it introduces a significant bias in large simulations requiring high resolution. This bias was recognized and assessed during preparations for an accident analysis study of nuclear power plants. This report describes a random number device based on the radioactive decay of alpha particles from a /sup 235/U source in a high-resolution gas proportional counter. The signals were fed to a 4096-channel analyzer and for each channel the frequency of signals registered in a 20,000-microsecond interval was recorded. The parity bits of these frequency counts (0 for an even count and 1 for an odd count) were then assembled in sequence to form 31-bit binary random numbers and transcribed to a magnetic tape. This cycle was repeated as many times as were necessary to create 3 million random numbers. The frequency distribution of counts from the present device conforms to the Brockwell-Moyal distribution, which takes into account the dead time of the counter (both the dead time and decay constant of the underlying Poisson process were estimated). Analysis of the count data and tests of randomness on a sample set of the 31-bit binary numbers indicate that this random number device is a highly reliable source of truly random numbers. Its use is, therefore, recommended in Monte Carlo simulations for which the congruential pseudorandom number generators are found to be inadequate. 6 figures, 5 tables.

  9. Comment on "Linguistic features of noncoding DNA sequences"

    CERN Document Server

    Israeloff, N E; Chan, K; Israeloff, N E; Kagalenko, M; Chan, K

    1995-01-01

    In a recent Physical Review Letter, Mantegna et. al., report that certain statistical signatures of natural language can be found in non-coding DNA sequences. In this comment we show that random noise with power-law correlation similar to 1/f noise, exhibits the same "linguistic" signature as those found in non-coding DNA. We conclude that these signa- tures cannot distinguish languages from noise.

  10. First steps in random walks from tools to applications

    CERN Document Server

    Klafter, J

    2011-01-01

    The name ""random walk"" for a problem of a displacement of a point in a sequence of independent random steps was coined by Karl Pearson in 1905 in a question posed to readers of ""Nature"". The same year, a similar problem was formulated by Albert Einstein in one of his Annus Mirabilis works. Even earlier such a problem was posed by Louis Bachelier in his thesis devoted to the theory of financial speculations in 1900. Nowadays the theory of random walks has proved useful in physics andchemistry (diffusion, reactions, mixing in flows), economics, biology (from animal spread to motion of subcel

  11. Improved motor sequence retention by motionless listening.

    Science.gov (United States)

    Lahav, Amir; Katz, Tal; Chess, Roxanne; Saltzman, Elliot

    2013-05-01

    This study examined the effect of listening to a newly learned musical piece on subsequent motor retention of the piece. Thirty-six non-musicians were trained to play an unfamiliar melody on a piano keyboard. Next, they were randomly assigned to participate in three follow-up listening sessions over 1 week. Subjects who, during their listening sessions, listened to the same initial piece showed significant improvements in motor memory and retention of the piece despite the absence of physical practice. These improvements included increased pitch accuracy, time accuracy, and dynamic intensity of key pressing. Similar improvements, though to a lesser degree, were observed in subjects who, during their listening sessions, were distracted by another task. Control subjects, who after learning the piece had listened to nonmusical sounds, showed impaired motoric retention of the piece at 1 week from the initial acquisition day. These results imply that motor sequences can be established in motor memory without direct access to motor-related information. In addition, the study revealed that the listening-induced improvements did not generalize to the learning of a new musical piece composed of the same notes as the initial piece learned, limiting the effects to musical motor sequences that are already part of the individual's motor repertoire.

  12. Effects of regularity on the processing of sound omission in a tone sequence in musicians and non-musicians.

    Science.gov (United States)

    Ono, Kentaro; Matsuhashi, Masao; Mima, Tatsuya; Fukuyama, Hidenao; Altmann, Christian F

    2013-09-01

    Numerous studies have reported that perceptual grouping affects the pre-attentive processing of sound omission in a sequence of tones. However, it remains unclear whether or not the perceptual grouping and musical experience affect the attentive processing of sound omission. To this end, we created a sequence of loud (L) and soft (S) tones grouped as 'LLSLLS…' and a random sequence of the L and S tones. The omission of the L tones was inserted pseudo-randomly in the random sequence, and there were two positions at which it was inserted. For within-group omission, the omission was after the first L tone within the 'LLS' pattern. For between-group omission, the omission was inserted between the patterns. The brain response to the omission in musicians and non-musicians was measured using magnetoencephalography. During the magnetoencephalography measurement, the subjects' performance in a task to detect the omission was faster in the random sequence than in the group sequence. Source analysis showed that the omission in the random sequence caused greater activity than that in the group sequence. The increase was found in the right inferior parietal lobe in musicians, whereas it was found in the left superior temporal gyrus in non-musicians. These results suggest that the attentive processing of perceptual grouping might implicate the left superior temporal gyrus or right inferior parietal lobe, depending on musical experience. © 2013 Federation of European Neuroscience Societies and John Wiley & Sons Ltd.

  13. Social intuition as a form of implicit learning: Sequences of body movements are learned less explicitly than letter sequences.

    Science.gov (United States)

    Norman, Elisabeth; Price, Mark C

    2012-01-01

    In the current paper, we first evaluate the suitability of traditional serial reaction time (SRT) and artificial grammar learning (AGL) experiments for measuring implicit learning of social signals. We then report the results of a novel sequence learning task which combines aspects of the SRT and AGL paradigms to meet our suggested criteria for how implicit learning experiments can be adapted to increase their relevance to situations of social intuition. The sequences followed standard finite-state grammars. Sequence learning and consciousness of acquired knowledge were compared between 2 groups of 24 participants viewing either sequences of individually presented letters or sequences of body-posture pictures, which were described as series of yoga movements. Participants in both conditions showed above-chance classification accuracy, indicating that sequence learning had occurred in both stimulus conditions. This shows that sequence learning can still be found when learning procedures reflect the characteristics of social intuition. Rule awareness was measured using trial-by-trial evaluation of decision strategy (Dienes & Scott, 2005; Scott & Dienes, 2008). For letters, sequence classification was best on trials where participants reported responding on the basis of explicit rules or memory, indicating some explicit learning in this condition. For body-posture, classification was not above chance on these types of trial, but instead showed a trend to be best on those trials where participants reported that their responses were based on intuition, familiarity, or random choice, suggesting that learning was more implicit. Results therefore indicate that the use of traditional stimuli in research on sequence learning might underestimate the extent to which learning is implicit in domains such as social learning, contributing to ongoing debate about levels of conscious awareness in implicit learning.

  14. EST sequencing of Onychophora and phylogenomic analysis of Metazoa.

    Science.gov (United States)

    Roeding, Falko; Hagner-Holler, Silke; Ruhberg, Hilke; Ebersberger, Ingo; von Haeseler, Arndt; Kube, Michael; Reinhardt, Richard; Burmester, Thorsten

    2007-12-01

    Onychophora (velvet worms) represent a small animal taxon considered to be related to Euarthropoda. We have obtained 1873 5' cDNA sequences (expressed sequence tags, ESTs) from the velvet worm Epiperipatus sp., which were assembled into 833 contigs. BLAST similarity searches revealed that 51.9% of the contigs had matches in the protein databases with expectation values lower than 10(-4). Most ESTs had the best hit with proteins from either Chordata or Arthropoda (approximately 40% respectively). The ESTs included sequences of 27 ribosomal proteins. The orthologous sequences from 28 other species of a broad range of phyla were obtained from the databases, including other EST projects. A concatenated amino acid alignment comprising 5021 positions was constructed, which covers 4259 positions when problematic regions were removed. Bayesian and maximum likelihood methods place Epiperipatus within the monophyletic Ecdysozoa (Onychophora, Arthropoda, Tardigrada and Nematoda), but its exact relation to the Euarthropoda remained unresolved. The "Articulata" concept was not supported. Tardigrada and Nematoda formed a well-supported monophylum, suggesting that Tardigrada are actually Cycloneuralia. In agreement with previous studies, we have demonstrated that random sequencing of cDNAs results in sequence information suitable for phylogenomic approaches to resolve metazoan relationships.

  15. In silico evidence for sequence-dependent nucleosome sliding

    Energy Technology Data Exchange (ETDEWEB)

    Lequieu, Joshua; Schwartz, David C.; de Pablo, Juan J.

    2017-10-18

    Nucleosomes represent the basic building block of chromatin and provide an important mechanism by which cellular processes are controlled. The locations of nucleosomes across the genome are not random but instead depend on both the underlying DNA sequence and the dynamic action of other proteins within the nucleus. These processes are central to cellular function, and the molecular details of the interplay between DNA sequence and nudeosome dynamics remain poorly understood. In this work, we investigate this interplay in detail by relying on a molecular model, which permits development of a comprehensive picture of the underlying free energy surfaces and the corresponding dynamics of nudeosome repositioning. The mechanism of nudeosome repositioning is shown to be strongly linked to DNA sequence and directly related to the binding energy of a given DNA sequence to the histone core. It is also demonstrated that chromatin remodelers can override DNA-sequence preferences by exerting torque, and the histone H4 tail is then identified as a key component by which DNA-sequence, histone modifications, and chromatin remodelers could in fact be coupled.

  16. Multilocus Sequence Typing of Total-Genome-Sequenced Bacteria

    DEFF Research Database (Denmark)

    Larsen, Mette Voldby; Cosentino, Salvatore; Rasmussen, Simon

    2012-01-01

    and between laboratories. Ideally, this information should also allow for comparison to historical data. We developed a Web-based method for MLST of 66 bacterial species based on WGS data. As input, the method uses short sequence reads from four sequencing platforms or preassembled genomes. Updates from......Accurate strain identification is essential for anyone working with bacteria. For many species, multilocus sequence typing (MLST) is considered the "gold standard" of typing, but it is traditionally performed in an expensive and time-consuming manner. As the costs of whole-genome sequencing (WGS......) continue to decline, it becomes increasingly available to scientists and routine diagnostic laboratories. Currently, the cost is below that of traditional MLST. The new challenges will be how to extract the relevant information from the large amount of data so as to allow for comparison over time...

  17. Analisis Teoritis dan Empiris Uji Craps dari Diehard Battery of Randomness Test untuk Pengujian Pembangkit Bilangan Acaksemu

    Directory of Open Access Journals (Sweden)

    Sari Agustini Hafman

    2013-05-01

    Full Text Available According to Kerchoffs (1883, the security system should only rely on cryptographic keys which is used in that system. Generally, the key sequences are generated by a Pseudo Random Number Generator (PRNG or Random Number Generator (RNG. There are three types of randomness sequences that generated by the RNG and PRNG i.e. pseudorandom sequence, cryptographically secure pseudorandom sequences, and real random sequences. Several statistical tests, including diehard battery of tests of randomness, is used to check the type of randomness sequences that generated by PRNG or RNG. Due to its purpose, the principle on taking the testing parameters and the test statistic are associated with the validity of the conclusion produced by a statistical test, then the theoretical analysis is performed by applying a variety of statistical theory to evaluate craps test, one of the test included in the diehard battery of randomness tests. Craps test, inspired by craps game, aims to examine whether a PRNG produces an independent and identically distributed (iid pseudorandom sequences. To demonstrate the process to produce a test statistics equation and to show how craps games applied on that test, will be carried out theoretical analysis by applying a variety of statistical theory. Furthermore, empirical observations will be done by applying craps test on a PRNG in order to check the test effectiveness in detecting the distribution and independency of sequences which produced by PRNG

  18. Random maintenance policies

    CERN Document Server

    Nakagawa, Toshio

    2014-01-01

    Exploring random maintenance models, this book provides an introduction to the implementation of random maintenance, and it is one of the first books to be written on this subject.  It aims to help readers learn new techniques for applying random policies to actual reliability models, and it provides new theoretical analyses of various models including classical replacement, preventive maintenance and inspection policies. These policies are applied to scheduling problems, backup policies of database systems, maintenance policies of cumulative damage models, and reliability of random redundant systems. Reliability theory is a major concern for engineers and managers, and in light of Japan’s recent earthquake, the reliability of large-scale systems has increased in importance. This also highlights the need for a new notion of maintenance and reliability theory, and how this can practically be applied to systems. Providing an essential guide for engineers and managers specializing in reliability maintenance a...

  19. Drawing a random number

    DEFF Research Database (Denmark)

    Wanscher, Jørgen Bundgaard; Sørensen, Majken Vildrik

    2006-01-01

    highly uniform multidimensional draws, which are highly relevant for todays traffic models. This paper shows among others combined shuffling and scrambling seems needless, that scrambling gives the lowest correlation and that there are detectable differences between random numbers, dependent...

  20. Theory of random sets

    CERN Document Server

    Molchanov, Ilya

    2017-01-01

    This monograph, now in a thoroughly revised second edition, offers the latest research on random sets. It has been extended to include substantial developments achieved since 2005, some of them motivated by applications of random sets to econometrics and finance. The present volume builds on the foundations laid by Matheron and others, including the vast advances in stochastic geometry, probability theory, set-valued analysis, and statistical inference. It shows the various interdisciplinary relationships of random set theory within other parts of mathematics, and at the same time fixes terminology and notation that often vary in the literature, establishing it as a natural part of modern probability theory and providing a platform for future development. It is completely self-contained, systematic and exhaustive, with the full proofs that are necessary to gain insight. Aimed at research level, Theory of Random Sets will be an invaluable reference for probabilists; mathematicians working in convex and integ...

  1. A note on the strong law of large numbers for associated sequences

    Directory of Open Access Journals (Sweden)

    A. Nezakati

    2005-01-01

    Full Text Available We prove that the sequence {bn−1∑i=1n(Xi−EXi}n≥1 converges a.e. to zero if {Xn,n≥1} is anassociated sequence of random variables with ∑n=1∞bkn−2Var(∑i=kn−1+1knXi<∞ where {bn,n≥1} is a positive nondecreasing sequence and {kn,n≥1} is a strictly increasing sequence, both tending to infinity as n tends to infinity and 0

  2. Central limit theorems for sequences with m(n)-dependent main part

    NARCIS (Netherlands)

    Nieuwenhuis, G.

    1992-01-01

    Let (Xi(n); n ϵ N, 1⩽i⩽h(n)) be a double sequence of random variables with h(n)→∞ as n→∞. Suppose that the sequence can be split into two parts: an m(n)-dependent sequence (Xi,m(n); n ϵ N, 1⩽i⩽h(n)) of main terms and a sequence (Xi,m(n); n ϵ N, 1⩽i⩽h(n)) of residual terms. Here (m(n)) may be

  3. Quasiclassical Random Matrix Theory

    OpenAIRE

    Prange, R. E.

    1996-01-01

    We directly combine ideas of the quasiclassical approximation with random matrix theory and apply them to the study of the spectrum, in particular to the two-level correlator. Bogomolny's transfer operator T, quasiclassically an NxN unitary matrix, is considered to be a random matrix. Rather than rejecting all knowledge of the system, except for its symmetry, [as with Dyson's circular unitary ensemble], we choose an ensemble which incorporates the knowledge of the shortest periodic orbits, th...

  4. Optimal sequence for Parrondo games

    Science.gov (United States)

    Dinis, Luis

    2008-02-01

    An algorithm based on backward induction is devised in order to compute the optimal sequence of games to be played in Parrondo games. The algorithm can be used to find the optimal sequence for any finite number of turns or in the steady state, showing that ABABB… is the sequence with the highest steady state average gain. The algorithm can also be generalized to find the optimal adaptive strategy in a multiplayer version of the games, where a finite number of players may choose, at every turn, the game the whole ensemble should play.

  5. G-quadruplex aptamer selection using capillary electrophoresis-LED-induced fluorescence and Illumina sequencing.

    Science.gov (United States)

    Ric, Audrey; Ecochard, Vincent; Iacovoni, Jason S; Boutonnet, Audrey; Ginot, Frédéric; Ong-Meang, Varravaddheay; Poinsot, Véréna; Paquereau, Laurent; Couderc, François

    2018-03-01

    One of the major difficulties that arises when selecting aptamers containing a G-quadruplex is the correct amplification of the ssDNA sequence. Can aptamers containing a G-quadruplex be selected from a degenerate library using non-equilibrium capillary electrophoresis (CE) of equilibrium mixtures (NECEEM) along with high-throughput Illumina sequencing? In this article, we present some mismatches of the G-quadruplex T29 aptamer specific to thrombin, which was PCR amplified and sequenced by Illumina sequencing. Then, we show the proportionality between the number of sequenced molecules of T29 added to the library and the number of sequences obtained in Illumina sequencing, and we find that T29 sequences from this aptamer can be detected in a random library of ssDNA after the sample is fractionated by NECEEM, amplified by PCR, and sequenced. Treatment of the data by the counting of double-stranded DNA T29 sequences containing a maximum of two mismatches reveals a good correlation with the enrichment factor (f E ). This factor is the ratio of the number of aptamer sequences found in the collected complex sample divided by the total number of sequencing reads (aptamer and non-aptamer) plus the quantity of T29 molecules (spiked into a DNA library) injected into CE.

  6. Quantum randomness and unpredictability

    Energy Technology Data Exchange (ETDEWEB)

    Jaeger, Gregg [Quantum Communication and Measurement Laboratory, Department of Electrical and Computer Engineering and Division of Natural Science and Mathematics, Boston University, Boston, MA (United States)

    2017-06-15

    Quantum mechanics is a physical theory supplying probabilities corresponding to expectation values for measurement outcomes. Indeed, its formalism can be constructed with measurement as a fundamental process, as was done by Schwinger, provided that individual measurements outcomes occur in a random way. The randomness appearing in quantum mechanics, as with other forms of randomness, has often been considered equivalent to a form of indeterminism. Here, it is argued that quantum randomness should instead be understood as a form of unpredictability because, amongst other things, indeterminism is not a necessary condition for randomness. For concreteness, an explication of the randomness of quantum mechanics as the unpredictability of quantum measurement outcomes is provided. Finally, it is shown how this view can be combined with the recently introduced view that the very appearance of individual quantum measurement outcomes can be grounded in the Plenitude principle of Leibniz, a principle variants of which have been utilized in physics by Dirac and Gell-Mann in relation to the fundamental processes. This move provides further support to Schwinger's ''symbolic'' derivation of quantum mechanics from measurement. (copyright 2016 WILEY-VCH Verlag GmbH and Co. KGaA, Weinheim)

  7. Random coil chemical shift for intrinsically disordered proteins

    DEFF Research Database (Denmark)

    Kjærgaard, Magnus; Brander, Søren; Poulsen, Flemming Martin

    2011-01-01

    Secondary chemical shift analysis is the main NMR method for detection of transiently formed secondary structure in intrinsically disordered proteins. The quality of the secondary chemical shifts is dependent on an appropriate choice of random coil chemical shifts. We report random coil chemical....... Temperature has a non-negligible effect on the (13)C random coil chemical shifts, so temperature coefficients are reported for the random coil chemical shifts to allow extrapolation to other temperatures. The pH dependence of the histidine random coil chemical shifts is investigated in a titration series...... shifts and sequence correction factors determined for a GGXGG peptide series following the approach of Schwarzinger et al. (J Am Chem Soc 123(13):2970-2978, 2001). The chemical shifts are determined at neutral pH in order to match the conditions of most studies of intrinsically disordered proteins...

  8. Fuzzy conditional random fields for temporal data mining

    Science.gov (United States)

    Nurma Yulita, Intan; Setiawan Abdullah, Atje

    2017-10-01

    Temporal data mining is one of the interesting problems in computer science and its application has been performed in a wide variety of fields. The difference between the temporal data mining and data mining is the use of variable time. Therefore, the method used must be capable of processing variables of time. Compared with other methods, conditional random field has advantages in the processing variables of time. The method is a directed graph models that has been widely applied for segmenting and labelling sequence data that appears in various domains. In this study, we proposed use of Fuzzy Logic to be applied in Conditional Random Fields to overcome the problems of uncertainty. The experiment is compared Fuzzy Conditional Random Fields, Conditional Random Fields, and Hidden Markov Models. The result showed that accuracy of Fuzzy Conditional Random Fields is the best.

  9. Multi-bit quantum random number generation by measuring positions of arrival photons.

    Science.gov (United States)

    Yan, Qiurong; Zhao, Baosheng; Liao, Qinghong; Zhou, Nanrun

    2014-10-01

    We report upon the realization of a novel multi-bit optical quantum random number generator by continuously measuring the arrival positions of photon emitted from a LED using MCP-based WSA photon counting imaging detector. A spatial encoding method is proposed to extract multi-bits random number from the position coordinates of each detected photon. The randomness of bits sequence relies on the intrinsic randomness of the quantum physical processes of photonic emission and subsequent photoelectric conversion. A prototype has been built and the random bit generation rate could reach 8 Mbit/s, with random bit generation efficiency of 16 bits per detected photon. FPGA implementation of Huffman coding is proposed to reduce the bias of raw extracted random bits. The random numbers passed all tests for physical random number generator.

  10. Cryptography, statistics and pseudo-randomness (Part 1)

    NARCIS (Netherlands)

    Brands, S.; Gill, R.D.

    1995-01-01

    In the classical approach to pseudo-random number generators, a generator is considered to perform well if its output sequences pass a battery of statistical tests that has become standard. In recent years, it has turned out that this approach is not satisfactory. Many generators have turned out to

  11. Statistical theory of neutral protein evolution by random site mutations

    Indian Academy of Sciences (India)

    Alternatively, a self-consistent mean-field based theory is developed to evaluate the protein neutrality through random single-point and multiple-point mutations by calculating the pair-wise probability profile of the amino acid residues in a library of sequences, consistent with a particular foldability criterion. The theory ...

  12. Models of Prime-Like Sequences Generated by Least Element Sieve Operations Like the Sieve of Eratosthenes

    OpenAIRE

    Baum, Leonard E.

    2017-01-01

    We suggest other models of sieve generated sequences like the Sieve of Eratosthenes to explain randomness properties of the prime numbers, like the twin prime conjecture, the lim sup conjecture, the Riemann conjecture, and the prime number theorem.

  13. Molecular beacon sequence design algorithm.

    Science.gov (United States)

    Monroe, W Todd; Haselton, Frederick R

    2003-01-01

    A method based on Web-based tools is presented to design optimally functioning molecular beacons. Molecular beacons, fluorogenic hybridization probes, are a powerful tool for the rapid and specific detection of a particular nucleic acid sequence. However, their synthesis costs can be considerable. Since molecular beacon performance is based on its sequence, it is imperative to rationally design an optimal sequence before synthesis. The algorithm presented here uses simple Microsoft Excel formulas and macros to rank candidate sequences. This analysis is carried out using mfold structural predictions along with other free Web-based tools. For smaller laboratories where molecular beacons are not the focus of research, the public domain algorithm described here may be usefully employed to aid in molecular beacon design.

  14. The Dynamics of DNA Sequencing.

    Science.gov (United States)

    Morvillo, Nancy

    1997-01-01

    Describes a paper-and-pencil activity that helps students understand DNA sequencing and expands student understanding of DNA structure, replication, and gel electrophoresis. Appropriate for advanced biology students who are familiar with the Sanger method. (DDR)

  15. Three subsets of sequence complexity and their relevance to biopolymeric information

    Directory of Open Access Journals (Sweden)

    Trevors Jack T

    2005-08-01

    Full Text Available Abstract Genetic algorithms instruct sophisticated biological organization. Three qualitative kinds of sequence complexity exist: random (RSC, ordered (OSC, and functional (FSC. FSC alone provides algorithmic instruction. Random and Ordered Sequence Complexities lie at opposite ends of the same bi-directional sequence complexity vector. Randomness in sequence space is defined by a lack of Kolmogorov algorithmic compressibility. A sequence is compressible because it contains redundant order and patterns. Law-like cause-and-effect determinism produces highly compressible order. Such forced ordering precludes both information retention and freedom of selection so critical to algorithmic programming and control. Functional Sequence Complexity requires this added programming dimension of uncoerced selection at successive decision nodes in the string. Shannon information theory measures the relative degrees of RSC and OSC. Shannon information theory cannot measure FSC. FSC is invariably associated with all forms of complex biofunction, including biochemical pathways, cycles, positive and negative feedback regulation, and homeostatic metabolism. The algorithmic programming of FSC, not merely its aperiodicity, accounts for biological organization. No empirical evidence exists of either RSC of OSC ever having produced a single instance of sophisticated biological organization. Organization invariably manifests FSC rather than successive random events (RSC or low-informational self-ordering phenomena (OSC.

  16. Sequencing Centers Panel at SFAF

    Energy Technology Data Exchange (ETDEWEB)

    Schilkey, Faye [NCGR; Ali, Johar [OICR; Grafham, Darren [Wellcome Trust Sanger Institute; Muzny, Donna [Baylor College of Medicine; Fulton, Bob [Washington University; Fitzgerald, Mike [Broad Institute; Hostetler, Jessica [J. Craig Venter Institute; Daum, Chris [DOE Joint Genome Institute

    2010-06-02

    From left to right: Faye Schilkey of NCGR, Johar Ali of OICR, Darren Grafham of Wellcome Trust Sanger Institute, Donna Muzny of the Baylor College of Medicine, Bob Fulton of Washington University, Mike Fitzgerald of the Broad Institute, Jessica Hostetler of the J. Craig Venter Institute and Chris Daum of the DOE Joint Genome Institute discuss sequencing technologies, applications and pipelines on June 2, 2010 at the "Sequencing, Finishing, Analysis in the Future" meeting in Santa Fe, NM

  17. DNA sequences at a glance.

    Directory of Open Access Journals (Sweden)

    Armando J Pinho

    Full Text Available Data summarization and triage is one of the current top challenges in visual analytics. The goal is to let users visually inspect large data sets and examine or request data with particular characteristics. The need for summarization and visual analytics is also felt when dealing with digital representations of DNA sequences. Genomic data sets are growing rapidly, making their analysis increasingly more difficult, and raising the need for new, scalable tools. For example, being able to look at very large DNA sequences while immediately identifying potentially interesting regions would provide the biologist with a flexible exploratory and analytical tool. In this paper we present a new concept, the "information profile", which provides a quantitative measure of the local complexity of a DNA sequence, independently of the direction of processing. The computation of the information profiles is computationally tractable: we show that it can be done in time proportional to the length of the sequence. We also describe a tool to compute the information profiles of a given DNA sequence, and use the genome of the fission yeast Schizosaccharomyces pombe strain 972 h(- and five human chromosomes 22 for illustration. We show that information profiles are useful for detecting large-scale genomic regularities by visual inspection. Several discovery strategies are possible, including the standalone analysis of single sequences, the comparative analysis of sequences from individuals from the same species, and the comparative analysis of sequences from different organisms. The comparison scale can be varied, allowing the users to zoom-in on specific details, or obtain a broad overview of a long segment. Software applications have been made available for non-commercial use at http://bioinformatics.ua.pt/software/dna-at-glance.

  18. Nanogrid rolling circle DNA sequencing

    Energy Technology Data Exchange (ETDEWEB)

    Church, George M.; Porreca, Gregory J.; Shendure, Jay; Rosenbaum, Abraham Meir

    2017-04-18

    The present invention relates to methods for sequencing a polynucleotide immobilized on an array having a plurality of specific regions each having a defined diameter size, including synthesizing a concatemer of a polynucleotide by rolling circle amplification, wherein the concatemer has a cross-sectional diameter greater than the diameter of a specific region, immobilizing the concatemer to the specific region to make an immobilized concatemer, and sequencing the immobilized concatemer.

  19. Optimization of sequence alignment for simple sequence repeat regions

    Directory of Open Access Journals (Sweden)

    Ogbonnaya Francis C

    2011-07-01

    Full Text Available Abstract Background Microsatellites, or simple sequence repeats (SSRs, are tandemly repeated DNA sequences, including tandem copies of specific sequences no longer than six bases, that are distributed in the genome. SSR has been used as a molecular marker because it is easy to detect and is used in a range of applications, including genetic diversity, genome mapping, and marker assisted selection. It is also very mutable because of slipping in the DNA polymerase during DNA replication. This unique mutation increases the insertion/deletion (INDELs mutation frequency to a high ratio - more than other types of molecular markers such as single nucleotide polymorphism (SNPs. SNPs are more frequent than INDELs. Therefore, all designed algorithms for sequence alignment fit the vast majority of the genomic sequence without considering microsatellite regions, as unique sequences that require special consideration. The old algorithm is limited in its application because there are many overlaps between different repeat units which result in false evolutionary relationships. Findings To overcome the limitation of the aligning algorithm when dealing with SSR loci, a new algorithm was developed using PERL script with a Tk graphical interface. This program is based on aligning sequences after determining the repeated units first, and the last SSR nucleotides positions. This results in a shifting process according to the inserted repeated unit type. When studying the phylogenic relations before and after applying the new algorithm, many differences in the trees were obtained by increasing the SSR length and complexity. However, less distance between different linage had been observed after applying the new algorithm. Conclusions The new algorithm produces better estimates for aligning SSR loci because it reflects more reliable evolutionary relations between different linages. It reduces overlapping during SSR alignment, which results in a more realistic

  20. Quantum Criticality of Hot Random Spin Chains

    Science.gov (United States)

    Vasseur, R.; Potter, A. C.; Parameswaran, S. A.

    2015-05-01

    We study the infinite-temperature properties of an infinite sequence of random quantum spin chains using a real-space renormalization group approach, and demonstrate that they exhibit nonergodic behavior at strong disorder. The analysis is conveniently implemented in terms of SU (2 )k anyon chains that include the Ising and Potts chains as notable examples. Highly excited eigenstates of these systems exhibit properties usually associated with quantum critical ground states, leading us to dub them "quantum critical glasses." We argue that random-bond Heisenberg chains self-thermalize and that the excited-state entanglement crosses over from volume-law to logarithmic scaling at a length scale that diverges in the Heisenberg limit k →∞. The excited state fixed points are generically distinct from their ground state counterparts, and represent novel nonequilibrium critical phases of matter.

  1. Complete mitochondrial DNA sequences of the green turtle and blue-tailed mole skink: statistical evidence for archosaurian affinity of turtles.

    Science.gov (United States)

    Kumazawa, Y; Nishida, M

    1999-06-01

    Turtles have highly specialized morphological characteristics, and their phylogenetic position has been under intensive debate. Previous molecular studies have not established a consistent and statistically well supported conclusion on this issue. In order to address this, complete mitochondrial DNA sequences were determined for the green turtle and the blue-tailed mole skink. These genomes possess an organization of genes which is typical of most other vertebrates, such as placental mammals, a frog, and bony fishes, but distinct from organizations of alligators and snakes. Molecular evolutionary rates of mitochondrial protein sequences appear to vary considerably among major reptilian lineages, with relatively rapid rates for snake and crocodilian lineages but slow rates for turtle and lizard lineages. In spite of this rate heterogeneity, phylogenetic analyses using amino acid sequences of 12 mitochondrial proteins reliably established the Archosauria (birds and crocodilians) and Lepidosauria (lizards and snakes) clades postulated from previous morphological studies. The phylogenetic analyses further suggested that turtles are a sister group of the archosaurs, and this untraditional relationship was provided with strong statistical evidence by both the bootstrap and the Kishino-Hasegawa tests. This is the first statistically significant molecular phylogeny on the placement of turtles relative to the archosaurs and lepidosaurs. It is therefore likely that turtles originated from a Permian-Triassic archosauromorph ancestor with two pairs of temporal fenestrae behind the skull orbit that were subsequently lost. The traditional classification of turtles in the Anapsida may thus need to be reconsidered.

  2. Facies Model for a Quaternary Hierarchical Depositional Sequences in the Niigata Basin, Central Japan. Approach to Prediction of Petroleum Reservoir Distribution on Bach-arc Basins

    Energy Technology Data Exchange (ETDEWEB)

    Arato, Hiroyuki. [Teikoku Oil Corp, Tokyo (Japan). Technical Research Center

    1999-01-01

    Dialectic prediction of reservoir distribution using conceptual facies models is one of the most direct techniques in petroleum exploration for reducing uncertainties about the factors in a petroleum system. If reservoir distribution could be predicted logically on the basis of generics of strata and sedimentary processes with inproved accuracy, then previously discovered petroleum systems might be reconsidered as future objectives of subtle entrapments. In this study a fourth-order daces model was constructed for Quaternary of the Niigata Basin within a back-arc setting, based on the concept of sequence stratigraphy. A progradational type fourth-order depositional sequence is subdivided into the following four systems tracts, which are defined by their morphologies and benthic foraminiferal faunas: (1) regressive progradational wedge systems tract (RPW), consisting of a forced-regressive strandplain system and associated depositional systems, (2) lowstand stable progradational wedge systems trac (LPW), consisting mainly of an incised-valley fill braidplain dalta system and associated systems, (3) transgressive aggradational sheet systems tract (TAS), consisting of a filled-estuary system and associated depositional systems, and (4) highstand stable progradational wedge systems tract (HPW), consisting of a fluvial-dominated dalta system and associated system. The results of this study demonstrate the effectiveness of sequence stratigraphic approaches and provide useful examples of occurrence, development, and sedimentary facies distribution for prograding coasts in ative margin basins. The development of such facies models improves our ability to the presence of sudetected standstone reservoirs, which is one of the most important factors of petroleum system. (autor)

  3. Pig genome sequence - analysis and publication strategy

    NARCIS (Netherlands)

    Archibald, A.L.; Bolund, L.; Churcher, C.; Fredholm, M.; Groenen, M.A.M.; Harlizius, B.

    2010-01-01

    Background - The pig genome is being sequenced and characterised under the auspices of the Swine Genome Sequencing Consortium. The sequencing strategy followed a hybrid approach combining hierarchical shotgun sequencing of BAC clones and whole genome shotgun sequencing. Results - Assemblies of the

  4. Tree morphisms, transducers, and integer sequences

    OpenAIRE

    Sunic, Zoran

    2006-01-01

    The notion of transducer integer sequences is considered through a series of examples. By definition, transducer integer sequences are integer sequences produced, under a suitable interpretation, by finite automata encoding tree morphisms (length and prefix preserving transformations of words). Transducer integer sequences are related to the notion of self-similar groups and semigroups, as well as to the notion of automatic sequences.

  5. Long-range barcode labeling-sequencing

    Energy Technology Data Exchange (ETDEWEB)

    Chen, Feng; Zhang, Tao; Singh, Kanwar K.; Pennacchio, Len A.; Froula, Jeff L.; Eng, Kevin S.

    2016-10-18

    Methods for sequencing single large DNA molecules by clonal multiple displacement amplification using barcoded primers. Sequences are binned based on barcode sequences and sequenced using a microdroplet-based method for sequencing large polynucleotide templates to enable assembly of haplotype-resolved complex genomes and metagenomes.

  6. A blackberry (Rubus L. expressed sequence tag library for the development of simple sequence repeat markers

    Directory of Open Access Journals (Sweden)

    Main Dorrie S

    2008-06-01

    Full Text Available Abstract Background The recent development of novel repeat-fruiting types of blackberry (Rubus L. cultivars, combined with a long history of morphological marker-assisted selection for thornlessness by blackberry breeders, has given rise to increased interest in using molecular markers to facilitate blackberry breeding. Yet no genetic maps, molecular markers, or even sequences exist specifically for cultivated blackberry. The purpose of this study is to begin development of these tools by generating and annotating the first blackberry expressed sequence tag (EST library, designing primers from the ESTs to amplify regions containing simple sequence repeats (SSR, and testing the usefulness of a subset of the EST-SSRs with two blackberry cultivars. Results A cDNA library of 18,432 clones was generated from expanding leaf tissue of the cultivar Merton Thornless, a progenitor of many thornless commercial cultivars. Among the most abundantly expressed of the 3,000 genes annotated were those involved with energy, cell structure, and defense. From individual sequences containing SSRs, 673 primer pairs were designed. Of a randomly chosen set of 33 primer pairs tested with two blackberry cultivars, 10 detected an average of 1.9 polymorphic PCR products. Conclusion This rate predicts that this library may yield as many as 940 SSR primer pairs detecting 1,786 polymorphisms. This may be sufficient to generate a genetic map that can be used to associate molecular markers with phenotypic traits, making possible molecular marker-assisted breeding to compliment existing morphological marker-assisted breeding in blackberry.

  7. Solid-phase sequencing on the gas-phase sequencer.

    Science.gov (United States)

    Sarin, V K; Kim, Y; Fox, J L

    1986-05-01

    Automated Edman degradation has been successfully used for determining the primary structure of numerous peptides and proteins. Quantitative solid-phase Edman degradation has great potential use for amino acid sequence analysis of synthetic peptides assembled on resin support by the Merrifield procedure. We report here the combined use of a modified gas-phase sequencer program and our improved reversed-phase HPLC analysis for PTH-amino acids to carry out the sequence analysis on synthesized peptide resins. This approach is far more sensitive than using glass beads on the conventional solid-phase sequencer. The peptide was assembled on copoly (styrene-1% divinylbenzene) resin beads at an initial substitution of 0.54 mmol/g. On a routine basis, 10-15 resin beads are used, and a repetitive yield of 94% is obtained: as few as 4 beads can be successfully sequenced. The HPLC PTH-amino acid analysis is sensitive down to subpicomole quantities. This procedure offers a sensitive and rapid analytical tool for checking the purity of peptides as they are being assembled on solid support.

  8. Sequencing and comparative analysis of the gorilla MHC genomic sequence

    Science.gov (United States)

    Wilming, Laurens G.; Hart, Elizabeth A.; Coggill, Penny C.; Horton, Roger; Gilbert, James G. R.; Clee, Chris; Jones, Matt; Lloyd, Christine; Palmer, Sophie; Sims, Sarah; Whitehead, Siobhan; Wiley, David; Beck, Stephan; Harrow, Jennifer L.

    2013-01-01

    Major histocompatibility complex (MHC) genes play a critical role in vertebrate immune response and because the MHC is linked to a significant number of auto-immune and other diseases it is of great medical interest. Here we describe the clone-based sequencing and subsequent annotation of the MHC region of the gorilla genome. Because the MHC is subject to extensive variation, both structural and sequence-wise, it is not readily amenable to study in whole genome shotgun sequence such as the recently published gorilla genome. The variation of the MHC also makes it of evolutionary interest and therefore we analyse the sequence in the context of human and chimpanzee. In our comparisons with human and re-annotated chimpanzee MHC sequence we find that gorilla has a trimodular RCCX cluster, versus the reference human bimodular cluster, and additional copies of Class I (pseudo)genes between Gogo-K and Gogo-A (the orthologues of HLA-K and -A). We also find that Gogo-H (and Patr-H) is coding versus the HLA-H pseudogene and, conversely, there is a Gogo-DQB2 pseudogene versus the HLA-DQB2 coding gene. Our analysis, which is freely available through the VEGA genome browser, provides the research community with a comprehensive dataset for comparative and evolutionary research of the MHC. PMID:23589541

  9. NAFASS: Discrete spectroscopy of random signals

    Energy Technology Data Exchange (ETDEWEB)

    Nigmatullin, R.R., E-mail: nigmat@knet.r [Institute of Physics, Kazan (Volga Region) Federal University, Kremlevskaya str.18, Kazan, Tatarstan 420008 (Russian Federation); Osokin, S.I. [Institute of Physics, Kazan (Volga Region) Federal University, Kremlevskaya str.18, Kazan, Tatarstan 420008 (Russian Federation); Toboev, V.A. [Department of Mathematics, Chuvash State University, Moskovskiy pr., 15, Cheboksary 428015 (Russian Federation)

    2011-04-15

    Research highlights: The successful solution of the Prony's problem has been obtained. It means that for any random signal its amplitude-frequency response can be found. This solution opens quite new possibilities in creation of new discrete spectroscopy in analysis of different nanoscopic and intermolecular signals. Real NIR spectra and biological data were considered and analyzed as examples. The conception of the pseudo-ergodic noise is introduced. It helps to fit the auto-correlation function that is related to remnant function. The three basic principles of the fluctuation metrology are formulated. - Abstract: In this paper we suggest a new discrete spectroscopy for analysis of random signals and fluctuations. This discrete spectroscopy is based on successful solution of the modified Prony's problem for the strongly-correlated random sequences. As opposed to the general Prony's problem where the set of frequencies is supposed to be unknown in the new approach suggested the distribution of the unknown frequencies can be found for the strongly-correlated random sequences. Preliminary information about the frequency distribution facilitates the calculations and attaches an additional stability in the presence of a noise. This spectroscopy uses only the informative-significant frequency band that helps to fit the given signal with high accuracy. It means that any random signal measured in t-domain can be 'read' in terms of its amplitude-frequency response (AFR) without model assumptions related to the behavior of this signal in the frequency region. The method overcomes some essential drawbacks of the conventional Prony's method and can be determined as the non-orthogonal amplitude frequency analysis of the smoothed sequences (NAFASS). In this paper we outline the basic principles of the NAFASS procedure and show its high potential possibilities based on analysis of some actual NIR data. The AFR obtained serves as a specific

  10. Coded Random Access

    DEFF Research Database (Denmark)

    Paolini, Enrico; Stefanovic, Cedomir; Liva, Gianluigi

    2015-01-01

    , in which the structure of the access protocol can be mapped to a structure of an erasure-correcting code defined on graph. This opens the possibility to use coding theory and tools for designing efficient random access protocols, offering markedly better performance than ALOHA. Several instances of coded......The rise of machine-to-machine communications has rekindled the interest in random access protocols as a support for a massive number of uncoordinatedly transmitting devices. The legacy ALOHA approach is developed under a collision model, where slots containing collided packets are considered...... as waste. However, if the common receiver (e.g., base station) is capable to store the collision slots and use them in a transmission recovery process based on successive interference cancellation, the design space for access protocols is radically expanded. We present the paradigm of coded random access...

  11. Sequence Factorization with Multiple References.

    Directory of Open Access Journals (Sweden)

    Sebastian Wandelt

    Full Text Available The success of high-throughput sequencing has lead to an increasing number of projects which sequence large populations of a species. Storage and analysis of sequence data is a key challenge in these projects, because of the sheer size of the datasets. Compression is one simple technology to deal with this challenge. Referential factorization and compression schemes, which store only the differences between input sequence and a reference sequence, gained lots of interest in this field. Highly-similar sequences, e.g., Human genomes, can be compressed with a compression ratio of 1,000:1 and more, up to two orders of magnitude better than with standard compression techniques. Recently, it was shown that the compression against multiple references from the same species can boost the compression ratio up to 4,000:1. However, a detailed analysis of using multiple references is lacking, e.g., for main memory consumption and optimality. In this paper, we describe one key technique for the referential compression against multiple references: The factorization of sequences. Based on the notion of an optimal factorization, we propose optimization heuristics and identify parameter settings which greatly influence 1 the size of the factorization, 2 the time for factorization, and 3 the required amount of main memory. We evaluate a total of 30 setups with a varying number of references on data from three different species. Our results show a wide range of factorization sizes (optimal to an overhead of up to 300%, factorization speed (0.01 MB/s to more than 600 MB/s, and main memory usage (few dozen MB to dozens of GB. Based on our evaluation, we identify the best configurations for common use cases. Our evaluation shows that multi-reference factorization is much better than single-reference factorization.

  12. Ossification sequence heterochrony among amphibians.

    Science.gov (United States)

    Harrington, Sean M; Harrison, Luke B; Sheil, Christopher A

    2013-01-01

    Heterochrony is an important mechanism in the evolution of amphibians. Although studies have centered on the relationship between size and shape and the rates of development, ossification sequence heterochrony also may have been important. Rigorous, phylogenetic methods for assessing sequence heterochrony are relatively new, and a comprehensive study of the relative timing of ossification of skeletal elements has not been used to identify instances of sequence heterochrony across Amphibia. In this study, a new version of the program Parsimov-based genetic inference (PGi) was used to identify shifts in ossification sequences across all extant orders of amphibians, for all major structural units of the skeleton. PGi identified a number of heterochronic sequence shifts in all analyses, the most interesting of which seem to be tied to differences in metamorphic patterns among major clades. Early ossification of the vomer, premaxilla, and dentary is retained by Apateon caducus and members of Gymnophiona and Urodela, which lack the strongly biphasic development seen in anurans. In contrast, bones associated with the jaws and face were identified as shifting late in the ancestor of Anura. The bones that do not shift late, and thereby occupy the earliest positions in the anuran cranial sequence, are those in regions of the skull that undergo the least restructuring throughout anuran metamorphosis. Additionally, within Anura, bones of the hind limb and pelvic girdle were also identified as shifting early in the sequence of ossification, which may be a result of functional constraints imposed by the drastic metamorphosis of most anurans. © 2013 Wiley Periodicals, Inc.

  13. Seismic sequences, swarms, and large earthquakes in Italy

    Science.gov (United States)

    Amato, Alessandro; Piana Agostinetti, Nicola; Selvaggi, Giulio; Mele, Franco

    2016-04-01

    In recent years, particularly after the L'Aquila 2009 earthquake and the 2012 Emilia sequence, the issue of earthquake predictability has been at the center of the discussion in Italy, not only within the scientific community but also in the courtrooms and in the media. Among the noxious effects of the L'Aquila trial there was an increase of scaremongering and false alerts during earthquake sequences and swarms, culminated in a groundless one-night evacuation in northern Tuscany in 2013. We have analyzed the Italian seismicity of the last decades in order to determine the rate of seismic sequences and investigate some of their characters, including frequencies, min/max durations, maximum magnitudes, main shock timing, etc. Selecting only sequences with an equivalent magnitude of 3.5 or above, we find an average of 30 sequences/year. Although there is an extreme variability in the examined parameters, we could set some boundaries, useful to obtain some quantitative estimates of the ongoing activity. In addition, the historical catalogue is rich of complex sequences in which one main shock is followed, seconds, days or months later, by another event with similar or higher magnitude We also analysed the Italian CPT11 catalogue (Rovida et al., 2011) between 1950 and 2006 to highlight the foreshock-mainshock event couples that were suggested in previous studies to exist (e.g. six couples, Marzocchi and Zhuang, 2011). Moreover, to investigate the probability of having random foreshock-mainshock couples over the investigated period, we produced 1000 synthetic catalogues, randomly distributing in time the events occured in such period. Preliminary results indicate that: (1) all but one of the the so-called foreshock-mainshock pairs found in Marzocchi and Zhuang (2011) fall inside previously well-known and studied seismic sequences (Belice, Friuli and Umbria-Marche), meaning that suggested foreshocks are also aftershocks; and (2) due to the high-rate of the italian

  14. Gift from statistical learning: Visual statistical learning enhances memory for sequence elements and impairs memory for items that disrupt regularities.

    Science.gov (United States)

    Otsuka, Sachio; Saiki, Jun

    2016-02-01

    Prior studies have shown that visual statistical learning (VSL) enhances familiarity (a type of memory) of sequences. How do statistical regularities influence the processing of each triplet element and inserted distractors that disrupt the regularity? Given that increased attention to triplets induced by VSL and inhibition of unattended triplets, we predicted that VSL would promote memory for each triplet constituent, and degrade memory for inserted stimuli. Across the first two experiments, we found that objects from structured sequences were more likely to be remembered than objects from random sequences, and that letters (Experiment 1) or objects (Experiment 2) inserted into structured sequences were less likely to be remembered than those inserted into random sequences. In the subsequent two experiments, we examined an alternative account for our results, whereby the difference in memory for inserted items between structured and random conditions is due to individuation of items within random sequences. Our findings replicated even when control letters (Experiment 3A) or objects (Experiment 3B) were presented before or after, rather than inserted into, random sequences. Our findings suggest that statistical learning enhances memory for each item in a regular set and impairs memory for items that disrupt the regularity. Copyright © 2015 Elsevier B.V. All rights reserved.

  15. Multisequence algorithm for coarse-grained biomolecular simulations: Exploring the sequence-structure relationship of proteins

    Science.gov (United States)

    Aina, A.; Wallin, S.

    2017-09-01

    We consider a generalized-ensemble algorithm for coarse-grained simulations of biomolecules which allows the thermodynamic behavior of two or more sequences to be determined in a single multisequence run. By carrying out a random walk in sequence space, the method also enhances conformational sampling. Escape from local energy minima is accelerated by visiting sequences for which the minima are more shallow or absent. We test the method on an intermediate-resolution coarse-grained model for protein folding with 3 amino acid types and explore the potential for a large-scale coverage of sequence space by applying the method to sets of more than 1000 sequences. The resulting thermodynamic data are used to analyze the structures and stability properties of sequences covering the space between folds with different secondary structures.

  16. Genome Sequencing of Steroid Producing Bacteria Using Ion Torrent Technology and a Reference Genome.

    Science.gov (United States)

    Sola-Landa, Alberto; Rodríguez-García, Antonio; Barreiro, Carlos; Pérez-Redondo, Rosario

    2017-01-01

    The Next-Generation Sequencing technology has enormously eased the bacterial genome sequencing and several tens of thousands of genomes have been sequenced during the last 10 years. Most of the genome projects are published as draft version, however, for certain applications the complete genome sequence is required.In this chapter, we describe the strategy that allowed the complete genome sequencing of Mycobacterium neoaurum NRRL B-3805, an industrial strain exploited for steroid production, using Ion Torrent sequencing reads and the genome of a close strain as the reference. This protocol can be applied to analyze the genetic variations between closely related strains; for example, to elucidate the point mutations between a parental strain and a random mutagenesis-derived mutant.

  17. Complete Moment Convergence and Mean Convergence for Arrays of Rowwise Extended Negatively Dependent Random Variables

    Directory of Open Access Journals (Sweden)

    Yongfeng Wu

    2014-01-01

    Full Text Available The authors first present a Rosenthal inequality for sequence of extended negatively dependent (END random variables. By means of the Rosenthal inequality, the authors obtain some complete moment convergence and mean convergence results for arrays of rowwise END random variables. The results in this paper extend and improve the corresponding theorems by Hu and Taylor (1997.

  18. Optimal Exact Simulation of Max-Stable and Related Random Fields

    OpenAIRE

    Liu, Zhipeng; Blanchet, Jose H.; Dieker, A. B.; Mikosch, Thomas

    2016-01-01

    We consider the random field M(t)=\\sup_{n\\geq 1}\\big\\{-\\log A_{n}+X_{n}(t)\\big\\}\\,,\\qquad t\\in T\\, for a set $T\\subset \\mathbb{R}^{m}$, where $(X_{n})$ is an iid sequence of centered Gaussian random fields on $T$ and $0

  19. CONVERGENCE OF THE FRACTIONAL PARTS OF THE RANDOM VARIABLES TO THE TRUNCATED EXPONENTIAL DISTRIBUTION

    Directory of Open Access Journals (Sweden)

    Bogdan Gheorghe Munteanu

    2013-01-01

    Full Text Available Using the stochastic approximations, in this paper it was studiedthe convergence in distribution of the fractional parts of the sum of random variables to the truncated exponential distribution with parameter lambda. This fact is feasible by means of the Fourier-Stieltjes sequence (FSS of the random variable.

  20. Levenshtein error-correcting barcodes for multiplexed DNA sequencing.

    Science.gov (United States)

    Buschmann, Tilo; Bystrykh, Leonid V

    2013-09-11

    of recovering the new length of the corrupted codeword and of correcting on average more random mutations than traditional Levenshtein or Hamming codes.As part of this work we prepared software for the flexible generation of DNA codes based on our new approach. To adapt codes to specific experimental conditions, the user can customize sequence filtering, the number of correctable mutations and barcode length for highest performance.