WorldWideScience

Sample records for random sequences reconsidered

  1. LPTAU, Quasi Random Sequence Generator

    International Nuclear Information System (INIS)

    Sobol, Ilya M.

    1993-01-01

    1 - Description of program or function: LPTAU generates quasi random sequences. These are uniformly distributed sets of L=M N points in the N-dimensional unit cube: I N =[0,1]x...x[0,1]. These sequences are used as nodes for multidimensional integration; as searching points in global optimization; as trial points in multi-criteria decision making; as quasi-random points for quasi Monte Carlo algorithms. 2 - Method of solution: Uses LP-TAU sequence generation (see references). 3 - Restrictions on the complexity of the problem: The number of points that can be generated is L 30 . The dimension of the space cannot exceed 51

  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. RANDNA: a random DNA sequence generator.

    Science.gov (United States)

    Piva, Francesco; Principato, Giovanni

    2006-01-01

    Monte Carlo simulations are useful to verify the significance of data. Genomic regularities, such as the nucleotide correlations or the not uniform distribution of the motifs throughout genomic or mature mRNA sequences, exist and their significance can be checked by means of the Monte Carlo test. The test needs good quality random sequences in order to work, moreover they should have the same nucleotide distribution as the sequences in which the regularities have been found. Random DNA sequences are also useful to estimate the background score of an alignment, that is a threshold below which the resulting score is merely due to chance. We have developed RANDNA, a free software which allows to produce random DNA or RNA sequences setting both their length and the percentage of nucleotide composition. Sequences having the same nucleotide distribution of exonic, intronic or intergenic sequences can be generated. Its graphic interface makes it possible to easily set the parameters that characterize the sequences being produced and saved in a text format file. The pseudo-random number generator function of Borland Delphi 6 is used, since it guarantees a good randomness, a long cycle length and a high speed. We have checked the quality of sequences generated by the software, by means of well-known tests, both by themselves and versus genuine random sequences. We show the good quality of the generated sequences. The software, complete with examples and documentation, is freely available to users from: http://www.introni.it/en/software.

  4. Bunches of random cross-correlated sequences

    International Nuclear Information System (INIS)

    Maystrenko, A A; Melnik, S S; Pritula, G M; Usatenko, O V

    2013-01-01

    The statistical properties of random cross-correlated sequences constructed by the convolution method (likewise referred to as the Rice or the inverse Fourier transformation) are examined. We clarify the meaning of the filtering function—the kernel of the convolution operator—and show that it is the value of the cross-correlation function which describes correlations between the initial white noise and constructed correlated sequences. The matrix generalization of this method for constructing a bunch of N cross-correlated sequences is presented. Algorithms for their generation are reduced to solving the problem of decomposition of the Fourier transform of the correlation matrix into a product of two mutually conjugate matrices. Different decompositions are considered. The limits of weak and strong correlations for the one-point probability and pair correlation functions of sequences generated by the method under consideration are studied. Special cases of heavy-tailed distributions of the generated sequences are analyzed. We show that, if the filtering function is rather smooth, the distribution function of generated variables has the Gaussian or Lévy form depending on the analytical properties of the distribution (or characteristic) functions of the initial white noise. Anisotropic properties of statistically homogeneous random sequences related to the asymmetry of a filtering function are revealed and studied. These asymmetry properties are expressed in terms of the third- or fourth-order correlation functions. Several examples of the construction of correlated chains with a predefined correlation matrix are given. (paper)

  5. 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.

  6. Long period pseudo random number sequence generator

    Science.gov (United States)

    Wang, Charles C. (Inventor)

    1989-01-01

    A circuit for generating a sequence of pseudo random numbers, (A sub K). There is an exponentiator in GF(2 sup m) for the normal basis representation of elements in a finite field GF(2 sup m) each represented by m binary digits and having two inputs and an output from which the sequence (A sub K). Of pseudo random numbers is taken. One of the two inputs is connected to receive the outputs (E sub K) of maximal length shift register of n stages. There is a switch having a pair of inputs and an output. The switch outputs is connected to the other of the two inputs of the exponentiator. One of the switch inputs is connected for initially receiving a primitive element (A sub O) in GF(2 sup m). Finally, there is a delay circuit having an input and an output. The delay circuit output is connected to the other of the switch inputs and the delay circuit input is connected to the output of the exponentiator. Whereby after the exponentiator initially receives the primitive element (A sub O) in GF(2 sup m) through the switch, the switch can be switched to cause the exponentiator to receive as its input a delayed output A(K-1) from the exponentiator thereby generating (A sub K) continuously at the output of the exponentiator. The exponentiator in GF(2 sup m) is novel and comprises a cyclic-shift circuit; a Massey-Omura multiplier; and, a control logic circuit all operably connected together to perform the function U(sub i) = 92(sup i) (for n(sub i) = 1 or 1 (for n(subi) = 0).

  7. Image encryption using random sequence generated from generalized information domain

    International Nuclear Information System (INIS)

    Zhang Xia-Yan; Wu Jie-Hua; Zhang Guo-Ji; Li Xuan; Ren Ya-Zhou

    2016-01-01

    A novel image encryption method based on the random sequence generated from the generalized information domain and permutation–diffusion architecture is proposed. The random sequence is generated by reconstruction from the generalized information file and discrete trajectory extraction from the data stream. The trajectory address sequence is used to generate a P-box to shuffle the plain image while random sequences are treated as keystreams. A new factor called drift factor is employed to accelerate and enhance the performance of the random sequence generator. An initial value is introduced to make the encryption method an approximately one-time pad. Experimental results show that the random sequences pass the NIST statistical test with a high ratio and extensive analysis demonstrates that the new encryption scheme has superior security. (paper)

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

    Directory of Open Access Journals (Sweden)

    Fiz-Palacios Omar

    2008-12-01

    Full Text Available Abstract Background 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. Results 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. Conclusion Although rate homogeneity was not rejected

  9. Design of Long Period Pseudo-Random Sequences from the Addition of -Sequences over

    Directory of Open Access Journals (Sweden)

    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 -sequences with pairwise-prime linear spans (AMPLS. Using -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 , a signal set is constructed.

  10. Generation of pseudo-random sequences for spread spectrum systems

    Science.gov (United States)

    Moser, R.; Stover, J.

    1985-05-01

    The characteristics of pseudo random radio signal sequences (PRS) are explored. The randomness of the PSR is a matter of artificially altering the sequence of binary digits broadcast. Autocorrelations of the two sequences shifted in time, if high, determine if the signals are the same and thus allow for position identification. Cross-correlation can also be calculated between sequences. Correlations closest to zero are obtained with large volume of prime numbers in the sequences. Techniques for selecting optimal and maximal lengths for the sequences are reviewed. If the correlations are near zero in the sequences, then signal channels can accommodate multiple users. Finally, Gold codes are discussed as a technique for maximizing the code lengths.

  11. Perceptions of randomness in binary sequences: Normative, heuristic, or both?

    Science.gov (United States)

    Reimers, Stian; Donkin, Chris; Le Pelley, Mike E

    2018-03-01

    When people consider a series of random binary events, such as tossing an unbiased coin and recording the sequence of heads (H) and tails (T), they tend to erroneously rate sequences with less internal structure or order (such as HTTHT) as more probable than sequences containing more structure or order (such as HHHHH). This is traditionally explained as a local representativeness effect: Participants assume that the properties of long sequences of random outcomes-such as an equal proportion of heads and tails, and little internal structure-should also apply to short sequences. However, recent theoretical work has noted that the probability of a particular sequence of say, heads and tails of length n, occurring within a larger (>n) sequence of coin flips actually differs by sequence, so P(HHHHH) rational norms based on limited experience. We test these accounts. Participants in Experiment 1 rated the likelihood of occurrence for all possible strings of 4, 5, and 6 observations in a sequence of coin flips. Judgments were better explained by representativeness in alternation rate, relative proportion of heads and tails, and sequence complexity, than by objective probabilities. Experiments 2 and 3 gave similar results using incentivized binary choice procedures. Overall the evidence suggests that participants are not sensitive to variation in objective probabilities of a sub-sequence occurring; they appear to use heuristics based on several distinct forms of representativeness. Copyright © 2017 Elsevier B.V. All rights reserved.

  12. Correlations of pseudo-random numbers of multiplicative sequence

    International Nuclear Information System (INIS)

    Bukin, A.D.

    1989-01-01

    An algorithm is suggested for searching with a computer in unit n-dimensional cube the sets of planes where all the points fall whose coordinates are composed of n successive pseudo-random numbers of multiplicative sequence. This effect should be taken into account in Monte-Carlo calculations with definite constructive dimension. The parameters of these planes are obtained for three random number generators. 2 refs.; 2 tabs

  13. Cryptographic pseudo-random sequence from the spatial chaotic map

    International Nuclear Information System (INIS)

    Sun Fuyan; Liu Shutang

    2009-01-01

    A scheme for pseudo-random binary sequence generation based on the spatial chaotic map is proposed. In order to face the challenge of using the proposed PRBS in cryptography, the proposed PRBS is subjected to statistical tests which are the well-known FIPS-140-1 in the area of cryptography, and correlation properties of the proposed sequences are investigated. The proposed PRBS successfully passes all these tests. Results of statistical testing of the sequences are found encouraging. The results of statistical tests suggest strong candidature for cryptographic applications.

  14. Parallel Mitogenome Sequencing Alleviates Random Rooting Effect in Phylogeography.

    Science.gov (United States)

    Hirase, Shotaro; Takeshima, Hirohiko; Nishida, Mutsumi; Iwasaki, Wataru

    2016-04-28

    Reliably rooted phylogenetic trees play irreplaceable roles in clarifying diversification in the patterns of species and populations. However, such trees are often unavailable in phylogeographic studies, particularly when the focus is on rapidly expanded populations that exhibit star-like trees. A fundamental bottleneck is known as the random rooting effect, where a distant outgroup tends to root an unrooted tree "randomly." We investigated whether parallel mitochondrial genome (mitogenome) sequencing alleviates this effect in phylogeography using a case study on the Sea of Japan lineage of the intertidal goby Chaenogobius annularis Eighty-three C. annularis individuals were collected and their mitogenomes were determined by high-throughput and low-cost parallel sequencing. Phylogenetic analysis of these mitogenome sequences was conducted to root the Sea of Japan lineage, which has a star-like phylogeny and had not been reliably rooted. The topologies of the bootstrap trees were investigated to determine whether the use of mitogenomes alleviated the random rooting effect. The mitogenome data successfully rooted the Sea of Japan lineage by alleviating the effect, which hindered phylogenetic analysis that used specific gene sequences. The reliable rooting of the lineage led to the discovery of a novel, northern lineage that expanded during an interglacial period with high bootstrap support. Furthermore, the finding of this lineage suggested the existence of additional glacial refugia and provided a new recent calibration point that revised the divergence time estimation between the Sea of Japan and Pacific Ocean lineages. This study illustrates the effectiveness of parallel mitogenome sequencing for solving the random rooting problem in phylogeographic studies. © The Author 2016. Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution.

  15. Automatic generation of randomized trial sequences for priming experiments.

    Science.gov (United States)

    Ihrke, Matthias; Behrendt, Jörg

    2011-01-01

    In most psychological experiments, a randomized presentation of successive displays is crucial for the validity of the results. For some paradigms, this is not a trivial issue because trials are interdependent, e.g., priming paradigms. We present a software that automatically generates optimized trial sequences for (negative-) priming experiments. Our implementation is based on an optimization heuristic known as genetic algorithms that allows for an intuitive interpretation due to its similarity to natural evolution. The program features a graphical user interface that allows the user to generate trial sequences and to interactively improve them. The software is based on freely available software and is released under the GNU General Public License.

  16. RANDOMNUMBERS, Random Number Sequence Generated from Gas Ionisation Chamber Data

    International Nuclear Information System (INIS)

    Frigerio, N.A.; Sanathanan, L.P.; Morley, M.; Tyler, S.A.; Clark, N.A.; Wang, J.

    1989-01-01

    1 - Description of problem or function: RANDOM NUMBERS is a data collection of almost 2.7 million 31-bit random numbers generated by using a high resolution gas ionization detector chamber in conjunction with a 4096-channel multichannel analyzer to record the radioactive decay of alpha particles from a U-235 source. The signals from the decaying alpha particles were fed to the 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 and odd count, were then assembled in sequence to form 31-bit random numbers and transcribed onto magnetic tape. This cycle was repeated to obtain the random numbers. 2 - Method of solution: The frequency distribution of counts from the device conforms to the Brockwell-Moyal distribution which takes into account the dead time of the counter. The count data were analyzed and tests for randomness on a sample indicate that the device is a highly reliable source of truly random numbers. 3 - Restrictions on the complexity of the problem: The RANDOM NUMBERS tape contains 2,669,568 31-bit numbers

  17. Reconsidering energy efficiency

    International Nuclear Information System (INIS)

    Goldoni, Giovanni

    2007-01-01

    Energy and environmental policies are reconsidering energy efficiency. In a perfect market, rational and well informed consumers reach economic efficiency which, at the given prices of energy and capital, corresponds to physical efficiency. In the real world, market failures and cognitive frictions distort the consumers from perfectly rational and informed choices. Green incentive schemes aim at balancing market failures and directing consumers toward more efficient goods and services. The problem is to fine tune the incentive schemes [it

  18. 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.

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

    Science.gov (United States)

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

    2012-01-03

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

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

    Directory of Open Access Journals (Sweden)

    Halperin Rebecca F

    2012-01-01

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

  1. Pseudo-random Trees: Multiple Independent Sequence Generators for Parallel and Branching Computations

    Science.gov (United States)

    Halton, John H.

    1989-09-01

    A class of families of linear congruential pseudo-random sequences is defined, for which it is possible to branch at any event without changing the sequence of random numbers used in the original random walk and for which the sequences in different branches show properties analogous to mutual statistical independence. This is a hitherto unavailable, and computationally desirable, tool.

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

    Directory of Open Access Journals (Sweden)

    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.

  3. Diverticular Disease: Reconsidering Conventional Wisdom

    Science.gov (United States)

    Peery, Anne F.; Sandler, Robert S.

    2013-01-01

    Colonic diverticula are common in developed countries and complications of colonic diverticulosis are responsible for a significant burden of disease. Several recent publications have called into question long held beliefs about diverticular disease. Contrary to conventional wisdom, studies have not shown that a high fiber diet protects against asymptomatic diverticulosis. The risk of developing diverticulitis among individuals with diverticulosis is lower than the 10–25% commonly quoted, and may be as low as 1% over 11 years. Nuts and seeds do not increase the risk of diverticulitis or diverticular bleeding. It is unclear whether diverticulosis, absent diverticulitis or overt colitis, is responsible for chronic gastrointestinal symptoms or worse quality of life. The role of antibiotics in acute diverticulitis has been challenged by a large randomized trial that showed no benefit in selected patients. The decision to perform elective surgery should be made on a case-by-case basis and not routinely after a second episode of diverticulitis, when there has been a complication, or in young people. A colonoscopy should be performed to exclude colon cancer after an attack of acute diverticulitis but may not alter outcomes among individuals who have had a colonoscopy prior to the attack. Given these surprising findings, it is time to reconsider conventional wisdom about diverticular disease. PMID:23669306

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

    Directory of Open Access Journals (Sweden)

    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.

  5. A symbolic dynamics approach for the complexity analysis of chaotic pseudo-random sequences

    International Nuclear Information System (INIS)

    Xiao Fanghong

    2004-01-01

    By considering a chaotic pseudo-random sequence as a symbolic sequence, authors present a symbolic dynamics approach for the complexity analysis of chaotic pseudo-random sequences. The method is applied to the cases of Logistic map and one-way coupled map lattice to demonstrate how it works, and a comparison is made between it and the approximate entropy method. The results show that this method is applicable to distinguish the complexities of different chaotic pseudo-random sequences, and it is superior to the approximate entropy method

  6. Golden Ratio Versus Pi as Random Sequence Sources for Monte Carlo Integration

    Science.gov (United States)

    Sen, S. K.; Agarwal, Ravi P.; Shaykhian, Gholam Ali

    2007-01-01

    We discuss here the relative merits of these numbers as possible random sequence sources. The quality of these sequences is not judged directly based on the outcome of all known tests for the randomness of a sequence. Instead, it is determined implicitly by the accuracy of the Monte Carlo integration in a statistical sense. Since our main motive of using a random sequence is to solve real world problems, it is more desirable if we compare the quality of the sequences based on their performances for these problems in terms of quality/accuracy of the output. We also compare these sources against those generated by a popular pseudo-random generator, viz., the Matlab rand and the quasi-random generator ha/ton both in terms of error and time complexity. Our study demonstrates that consecutive blocks of digits of each of these numbers produce a good random sequence source. It is observed that randomly chosen blocks of digits do not have any remarkable advantage over consecutive blocks for the accuracy of the Monte Carlo integration. Also, it reveals that pi is a better source of a random sequence than theta when the accuracy of the integration is concerned.

  7. 42 CFR 405.715 - Reconsidered determination.

    Science.gov (United States)

    2010-10-01

    ... 42 Public Health 2 2010-10-01 2010-10-01 false Reconsidered determination. 405.715 Section 405.715... Part A § 405.715 Reconsidered determination. (a) In reconsidering an initial determination, the CMS shall review such initial determination, the evidence and findings upon which such determination was...

  8. 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.

  9. Humans can consciously generate random number sequences: a possible test for artificial intelligence.

    Science.gov (United States)

    Persaud, Navindra

    2005-01-01

    Computer algorithms can only produce seemingly random or pseudorandom numbers whereas certain natural phenomena, such as the decay of radioactive particles, can be utilized to produce truly random numbers. In this study, the ability of humans to generate random numbers was tested in healthy adults. Subjects were simply asked to generate and dictate random numbers. Generated numbers were tested for uniformity, independence and information density. The results suggest that humans can generate random numbers that are uniformly distributed, independent of one another and unpredictable. If humans can generate sequences of random numbers then neural networks or forms of artificial intelligence, which are purported to function in ways essentially the same as the human brain, should also be able to generate sequences of random numbers. Elucidating the precise mechanism by which humans generate random number sequences and the underlying neural substrates may have implications in the cognitive science of decision-making. It is possible that humans use their random-generating neural machinery to make difficult decisions in which all expected outcomes are similar. It is also possible that certain people, perhaps those with neurological or psychiatric impairments, are less able or unable to generate random numbers. If the random-generating neural machinery is employed in decision making its impairment would have profound implications in matters of agency and free will.

  10. 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, ...

  11. Reconsidering Our Domestic Violence System.

    Science.gov (United States)

    Starsoneck, Leslie; Ake, George

    2018-01-01

    Children's exposure to domestic violence is well established as an adverse childhood experience (ACE). Much is known about the impact of this exposure, but efforts to ameliorate its effects are too often unsuccessful. Reconsidering our response requires a candid assessment of whether convening large and disparate systems leads to the best outcome. ©2018 by the North Carolina Institute of Medicine and The Duke Endowment. All rights reserved.

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

    Directory of Open Access Journals (Sweden)

    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.

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

    Science.gov (United States)

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

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

  14. GenRGenS: Software for Generating Random Genomic Sequences and Structures

    OpenAIRE

    Ponty , Yann; Termier , Michel; Denise , Alain

    2006-01-01

    International audience; GenRGenS is a software tool dedicated to randomly generating genomic sequences and structures. It handles several classes of models useful for sequence analysis, such as Markov chains, hidden Markov models, weighted context-free grammars, regular expressions and PROSITE expressions. GenRGenS is the only program that can handle weighted context-free grammars, thus allowing the user to model and to generate structured objects (such as RNA secondary structures) of any giv...

  15. Magnetic nanoparticle imaging by random and maximum length sequences of inhomogeneous activation fields.

    Science.gov (United States)

    Baumgarten, Daniel; Eichardt, Roland; Crevecoeur, Guillaume; Supriyanto, Eko; Haueisen, Jens

    2013-01-01

    Biomedical applications of magnetic nanoparticles require a precise knowledge of their biodistribution. From multi-channel magnetorelaxometry measurements, this distribution can be determined by means of inverse methods. It was recently shown that the combination of sequential inhomogeneous excitation fields in these measurements is favorable regarding the reconstruction accuracy when compared to homogeneous activation . In this paper, approaches for the determination of activation sequences for these measurements are investigated. Therefor, consecutive activation of single coils, random activation patterns and families of m-sequences are examined in computer simulations involving a sample measurement setup and compared with respect to the relative condition number of the system matrix. We obtain that the values of this condition number decrease with larger number of measurement samples for all approaches. Random sequences and m-sequences reveal similar results with a significant reduction of the required number of samples. We conclude that the application of pseudo-random sequences for sequential activation in the magnetorelaxometry imaging of magnetic nanoparticles considerably reduces the number of required sequences while preserving the relevant measurement information.

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

    Directory of Open Access Journals (Sweden)

    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.

  17. Reduced randomness in quantum cryptography with sequences of qubits encoded in the same basis

    International Nuclear Information System (INIS)

    Lamoureux, L.-P.; Cerf, N. J.; Bechmann-Pasquinucci, H.; Gisin, N.; Macchiavello, C.

    2006-01-01

    We consider the cloning of sequences of qubits prepared in the states used in the BB84 or six-state quantum cryptography protocol, and show that the single-qubit fidelity is unaffected even if entire sequences of qubits are prepared in the same basis. This result is only valid provided that the sequences are much shorter than the total key. It is of great importance for practical quantum cryptosystems because it reduces the need for high-speed random number generation without impairing on the security against finite-size cloning attacks

  18. Random sequences are an abundant source of bioactive RNAs or peptides

    DEFF Research Database (Denmark)

    Neme, Rafik; Amador, Cristina; Yildirim, Burcin

    2017-01-01

    It is generally assumed that new genes arise through duplication and/or recombination of existing genes. The probability that a new functional gene could arise out of random non-coding DNA is so far considered to be negligible, as it seems unlikely that such an RNA or protein sequence could have ...

  19. Statistical distributions of optimal global alignment scores of random protein sequences

    Directory of Open Access Journals (Sweden)

    Tang Jiaowei

    2005-10-01

    Full Text Available Abstract Background The inference of homology from statistically significant sequence similarity is a central issue in sequence alignments. So far the statistical distribution function underlying the optimal global alignments has not been completely determined. Results In this study, random and real but unrelated sequences prepared in six different ways were selected as reference datasets to obtain their respective statistical distributions of global alignment scores. All alignments were carried out with the Needleman-Wunsch algorithm and optimal scores were fitted to the Gumbel, normal and gamma distributions respectively. The three-parameter gamma distribution performs the best as the theoretical distribution function of global alignment scores, as it agrees perfectly well with the distribution of alignment scores. The normal distribution also agrees well with the score distribution frequencies when the shape parameter of the gamma distribution is sufficiently large, for this is the scenario when the normal distribution can be viewed as an approximation of the gamma distribution. Conclusion We have shown that the optimal global alignment scores of random protein sequences fit the three-parameter gamma distribution function. This would be useful for the inference of homology between sequences whose relationship is unknown, through the evaluation of gamma distribution significance between sequences.

  20. Pseudo-Random Sequences Generated by a Class of One-Dimensional Smooth Map

    Science.gov (United States)

    Wang, Xing-Yuan; Qin, Xue; Xie, Yi-Xin

    2011-08-01

    We extend a class of a one-dimensional smooth map. We make sure that for each desired interval of the parameter the map's Lyapunov exponent is positive. Then we propose a novel parameter perturbation method based on the good property of the extended one-dimensional smooth map. We perturb the parameter r in each iteration by the real number xi generated by the iteration. The auto-correlation function and NIST statistical test suite are taken to illustrate the method's randomness finally. We provide an application of this method in image encryption. Experiments show that the pseudo-random sequences are suitable for this application.

  1. Pseudo-Random Sequences Generated by a Class of One-Dimensional Smooth Map

    International Nuclear Information System (INIS)

    Wang Xing-Yuan; Qin Xue; Xie Yi-Xin

    2011-01-01

    We extend a class of a one-dimensional smooth map. We make sure that for each desired interval of the parameter the map's Lyapunov exponent is positive. Then we propose a novel parameter perturbation method based on the good property of the extended one-dimensional smooth map. We perturb the parameter r in each iteration by the real number x i generated by the iteration. The auto-correlation function and NIST statistical test suite are taken to illustrate the method's randomness finally. We provide an application of this method in image encryption. Experiments show that the pseudo-random sequences are suitable for this application. (general)

  2. Configurational statistics of a polymer chain with random sequence of elements

    International Nuclear Information System (INIS)

    Obukhov, S.P.

    1984-10-01

    It is shown that for a disordered polymer chain the upper critical dimension is d c =3. At d≤3 the effect of randomness increases on large scales due to the space correlations of attractive and repulsive monomers, but it can also be screened by repulsive two- or three-body interaction. The renorm group equations indicate that near the theta point it can be the large dispersion of sizes of polymers which differ only in sequences of elements. (orig.)

  3. Kinship and Beyond: The Genealogical Model Reconsidered

    Directory of Open Access Journals (Sweden)

    Ryan Schram

    2010-08-01

    Full Text Available Review of Kinship and Beyond: The Genealogical Model Reconsidered. Sandra Bamford and James Leach, eds. 2009. Berghahn Books, New York. 292 pp., 21 illustrations, bibliography, index. $95.00 (hardback. ISBN 9781845454227.

  4. Multiple ECG Fiducial Points-Based Random Binary Sequence Generation for Securing Wireless Body Area Networks.

    Science.gov (United States)

    Zheng, Guanglou; Fang, Gengfa; Shankaran, Rajan; Orgun, Mehmet A; Zhou, Jie; Qiao, Li; Saleem, Kashif

    2017-05-01

    Generating random binary sequences (BSes) is a fundamental requirement in cryptography. A BS is a sequence of N bits, and each bit has a value of 0 or 1. For securing sensors within wireless body area networks (WBANs), electrocardiogram (ECG)-based BS generation methods have been widely investigated in which interpulse intervals (IPIs) from each heartbeat cycle are processed to produce BSes. Using these IPI-based methods to generate a 128-bit BS in real time normally takes around half a minute. In order to improve the time efficiency of such methods, this paper presents an ECG multiple fiducial-points based binary sequence generation (MFBSG) algorithm. The technique of discrete wavelet transforms is employed to detect arrival time of these fiducial points, such as P, Q, R, S, and T peaks. Time intervals between them, including RR, RQ, RS, RP, and RT intervals, are then calculated based on this arrival time, and are used as ECG features to generate random BSes with low latency. According to our analysis on real ECG data, these ECG feature values exhibit the property of randomness and, thus, can be utilized to generate random BSes. Compared with the schemes that solely rely on IPIs to generate BSes, this MFBSG algorithm uses five feature values from one heart beat cycle, and can be up to five times faster than the solely IPI-based methods. So, it achieves a design goal of low latency. According to our analysis, the complexity of the algorithm is comparable to that of fast Fourier transforms. These randomly generated ECG BSes can be used as security keys for encryption or authentication in a WBAN system.

  5. Economic planning: Time to reconsider?

    Directory of Open Access Journals (Sweden)

    Kafouros Wassily

    2009-01-01

    Full Text Available Together with the collapse of what was once called the socialist system, was also the collapse of research on any other form of economic organization of a society. Administrative methods for running an economy, with economic planning foremost among them, were inseparably linked to the collapse of the socialist system and, in essence, were held responsible for it. Thus, although the dominant economic paradigm has once again failed to deliver in recent years, the research for other methods fell into oblivion along with the system they were attached to. This work represents an attempt to reconsider the potential of economic planning as a means of organizing an economy at various levels, at various degrees and in various environments. I shall try to illustrate that the blame for the collapse of different socialist systems should not have fallen on the systemic deficiencies of economic planning but, instead, on the political institutions responsible for its application. In addition, I will stress that economic planning has been condemned by non-economic parameters and the application of wrong planning methods. In making this argument I hope to provide an angle through which the discussion of economic organization can be opened to a broader scope of research.

  6. Prediction of protein-protein interaction sites in sequences and 3D structures by random forests.

    Directory of Open Access Journals (Sweden)

    Mile Sikić

    2009-01-01

    Full Text Available Identifying interaction sites in proteins provides important clues to the function of a protein and is becoming increasingly relevant in topics such as systems biology and drug discovery. Although there are numerous papers on the prediction of interaction sites using information derived from structure, there are only a few case reports on the prediction of interaction residues based solely on protein sequence. Here, a sliding window approach is combined with the Random Forests method to predict protein interaction sites using (i a combination of sequence- and structure-derived parameters and (ii sequence information alone. For sequence-based prediction we achieved a precision of 84% with a 26% recall and an F-measure of 40%. When combined with structural information, the prediction performance increases to a precision of 76% and a recall of 38% with an F-measure of 51%. We also present an attempt to rationalize the sliding window size and demonstrate that a nine-residue window is the most suitable for predictor construction. Finally, we demonstrate the applicability of our prediction methods by modeling the Ras-Raf complex using predicted interaction sites as target binding interfaces. Our results suggest that it is possible to predict protein interaction sites with quite a high accuracy using only sequence information.

  7. 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.

  8. Alignment efficiency and discomfort of three orthodontic archwire sequences: a randomized clinical trial.

    Science.gov (United States)

    Ong, Emily; Ho, Christopher; Miles, Peter

    2011-03-01

    To compare the efficiency of orthodontic archwire sequences produced by three manufacturers. Prospective, randomized clinical trial with three parallel groups. Private orthodontic practice in Caloundra, QLD, Australia. One hundred and thirty-two consecutive patients were randomized to one of three archwire sequence groups: (i) 3M Unitek, 0·014 inch Nitinol, 0·017 inch × 0·017 inch heat activated Ni-Ti; (ii) GAC international, 0·014 inch Sentalloy, 0·016 × 0·022 inch Bioforce; and (iii) Ormco corporation, 0·014 inch Damon Copper Ni-Ti, 0·014 × 0·025 inch Damon Copper Ni-Ti. All patients received 0·018 × 0·025 inch slot Victory Series™ brackets. Mandibular impressions were taken before the insertion of each archwire. Patients completed discomfort surveys according to a seven-point Likert Scale at 4 h, 24 h, 3 days and 7 days after the insertion of each archwire. Efficiency was measured by time required to reach the working archwire, mandibular anterior alignment and level of discomfort. No significant differences were found in the reduction of irregularity between the archwire sequences at any time-point (T1: P = 0·12; T2: P = 0·06; T3: P = 0·21) or in the time to reach the working archwire (P = 0·28). No significant differences were found in the overall discomfort scores between the archwire sequences (4 h: P = 0·30; 24 h: P = 0·18; 3 days: P = 0·53; 7 days: P = 0·47). When the time-points were analysed individually, the 3M Unitek archwire sequence induced significantly less discomfort than GAC and Ormco archwires 24 h after the insertion of the third archwire (P = 0·02). This could possibly be attributed to the progression in archwire material and archform. The archwire sequences were similar in alignment efficiency and overall discomfort. Progression in archwire dimension and archform may contribute to discomfort levels. This study provides clinical justification for three common archwire sequences in 0·018 × 0·025 inch slot brackets.

  9. 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.

  10. 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 (V̇O 2 ) kinetics as well as heart rate kinetics were expected to be similar for walking and cycling. Cardiac data and V̇O 2 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 V̇O 2 kinetics were estimated from heart rate and pulmonary V̇O 2 using a circulatory model. Muscular (walking vs. cycling [mean±SD in arbitrary units]: 0.40±0.08 vs. 0.41±0.08) and pulmonary V̇O 2 kinetics (0.35±0.06 vs. 0.35±0.06) were not different, although the time courses of the cross-correlation functions of pulmonary V̇O 2 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 V̇O 2 during walking, the assessment of muscular V̇O 2 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.

  11. 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)....... lognormal variables or polynomials of standard Gaussian variables. The dependency structure is induced by specifying the autocorrelation structure of the sequence of standard Gaussian variables. Particularly useful polynomials are the Winterstein approximations that distributionally fit with non...

  12. A Novel Motion Compensation Method for Random Stepped Frequency Radar with M-sequence

    Science.gov (United States)

    Liao, Zhikun; Hu, Jiemin; Lu, Dawei; Zhang, Jun

    2018-01-01

    The random stepped frequency radar is a new kind of synthetic wideband radar. In the research, it has been found that it possesses a thumbtack-like ambiguity function which is considered to be the ideal one. This also means that only a precise motion compensation could result in the correct high resolution range profile. In this paper, we will introduce the random stepped frequency radar coded by M-sequence firstly and briefly analyse the effect of relative motion between target and radar on the distance imaging, which is called defocusing problem. Then, a novel motion compensation method, named complementary code cancellation, will be put forward to solve this problem. Finally, the simulated experiments will demonstrate its validity and the computational analysis will show up its efficiency.

  13. Growth rate for the expected value of a generalized random Fibonacci sequence

    International Nuclear Information System (INIS)

    Janvresse, Elise; De la Rue, Thierry; Rittaud, BenoIt

    2009-01-01

    We study the behaviour of generalized random Fibonacci sequences defined by the relation g n = |λg n-1 ± g n-2 |, where the ± sign is given by tossing an unbalanced coin, giving probability p to the + sign. We prove that the expected value of g n grows exponentially fast for any 0 (2 - λ)/4 when λ is of the form 2cos(π/k) for some fixed integer k ≥ 3. In both cases, we give an algebraic expression for the growth rate

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

    KAUST Repository

    Ganesan, Pugalenthi; Kandaswamy, Krishna Kumar Umar; Chou -, Kuochen; Vivekanandan, Saravanan; Kolatkar, Prasanna R.

    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

  15. 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

  16. The MedSeq Project: a randomized trial of integrating whole genome sequencing into clinical medicine.

    Science.gov (United States)

    Vassy, Jason L; Lautenbach, Denise M; McLaughlin, Heather M; Kong, Sek Won; Christensen, Kurt D; Krier, Joel; Kohane, Isaac S; Feuerman, Lindsay Z; Blumenthal-Barby, Jennifer; Roberts, J Scott; Lehmann, Lisa Soleymani; Ho, Carolyn Y; Ubel, Peter A; MacRae, Calum A; Seidman, Christine E; Murray, Michael F; McGuire, Amy L; Rehm, Heidi L; Green, Robert C

    2014-03-20

    Whole genome sequencing (WGS) is already being used in certain clinical and research settings, but its impact on patient well-being, health-care utilization, and clinical decision-making remains largely unstudied. It is also unknown how best to communicate sequencing results to physicians and patients to improve health. We describe the design of the MedSeq Project: the first randomized trials of WGS in clinical care. This pair of randomized controlled trials compares WGS to standard of care in two clinical contexts: (a) disease-specific genomic medicine in a cardiomyopathy clinic and (b) general genomic medicine in primary care. We are recruiting 8 to 12 cardiologists, 8 to 12 primary care physicians, and approximately 200 of their patients. Patient participants in both the cardiology and primary care trials are randomly assigned to receive a family history assessment with or without WGS. Our laboratory delivers a genome report to physician participants that balances the needs to enhance understandability of genomic information and to convey its complexity. We provide an educational curriculum for physician participants and offer them a hotline to genetics professionals for guidance in interpreting and managing their patients' genome reports. Using varied data sources, including surveys, semi-structured interviews, and review of clinical data, we measure the attitudes, behaviors and outcomes of physician and patient participants at multiple time points before and after the disclosure of these results. The impact of emerging sequencing technologies on patient care is unclear. We have designed a process of interpreting WGS results and delivering them to physicians in a way that anticipates how we envision genomic medicine will evolve in the near future. That is, our WGS report provides clinically relevant information while communicating the complexity and uncertainty of WGS results to physicians and, through physicians, to their patients. This project will not only

  17. Succinylcholine versus rocuronium for rapid sequence intubation in intensive care: a prospective, randomized controlled trial

    Science.gov (United States)

    2011-01-01

    Introduction Succinylcholine and rocuronium are widely used to facilitate rapid sequence induction (RSI) intubation in intensive care. Concerns relate to the side effects of succinylcholine and to slower onset and inferior intubation conditions associated with rocuronium. So far, succinylcholine and rocuronium have not been compared in an adequately powered randomized trial in intensive care. Accordingly, the aim of the present study was to compare the incidence of hypoxemia after rocuronium or succinylcholine in critically ill patients requiring an emergent RSI. Methods This was a prospective randomized controlled single-blind trial conducted from 2006 to 2010 at the University Hospital of Basel. Participants were 401 critically ill patients requiring emergent RSI. Patients were randomized to receive 1 mg/kg succinylcholine or 0.6 mg/kg rocuronium for neuromuscular blockade. The primary outcome was the incidence of oxygen desaturations defined as a decrease in oxygen saturation ≥ 5%, assessed by continuous pulse oxymetry, at any time between the start of the induction sequence and two minutes after the completion of the intubation. A severe oxygen desaturation was defined as a decrease in oxygen saturation ≥ 5% leading to a saturation value of ≤ 80%. Results There was no difference between succinylcholine and rocuronium regarding oxygen desaturations (succinylcholine 73/196; rocuronium 66/195; P = 0.67); severe oxygen desaturations (succinylcholine 20/196; rocuronium 20/195; P = 1.0); and extent of oxygen desaturations (succinylcholine -14 ± 12%; rocuronium -16 ± 13%; P = 0.77). The duration of the intubation sequence was shorter after succinycholine than after rocuronium (81 ± 38 sec versus 95 ± 48 sec; P = 0.002). Intubation conditions (succinylcholine 8.3 ± 0.8; rocuronium 8.2 ± 0.9; P = 0.7) and failed first intubation attempts (succinylcholine 32/200; rocuronium 36/201; P = 1.0) did not differ between the groups. Conclusions In critically ill

  18. Entropy of finite random binary sequences with weak long-range correlations.

    Science.gov (United States)

    Melnik, S S; Usatenko, O V

    2014-11-01

    We study the N-step binary stationary ergodic Markov chain and analyze its differential entropy. Supposing that the correlations are weak we express the conditional probability function of the chain through the pair correlation function and represent the entropy as a functional of the pair correlator. Since the model uses the two-point correlators instead of the block probability, it makes it possible to calculate the entropy of strings at much longer distances than using standard methods. A fluctuation contribution to the entropy due to finiteness of random chains is examined. This contribution can be of the same order as its regular part even at the relatively short lengths of subsequences. A self-similar structure of entropy with respect to the decimation transformations is revealed for some specific forms of the pair correlation function. Application of the theory to the DNA sequence of the R3 chromosome of Drosophila melanogaster is presented.

  19. 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.

  20. Fast selection of miRNA candidates based on large-scale pre-computed MFE sets of randomized sequences.

    Science.gov (United States)

    Warris, Sven; Boymans, Sander; Muiser, Iwe; Noback, Michiel; Krijnen, Wim; Nap, Jan-Peter

    2014-01-13

    Small RNAs are important regulators of genome function, yet their prediction in genomes is still a major computational challenge. Statistical analyses of pre-miRNA sequences indicated that their 2D structure tends to have a minimal free energy (MFE) significantly lower than MFE values of equivalently randomized sequences with the same nucleotide composition, in contrast to other classes of non-coding RNA. The computation of many MFEs is, however, too intensive to allow for genome-wide screenings. Using a local grid infrastructure, MFE distributions of random sequences were pre-calculated on a large scale. These distributions follow a normal distribution and can be used to determine the MFE distribution for any given sequence composition by interpolation. It allows on-the-fly calculation of the normal distribution for any candidate sequence composition. The speedup achieved makes genome-wide screening with this characteristic of a pre-miRNA sequence practical. Although this particular property alone will not be able to distinguish miRNAs from other sequences sufficiently discriminative, the MFE-based P-value should be added to the parameters of choice to be included in the selection of potential miRNA candidates for experimental verification.

  1. 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

  2. Non-random alkylation of DNA sequences induced in vivo by chemical mutagens

    Energy Technology Data Exchange (ETDEWEB)

    Durante, M.; Geri, C.; Bonatti, S.; Parenti, R. (Universita di Pisa (Italy))

    1989-08-01

    Previous studies of the interaction of alkylating agents on the eukaryotic genome support the idea that induction of DNA adducts is at specific genomic sites. Here we show molecular and cytological evidence that alkylation is rather specific. Mammalian cell cultures were exposed to different doses of mutagens and the DNA was analyzed by density gradient ultracentrifugation, hydroxylapatite fractionation, and by restriction enzyme analysis. Studies with the labelled mutagens N-ethyl-N-nitrosourea and N-methyl-N'-nitro-N-nitrosoguanidine show that there is a non-random distribution of the adducts. The adducts are found more frequently in A-T, G-C rich satellite DNA and highly repetitive sequences. Analysis with restriction enzymes shows that both methyl and ethyl groups influence the restriction patterns of the enzymes HpaII and MspI that recognize specific endogenous DNA methylation. These data suggest, as a subsequent mechanism, a modification in the pattern of the normal endogenous methylation of 5-methylcytosine.

  3. 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.

  4. 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 diff...

  5. 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.

  6. A high-speed on-chip pseudo-random binary sequence generator for multi-tone phase calibration

    Science.gov (United States)

    Gommé, Liesbeth; Vandersteen, Gerd; Rolain, Yves

    2011-07-01

    An on-chip reference generator is conceived by adopting the technique of decimating a pseudo-random binary sequence (PRBS) signal in parallel sequences. This is of great benefit when high-speed generation of PRBS and PRBS-derived signals is the objective. The design implemented standard CMOS logic is available in commercial libraries to provide the logic functions for the generator. The design allows the user to select the periodicity of the PRBS and the PRBS-derived signals. The characterization of the on-chip generator marks its performance and reveals promising specifications.

  7. A high-speed on-chip pseudo-random binary sequence generator for multi-tone phase calibration

    International Nuclear Information System (INIS)

    Gommé, Liesbeth; Vandersteen, Gerd; Rolain, Yves

    2011-01-01

    An on-chip reference generator is conceived by adopting the technique of decimating a pseudo-random binary sequence (PRBS) signal in parallel sequences. This is of great benefit when high-speed generation of PRBS and PRBS-derived signals is the objective. The design implemented standard CMOS logic is available in commercial libraries to provide the logic functions for the generator. The design allows the user to select the periodicity of the PRBS and the PRBS-derived signals. The characterization of the on-chip generator marks its performance and reveals promising specifications

  8. 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.

  9. 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 ...

  10. A structuralist theory of evolution reconsidered.

    Science.gov (United States)

    van der Hammen, L

    1997-01-01

    The structuralist theory of evolution is reconsidered in the light of new discoveries. According to this theory, the evolutionary potentialities are in the genotype (a hierarchically ordered set of interacting elements) and manifest themselves in the course of morphogenesis in association with changes in the environment. It is demonstrated that this theory is in fact the development of a long philosophical tradition, in which Darwin and Neo-Darwinism did not participate. New discoveries in the field of molecular cytogenetics confirm the ideas of evolutionary potentiality and hierarchical genotypic ordering. It is demonstrated that gene regulation can manifest itself in association with instabilities of the morphogenetic field and the attainment of a new equilibrium; this change could be connected with changes in the environment, but has nothing to do with natural selection.

  11. A weak zero-one law for sequences of random distance graphs

    Energy Technology Data Exchange (ETDEWEB)

    Zhukovskii, Maksim E [M. V. Lomonosov Moscow State University, Faculty of Mechanics and Mathematics, Moscow (Russian Federation)

    2012-07-31

    We study zero-one laws for properties of random distance graphs. Properties written in a first-order language are considered. For p(N) such that pN{sup {alpha}}{yields}{infinity} as N{yields}{infinity}, and (1-p)N{sup {alpha}} {yields} {infinity} as N {yields} {infinity} for any {alpha}>0, we succeed in refuting the law. In this connection, we consider a weak zero-one j-law. For this law, we obtain results for random distance graphs which are similar to the assertions concerning the classical zero-one law for random graphs. Bibliography: 18 titles.

  12. 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.

  13. High-resolution characterization of sequence signatures due to non-random cleavage of cell-free DNA.

    Science.gov (United States)

    Chandrananda, Dineika; Thorne, Natalie P; Bahlo, Melanie

    2015-06-17

    High-throughput sequencing of cell-free DNA fragments found in human plasma has been used to non-invasively detect fetal aneuploidy, monitor organ transplants and investigate tumor DNA. However, many biological properties of this extracellular genetic material remain unknown. Research that further characterizes circulating DNA could substantially increase its diagnostic value by allowing the application of more sophisticated bioinformatics tools that lead to an improved signal to noise ratio in the sequencing data. In this study, we investigate various features of cell-free DNA in plasma using deep-sequencing data from two pregnant women (>70X, >50X) and compare them with matched cellular DNA. We utilize a descriptive approach to examine how the biological cleavage of cell-free DNA affects different sequence signatures such as fragment lengths, sequence motifs at fragment ends and the distribution of cleavage sites along the genome. We show that the size distributions of these cell-free DNA molecules are dependent on their autosomal and mitochondrial origin as well as the genomic location within chromosomes. DNA mapping to particular microsatellites and alpha repeat elements display unique size signatures. We show how cell-free fragments occur in clusters along the genome, localizing to nucleosomal arrays and are preferentially cleaved at linker regions by correlating the mapping locations of these fragments with ENCODE annotation of chromatin organization. Our work further demonstrates that cell-free autosomal DNA cleavage is sequence dependent. The region spanning up to 10 positions on either side of the DNA cleavage site show a consistent pattern of preference for specific nucleotides. This sequence motif is present in cleavage sites localized to nucleosomal cores and linker regions but is absent in nucleosome-free mitochondrial DNA. These background signals in cell-free DNA sequencing data stem from the non-random biological cleavage of these fragments. This

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

    Indian Academy of Sciences (India)

    2-dimensional chaotic maps for the generation of pseudorandom sequences. 3. ... map. Consider the bit-stream Bx formed by choosing every Pth bit of Sx, ... Similarly, the probability of the linear complexity C assuming the value c(c < N) when.

  15. Prehospital rapid sequence intubation improves functional outcome for patients with severe traumatic brain injury: a randomized controlled trial.

    Science.gov (United States)

    Bernard, Stephen A; Nguyen, Vina; Cameron, Peter; Masci, Kevin; Fitzgerald, Mark; Cooper, David J; Walker, Tony; Std, B Paramed; Myles, Paul; Murray, Lynne; David; Taylor; Smith, Karen; Patrick, Ian; Edington, John; Bacon, Andrew; Rosenfeld, Jeffrey V; Judson, Rodney

    2010-12-01

    To determine whether paramedic rapid sequence intubation in patients with severe traumatic brain injury (TBI) improves neurologic outcomes at 6 months compared with intubation in the hospital. Severe TBI is associated with a high rate of mortality and long-term morbidity. Comatose patients with TBI routinely undergo endo-tracheal intubation to protect the airway, prevent hypoxia, and control ventilation. In many places, paramedics perform intubation prior to hospital arrival. However, it is unknown whether this approach improves outcomes. In a prospective, randomized, controlled trial, we assigned adults with severe TBI in an urban setting to either prehospital rapid sequence intubation by paramedics or transport to a hospital emergency department for intubation by physicians. The primary outcome measure was the median extended Glasgow Outcome Scale (GOSe) score at 6 months. Secondary end-points were favorable versus unfavorable outcome at 6 months, length of intensive care and hospital stay, and survival to hospital discharge. A total of 312 patients with severe TBI were randomly assigned to paramedic rapid sequence intubation or hospital intubation. The success rate for paramedic intubation was 97%. At 6 months, the median GOSe score was 5 (interquartile range, 1-6) in patients intubated by paramedics compared with 3 (interquartile range, 1-6) in the patients intubated at hospital (P = 0.28).The proportion of patients with favorable outcome (GOSe, 5-8) was 80 of 157 patients (51%) in the paramedic intubation group compared with 56 of 142 patients (39%) in the hospital intubation group (risk ratio, 1.28; 95% confidence interval, 1.00-1.64; P = 0.046). There were no differences in intensive care or hospital length of stay, or in survival to hospital discharge. In adults with severe TBI, prehospital rapid sequence intubation by paramedics increases the rate of favorable neurologic outcome at 6 months compared with intubation in the hospital.

  16. The simultaneous use of several pseudo-random binary sequences in the identification of linear multivariable dynamic systems

    International Nuclear Information System (INIS)

    Cummins, J.D.

    1965-02-01

    With several white noise sources the various transmission paths of a linear multivariable system may be determined simultaneously. This memorandum considers the restrictions on pseudo-random two state sequences to effect simultaneous identification of several transmission paths and the consequential rejection of cross-coupled signals in linear multivariable systems. The conditions for simultaneous identification are established by an example, which shows that the integration time required is large i.e. tends to infinity, as it does when white noise sources are used. (author)

  17. 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

  18. Exact distribution of a pattern in a set of random sequences generated by a Markov source: applications to biological data.

    Science.gov (United States)

    Nuel, Gregory; Regad, Leslie; Martin, Juliette; Camproux, Anne-Claude

    2010-01-26

    In bioinformatics it is common to search for a pattern of interest in a potentially large set of rather short sequences (upstream gene regions, proteins, exons, etc.). Although many methodological approaches allow practitioners to compute the distribution of a pattern count in a random sequence generated by a Markov source, no specific developments have taken into account the counting of occurrences in a set of independent sequences. We aim to address this problem by deriving efficient approaches and algorithms to perform these computations both for low and high complexity patterns in the framework of homogeneous or heterogeneous Markov models. The latest advances in the field allowed us to use a technique of optimal Markov chain embedding based on deterministic finite automata to introduce three innovative algorithms. Algorithm 1 is the only one able to deal with heterogeneous models. It also permits to avoid any product of convolution of the pattern distribution in individual sequences. When working with homogeneous models, Algorithm 2 yields a dramatic reduction in the complexity by taking advantage of previous computations to obtain moment generating functions efficiently. In the particular case of low or moderate complexity patterns, Algorithm 3 exploits power computation and binary decomposition to further reduce the time complexity to a logarithmic scale. All these algorithms and their relative interest in comparison with existing ones were then tested and discussed on a toy-example and three biological data sets: structural patterns in protein loop structures, PROSITE signatures in a bacterial proteome, and transcription factors in upstream gene regions. On these data sets, we also compared our exact approaches to the tempting approximation that consists in concatenating the sequences in the data set into a single sequence. Our algorithms prove to be effective and able to handle real data sets with multiple sequences, as well as biological patterns of

  19. ACORN—A new method for generating sequences of uniformly distributed Pseudo-random Numbers

    Science.gov (United States)

    Wikramaratna, R. S.

    1989-07-01

    A new family of pseudo-random number generators, the ACORN ( additive congruential random number) generators, is proposed. The resulting numbers are distributed uniformly in the interval [0, 1). The ACORN generators are defined recursively, and the ( k + 1)th order generator is easily derived from the kth order generator. Some theorems concerning the period length are presented and compared with existing results for linear congruential generators. A range of statistical tests are applied to the ACORN generators, and their performance is compared with that of the linear congruential generators and the Chebyshev generators. The tests show the ACORN generators to be statistically superior to the Chebyshev generators, while being statistically similar to the linear congruential generators. However, the ACORN generators execute faster than linear congruential generators for the same statistical faithfulness. The main advantages of the ACORN generator are speed of execution, long period length, and simplicity of coding.

  20. Reconsidering the role of nuclear energy

    International Nuclear Information System (INIS)

    Uematsu, K.

    1990-01-01

    The use of nuclear power is being reconsidered in the light of the present environmental debate. The extreme rise in the world-wide consumption of fossil energy resources has given rise to the climatological problem and will, at some point in time, lead to the depletion of fossil resources. There is no doubt that the use of nuclear power does not generate any CO 2 emissions, but nuclear power alone is not able to meet tomorrow's world energy requirement. Expanding the worldwide use of fossil fuels is no solution either. To what extent nuclear power will be used depends on the severity of the environmental problems, but also on the alternatives made available economically by new technical concepts. A major role is palyed by the human attitude to nuclear power, which is now influenced by too many emotions. Weighing the risks inherent in all energy resources, and considering the growing energy requirement in the developing countries, will lead to parameters which will be instrumental in determining the future of nuclear power. (orig.) [de

  1. 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.

  2. Analysis of using interpulse intervals to generate 128-bit biometric random binary sequences for securing wireless body sensor networks.

    Science.gov (United States)

    Zhang, Guang-He; Poon, Carmen C Y; Zhang, Yuan-Ting

    2012-01-01

    Wireless body sensor network (WBSN), a key building block for m-Health, demands extremely stringent resource constraints and thus lightweight security methods are preferred. To minimize resource consumption, utilizing information already available to a WBSN, particularly common to different sensor nodes of a WBSN, for security purposes becomes an attractive solution. In this paper, we tested the randomness and distinctiveness of the 128-bit biometric binary sequences (BSs) generated from interpulse intervals (IPIs) of 20 healthy subjects as well as 30 patients suffered from myocardial infarction and 34 subjects with other cardiovascular diseases. The encoding time of a biometric BS on a WBSN node is on average 23 ms and memory occupation is 204 bytes for any given IPI sequence. The results from five U.S. National Institute of Standards and Technology statistical tests suggest that random biometric BSs can be generated from both healthy subjects and cardiovascular patients and can potentially be used as authentication identifiers for securing WBSNs. Ultimately, it is preferred that these biometric BSs can be used as encryption keys such that key distribution over the WBSN can be avoided.

  3. Randomness control of vehicular motion through a sequence of traffic signals at irregular intervals

    International Nuclear Information System (INIS)

    Nagatani, Takashi

    2010-01-01

    We study the regularization of irregular motion of a vehicle moving through the sequence of traffic signals with a disordered configuration. Each traffic signal is controlled by both cycle time and phase shift. The cycle time is the same for all signals, while the phase shift varies from signal to signal by synchronizing with intervals between a signal and the next signal. The nonlinear dynamic model of the vehicular motion is presented by the stochastic nonlinear map. The vehicle exhibits the very complex behavior with varying both cycle time and strength of irregular intervals. The irregular motion induced by the disordered configuration is regularized by adjusting the phase shift within the regularization regions.

  4. 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

  5. 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.

  6. Reconsidering connectivity in the sub-Antarctic.

    Science.gov (United States)

    Moon, Katherine L; Chown, Steven L; Fraser, Ceridwen I

    2017-11-01

    Extreme and remote environments provide useful settings to test ideas about the ecological and evolutionary drivers of biological diversity. In the sub-Antarctic, isolation by geographic, geological and glaciological processes has long been thought to underpin patterns in the region's terrestrial and marine diversity. Molecular studies using increasingly high-resolution data are, however, challenging this perspective, demonstrating that many taxa disperse among distant sub-Antarctic landmasses. Here, we reconsider connectivity in the sub-Antarctic region, identifying which taxa are relatively isolated, which are well connected, and the scales across which this connectivity occurs in both terrestrial and marine systems. Although many organisms show evidence of occasional long-distance, trans-oceanic dispersal, these events are often insufficient to maintain gene flow across the region. Species that do show evidence of connectivity across large distances include both active dispersers and more sedentary species. Overall, connectivity patterns in the sub-Antarctic at intra- and inter-island scales are highly complex, influenced by life-history traits and local dynamics such as relative dispersal capacity and propagule pressure, natal philopatry, feeding associations, the extent of human exploitation, past climate cycles, contemporary climate, and physical barriers to movement. An increasing use of molecular data - particularly genomic data sets that can reveal fine-scale patterns - and more effective international collaboration and communication that facilitates integration of data from across the sub-Antarctic, are providing fresh insights into the processes driving patterns of diversity in the region. These insights offer a platform for assessing the ways in which changing dispersal mechanisms, such as through increasing human activity and changes to wind and ocean circulation, may alter sub-Antarctic biodiversity patterns in the future. © 2017 Cambridge

  7. 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.

  8. Treatment Sequencing for Childhood ADHD: A Multiple-Randomization Study of Adaptive Medication and Behavioral Interventions.

    Science.gov (United States)

    Pelham, William E; Fabiano, Gregory A; Waxmonsky, James G; Greiner, Andrew R; Gnagy, Elizabeth M; Pelham, William E; Coxe, Stefany; Verley, Jessica; Bhatia, Ira; Hart, Katie; Karch, Kathryn; Konijnendijk, Evelien; Tresco, Katy; Nahum-Shani, Inbal; Murphy, Susan A

    2016-01-01

    Behavioral and pharmacological treatments for children with attention deficit/hyperactivity disorder (ADHD) were evaluated to address whether endpoint outcomes are better depending on which treatment is initiated first and, in case of insufficient response to initial treatment, whether increasing dose of initial treatment or adding the other treatment modality is superior. Children with ADHD (ages 5-12, N = 146, 76% male) were treated for 1 school year. Children were randomized to initiate treatment with low doses of either (a) behavioral parent training (8 group sessions) and brief teacher consultation to establish a Daily Report Card or (b) extended-release methylphenidate (equivalent to .15 mg/kg/dose bid). After 8 weeks or at later monthly intervals as necessary, insufficient responders were rerandomized to secondary interventions that either increased the dose/intensity of the initial treatment or added the other treatment modality, with adaptive adjustments monthly as needed to these secondary treatments. The group beginning with behavioral treatment displayed significantly lower rates of observed classroom rule violations (the primary outcome) at study endpoint and tended to have fewer out-of-class disciplinary events. Further, adding medication secondary to initial behavior modification resulted in better outcomes on the primary outcomes and parent/teacher ratings of oppositional behavior than adding behavior modification to initial medication. Normalization rates on teacher and parent ratings were generally high. Parents who began treatment with behavioral parent training had substantially better attendance than those assigned to receive training following medication. Beginning treatment with behavioral intervention produced better outcomes overall than beginning treatment with medication.

  9. 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.

  10. 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 decision? 134.715 Section 134.715 Business Credit and Assistance SMALL BUSINESS ADMINISTRATION RULES OF....715 Can a Judge reconsider his decision? (a) The Judge may reconsider an appeal decision within 20...

  11. Reconsidering Replication: New Perspectives on Large-Scale School Improvement

    Science.gov (United States)

    Peurach, Donald J.; Glazer, Joshua L.

    2012-01-01

    The purpose of this analysis is to reconsider organizational replication as a strategy for large-scale school improvement: a strategy that features a "hub" organization collaborating with "outlet" schools to enact school-wide designs for improvement. To do so, we synthesize a leading line of research on commercial replication to construct a…

  12. Reconsidering Children's Encounters with Nature and Place Using Posthumanism

    Science.gov (United States)

    Malone, Karen

    2016-01-01

    This article explores and reconsiders the view of children's encounters with place as central to a place-based pedagogy that seeks to dismantle rather than support constructions of a nature-culture binary. I unpack the current fervour for reinserting the child in nature and nature-based education as a significant phenomenon in environmental and…

  13. 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…

  14. 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 ...

  15. 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˙O 2 pulm) and predicted muscular (V˙O 2 musc) 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˙O 2 pulm were measured beat-to-beat and breath-by-breath, respectively. V˙O 2 musc 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˙O 2 musc kinetics seem to be independent of WR intensity (p>0.05). V˙O 2 pulm kinetics show prominent differences in the lag of the CCF maximum (39±9s; 31±4s; p<0.05). A mean difference of 14W between the PRBS WR amplitudes impacts venous return significantly, while HR and V˙O 2 musc kinetics remain unchanged. Copyright © 2017 Elsevier B.V. All rights reserved.

  16. A randomized clinical trial of a new orthodontic appliance to improve upper airway obstruction in infants with Pierre Robin sequence.

    Science.gov (United States)

    Buchenau, Wolfgang; Urschitz, Michael S; Sautermeister, Judit; Bacher, Margit; Herberts, Tina; Arand, Joerg; Poets, Christian F

    2007-08-01

    To test the hypothesis that a new orthodontic appliance with a velar extension that shifts the tongue anteriorly would reduce upper airway obstruction in infants with Pierre Robin sequence (PRS). Eleven infants with PRS (median age, 3 days) and an apnea index (AI) >3 were studied. The effect of the new appliance on the AI was compared with that of a conventional appliance without a velar extension by using a crossover study design with random allocation. Compared with baseline (mean AI, 13.8), there was a significant decrease in the AI with the new appliance (3.9; P value appliance (14.8; P = .842). Thus, the relative change in AI was -71% (95% CI, -84--49) for the new appliance and +8% (95% CI, -52-142) for the conventional appliance, which was significantly different (P = .004). No severe adverse effects were observed. This new orthodontic appliance appears to be safe and effective in reducing upper airway obstruction in infants with PRS.

  17. CNV-RF Is a Random Forest-Based Copy Number Variation Detection Method Using Next-Generation Sequencing.

    Science.gov (United States)

    Onsongo, Getiria; Baughn, Linda B; Bower, Matthew; Henzler, Christine; Schomaker, Matthew; Silverstein, Kevin A T; Thyagarajan, Bharat

    2016-11-01

    Simultaneous detection of small copy number variations (CNVs) (<0.5 kb) and single-nucleotide variants in clinically significant genes is of great interest for clinical laboratories. The analytical variability in next-generation sequencing (NGS) and artifacts in coverage data because of issues with mappability along with lack of robust bioinformatics tools for CNV detection have limited the utility of targeted NGS data to identify CNVs. We describe the development and implementation of a bioinformatics algorithm, copy number variation-random forest (CNV-RF), that incorporates a machine learning component to identify CNVs from targeted NGS data. Using CNV-RF, we identified 12 of 13 deletions in samples with known CNVs, two cases with duplications, and identified novel deletions in 22 additional cases. Furthermore, no CNVs were identified among 60 genes in 14 cases with normal copy number and no CNVs were identified in another 104 patients with clinical suspicion of CNVs. All positive deletions and duplications were confirmed using a quantitative PCR method. CNV-RF also detected heterozygous deletions and duplications with a specificity of 50% across 4813 genes. The ability of CNV-RF to detect clinically relevant CNVs with a high degree of sensitivity along with confirmation using a low-cost quantitative PCR method provides a framework for providing comprehensive NGS-based CNV/single-nucleotide variant detection in a clinical molecular diagnostics laboratory. Copyright © 2016 American Society for Investigative Pathology and the Association for Molecular Pathology. Published by Elsevier Inc. All rights reserved.

  18. Estimating Genetic Conformism of Korean Mulberry Cultivars Using Random Amplified Polymorphic DNA and Inter-Simple Sequence Repeat Profiling

    Directory of Open Access Journals (Sweden)

    Sunirmal Sheet

    2018-03-01

    Full Text Available Apart from being fed to silkworms in sericulture, the ecologically important Mulberry plant has been used for traditional medicine in Asian countries as well as in manufacturing wine, food, and beverages. Germplasm analysis among Mulberry cultivars originating from South Korea is crucial in the plant breeding program for cultivar development. Hence, the genetic deviations and relations among 8 Morus alba plants, and one Morus lhou plant, of different cultivars collected from South Korea were investigated using 10 random amplified polymorphic DNA (RAPD and 10 inter-simple sequence repeat (ISSR markers in the present study. The ISSR markers exhibited a higher polymorphism (63.42% among mulberry genotypes in comparison to RAPD markers. Furthermore, the similarity coefficient was estimated for both markers and found to be varying between 0.183 and 0.814 for combined pooled data of ISSR and RAPD. The phenogram drawn using the UPGMA cluster method based on combined pooled data of RAPD and ISSR markers divided the nine mulberry genotypes into two divergent major groups and the two individual independent accessions. The distant relationship between Dae-Saug (SM1 and SangchonJo Sang Saeng (SM5 offers a possibility of utilizing them in mulberry cultivar improvement of Morus species of South Korea.

  19. Improvement of the Gravitational Search Algorithm by means of Low-Discrepancy Sobol Quasi Random-Number Sequence Based Initialization

    Directory of Open Access Journals (Sweden)

    ALTINOZ, O. T.

    2014-08-01

    Full Text Available Nature-inspired optimization algorithms can obtain the optima by updating the position of each member in the population. At the beginning of the algorithm, the particles of the population are spread into the search space. The initial distribution of particles corresponds to the beginning points of the search process. Hence, the aim is to alter the position for each particle beginning with this initial position until the optimum solution will be found with respect to the pre-determined conditions like maximum iteration, and specific error value for the fitness function. Therefore, initial positions of the population have a direct effect on both accuracy of the optima and the computational cost. If any member in the population is close enough to the optima, this eases the achievement of the exact solution. On the contrary, individuals grouped far away from the optima might yield pointless efforts. In this study, low-discrepancy quasi-random number sequence is preferred for the localization of the population at the initialization phase. By this way, the population is distributed into the search space in a more uniform manner at the initialization phase. The technique is applied to the Gravitational Search Algorithm and compared via the performance on benchmark function solutions.

  20. 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

    2018-03-01

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

  1. Dividend announcements reconsidered: Dividend changes versus dividend surprises

    OpenAIRE

    Andres, Christian; Betzer, André; van den Bongard, Inga; Haesner, Christian; Theissen, Erik

    2012-01-01

    This paper reconsiders the issue of share price reactions to dividend announcements. Previous papers rely almost exclusively on a naive dividend model in which the dividend change is used as a proxy for the dividend surprise. We use the difference between the actual dividend and the analyst consensus forecast as obtained from I/B/E/S as a proxy for the dividend surprise. Using data from Germany, we find significant share price reactions after dividend announcements. Once we control for analys...

  2. 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

  3. Paleomagnetism of ~635 Ma "Elatina Rhythmites," Reconsidered

    Science.gov (United States)

    Raub, T. D.; Raub, T. M.

    2007-12-01

    Extraordinary laminated sand-siltstone of South Australia's synglacial/deglacial Elatina Formation-equivalent at Pichi Richi Pass is an iconic outcrop for paleomagnetists, paleoclimatologists, and astrophysicists. Cyclic- bedded stacks of coarse/fine-grained doublets have been interpreted as rhythmites of semi-diurnal tidal origin in a deep-water delta front environment. Cycle analysis has yielded estimates of Earth's paleorotation and revolution periods and lunar distance. The reported 10 m (interpreted 60 year) record disagrees somewhat with coeval and younger biological "sediment-clocks," and Williams (2000) argues that the sedimentological context and extraordinary preservation of Elatina rhythmites makes that record preferable. A paleomagnetic "synsedimentary fold" test on 50 cm packages to culminate in unambiguous ladderback ripples. This shallowing-upward sequence reflects high sediment supply over 60 years and/or else significant sea level regression during (possibly longer) rhythmite deposition. The exceptional character of climbing-ripple rhythmites can be explained by pervasive microbial binding of sediment, in the anomalous mode characterizing many Ediacaran siliciclastic environments. Detrital magnetization seemingly should not around ripple crests. Either the interval of Snowball Earth deglaciation was characterized by unusually low geomagnetic field strength, biasing magnetization fidelity, or else Elatina rhythmites do not record DRM over a continuous 60-year timescale. This latter alternative may find support in the original studies, which document considerable dispersion, unexpected for a VGP. Kirschvink, 1992. in Schopf, J.W. and Klein, C., eds. The Proterozoic Biosphere, Cambridge University Press, Cambridge, pp. 51-52. Schmidt and Williams, 1995. Earth and Planetary Science Letters, v. 134, pp. 107-124. Sohl, Christie-Blick, and Kent, 1999. Geological Society of America Bulletin, v. 111, pp. 1120-1139. Sumner, Kirschvink, and Runnegar, 1987

  4. Modelling estimation and analysis of dynamic processes from image sequences using temporal random closed sets and point processes with application to the cell exocytosis and endocytosis

    OpenAIRE

    Díaz Fernández, Ester

    2010-01-01

    In this thesis, new models and methodologies are introduced for the analysis of dynamic processes characterized by image sequences with spatial temporal overlapping. The spatial temporal overlapping exists in many natural phenomena and should be addressed properly in several Science disciplines such as Microscopy, Material Sciences, Biology, Geostatistics or Communication Networks. This work is related to the Point Process and Random Closed Set theories, within Stochastic Ge...

  5. AFLP fragment isolation technique as a method to produce random sequences for single nucleotide polymorphism discovery in the green turtle, Chelonia mydas.

    Science.gov (United States)

    Roden, Suzanne E; Dutton, Peter H; Morin, Phillip A

    2009-01-01

    The green sea turtle, Chelonia mydas, was used as a case study for single nucleotide polymorphism (SNP) discovery in a species that has little genetic sequence information available. As green turtles have a complex population structure, additional nuclear markers other than microsatellites could add to our understanding of their complex life history. Amplified fragment length polymorphism technique was used to generate sets of random fragments of genomic DNA, which were then electrophoretically separated with precast gels, stained with SYBR green, excised, and directly sequenced. It was possible to perform this method without the use of polyacrylamide gels, radioactive or fluorescent labeled primers, or hybridization methods, reducing the time, expense, and safety hazards of SNP discovery. Within 13 loci, 2547 base pairs were screened, resulting in the discovery of 35 SNPs. Using this method, it was possible to yield a sufficient number of loci to screen for SNP markers without the availability of prior sequence information.

  6. The administration sequence of propofol and remifentanil does not affect the ED50 and ED95 of rocuronium in rapid sequence induction of anesthesia: a double-blind randomized controlled trial.

    Science.gov (United States)

    Ozcelik, M; Guclu, C; Bermede, O; Baytas, V; Altay, N; Karahan, M A; Erdogan, B; Can, O

    2016-04-01

    The topic of drug administration sequence in rapid sequence induction (RSI) is still an object of interest in terms of rocuronium effectiveness. The aim of this prospective, randomized trial was to evaluate the effect of administration sequence of propofol and remifentanil on ED50 and ED95 of rocuronium in a RSI model. Eighty-four patients were randomized into Group Remifentanil (Group R, n = 43), where induction of general anesthesia started with remifentanil (2 µg/kg) and followed by propofol (2 mg/kg) and rocuronium administrations; and Group Propofol (Group P, n = 41), where induction of general anesthesia started with propofol and followed by remifentanil and rocuronium. First patients in each group were paralyzed by 0.8 mg/kg rocuronium. In case of acceptable intubation as evaluated according to the criteria described by Viby-Mogensen et al, rocuronium dose was decreased by 0.1 mg/kg for the next patient; otherwise, rocuronium dose was increased by 0.1 mg/kg. After three crossover points, increments or decrements in rocuronium dosage were set to 0.05 mg/kg. The process was repeated until a total of ten crossover points were obtained. The ED50 and ED95 doses of rocuronium were similar in Group R (0.182 mg/kg, and 0.244 mg/kg, respectively) and Group P (0.121 mg/kg, and 0.243 mg/kg, respectively) according to 95% CI of the estimates. There was no statistically significant difference in terms of clinically acceptable intubation conditions between the two groups (56.1% in Group R vs. 59% in Group P, p = 0.795). The choice of administration sequence of propofol and remifentanil does not have an impact on estimated ED50 and ED95 of rocuronium in providing acceptable intubation conditions in the RSI technique.

  7. 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.

  8. 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 previ......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...... to the surface of the film. The value of the effective diffusion coefficient of water vapour in the dry and partly coalesced layer (7 x 10(-7) m(2)/s at 19-24 degrees C), the adjustable parameter of the model for the falling rate period, was found to be independent of initial wet film thickness (89-1322 mu m...

  9. 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

    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....... 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...... in the conformational ensemble are an important source of neighbor effects in disordered proteins. Glutamine derived random coil chemical shifts and correction factors modestly improve our ability to predict (13)C chemical shifts of intrinsically disordered proteins compared to existing datasets, and may thus improve...

  10. Comparison of single-use and reusable metal laryngoscope blades for orotracheal intubation during rapid sequence induction of anesthesia: a multicenter cluster randomized study.

    Science.gov (United States)

    Amour, Julien; Le Manach, Yannick Le; Borel, Marie; Lenfant, François; Nicolas-Robin, Armelle; Carillion, Aude; Ripart, Jacques; Riou, Bruno; Langeron, Olivier

    2010-02-01

    Single-use metal laryngoscope blades are cheaper and carry a lower risk of infection than reusable metal blades. The authors compared single-use and reusable metal blades during rapid sequence induction of anesthesia in a multicenter cluster randomized trial. One thousand seventy-two adult patients undergoing general anesthesia under emergency conditions and requiring rapid sequence induction were randomly assigned on a weekly basis to either single-use or reusable metal blades (cluster randomization). After induction, a 60-s period was allowed to complete intubation. In the case of failed intubation, a second attempt was performed using the opposite type of blade. The primary endpoint was the rate of failed intubation, and the secondary endpoints were the incidence of complications (oxygen desaturation, lung aspiration, and/or oropharynx trauma) and the Cormack and Lehane score. Both groups were similar in their main characteristics, including the risk factors for difficult intubation. The rate of failed intubation was significantly decreased with single-use metal blades at the first attempt compared with reusable blades (2.8 vs. 5.4%, P < 0.05). In addition, the proportion of grades III and IV in Cormack and Lehane score were also significantly decreased with single-use metal blades (6 vs. 10%, P < 0.05). The global complication rate did not reach statistical significance, although the same trend was noted (6.8% vs. 11.5%, P = not significant). An investigator survey and a measure of illumination pointed that illumination might have been responsible for this result. The single-use metal blade was more efficient than a reusable metal blade in rapid sequence induction of anesthesia.

  11. Frequency characteristic measurement of a fiber optic gyroscope using a correlation spectrum analysis method based on a pseudo-random sequence

    International Nuclear Information System (INIS)

    Li, Yang; Chen, Xingfan; Liu, Cheng

    2015-01-01

    The frequency characteristic is an important indicator of a system’s dynamic performance. The identification of a fiber optic gyroscope (FOG)’s frequency characteristic using a correlation spectrum analysis method based on a pseudo-random sequence is proposed. Taking the angle vibrator as the source of the test rotation stimulation and a pseudo-random sequence as the test signal, the frequency characteristic of a FOG is calculated according to the power spectral density of the rotation rate signal and the cross-power spectral density of the FOG’s output signal and rotation rate signal. A theoretical simulation is done to confirm the validity of this method. An experiment system is built and the test results indicate that the measurement error of the normalized amplitude–frequency response is less than 0.01, that the error of the phase–frequency response is less than 0.3 rad, and the overall measurement accuracy is superior to the traditional frequency-sweep method. By using this method, the FOG’s amplitude–frequency response and phase–frequency response can be measured simultaneously, quickly, accurately, and with a high frequency resolution. The described method meets the requirements of engineering applications. (paper)

  12. 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...

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

    Science.gov (United States)

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

    2005-08-01

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

  14. 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.

  15. Absence of zero-temperature transmission rate of a double-chain tight-binding model for DNA with random sequence of nucleotides in thermodynamic limit

    International Nuclear Information System (INIS)

    Xiong Gang; Wang, X.R.

    2005-01-01

    The zero-temperature transmission rate spectrum of a double-chain tight-binding model for real DNA is calculated. It is shown that a band of extended-like states exists only for finite chain length with strong inter-chain coupling. While the whole spectrum tends to zero in thermodynamic limit, regardless of the strength of inter-chain coupling. It is also shown that a more faithful model for real DNA with periodic sugar-phosphate chains in backbone structures can be mapped into the above simple double-chain tight-binding model. Combined with above results, the transmission rate of real DNA with long random sequence of nucleotides is expected to be poor

  16. 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.

  17. A Developmental and Sequenced One-to-One Educational Intervention for Autism Spectrum Disorder: A Randomized Single-Blind Controlled Trial.

    Science.gov (United States)

    Tanet, Antoine; Hubert-Barthelemy, Annik; Crespin, Graciela C; Bodeau, Nicolas; Cohen, David; Saint-Georges, Catherine

    2016-01-01

    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). We implemented a novel model called the "Developmental and Sequenced One-to-One Educational Intervention" (DS1-EI) in 5- to 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 behaviors, 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 min 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. We enrolled 75 participants: 38 were randomized to the DS1-EI and 37 to the TAU groups. At enrollment, 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 the DS1-EI group vs. 3.4 (±4.5) h/week in the TAU group, Student's t

  18. German nuclear policy reconsidered. Implications for the electricity market

    International Nuclear Information System (INIS)

    Fuersch, Michaela; Lindenberger, Dietmar; Malischek, Raimund; Nagl, Stephan; Panke, Timo; Trueby, Johannes

    2011-01-01

    In the aftermath of the nuclear catastrophe in Fukushima, German nuclear policy has been reconsidered. This paper demonstrates the economic effects of an accelerated nuclear phase-out on the German electricity generation sector. A detailed optimization model for European electricity markets is used to analyze two scenarios with different lifetimes for nuclear plants (phase-out vs. prolongation). Based on political targets, both scenarios assume significant electricity demand reductions and a high share of generation from renewable energy sources in Germany. Our principal findings are: First, nuclear capacities are mainly replaced by longer lifetimes of existing coal-fired plants and the construction of new gas-fired plants. Second, fossil fuel-based generation and power imports increase, while power exports are reduced in response to the lower nuclear generation. Third, despite the increased fossil generation, challenging climate protection goals can still be achieved within the framework of the considered scenarios. Finally, system costs and electricity prices are clearly higher. We conclude that the generation sector can generally cope with an accelerated nuclear phase-out under the given assumptions. Yet, we emphasize that such a policy requires a substantial and costly transformation of the supply and the demand side.

  19. Counter-Terrorism, Technology and Transparency: Reconsidering State Accountability

    Directory of Open Access Journals (Sweden)

    Quirine Eijkman

    2012-02-01

    Full Text Available In this Discussion Paper, Dr. Quirine Eijkman discusses the use of surveillance, storage of personal information, biometrics, satellite technology and other forms of ICT technology used in the fight against terrorism. Although technology is a powerful tool to fight terrorism, it is also a means for increasing social control by the state. Henceforth, there is a risk that panoptic surveillance – where the few view the many – could develop. Therefore accountability in relation to use of technological counter-terrorism measures such as smart surveillance cameras, biometric devices or the tracking of personal data is discussed in this article. The extra powers that both public authorities and private companies gain through new (surveillance technologies should be counterbalanced. In this context the role of the state, because of its monopoly to use force and its duty to protect the rule of law, is crucial. By reconsidering how to enforce accountability by the state, the effects of technological counter-terrorism measures could be checked and balanced.

  20. Land in China: Re-considering comparability in financial reporting

    Directory of Open Access Journals (Sweden)

    Ying Zhang

    2010-03-01

    Full Text Available This paper re-considers the notion of ‘comparability’ as it has been applied to the accounting standardharmonisation project and its implications for accounting practices that are emerging in China.Comparability is a concept that has been widely referred to within the accounting literature, but has remainedlargely unexplored. In order to encourage what Zeff (2007 described as “genuine comparability” we arguethat the underlying economic substance of an event should be the focus of our accounting choices in order toenable appropriate comparisons. If we focus too heavily on regulatory standardisation that prescribescomparable techniques without considering the broader economic context in which these are applied, theaccounting representations could mislead users. The techniques may distort representations of theunderlying economic substance of business activities, which would hinder the level of a genuinecomparability in global financial reporting. In order to explore this, given the unique legal status of land inChina, we consider how it is classified and represented in Chinese financial reports. This example shows thatthere are still significant challenges that need to be overcome in order to implement IFRS in China and thereare still substantial comparability problems for cross-border users.

  1. 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

  2. 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

  3. 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

    International Nuclear Information System (INIS)

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

    2016-01-01

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

  4. 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.

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

    Science.gov (United States)

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

    2015-06-01

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

  6. 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.

  7. Bioavailability of two single-dose oral formulations of omeprazole 20 mg: an open-label, randomized sequence, two-period crossover comparison in healthy Mexican adult volunteers.

    Science.gov (United States)

    Poo, Jorge Luis; Galán, Juan Francisco; Rosete, Alejandra; de Lago, Alberto; Oliva, Iván; González-de la Parra, Mario; Jiménez, Patricia; Burke-Fraga, Victoria; Namur, Salvador

    2008-04-01

    Omeprazole is a proton-pump inhibitor that acts to reduce acid secretion in the stomach and is used for treating various acid-related gastrointestinal disorders. There are several generic formulations of omeprazole available in Mexico; however, a literature search failed to identify published data concerning the bioavailability of these formulations in the Mexican population. The aim of this study was to compare the bioavailability of 2 oral formulations of omeprazole 20-mg capsules, marketed for use in Mexico, in healthy volunteers: Inhibitron (test formulation) and LosecA 20 mg (reference formulation). This study used a single-dose, open-label, randomized sequence, 2 x 2 crossover (2 administration periods x 2 treatments) design to compare the 2 formulations. Eligible subjects were healthy adult Mexican volunteers of both sexes. Subjects were randomly assigned in a 1:1 ratio to receive a single 20-mg dose of the test formulation followed by the reference formulation, or vice versa, with a 7-day washout period between administration periods. After a 12-hour (overnight) fast, subjects received a single, 20-mg dose of the corresponding formulation. Plasma samples were obtained over a 12-hour period after administration. Plasma omeprazole concentrations were analyzed by a nonstereospecific high-performance liquid chromatography method. For analysis of pharmacokinetic properties, including C(max), AUC from time 0 (baseline) to time t (AUC(0-t)), and AUC from baseline to infinity (AUC(0-infinity)), blood samples were drawn at baseline and 0.17, 0.33, 0.50, 0.75, 1, 1.25, 1.50, 1.75, 2, 2.50, 3, 4, 6, 8, and 12 hours after administration. The formulations were considered bioequivalent if the natural log (ln)-transformed ratios of C(max) and AUC were within the predetermined equivalence range of 80% to 125%, and if P disability, or required intervention to prevent permanent impairment or damage. Thirty-four subjects were enrolled and completed the study (25 men and 9

  8. 14 CFR 11.101 - May I ask FAA to reconsider my petition for rulemaking or petition for exemption if it is denied?

    Science.gov (United States)

    2010-01-01

    ... 14 Aeronautics and Space 1 2010-01-01 2010-01-01 false May I ask FAA to reconsider my petition for... Rulemaking Procedures Petitions for Rulemaking and for Exemption § 11.101 May I ask FAA to reconsider my petition for rulemaking or petition for exemption if it is denied? Yes, you may petition FAA to reconsider...

  9. Lithium evolution in metal-poor stars: from Pre-Main Sequence to the Spite plateau

    OpenAIRE

    Fu, Xiaoting; Bressan, Alessandro; Molaro, Paolo; Marigo, Paola

    2015-01-01

    Lithium abundance derived in metal-poor main sequence stars is about three times lower than the value of primordial Li predicted by the standard Big Bang nucleosynthesis when the baryon density is taken from the CMB or the deuterium measurements. This disagreement is generally referred as the lithium problem. We here reconsider the stellar Li evolution from the pre-main sequence to the end of the main sequence phase by introducing the effects of convective overshooting and residual mass accre...

  10. 15 CFR 325.9 - Reconsidering an application that has been denied.

    Science.gov (United States)

    2010-01-01

    ... 15 Commerce and Foreign Trade 2 2010-01-01 2010-01-01 false Reconsidering an application that has been denied. 325.9 Section 325.9 Commerce and Foreign Trade Regulations Relating to Commerce and Foreign Trade (Continued) INTERNATIONAL TRADE ADMINISTRATION, DEPARTMENT OF COMMERCE MISCELLANEOUS...

  11. (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…

  12. 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…

  13. 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.

  14. The capital-asset pricing model reconsidered: tests in real terms on ...

    African Journals Online (AJOL)

    This paper extends previous work of the authors to reconsider the capital-asset pricing model (CAPM) in South Africa in real terms. As in that work, the main question this study aimed to answer remains: Can the CAPM be accepted in the South African market for the purposes of the stochastic modelling of investment returns ...

  15. 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

  16. 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

  17. Phylogeny of Marsileaceous Ferns and Relationships of the Fossil Hydropteris pinnata Reconsidered.

    Science.gov (United States)

    Pryer

    1999-09-01

    Recent phylogenetic studies have provided compelling evidence that confirms the once disputed hypothesis of monophyly for heterosporous leptosporangiate ferns (Marsileaceae and Salviniaceae). Hypotheses for relationships among the three genera of Marsileaceae (Marsilea, Regnellidium, and Pilularia), however, have continued to be in conflict. The phylogeny of Marsileaceae is investigated here using information from morphology and rbcL sequence data. In addition, relationships among all heterosporous ferns, including the whole-plant fossil Hydropteris pinnata are reconsidered. Data sets of 71 morphological and 1239 rbcL characters for 23 leptosporangiate ferns, including eight heterosporous ingroup taxa and 15 homosporous outgroup taxa, were subjected to maximum parsimony analysis. Morphological analyses were carried out both with and without the fossil Hydropteris, and it was excluded from all analyses with rbcL data. An annotated list of the 71 morphological characters is provided in the appendix. For comparative purposes, the Rothwell and Stockey (1994) data set was also reanalyzed here. The best estimate of phylogenetic relationships for Marsileaceae in all analyses is that Pilularia and Regnellidium are sister taxa and Marsilea is sister to that clade. Morphological synapomorphies for various nodes are discussed. Analyses that included Hydropteris resulted in two most-parsimonious trees that differ only in the placement of the fossil. One topology is identical to the relationship found by Rothwell and Stockey (1994), placing the fossil sister to the Azolla plus Salvinia clade. The alternative topology places Hydropteris as the most basal member of the heterosporous fern clade. Equivocal interpretations for character evolution in heterosporous ferns are discussed in the context of these two most-parsimonious trees. Because of the observed degree of character ambiguity, the phylogenetic placement of Hydropteris is best viewed as unresolved, and recognition of the

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

    Energy Technology Data Exchange (ETDEWEB)

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

    1995-07-01

    Purpose: To determine the effects of different sequences of CT and RT following CS for pts with clinical Stage I or II breast carcinoma. Methods and Materials: From 6/84-12/92, 244 pts were randomized following CS to receive CT (4 cycles of CAMFP at 3-wk intervals) either before or after RT. Median pt age was 45 yrs (range, 20-68). 164 pts were pre-, 18 pts peri-, and 62 pts were postmenopausal. 209 pts were node-positive (61 had 4 or more positive nodes); after 6/88, 35 selected node-negative pts were also included. 45 Gy was prescribed to the entire breast, followed by a boost of 16 Gy; nodal RT was optional. The medians ( and ranges) of the surgery-radiotherapy interval (SRI) according to assigned arm were: RT-first, 36 days (14-234); CT-first, 126 days (98-185). Drug doses were based on ideal body weight. Doses (per square meter) and schedule were: methotrexate, 200 mg, d.1 and 15; leucovorin, 10 mg, q6H x 12, start d.2 and 16; 5-fluorouracil, 500 mg, d.1; cyclophosphamide, 500 mg, d.1; prednisone, 40 mg/day x 5d, start d.1; and doxorubicin, 45 mg, d.3. All except leucovorin and prednisone were given by IV bolus. Dose reductions were based on the granulocyte nadir from the previous cycle, with an attempt to reescalate doses in subsequent cycles. Tamoxifen 10 mg BID was prescribed to postmenopausal pts with ER+ tumors following both RT and CT. 4 pts were ineligible due to prior malignancies, 2 pts on the RT-first arm refused their assigned sequence and received CT first, 2 pts on the RT-first arm and 1 pt on the CT-first arm refused to start or complete CT, 1 pt on the CT-arm underwent elective mastectomy prior to starting RT, and 1 pt on each arm received nonprotocol CT. Possible prognostic factors including age, menopausal status, ERP status, nodal status, and lymphatic vessel invasion were distributed nearly uniformly between the 2 arms. There was an excess of pts with EIC-positive tumors on the RT-first arm (25%) compared to the CT-first arm (11%) (p-bar=0

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

    International Nuclear Information System (INIS)

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

    1995-01-01

    Purpose: To determine the effects of different sequences of CT and RT following CS for pts with clinical Stage I or II breast carcinoma. Methods and Materials: From 6/84-12/92, 244 pts were randomized following CS to receive CT (4 cycles of CAMFP at 3-wk intervals) either before or after RT. Median pt age was 45 yrs (range, 20-68). 164 pts were pre-, 18 pts peri-, and 62 pts were postmenopausal. 209 pts were node-positive (61 had 4 or more positive nodes); after 6/88, 35 selected node-negative pts were also included. 45 Gy was prescribed to the entire breast, followed by a boost of 16 Gy; nodal RT was optional. The medians ( and ranges) of the surgery-radiotherapy interval (SRI) according to assigned arm were: RT-first, 36 days (14-234); CT-first, 126 days (98-185). Drug doses were based on ideal body weight. Doses (per square meter) and schedule were: methotrexate, 200 mg, d.1 and 15; leucovorin, 10 mg, q6H x 12, start d.2 and 16; 5-fluorouracil, 500 mg, d.1; cyclophosphamide, 500 mg, d.1; prednisone, 40 mg/day x 5d, start d.1; and doxorubicin, 45 mg, d.3. All except leucovorin and prednisone were given by IV bolus. Dose reductions were based on the granulocyte nadir from the previous cycle, with an attempt to reescalate doses in subsequent cycles. Tamoxifen 10 mg BID was prescribed to postmenopausal pts with ER+ tumors following both RT and CT. 4 pts were ineligible due to prior malignancies, 2 pts on the RT-first arm refused their assigned sequence and received CT first, 2 pts on the RT-first arm and 1 pt on the CT-first arm refused to start or complete CT, 1 pt on the CT-arm underwent elective mastectomy prior to starting RT, and 1 pt on each arm received nonprotocol CT. Possible prognostic factors including age, menopausal status, ERP status, nodal status, and lymphatic vessel invasion were distributed nearly uniformly between the 2 arms. There was an excess of pts with EIC-positive tumors on the RT-first arm (25%) compared to the CT-first arm (11%) (p-bar=0

  20. 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.

  1. The Tangled Nature Model of evolutionary dynamics reconsidered

    DEFF Research Database (Denmark)

    Andersen, Christian Walther; Sibani, Paolo

    2016-01-01

    The Tangled Nature Model of biological and cultural evolution features interacting agents which compete for limited resources and reproduce in an error prone fashion and at a rate depending on the `tangle' of interactions they maintain with others. The set of interactions linking a TNM individual....... To bring out the structural and dynamical effects of trait inheritance , we introduce and numerically analyze a family of TNM models where a positive integer $K$ parametrises correlations between the interactions of an agent and those of its mutated offspring. For $K=1$ a single point mutation randomizes...

  2. Random matrices and random difference equations

    International Nuclear Information System (INIS)

    Uppuluri, V.R.R.

    1975-01-01

    Mathematical models leading to products of random matrices and random difference equations are discussed. A one-compartment model with random behavior is introduced, and it is shown how the average concentration in the discrete time model converges to the exponential function. This is of relevance to understanding how radioactivity gets trapped in bone structure in blood--bone systems. The ideas are then generalized to two-compartment models and mammillary systems, where products of random matrices appear in a natural way. The appearance of products of random matrices in applications in demography and control theory is considered. Then random sequences motivated from the following problems are studied: constant pulsing and random decay models, random pulsing and constant decay models, and random pulsing and random decay models

  3. Reconsidering the autohypnotic model of the dissociative disorders.

    Science.gov (United States)

    Dell, Paul F

    2018-03-22

    The dissociative disorders field and the hypnosis field currently reject the autohypnotic model of the dissociative disorders, largely because many correlational studies have shown hypnotizability and dissociation to be minimally related (r = .12). Curiously, it is also widely accepted that dissociative patients are highly hypnotizable. If dissociative patients are highly hypnotizable because only highly hypnotizable individuals can develop a dissociative disorder - as the author proposes - then the methodology of correlational studies of hypnotizability and dissociation in random clinical and community samples would necessarily be constitutively unable to detect, and statistically unable to reflect, that fact. That is, the autohypnotic, dissociative distancing of that small subset of highly hypnotizable individuals who repeatedly encountered intolerable circumstances is statistically lost among the data of (1) the highly hypnotizable subjects who do not dissociate and (2) subjects (of all levels of hypnotizability) who manifest other kinds of dissociation. The author proposes that, when highly hypnotizable individuals repeatedly engage in autohypnotic distancing from intolerable circumstances, they develop an overlearned, highly-motivated, automatized pattern of dissociative self-protection (i.e., a dissociative disorder). The author urges that theorists of hypnosis and the dissociative disorders explicitly include in their theories (a) the trait of high hypnotizability, (b) the phenomena of autohypnosis, and (c) the manifestations of systematized, autohypnotic pathology. Said differently, the author is suggesting that autohypnosis and autohypnotic pathology are unacknowledged nodes in the nomothetic networks of both hypnosis and dissociation.

  4. Reconsidering the psychometrics of quality of life assessment in light of response shift and appraisal

    Directory of Open Access Journals (Sweden)

    Schwartz Carolyn E

    2004-03-01

    Full Text Available Abstract The increasing evidence for response shift phenomena in quality of life (QOL assessment points to the necessity to reconsider both the measurement model and the application of psychometric analyses. The proposed psychometric model posits that the QOL true score is always contingent upon parameters of the appraisal process. This new model calls into question existing methods for establishing the reliability and validity of QOL assessment tools and suggests several new approaches for describing the psychometric properties of these scales. Recommendations for integrating the assessment of appraisal into QOL research and clinical practice are discussed.

  5. Reconsidering the psychometrics of quality of life assessment in light of response shift and appraisal

    Science.gov (United States)

    Schwartz, Carolyn E; Rapkin, Bruce D

    2004-01-01

    The increasing evidence for response shift phenomena in quality of life (QOL) assessment points to the necessity to reconsider both the measurement model and the application of psychometric analyses. The proposed psychometric model posits that the QOL true score is always contingent upon parameters of the appraisal process. This new model calls into question existing methods for establishing the reliability and validity of QOL assessment tools and suggests several new approaches for describing the psychometric properties of these scales. Recommendations for integrating the assessment of appraisal into QOL research and clinical practice are discussed. PMID:15038830

  6. 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.

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

    Science.gov (United States)

    Yaari, Gur; Eisenmann, Shmuel

    2011-01-01

    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.

  8. Congruence Reconsidered.

    Science.gov (United States)

    Tudor, Keith; Worrall, Mike

    1994-01-01

    Discusses Carl Rogers' definitions of congruence, and identifies four specific requirements for the concept and practice of therapeutic congruence. Examines the interface between congruence and the other necessary and sufficient conditions of change, drawing on examples from practice. (JPS)

  9. Reconsidering Innovation

    DEFF Research Database (Denmark)

    Vaaben, Nana Katrine

    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...

  10. Reconsidering IUDs.

    Science.gov (United States)

    Goldberg, B

    1992-07-01

    The Population Council reported in April 1992 that the modern IUD has become the world's most widely used reversible contraceptive method. The Dalkon Shield was associated with pelvic inflammatory disease (PID), and in 1985 its manufacturer, A.H. Robins Company, went bankrupt. A new study from WHO showed no increased risk of PID among IUD users at low risk for sexually transmitted diseases, although the risk of PID appears to be greater in the 1st month after insertion. With proper patient selection IUDs are a good contraceptive choice for many women. US and international staff members of the Association for Voluntary Surgical Contraception (AVSC) were among professionals at a New York conference of IUD use in developed and developing countries. The current copper-bearing IUD (Copper T 380A) is effective for up to 8 years, but is also appropriate for shorter-term use. A study was presented about women who had their IUDs removed: 80% became pregnant within the 1st year and 95% within 3 years after removal. A longterm, continuing study of the Copper T 380A found it safe, effective, long-lasting, and inexpensive to manufacture. The Copper T 380A was 1st marketed in the US in 1988. Because of its long-term effectiveness, the Copper T 380A is a possible alternative for women who desire no children but have decided against surgical sterilization. A survey revealed that only 27% of US obstetrics and gynecology training programs teach IUD insertion and removal, and 37% of chief residents have never inserted an IUD. The conference examined new copper and hormonal IUDs, including levonorgestrel-releasing IUD which is effective for up to 5 years (LNG-20) expected to be approved for use in the US by 1995. More than 20 presenters addressed IUD performance, mechanisms of action, complications and their prevention, ectopic pregnancy, infertility, and postremoval conception rates.

  11. 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 [...

  12. Reconsidering Facebook

    OpenAIRE

    Hilary Davis

    2011-01-01

    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 [...

  13. A phase III randomized study on the sequencing of radiotherapy and chemotherapy in the conservative management of early-stage breast cancer

    International Nuclear Information System (INIS)

    Arcangeli, Giorgio; Pinnaro, Paola; Rambone, Rita; Giannarelli, Diana; Benassi, Marcello

    2006-01-01

    Purpose: To compare two different timings of radiation treatment in patients with breast cancer who underwent conservative surgery and were candidates to receive adjuvant cyclophosphamide, methotrexate, and fluorouracil (CMF) chemotherapy. Methods and Materials: A total of 206 patients who had quadrantectomy and axillary dissection for breast cancer and were planned to receive adjuvant CMF chemotherapy were randomized to concurrent or sequential radiotherapy. Radiotherapy was delivered only to the whole breast through tangential fields to a dose of 50 Gy in 20 fractions over 4 weeks, followed by an electron boost of 10-15 Gy in 4-6 fractions to the tumor bed. Results: No differences in 5-year breast recurrence-free, metastasis-free, disease-free, and overall survival were observed in the two treatment groups. All patients completed the planned radiotherapy. No evidence of an increased risk of toxicity was observed between the two arms. No difference in radiotherapy and in the chemotherapy dose intensity was observed in the two groups. Conclusions: In patients with negative surgical margins receiving adjuvant chemotherapy, radiotherapy can be delayed to up to 7 months. Concurrent administration of CMF chemotherapy and radiotherapy is safe and might be reserved for patients at high risk of local recurrence, such as those with positive surgical margins or larger tumor diameters

  14. 多重随机序列在算术编码中的应用%Application of Multiple Random Sequence in Arithmetic Coding

    Institute of Scientific and Technical Information of China (English)

    周明; 冯民富

    2012-01-01

    Arithmetic coding, for its high compression ratio and moderate coding efficiency, plays an important role in the standard of image compression technology. This algorithm depends on only one argument: the occurrence probability of information source symbols. This probability determines the efficiency of compression, and the interval of information source symbols as well. However, the classical arithmetic coding considers no internal structure of the input sequence of information source symbols, but only the probability of single symbols. Finally to which special combinations the coding intervals should be allocated, and whether there exists an effective allocation algorithm, these are still problems to been considered and settled.%算术编码凭借其高效的压缩比以及适度的编码效率,在图像压缩技术标准(比如JPEG等)中有着重要的地位。该算法仅仅依赖于一个参数:信源符号出现的概率。该概率决定了压缩编码的效率,同时也决定了编码过程中信源符号的间隔。然而,经典的算术编码都没有考虑信源符号输入序列的内在结构,仅仅是考虑单个的符号。这些连续的输入组合中的某些组合若大量出现在信源符号中,就有必要考虑这些组合的出现概率了。而最终需要给哪些特定的组合分配编码区间,以及是否有行之有效的分配算法,都需要考虑。

  15. Reconsidering Feminisms and the Work of Norbert Elias for Understanding Gender, Sport and Sport-Related Activities

    Science.gov (United States)

    Mansfield, Louise

    2008-01-01

    This paper reconsiders the relationships between feminist perspectives and the figurational/process-sociological perspective of Norbert Elias for understanding gender, sport and sport-related activities. The main aim of the article is to respond to Colwell's claim that there are differences between feminist and figurational approaches to…

  16. A Philosopher's War on Poverty of the Stimulus Arguments: A Review of Fiona Cowie's "What's Within? Nativism Reconsidered"

    Science.gov (United States)

    Schoneberger, Ted

    2005-01-01

    In "What's Within? Nativism Reconsidered" (1999) Fiona Cowie addresses three questions: (1) What is nativism? (2) What is meant by calling some trait "innate"? and (3) What types of evidence should be offered when claiming innateness? This review concentrates on these questions as they pertain to Chomsky's faculties-based account of language…

  17. 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... entitlement of a party was established, is later found to be alive; or (4) The death of the individual on whose account a party's claim was denied for lack of proof of death is established— (i) By reason of an...

  18. Speaking of That: Terms to Avoid or Reconsider in the Eating Disorders Field.

    Science.gov (United States)

    Weissman, Ruth S; Becker, Anne E; Bulik, Cynthia M; Frank, Guido K W; Klump, Kelly L; Steiger, Howard; Strober, Michael; Thomas, Jennifer; Waller, Glenn; Walsh, B Timothy

    2016-04-01

    Inspired by an article on 50 terms that, in the interest of clarity in scientific reasoning and communication in psychology, psychiatry, and allied fields, "should be avoided or at most be used sparingly and only with explicit caveats,"(1) we propose a list of terms to avoid or think twice about before using when writing for the International Journal of Eating Disorders (IJED). Drawing upon our experience as reviewers or editors for the IJED, we generated an abridged list of such terms. For each term, we explain why it made our list and what alternatives we recommend. We hope that our list will contribute to improved clarity in scientific thinking about eating disorders, and that it will stimulate discussion of terms that may need to be reconsidered in our field's vocabulary to ensure the use of language that is respectful and sensitive to individuals who experience an eating disorder. © 2016 Wiley Periodicals, Inc.

  19. 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.

  20. Sequence assembly

    DEFF Research Database (Denmark)

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

    2009-01-01

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

  1. Genome Sequencing

    DEFF Research Database (Denmark)

    Sato, Shusei; Andersen, Stig Uggerhøj

    2014-01-01

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

  2. 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

  3. How random are random numbers generated using photons?

    International Nuclear Information System (INIS)

    Solis, Aldo; Angulo Martínez, Alí M; Ramírez Alarcón, Roberto; Cruz Ramírez, Hector; U’Ren, Alfred B; Hirsch, Jorge G

    2015-01-01

    Randomness is fundamental in quantum theory, with many philosophical and practical implications. In this paper we discuss the concept of algorithmic randomness, which provides a quantitative method to assess the Borel normality of a given sequence of numbers, a necessary condition for it to be considered random. We use Borel normality as a tool to investigate the randomness of ten sequences of bits generated from the differences between detection times of photon pairs generated by spontaneous parametric downconversion. These sequences are shown to fulfil the randomness criteria without difficulties. As deviations from Borel normality for photon-generated random number sequences have been reported in previous work, a strategy to understand these diverging findings is outlined. (paper)

  4. Relative bioavailability of generic and branded 250-mg and 500-mg oral chlorphenesin carbamate tablets in healthy Korean volunteers: a single-dose, randomized-sequence, open-label, two-period crossover trial.

    Science.gov (United States)

    Yu, Ji-young; Song, Hyun Ho; Kim, Bo Gyeom; Park, Hyeon Ju; Choi, Kwang Sik; Kwon, Young Ee

    2009-11-01

    Chlorphenesin carbamate is a skeletal muscle relaxant approved in Korea for use in the treatment of pain and discomfort related to skeletal muscle trauma and inflammation. The aim of this study was to assess the bioequivalence of a generic formulation of chlorphenesin carbamate at doses of 250 and 500 mg and 2 branded formulations of the same doses in healthy Korean adults. This single-dose, randomized-sequence, open-label, 2-period crossover study was conducted in healthy Korean male and female volunteers. Subjects were assigned to receive, in a randomized sequence, a single dose of the generic (test) and branded (reference) formulations of chlorphenesin carbamate at a dose of 250 or 500 mg. Blood samples were drawn at 0, 0.33, 0.67, 1, 1.5, 2, 3, 4, 6, 9, 12, and 15 hours after administration. Pharmacokinetic properties (C(max), T(max), AUC(0-t) AUC(0-infinity), t(1/2), and ke) were determined using HPLC. The formulations were to be considered bioequivalent if the 90% CIs of the treatment ratios of the geometric means of C(max) and AUC(0-t) were within a predetermined range of log 0.80 to log 1.25 based on regulatory criteria. Tolerability was assessed by monitoring for adverse events (AEs) on physical examination and/or e-mail and personal interview at the beginning and end of each study period. Twenty-eight subjects (22 men, 6 women) received chlorphenesin carbamate at the 250-mg dose, and 24 male subjects received the 500-mg dose. The mean (SD) ages of the subjects were 24.0 (2.6) and 24.0 (1.9) years in the 250- and 500-mg groups, respectively. No significant differences were found between the test and reference formulations (90% CIs: C(max), 1.0048-1.1153 with the 250-mg dose and 0.9630-1.1189 with the 500-mg dose; AUC(0-t), 0.9882-1.0546 and 0.9842-1.0578, respectively). No clinically significant AEs (upper gastric pain, abdominal bloating, pyrexia, edema, nausea, heartburn, constipation, headache, dizziness, drowsiness, or fatigue) were reported throughout

  5. Comparative bioavailability and tolerability of a single 20-mg dose of two fluoxetine hydrochloride dispersible tablet formulations in fasting, healthy Chinese male volunteers: an open-label, randomized-sequence, two-period crossover study.

    Science.gov (United States)

    Shi, Shaojun; Liu, Yani; Wu, Jianhong; Li, Zhongfang; Zhao, Yan; Zhong, Dafang; Zeng, Fandian

    2010-10-01

    The proprietary formulation of fluoxetine hydrochloride is an antidepressant of the selective serotonin reuptake inhibitor class. Pharmacokinetic studies investigating the bioequivalence of generic and branded formulations are needed to market generic fluoxetine in China. The aim of this study was to compare the bioavailability and tolerability of the proposed generic formulation with the established reference formulation of fluoxetine hydrochloride 20 mg in a fasting, healthy Chinese male population. This 10-week, open-label, randomized-sequence, single-dose, 2-period crossover study was conducted in healthy native Han Chinese male volunteers. Eligible subjects were randomly assigned in a 1:1 ratio to receive a single 20-mg dose of the test or reference formulation, followed by a 35-day washout period and administration of the alternate formulation. Doses were administered after a 12-hour overnight fast. For analysis of pharmacokinetic properties (including C(max), T(max), AUC(0-t), AUC(0-∞), and t(½)), blood samples were obtained over a 672-hour period after dosing. Plasma concentrations of fluoxetine and its active metabolite, norfluoxetine, were analyzed using a validated LC-MS/MS method. The formulations were to be considered bioequivalent if the ln-transformed ratios (test/ reference) of C(max) and AUC were within the predetermined bioequivalence range of 80% to 125%, as established by the US Food and Drug Administration, and if the P values were fasting, healthy Chinese male volunteers. Both formulations appeared to be well tolerated. Copyright © 2010 Excerpta Medica Inc. All rights reserved.

  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. ‘Developmental Delay’ Reconsidered: The Critical Role of Age-Dependent, Co-variant Development

    Directory of Open Access Journals (Sweden)

    Yonata Levy

    2018-04-01

    Full Text Available In memory of Annette Karmiloff-Smith.This paper reviews recent neurobiological research reporting structural co-variance and temporal dependencies in age-dependent gene expression, parameters of cortical maturation, long range connectivity and interaction of the biological network with the environment. This research suggests that age by size trajectories of brain structures relate to functional properties more than absolute sizes. In line with these findings, recent behavioral studies of typically developing children whose language development was delayed reported long term consequences of such delays. As for neurodevelopmental disorders, disrupted developmental timing and slow acquisitional pace are hallmarks of these populations. It is argued that these behavioral and neuro-biological results highlight the need to commit to a developmental model which will reflect the fact that temporal dependencies overseeing structural co-variance among developmental components are major regulatory factors of typical development of the brain/mind network. Consequently, the concept of ‘developmental delay’ in developmental theorizing needs to be reconsidered.

  8. 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.

  9. [Reconsidering evaluation criteria regarding health care research: toward an integrative framework of quantitative and qualitative criteria].

    Science.gov (United States)

    Miyata, Hiroaki; Kai, Ichiro

    2006-05-01

    Debate about the relationship between quantitative and qualitative paradigms is often muddled and confused and the clutter of terms and arguments has resulted in the concepts becoming obscure and unrecognizable. It is therefore very important to reconsider evaluation criteria regarding rigor in social science. As Lincoln & Guba have already compared quantitative paradigms (validity, reliability, neutrality, generalizability) with qualitative paradigms (credibility, dependability, confirmability, transferability), we have discuss use of evaluation criteria based on pragmatic perspective. Validity/Credibility is the paradigm concerned to observational framework, while Reliability/Dependability refer to the range of stability in observations, Neutrality/Confirmability reflect influences between observers and subjects, Generalizability/Transferability have epistemological difference in the way findings are applied. Qualitative studies, however, does not always chose the qualitative paradigms. If we assume the stability to some extent, it is better to use the quantitative paradigm (reliability). Moreover as a quantitative study can not always guarantee a perfect observational framework, with stability in all phases of observations, it is useful to use qualitative paradigms to enhance the rigor in the study.

  10. (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.

  11. 3rd Circuit hints it may reconsider McNemar reasoning.

    Science.gov (United States)

    1997-10-17

    The [name removed] v. The Disney Store ruling is under criticism and the 3rd U.S. Circuit Court of Appeals may reconsider its 1996 decision to not allow employees who receive disability benefits to sue under the Americans with Disabilities Act (ADA). A panel of 3rd Circuit judges, working on [name removed] v. American Sterilizer Co., asserts that the [name removed] decision should not be used to assume that an individual's ADA claims are barred because of prior representations of disability. [Name removed] is suing American Sterilizer under the retaliation provisions of the ADA. Other courts are criticizing the [name removed] decision, including the District of Columbia Court in [name removed] v. Washington Metropolitan Area Transit Authority. The [name removed] court assets that a statement made in the context of a disability application does not preclude an ADA claim brought by a worker for illegal discrimination because the ADA and the Social Security Act differ in their statutory intent. AIDS advocates state that the [name removed] decision places a plaintiff in the position of having to choose between asserting a legal right or maintaining an income. Alan Epstein, who represented [name removed], is pleased by the criticism but explains that [name removed], who died this summer, will not be vindicated.

  12. Bioequivalence of two film-coated tablets of imatinib mesylate 400 mg: a randomized, open-label, single-dose, fasting, two-period, two-sequence crossover comparison in healthy male South American volunteers.

    Science.gov (United States)

    Parrillo-Campiglia, Susana; Ercoli, Mónica Cedres; Umpierrez, Ofelia; Rodríguez, Patricia; Márquez, Sara; Guarneri, Carolina; Estevez-Parrillo, Francisco T; Laurenz, Marilena; Estevez-Carrizo, Francisco E

    2009-10-01

    Imatinib is a tyrosine kinase inhibitor that has been established as a highly effective therapy for chronic myelogenous leukemia and gastrointestinal stromal tumors. A new generic, once-daily 400-mg tablet of imatinib has been developed by a pharmaceutical company in Argentina, where the regulatory standard for marketing authorization of an imatinib generic is in vitro dissolution testing. The aim of this study was to assess the bioequivalence of a new generic film-coated test tablet formulation versus a film-coated reference tablet formulation of imatinib 400 mg. The local manufacturer seeks to validate the in vitro performance of this new formulation with a bioequivalence study. A randomized, open-label, single-dose, fasting, 2-period, 2-sequence crossover design with a 2-week washout period was used in this study. The study population consisted of healthy male South American (Uruguayan) volunteers, who were assigned in a 1:1 ratio to a randomized sequence (test-reference or reference-test). In each period, the test or reference formulation was administered after an overnight fast. During the 72-hour follow-up period, participants were monitored for vital signs and symptoms. Blood samples were collected at 15 time points, including baseline, until 72 hours. Physical examination and laboratory tests (blood, urine) were repeated 1 week after study completion. A noncompartmental model was used to determine the pharmacokinetic parameters of imatinib. The 90% CIs of the test/reference ratios for AUC(0-infinity) and C(max) were determined; the test and reference formulations were considered bioequivalent if the 90% CIs were between 0.80 and 1.25. Adverse events were assessed by a nurse who administered a questionnaire while the healthy volunteers were admitted in the unit. The bioequivalence study was conducted in 30 Uruguayan male volunteers. Demographic characteristics (mean [SD]) included age, 27.8 (6.5) years; weight, 71.2 (9.8) kg; height, 1.71 (0.09) m; and body

  13. 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

  14. 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

  15. 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.

  16. Drawing a random number

    DEFF Research Database (Denmark)

    Wanscher, Jørgen Bundgaard; Sørensen, Majken Vildrik

    2006-01-01

    Random numbers are used for a great variety of applications in almost any field of computer and economic sciences today. Examples ranges from stock market forecasting in economics, through stochastic traffic modelling in operations research to photon and ray tracing in graphics. The construction...... distributions into others with most of the required characteristics. In essence, a uniform sequence which is transformed into a new sequence with the required distribution. The subject of this article is to consider the well known highly uniform Halton sequence and modifications to it. The intent is to generate...

  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. Pseudo-random number generator based on asymptotic deterministic randomness

    Science.gov (United States)

    Wang, Kai; Pei, Wenjiang; Xia, Haishan; Cheung, Yiu-ming

    2008-06-01

    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.

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

    International Nuclear Information System (INIS)

    Wang Kai; Pei Wenjiang; Xia Haishan; Cheung Yiuming

    2008-01-01

    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

  20. Bioequivalence and pharmacokinetic evaluation of two formulations of risperidone 2 mg : an open-label, single-dose, fasting, randomized-sequence, two-way crossover study in healthy male Chinese volunteers.

    Science.gov (United States)

    Liu, Yun; Zhang, Meng-qi; Jia, Jing-ying; Liu, Yan-mei; Liu, Gang-yi; Li, Shui-jun; Wang, Wei; Weng, Li-ping; Yu, Chen

    2013-03-01

    Risperidone is a benzisoxazole derivate and is effective in the treatment of schizophrenia and other psychiatric illnesses in adults and children. Although there are a few reports in the literature regarding the pharmacokinetic characteristics of risperidone, insufficient data on its pharmacokinetic properties in a Chinese population are available. To meet the requirements for marketing a new generic product, this study was designed to compare the pharmacokinetic properties and bioequivalence of two 2 mg tablet formulations of risperidone: a newly developed generic formulation (test) and a branded formulation (reference) in healthy adult male Chinese volunteers. A single-dose, open-label, randomized-sequence, 2 × 2 crossover study was conducted in fasted healthy male Chinese volunteers. Eligible participants were randomly assigned in a 1:1 ratio to receive 1 tablet (2 mg each) of the test formulation (Risperidone tablet; Dr. Reddy's Laboratories Ltd., Hyderabad, India) or the reference formulation (Risperdal(®) tablet; Xian-Janssen Pharmaceutical Ltd., Xi-an, China), followed by a 2-week washout period and subsequent administration of the alternate formulation. The study drugs were administered after a 10-hour overnight fast. Plasma samples were collected over 96 hours. Plasma concentrations of the parent drug, risperidone, and its active metabolite, 9-hydroxy-risperidone, were analyzed by a liquid chromatography-tandem mass spectrometry method. The formulations would be considered bioequivalent if the 90% confidence intervals (CIs) of the natural log-transformed values were within the predetermined 80-125% equivalence range for the maximum plasma drug concentration (Cmax) and the area under the plasma concentration-time curve (AUC), in accordance with guidelines issued by the US Food and Drug Administration. Assessment of tolerability was based on recording of adverse events (AEs), monitoring of vital signs, electrocardiograms, and laboratory tests at baseline

  1. Relative bioavailability of two oral formulations of risperidone 2 mg: A single-dose, randomized-sequence, open-label, two-period crossover comparison in healthy Brazilian volunteers.

    Science.gov (United States)

    Belotto, Karisa Cristina Rodrigues; Raposo, Nádia Rezende Barbosa; Ferreira, Aline Siqueira; Gattaz, Wagner Farid

    2010-11-01

    Risperidone (RSP) is a benzisoxazole antipsychotic agent used to treat schizophrenia and other psychiatric illnesses in adults and children (including those with autism). After oral administration, RSP is completely absorbed from the gastrointestinal tract and undergoes hydroxylation to yield 9-hydroxyrisperidone (9-OH-RSP), an active metabolite that has a pharmacologic profile and potency similar to RSP. The aims of this study were to compare the relative bioavailability of a pharmaceutical-equivalent (test) formulation with a reference formulation of oral RSP 2 mg, both available commercially on the Brazilian pharmaceutical market, and to generate data regarding the oral bioavailability of the tested drug in healthy Brazilian volunteers. This single-dose, randomized-sequence, open-label, 2-period crossover study was conducted in healthy Brazilian volunteers from August to December 2008. Subjects were randomly assigned to receive the test formulation followed by the reference formulation or vice versa, with a 30-day washout period between doses. Study drugs were administered after a 12-hour overnight fast. For pharmacokinetic analysis, blood samples were drawn at 0 (baseline), 0.25, 0.5, 1, 1.5, 3, 5, 8, 12, 24, 48, 72, 96, and 120 hours after administration. Plasma concentrations of RSP and 9-OH-RSP were determined using LC-MS/MS. The test and reference formulations were to be considered bioequivalent if the 90% CIs for the geometric mean test/reference ratios were within a predetermined range of 80% to 125%, in accordance with the policies of the Brazilian Sanitary Surveillance Agency and the US Food and Drug Administration. Tolerability was determined using clinical assessments, monitoring of vital signs, analysis of laboratory test results, and subject interviews regarding adverse events. A total of 22 subjects were enrolled (11 men, 11 women; mean [SD] age, 32 [12] years [range, 1858 years]; weight, 70.4 [11.9] kg [range, 50-103 kg]; height, 1.67 [0.08] m

  2. Randomness at the root of things 1: Random walks

    Science.gov (United States)

    Ogborn, Jon; Collins, Simon; Brown, Mick

    2003-09-01

    This is the first of a pair of articles about randomness in physics. In this article, we use some variations on the idea of a `random walk' to consider first the path of a particle in Brownian motion, and then the random variation to be expected in radioactive decay. The arguments are set in the context of the general importance of randomness both in physics and in everyday life. We think that the ideas could usefully form part of students' A-level work on random decay and quantum phenomena, as well as being good for their general education. In the second article we offer a novel and simple approach to Poisson sequences.

  3. 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.

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

    Science.gov (United States)

    Deroost, Natacha; Coomans, Daphné

    2018-02-01

    We examined the role of sequence awareness in a pure perceptual sequence learning design. Participants had to react to the target's colour that changed according to a perceptual sequence. By varying the mapping of the target's colour onto the response keys, motor responses changed randomly. The effect of sequence awareness on perceptual sequence learning was determined by manipulating the learning instructions (explicit versus implicit) and assessing the amount of sequence awareness after the experiment. In the explicit instruction condition (n = 15), participants were instructed to intentionally search for the colour sequence, whereas in the implicit instruction condition (n = 15), they were left uninformed about the sequenced nature of the task. Sequence awareness after the sequence learning task was tested by means of a questionnaire and the process-dissociation-procedure. The results showed that the instruction manipulation had no effect on the amount of perceptual sequence learning. Based on their report to have actively applied their sequence knowledge during the experiment, participants were subsequently regrouped in a sequence strategy group (n = 14, of which 4 participants from the implicit instruction condition and 10 participants from the explicit instruction condition) and a no-sequence strategy group (n = 16, of which 11 participants from the implicit instruction condition and 5 participants from the explicit instruction condition). Only participants of the sequence strategy group showed reliable perceptual sequence learning and sequence awareness. These results indicate that perceptual sequence learning depends upon the continuous employment of strategic cognitive control processes on sequence knowledge. Sequence awareness is suggested to be a necessary but not sufficient condition for perceptual learning to take place. Copyright © 2018 Elsevier B.V. All rights reserved.

  5. The RANDOM computer program: A linear congruential random number generator

    Science.gov (United States)

    Miles, R. F., Jr.

    1986-01-01

    The RANDOM Computer Program is a FORTRAN program for generating random number sequences and testing linear congruential random number generators (LCGs). The linear congruential form of random number generator is discussed, and the selection of parameters of an LCG for a microcomputer described. This document describes the following: (1) The RANDOM Computer Program; (2) RANDOM.MOD, the computer code needed to implement an LCG in a FORTRAN program; and (3) The RANCYCLE and the ARITH Computer Programs that provide computational assistance in the selection of parameters for an LCG. The RANDOM, RANCYCLE, and ARITH Computer Programs are written in Microsoft FORTRAN for the IBM PC microcomputer and its compatibles. With only minor modifications, the RANDOM Computer Program and its LCG can be run on most micromputers or mainframe computers.

  6. Memory and learning with rapid audiovisual sequences

    Science.gov (United States)

    Keller, Arielle S.; Sekuler, Robert

    2015-01-01

    We examined short-term memory for sequences of visual stimuli embedded in varying multisensory contexts. In two experiments, subjects judged the structure of the visual sequences while disregarding concurrent, but task-irrelevant auditory sequences. Stimuli were eight-item sequences in which varying luminances and frequencies were presented concurrently and rapidly (at 8 Hz). Subjects judged whether the final four items in a visual sequence identically replicated the first four items. Luminances and frequencies in each sequence were either perceptually correlated (Congruent) or were unrelated to one another (Incongruent). Experiment 1 showed that, despite encouragement to ignore the auditory stream, subjects' categorization of visual sequences was strongly influenced by the accompanying auditory sequences. Moreover, this influence tracked the similarity between a stimulus's separate audio and visual sequences, demonstrating that task-irrelevant auditory sequences underwent a considerable degree of processing. Using a variant of Hebb's repetition design, Experiment 2 compared musically trained subjects and subjects who had little or no musical training on the same task as used in Experiment 1. Test sequences included some that intermittently and randomly recurred, which produced better performance than sequences that were generated anew for each trial. The auditory component of a recurring audiovisual sequence influenced musically trained subjects more than it did other subjects. This result demonstrates that stimulus-selective, task-irrelevant learning of sequences can occur even when such learning is an incidental by-product of the task being performed. PMID:26575193

  7. Memory and learning with rapid audiovisual sequences.

    Science.gov (United States)

    Keller, Arielle S; Sekuler, Robert

    2015-01-01

    We examined short-term memory for sequences of visual stimuli embedded in varying multisensory contexts. In two experiments, subjects judged the structure of the visual sequences while disregarding concurrent, but task-irrelevant auditory sequences. Stimuli were eight-item sequences in which varying luminances and frequencies were presented concurrently and rapidly (at 8 Hz). Subjects judged whether the final four items in a visual sequence identically replicated the first four items. Luminances and frequencies in each sequence were either perceptually correlated (Congruent) or were unrelated to one another (Incongruent). Experiment 1 showed that, despite encouragement to ignore the auditory stream, subjects' categorization of visual sequences was strongly influenced by the accompanying auditory sequences. Moreover, this influence tracked the similarity between a stimulus's separate audio and visual sequences, demonstrating that task-irrelevant auditory sequences underwent a considerable degree of processing. Using a variant of Hebb's repetition design, Experiment 2 compared musically trained subjects and subjects who had little or no musical training on the same task as used in Experiment 1. Test sequences included some that intermittently and randomly recurred, which produced better performance than sequences that were generated anew for each trial. The auditory component of a recurring audiovisual sequence influenced musically trained subjects more than it did other subjects. This result demonstrates that stimulus-selective, task-irrelevant learning of sequences can occur even when such learning is an incidental by-product of the task being performed.

  8. Subjective randomness as statistical inference.

    Science.gov (United States)

    Griffiths, Thomas L; Daniels, Dylan; Austerweil, Joseph L; Tenenbaum, Joshua B

    2018-06-01

    Some events seem more random than others. For example, when tossing a coin, a sequence of eight heads in a row does not seem very random. Where do these intuitions about randomness come from? We argue that subjective randomness can be understood as the result of a statistical inference assessing the evidence that an event provides for having been produced by a random generating process. We show how this account provides a link to previous work relating randomness to algorithmic complexity, in which random events are those that cannot be described by short computer programs. Algorithmic complexity is both incomputable and too general to capture the regularities that people can recognize, but viewing randomness as statistical inference provides two paths to addressing these problems: considering regularities generated by simpler computing machines, and restricting the set of probability distributions that characterize regularity. Building on previous work exploring these different routes to a more restricted notion of randomness, we define strong quantitative models of human randomness judgments that apply not just to binary sequences - which have been the focus of much of the previous work on subjective randomness - but also to binary matrices and spatial clustering. Copyright © 2018 Elsevier Inc. All rights reserved.

  9. Random walk on random walks

    NARCIS (Netherlands)

    Hilário, M.; Hollander, den W.Th.F.; Sidoravicius, V.; Soares dos Santos, R.; Teixeira, A.

    2014-01-01

    In this paper we study a random walk in a one-dimensional dynamic random environment consisting of a collection of independent particles performing simple symmetric random walks in a Poisson equilibrium with density ¿¿(0,8). At each step the random walk performs a nearest-neighbour jump, moving to

  10. 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.

  11. 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...

  12. 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.

  13. 14 CFR 406.177 - Petition to reconsider or modify a final decision and order of the FAA decisionmaker on appeal.

    Science.gov (United States)

    2010-01-01

    ... decision and order of the FAA decisionmaker on appeal. 406.177 Section 406.177 Aeronautics and Space... INVESTIGATIONS, ENFORCEMENT, AND ADMINISTRATIVE REVIEW Rules of Practice in FAA Space Transportation Adjudications § 406.177 Petition to reconsider or modify a final decision and order of the FAA decisionmaker on...

  14. 14 CFR 13.234 - Petition to reconsider or modify a final decision and order of the FAA decisionmaker on appeal.

    Science.gov (United States)

    2010-01-01

    ... decision and order of the FAA decisionmaker on appeal. 13.234 Section 13.234 Aeronautics and Space FEDERAL... PROCEDURES Rules of Practice in FAA Civil Penalty Actions § 13.234 Petition to reconsider or modify a final decision and order of the FAA decisionmaker on appeal. (a) General. Any party may petition the FAA...

  15. 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...

  16. 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

  17. Random magnetism

    International Nuclear Information System (INIS)

    Tahir-Kheli, R.A.

    1975-01-01

    A few simple problems relating to random magnetic systems are presented. Translational symmetry, only on the macroscopic scale, is assumed for these systems. A random set of parameters, on the microscopic scale, for the various regions of these systems is also assumed. A probability distribution for randomness is obeyed. Knowledge of the form of these probability distributions, is assumed in all cases [pt

  18. 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...

  19. ‘Cut in two’, Part 2: Reconsidering the redaction of Q 12:42−46

    Directory of Open Access Journals (Sweden)

    Llewellyn Howes

    2015-06-01

    Full Text Available In his influential 1987 monograph, Kloppenborg identified three layers in the Sayings Gospel Q: the ‘formative stratum’ (or Q¹, the ‘main redaction’ (or Q², and the ‘final recension’ (or Q³. He ascribed the cluster of sayings in Q 12:39–59 to the main redaction. Within this cluster appears the parable of the loyal and wise slave (Q 12:42–46. In my view, some portions of this parable actually originate with the formative stratum. The aim of the current article is to reconsider the redactional make-up of this parable by appealing to Kloppenborg’s own criteria for distinguishing between Q1 and Q2, including those of ‘characteristic forms’, ‘characteristic motifs’ and ‘implied audience’.

  20. Reconsidering Evaluation Criteria for Scientific Adequacy in Health Care Research: An Integrative Framework of Quantitative and Qualitative Criteria

    Directory of Open Access Journals (Sweden)

    Hiroaki Miyata PhD

    2009-03-01

    Full Text Available It is important to reconsider evaluation criteria regarding scientific adequacy in health care research. In this article the authors review the four pairs of quantitative/qualitative paradigms. They discuss the use of evaluation criteria based on a pragmatic perspective after examining the epistemological issues behind the criteria. Validity/credibility is concerned with research framework, whereas reliability/dependability refers to the range of stability in observations, objectivity/ confirmability reflects influences between observers and subjects, and generalizability/transferability has epistemological differences in the way findings are applied. Qualitative studies should not always choose qualitative paradigms, and vice versa. If stability can be assumed to some extent in a qualitative study, it is better to use a quantitative paradigm. Regardless of whether it is quantitative or qualitative research, it is important to recognize the four epistemological axes.

  1. Randomized random walk on a random walk

    International Nuclear Information System (INIS)

    Lee, P.A.

    1983-06-01

    This paper discusses generalizations of the model introduced by Kehr and Kunter of the random walk of a particle on a one-dimensional chain which in turn has been constructed by a random walk procedure. The superimposed random walk is randomised in time according to the occurrences of a stochastic point process. The probability of finding the particle in a particular position at a certain instant is obtained explicitly in the transform domain. It is found that the asymptotic behaviour for large time of the mean-square displacement of the particle depends critically on the assumed structure of the basic random walk, giving a diffusion-like term for an asymmetric walk or a square root law if the walk is symmetric. Many results are obtained in closed form for the Poisson process case, and these agree with those given previously by Kehr and Kunter. (author)

  2. Random number generation and creativity.

    Science.gov (United States)

    Bains, William

    2008-01-01

    A previous paper suggested that humans can generate genuinely random numbers. I tested this hypothesis by repeating the experiment with a larger number of highly numerate subjects, asking them to call out a sequence of digits selected from 0 through 9. The resulting sequences were substantially non-random, with an excess of sequential pairs of numbers and a deficit of repeats of the same number, in line with previous literature. However, the previous literature suggests that humans generate random numbers with substantial conscious effort, and distractions which reduce that effort reduce the randomness of the numbers. I reduced my subjects' concentration by asking them to call out in another language, and with alcohol - neither affected the randomness of their responses. This suggests that the ability to generate random numbers is a 'basic' function of the human mind, even if those numbers are not mathematically 'random'. I hypothesise that there is a 'creativity' mechanism, while not truly random, provides novelty as part of the mind's defence against closed programming loops, and that testing for the effects seen here in people more or less familiar with numbers or with spontaneous creativity could identify more features of this process. It is possible that training to perform better at simple random generation tasks could help to increase creativity, through training people to reduce the conscious mind's suppression of the 'spontaneous', creative response to new questions.

  3. The sequence of spacers between the consensus sequences modulates the strength of procaryotic promoters

    DEFF Research Database (Denmark)

    Jensen, Peter Ruhdal; Hammer, Karin

    1998-01-01

    A library of synthetic promoters for Lactococcus lactis was constructed, in which the known consensus sequences were kept constant while the sequences of the separating spacers were randomized. The library consists of 38 promoters which differ in strength from 0.3 relative units, and up to more t......-reactors and cell factories....

  4. 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.

  5. Shotgun protein sequencing.

    Energy Technology Data Exchange (ETDEWEB)

    Faulon, Jean-Loup Michel; Heffelfinger, Grant S.

    2009-06-01

    A novel experimental and computational technique based on multiple enzymatic digestion of a protein or protein mixture that reconstructs protein sequences from sequences of overlapping peptides is described in this SAND report. This approach, analogous to shotgun sequencing of DNA, is to be used to sequence alternative spliced proteins, to identify post-translational modifications, and to sequence genetically engineered proteins.

  6. Randomizer for High Data Rates

    Science.gov (United States)

    Garon, Howard; Sank, Victor J.

    2018-01-01

    NASA as well as a number of other space agencies now recognize that the current recommended CCSDS randomizer used for telemetry (TM) is too short. When multiple applications of the PN8 Maximal Length Sequence (MLS) are required in order to fully cover a channel access data unit (CADU), spectral problems in the form of elevated spurious discretes (spurs) appear. Originally the randomizer was called a bit transition generator (BTG) precisely because it was thought that its primary value was to insure sufficient bit transitions to allow the bit/symbol synchronizer to lock and remain locked. We, NASA, have shown that the old BTG concept is a limited view of the real value of the randomizer sequence and that the randomizer also aids in signal acquisition as well as minimizing the potential for false decoder lock. Under the guidelines we considered here there are multiple maximal length sequences under GF(2) which appear attractive in this application. Although there may be mitigating reasons why another MLS sequence could be selected, one sequence in particular possesses a combination of desired properties which offsets it from the others.

  7. Random walks in Euclidean space

    OpenAIRE

    Varjú, Péter Pál

    2012-01-01

    Consider a sequence of independent random isometries of Euclidean space with a previously fixed probability law. Apply these isometries successively to the origin and consider the sequence of random points that we obtain this way. We prove a local limit theorem under a suitable moment condition and a necessary non-degeneracy condition. Under stronger hypothesis, we prove a limit theorem on a wide range of scales: between e^(-cl^(1/4)) and l^(1/2), where l is the number of steps.

  8. Reconsidering the Rhizome: A Textual Analysis of Web Search Engines as Gatekeepers of the Internet

    Science.gov (United States)

    Hess, A.

    Critical theorists have often drawn from Deleuze and Guattari's notion of the rhizome when discussing the potential of the Internet. While the Internet may structurally appear as a rhizome, its day-to-day usage by millions via search engines precludes experiencing the random interconnectedness and potential democratizing function. Through a textual analysis of four search engines, I argue that Web searching has grown hierarchies, or "trees," that organize data in tracts of knowledge and place users in marketing niches rather than assist in the development of new knowledge.

  9. Multimodal sequence learning.

    Science.gov (United States)

    Kemény, Ferenc; Meier, Beat

    2016-02-01

    While sequence learning research models complex phenomena, previous studies have mostly focused on unimodal sequences. The goal of the current experiment is to put implicit sequence learning into a multimodal context: to test whether it can operate across different modalities. We used the Task Sequence Learning paradigm to test whether sequence learning varies across modalities, and whether participants are able to learn multimodal sequences. Our results show that implicit sequence learning is very similar regardless of the source modality. However, the presence of correlated task and response sequences was required for learning to take place. The experiment provides new evidence for implicit sequence learning of abstract conceptual representations. In general, the results suggest that correlated sequences are necessary for implicit sequence learning to occur. Moreover, they show that elements from different modalities can be automatically integrated into one unitary multimodal sequence. Copyright © 2015 Elsevier B.V. All rights reserved.

  10. 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...

  11. Chelation therapy to treat atherosclerosis, particularly in diabetes: is it time to reconsider?

    Science.gov (United States)

    Lamas, Gervasio A; Ergui, Ian

    2016-08-01

    Case reports and case series have suggested a possible beneficial effect of chelation therapy in patients with atherosclerotic disease. Small randomized trials conducted in patients with angina or peripheral artery disease, however, were not sufficiently powered to provide conclusive evidence on clinical outcomes. The Trial to Assess Chelation Therapy (TACT) was the first randomized trial adequately powered to detect the effects of chelation therapy on clinical endpoints. We discuss results and future research. Expert commentary: Chelation reduced adverse cardiovascular events in a post myocardial infarction (MI) population. Patients with diabetes demonstrated even greater benefit, with a number needed to treat of 6.5 patients to prevent a cardiac event over 5 years, with a 41% relative reduction in risk of a cardiac event (p = 0.0002). These results led to the revision of the ACC/AHA guideline recommendations for chelation therapy, changing its classification from class III to class IIb. TACT2, a replicative trial, will assess the effects of chelation therapy on cardiovascular outcomes in diabetic patients with a prior myocardial infarction. We are seeking participating sites for TACT2.

  12. Random Fields

    Science.gov (United States)

    Vanmarcke, Erik

    1983-03-01

    Random variation over space and time is one of the few attributes that might safely be predicted as characterizing almost any given complex system. Random fields or "distributed disorder systems" confront astronomers, physicists, geologists, meteorologists, biologists, and other natural scientists. They appear in the artifacts developed by electrical, mechanical, civil, and other engineers. They even underlie the processes of social and economic change. The purpose of this book is to bring together existing and new methodologies of random field theory and indicate how they can be applied to these diverse areas where a "deterministic treatment is inefficient and conventional statistics insufficient." Many new results and methods are included. After outlining the extent and characteristics of the random field approach, the book reviews the classical theory of multidimensional random processes and introduces basic probability concepts and methods in the random field context. It next gives a concise amount of the second-order analysis of homogeneous random fields, in both the space-time domain and the wave number-frequency domain. This is followed by a chapter on spectral moments and related measures of disorder and on level excursions and extremes of Gaussian and related random fields. After developing a new framework of analysis based on local averages of one-, two-, and n-dimensional processes, the book concludes with a chapter discussing ramifications in the important areas of estimation, prediction, and control. The mathematical prerequisite has been held to basic college-level calculus.

  13. Estimation of the time since death--reconsidering the re-establishment of rigor mortis.

    Science.gov (United States)

    Anders, Sven; Kunz, Michaela; Gehl, Axel; Sehner, Susanne; Raupach, Tobias; Beck-Bornholdt, Hans-Peter

    2013-01-01

    In forensic medicine, there is an undefined data background for the phenomenon of re-establishment of rigor mortis after mechanical loosening, a method used in establishing time since death in forensic casework that is thought to occur up to 8 h post-mortem. Nevertheless, the method is widely described in textbooks on forensic medicine. We examined 314 joints (elbow and knee) of 79 deceased at defined time points up to 21 h post-mortem (hpm). Data were analysed using a random intercept model. Here, we show that re-establishment occurred in 38.5% of joints at 7.5 to 19 hpm. Therefore, the maximum time span for the re-establishment of rigor mortis appears to be 2.5-fold longer than thought so far. These findings have major impact on the estimation of time since death in forensic casework.

  14. Treatment of hyperthyroidism with radioiodine: adjunctive therapy with antithyroid drugs reconsidered

    International Nuclear Information System (INIS)

    Velkeniers, B.; Vanhaelst, L.; Cytryn, R.; Jonckheer, M.H.

    1988-01-01

    To assess the value of antithyroid drugs as an adjunct to radioactive iodine for the treatment of hyperthyroidism the incidence of relapse or hypothyroidism after a mean follow-up of 51/2 years (range 2-7 years) was reviewed retrospectively for 206 patients, some treated with and others without antithyroid drugs after radioiodine therapy. Allocation to treatment group had been random, and both groups were similar in all respects except for the adjunctive treatment with antithyroid drugs. All doses of 131 I had been calculated by one physician. Compared with those who received 131 I alone, those starting on antithyroid drugs within 8 days after 131 I had a lower incidence of hypothyroidism but a higher incidence of early post-treatment recurrence or persistence of hyperthyroidism, and considerably lower incidence of remission. (author)

  15. 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.

  16. Gene Discovery through Genomic Sequencing of Brucella abortus

    OpenAIRE

    Sánchez, Daniel O.; Zandomeni, Ruben O.; Cravero, Silvio; Verdún, Ramiro E.; Pierrou, Ester; Faccio, Paula; Diaz, Gabriela; Lanzavecchia, Silvia; Agüero, Fernán; Frasch, Alberto C. C.; Andersson, Siv G. E.; Rossetti, Osvaldo L.; Grau, Oscar; Ugalde, Rodolfo A.

    2001-01-01

    Brucella abortus is the etiological agent of brucellosis, a disease that affects bovines and human. We generated DNA random sequences from the genome of B. abortus strain 2308 in order to characterize molecular targets that might be useful for developing immunological or chemotherapeutic strategies against this pathogen. The partial sequencing of 1,899 clones allowed the identification of 1,199 genomic sequence surveys (GSSs) with high homology (BLAST expect value < 10−5) to sequences deposit...

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

    Energy Technology Data Exchange (ETDEWEB)

    Huang Yanzhao [Biomolecular Physics and Modeling Group, Department of Physics, Huazhong University of Science and Technology, Wuhan 430074, Hubei (China); Li Mingfeng [Biomolecular Physics and Modeling Group, Department of Physics, Huazhong University of Science and Technology, Wuhan 430074, Hubei (China); Xiao Yi [Biomolecular Physics and Modeling Group, Department of Physics, Huazhong University of Science and Technology, Wuhan 430074, Hubei (China)]. E-mail: lmf_bill@sina.com

    2007-11-15

    Many multi-domain proteins have repetitive three-dimensional structures but nearly-random amino acid sequences. In the present paper, by using a modified recurrence plot proposed by us previously, we show that these amino acid sequences have hidden repetitions in fact. These results indicate that the repetitive domain structures are encoded by the repetitive sequences. This also gives a method to detect the repetitive domain structures directly from amino acid sequences.

  18. Male bladder outlet obstruction: Time to re-evaluate the definition and reconsider our diagnostic pathway? ICI-RS 2015.

    Science.gov (United States)

    Rademakers, Kevin; Drake, Marcus J; Gammie, Andrew; Djurhuus, Jens C; Rosier, Peter F W M; Abrams, Paul; Harding, Christopher

    2017-04-01

    The diagnosis of bladder outlet obstruction (BOO) in the male is dependent on measurements of pressure and flow made during urodynamic studies. The procedure of urodynamics and the indices used to delineate BOO are well standardized largely as a result of the work of the International Continence Society. The clinical utility of the diagnosis of BOO is however, less well defined and there are several shortcomings and gaps in the currently available medical literature. Consequently the International Consultation on Incontinence Research Society (ICI-RS) held a think tank session in 2015 entitled "Male bladder outlet obstruction: Time to re-evaluate the definition and reconsider our diagnostic pathway?" This manuscript details the discussions that took place within that think tank setting out the pros and cons of the current definition of BOO and exploring alternative clinical tests (alone or in combination) which may be useful in the future investigation of male patients with lower urinary tract symptoms. The think tank panel concluded that pressure-flow studies remain the diagnostic gold-standard for BOO although there is still a lack of high quality evidence. Newer, less invasive, investigations have shown promise in terms of diagnostic accuracy for BOO but similar criticisms can be levelled against these tests. Therefore, the think tank suggests further research with regard to these alternative indicators to determine their clinical utility. © 2017 Wiley Periodicals, Inc.

  19. Reconsidering identity: the ethnic and political dimensions of hybridity among majority and Turkish youth in Germany and England.

    Science.gov (United States)

    Faas, Daniel

    2009-06-01

    Sociological research has hitherto largely focused on majority and minority ethnic identities or citizenship identities. However, the social connections between youth are not simply ethnic dynamics but also political dynamics involving citizenship categories. This article argues that in postmodern societies, it is important to reconsider the ways we think about youth identities. Drawing upon qualitative data from a study into the political identities of majority (German and British) youth and Turkish youth, educated in two Stuttgart and two London secondary schools, the research found that fifteen-year-olds had no singular identity but hybrid ethno-national, ethno-local and national-European identities as a result of governmental policies, their schooling and community experience, social class positioning, ethnicity and migration history. In working-class educational contexts, many majority and Turkish youth privileged the ethnic dimension of hybridity whereas majority and Turkish youth in the two middle-class dominated schools emphasized the political dimension of hybridity. The article demonstrates that social class and schooling (e.g. ethos and peer cultures) have a considerable role to play in who can afford to take on the more hybridized cosmopolitan identities on offer.

  20. Environmental imperatives reconsidered: demographic crises in western North America during the medieval climatic anomaly.

    Science.gov (United States)

    Jones, T L; Brown, G M; Raab, L M; McVickar, J L; Spaulding, W G; Kennett, D J; York, A; Wlaker, P L

    1999-04-01

    Review of late Holocene paleoenvironmental and cultural sequences from four regions of western North America show striking correlations between drought and changes in subsistence, population, exchange, health, and interpersonal violence during the Medieval Climatic Anomaly (A.D. 800-1350). While ultimate causality is difficult to identify in the archaeological record, synchrony of the environmental and cultural changes and the negative character of many human responses--increased interpersonal violence, deterioration of long-distance exchange relationships, and regional abandonments--suggest widespread demographic crises caused by decreased environmental productivity. The medieval droughts occurred at a unique juncture in the demographic history of western North America when unusually large populations of both hunter-gathers and agriculturalists had evolved highly intensified economies that put them in unprecedented ecological jeopardy. Long-term patterns in the archaeological record are inconsistent with the predicted outcomes of simple adaptation or continuous economic intensification, suggesting that in this instance environmental dynamics played a major role in cultural transformations across a wide expanse of western North America among groups with diverse subsistence strategies. These events suggest that environment should not be overlooked as a potential cause of prehistoric culture change.

  1. Reconsidering the Gatekeeper Paradigm for Percutaneous Coronary Intervention in Stable Coronary Disease Management.

    Science.gov (United States)

    Schulman-Marcus, Joshua; Weintraub, William S; Boden, William E

    2017-10-15

    Major randomized clinical trials over the last decade support the role of optimal medical therapy for the initial management approach for patients with stable coronary artery disease (CAD), whereas percutaneous coronary intervention (PCI) ought to be reserved for patients with persistent symptoms despite optimal medical therapy. Likewise, several studies have continued to demonstrate the superiority of coronary artery bypass grafting surgery over PCI in many patients with extensive multivessel CAD, especially those with diabetes. Nevertheless, the decision-making paradigm for patients with stable CAD often continues to propagate the upfront use of "ad hoc PCI" and disadvantages alternative therapeutic approaches. In our editorial, we discuss how multiple systemic and interpersonal factors continue to favor early revascularization with PCI in stable patients. We discuss whether the interventional cardiologist can be an unbiased "gatekeeper" for the use of PCI or whether other physicians should also be involved with the patient in decision-making. Finally, we offer suggestions that can redefine the gatekeeper role to facilitate an evidence-based approach that embraces shared decision-making. Copyright © 2017 Elsevier Inc. All rights reserved.

  2. Nonparametric combinatorial sequence models.

    Science.gov (United States)

    Wauthier, Fabian L; Jordan, Michael I; Jojic, Nebojsa

    2011-11-01

    This work considers biological sequences that exhibit combinatorial structures in their composition: groups of positions of the aligned sequences are "linked" and covary as one unit across sequences. If multiple such groups exist, complex interactions can emerge between them. Sequences of this kind arise frequently in biology but methodologies for analyzing them are still being developed. This article presents a nonparametric prior on sequences which allows combinatorial structures to emerge and which induces a posterior distribution over factorized sequence representations. We carry out experiments on three biological sequence families which indicate that combinatorial structures are indeed present and that combinatorial sequence models can more succinctly describe them than simpler mixture models. We conclude with an application to MHC binding prediction which highlights the utility of the posterior distribution over sequence representations induced by the prior. By integrating out the posterior, our method compares favorably to leading binding predictors.

  3. Order and correlations in genomic DNA sequences. The spectral approach

    International Nuclear Information System (INIS)

    Lobzin, Vasilii V; Chechetkin, Vladimir R

    2000-01-01

    The structural analysis of genomic DNA sequences is discussed in the framework of the spectral approach, which is sufficiently universal due to the reciprocal correspondence and mutual complementarity of Fourier transform length scales. The spectral characteristics of random sequences of the same nucleotide composition possess the property of self-averaging for relatively short sequences of length M≥100-300. Comparison with the characteristics of random sequences determines the statistical significance of the structural features observed. Apart from traditional applications to the search for hidden periodicities, spectral methods are also efficient in studying mutual correlations in DNA sequences. By combining spectra for structure factors and correlation functions, not only integral correlations can be estimated but also their origin identified. Using the structural spectral entropy approach, the regularity of a sequence can be quantitatively assessed. A brief introduction to the problem is also presented and other major methods of DNA sequence analysis described. (reviews of topical problems)

  4. 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.

  5. Random Item Generation Is Affected by Age

    Science.gov (United States)

    Multani, Namita; Rudzicz, Frank; Wong, Wing Yiu Stephanie; Namasivayam, Aravind Kumar; van Lieshout, Pascal

    2016-01-01

    Purpose: Random item generation (RIG) involves central executive functioning. Measuring aspects of random sequences can therefore provide a simple method to complement other tools for cognitive assessment. We examine the extent to which RIG relates to specific measures of cognitive function, and whether those measures can be estimated using RIG…

  6. 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

  7. Random magnetism

    International Nuclear Information System (INIS)

    Tsallis, C.

    1980-03-01

    The 'ingredients' which control a phase transition in well defined system as well as in random ones (e.g. random magnetic systems) are listed and discussed within a somehow unifying perspective. Among these 'ingredients' we find the couplings and elements responsible for the cooperative phenomenon, the topological connectivity as well as possible topological incompatibilities, the influence of new degrees of freedom, the order parameter dimensionality, the ground state degeneracy and finally the 'quanticity' of the system. The general trends, though illustrated in magnetic systems, essentially hold for all phase transitions, and give a basis for connection of this area with Field theory, Theory of dynamical systems, etc. (Author) [pt

  8. Random magnetism

    International Nuclear Information System (INIS)

    Tsallis, C.

    1981-01-01

    The 'ingredients' which control a phase transition in well defined systems as well as in random ones (e.q. random magnetic systems) are listed and discussed within a somehow unifying perspective. Among these 'ingredients' the couplings and elements responsible for the cooperative phenomenon, the topological connectivity as well as possible topological incompatibilities, the influence of new degrees of freedom, the order parameter dimensionality, the ground state degeneracy and finally the 'quanticity' of the system are found. The general trends, though illustrated in magnetic systems, essentially hold for all phase transitions, and give a basis for connection of this area with Field theory, Theory of dynamical systems, etc. (Author) [pt

  9. Selective retrieval of memory and concept sequences through neuro-windows

    OpenAIRE

    Kakeya, Hideki; Okabe, Yoichi

    1999-01-01

    This letter presents a crosscorrelational associative memory model which realizes selective retrieval of pattern sequences. When hierarchically correlated sequences are memorized, sequences of the correlational centers can be defined as the concept sequences. The authors propose a modified neuro-window method which enables selective retrieval of memory sequences and concept sequences. It is also shown that the proposed model realizes capacity expansion of the memory which stores random sequen...

  10. Early Nonresponse in the Antipsychotic Treatment of Acute Mania: A Criterion for Reconsidering Treatment? Results From an Individual Patient Data Meta-Analysis.

    Science.gov (United States)

    Welten, Carlijn C M; Koeter, Maarten W J; Wohlfarth, Tamar D; Storosum, Jitschak G; van den Brink, Wim; Gispen-de Wied, Christine C; Leufkens, Hubert G M; Denys, Damiaan A J P

    2016-09-01

    To investigate whether early nonresponse to antipsychotic treatment of acute mania predicts treatment failure and, if so, to establish the best definition or criterion of an early nonresponse. Short-term efficacy studies assessing antipsychotics that were submitted to the Dutch Medicines Evaluation Board during an 11-year period as part of the marketing authorization application for the indication of acute manic episode of bipolar disorder. Pharmaceutical companies provided their raw patient data, which enabled us to perform an individual patient data meta-analysis. All double-blind, randomized, placebo-controlled trials assessing the efficacy of antipsychotics for acute manic episode of bipolar disorder were included (10 trials). All patients with data available for completer analysis (N = 1,243), symptom severity scores on the Young Mania Rating Scale (YMRS) at weeks 0, 1, and 2 and at study end point (week 3 or 4). The a priori chances of nonresponse and nonremission at study end point were 40.9% (95% CI, 38.2%-43.6%) and 65.3% (95% CI, 62.0%-68.6%), respectively. Early nonresponse in weeks 1 and 2, defined by cutoff scores ranging from a ≤ 10% to a ≤ 50% reduction in symptoms compared to baseline on the YMRS, significantly predicted nonresponse (≤ 0% symptom reduction) and nonremission (YMRS score higher than 8) in week 3. The predictive value of early nonresponse (PVnr_se) at week 1 for both nonresponse and nonremission at study end point declined linearly with increasing cutoff scores of early nonresponse; nonresponse: 76.0% (95% CI, 69.7%-82.3%) for a ≤ 10% response to 48.7% (95% CI, 45.5%-51.9%) for a ≤ 50% response; nonremission: 92.2% (95% CI, 88.3%-96.1%) for a ≤ 10% response to 76.8% (95% CI, 74.4%-79.5%) for a ≤ 50% response. A similar linear decline was observed for increasing cutoff scores of early nonresponse at week 2 for nonresponse, but not for nonremission at end point: nonresponse 90.3% (95% CI, 84.6%-96.0%) for a ≤ 10% response

  11. Long sequence correlation coprocessor

    Science.gov (United States)

    Gage, Douglas W.

    1994-09-01

    A long sequence correlation coprocessor (LSCC) accelerates the bitwise correlation of arbitrarily long digital sequences by calculating in parallel the correlation score for 16, for example, adjacent bit alignments between two binary sequences. The LSCC integrated circuit is incorporated into a computer system with memory storage buffers and a separate general purpose computer processor which serves as its controller. Each of the LSCC's set of sequential counters simultaneously tallies a separate correlation coefficient. During each LSCC clock cycle, computer enable logic associated with each counter compares one bit of a first sequence with one bit of a second sequence to increment the counter if the bits are the same. A shift register assures that the same bit of the first sequence is simultaneously compared to different bits of the second sequence to simultaneously calculate the correlation coefficient by the different counters to represent different alignments of the two sequences.

  12. 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.

  13. 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...

  14. 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.

  15. 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....

  16. All-optical fast random number generator.

    Science.gov (United States)

    Li, Pu; Wang, Yun-Cai; Zhang, Jian-Zhong

    2010-09-13

    We propose a scheme of all-optical random number generator (RNG), which consists of an ultra-wide bandwidth (UWB) chaotic laser, an all-optical sampler and an all-optical comparator. Free from the electric-device bandwidth, it can generate 10Gbit/s random numbers in our simulation. The high-speed bit sequences can pass standard statistical tests for randomness after all-optical exclusive-or (XOR) operation.

  17. Quality pseudo-random number generator

    International Nuclear Information System (INIS)

    Tarasiuk, J.

    1996-01-01

    The pseudo-random number generator (RNG) was written to match needs of nuclear and high-energy physics computation which in some cases require very long and independent random number sequences. In this random number generator the repetition period is about 10 36 what should be sufficient for all computers in the world. In this article the test results of RNG correlation, speed and identity of computations for PC, Sun4 and VAX computer tests are presented

  18. 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.

  19. Application of quasi-random numbers for simulation

    International Nuclear Information System (INIS)

    Kazachenko, O.N.; Takhtamyshev, G.G.

    1985-01-01

    Application of the Monte-Carlo method for multidimensional integration is discussed. The main goal is to check the statement that the application of quasi-random numbers instead of regular pseudo-random numbers provides more rapid convergency. The Sobol, Richtmayer and Halton algorithms of quasi-random sequences are described. Over 50 tests to compare these quasi-random numbers as well as pseudo-random numbers were fulfilled. In all cases quasi-random numbers have clearly demonstrated a more rapid convergency as compared with pseudo-random ones. Positive test results on quasi-random trend in Monte-Carlo method seem very promising

  20. Random Decrement

    DEFF Research Database (Denmark)

    Asmussen, J.C.; Ibrahim, S.R.; Brincker, Rune

    Abstraet Thispaper demansirates how to use the Random Decrement (RD) technique for identification o flinear structures subjected to ambient excitation. The theory behind the technique will be presented and guidelines how to choose the different variables will be given. This is done by introducing...

  1. Random Decrement

    DEFF Research Database (Denmark)

    Asmussen, J. C.; Ibrahim, S. R.; Brincker, Rune

    This paper demonstrates how to use the Random Decrement (RD) technique for identification of linear structures subjected to ambient excitation. The theory behind the technique will be presented and guidelines how to choose the different variables will be given. This is done by introducing a new...

  2. Random Decrement

    DEFF Research Database (Denmark)

    Asmussen, J. C.; Ibrahim, R.; Brincker, Rune

    1998-01-01

    This paper demonstrates how to use the Random Decrement (RD) technique for identification of linear structures subjected to ambient excitation. The theory behind the technique will be presented and guidelines how to choose the different variables will be given. This is done by introducing a new...

  3. Random dynamics

    International Nuclear Information System (INIS)

    Bennett, D.L.; Brene, N.; Nielsen, H.B.

    1986-06-01

    The goal of random dynamics is the derivation of the laws of Nature as we know them (standard model) from inessential assumptions. The inessential assumptions made here are expressed as sets of general models at extremely high energies: gauge glass and spacetime foam. Both sets of models lead tentatively to the standard model. (orig.)

  4. Random dynamics

    International Nuclear Information System (INIS)

    Bennett, D.L.

    1987-01-01

    The goal of random dynamics is the derivation of the laws of Nature as we know them (standard model) from inessential assumptions. The inessential assumptions made here are expressed as sets of general models at extremely high energies: Gauge glass and spacetime foam. Both sets of models lead tentatively to the standard model. (orig.)

  5. Random Dynamics

    Science.gov (United States)

    Bennett, D. L.; Brene, N.; Nielsen, H. B.

    1987-01-01

    The goal of random dynamics is the derivation of the laws of Nature as we know them (standard model) from inessential assumptions. The inessential assumptions made here are expressed as sets of general models at extremely high energies: gauge glass and spacetime foam. Both sets of models lead tentatively to the standard model.

  6. Basic randomness of nature and ether-drift experiments

    International Nuclear Information System (INIS)

    Consoli, M.; Pluchino, A.; Rapisarda, A.

    2011-01-01

    Highlights: ► We re-consider the idea of a basic randomness of nature. ► We adopt Stochastic Electro Dynamics as a heuristic model. ► We represent the vacuum as a form of turbulent ether. ► This picture can be tested with forthcoming ether-drift experiments. - Abstract: We re-consider the idea that quantum fluctuations might reflect the existence of an ‘objective randomness’, i.e. a basic property of the vacuum state which is independent of any experimental accuracy of the observations or limited knowledge of initial conditions. Besides being responsible for the observed quantum behavior, this might introduce a weak, residual form of ‘noise’ which is intrinsic to natural phenomena and could be important for the emergence of complexity at higher physical levels. By adopting Stochastic Electro Dynamics as a heuristic model, we are driven to a picture of the vacuum as a form of highly turbulent ether, which is deep-rooted into the basic foundational aspects of both quantum physics and relativity, and to search for experimental tests of this scenario. An analysis of the most precise ether-drift experiments, operating both at room temperature and in the cryogenic regime, shows that, at present, there is some ambiguity in the interpretation of the data. In fact the average amplitude of the signal has precisely the magnitude expected, in a ‘Lorentzian’ form of relativity, from an underlying stochastic ether and, as such, might not be a spurious instrumental effect. This puzzle, however, should be solved in a next future with the use of new cryogenically cooled optical resonators whose stability should improve by about two orders of magnitude. In these new experimental conditions, the persistence of the present amplitude would represent a clean evidence for the type of random vacuum we are envisaging.

  7. Sequence complexity and work extraction

    International Nuclear Information System (INIS)

    Merhav, Neri

    2015-01-01

    We consider a simplified version of a solvable model by Mandal and Jarzynski, which constructively demonstrates the interplay between work extraction and the increase of the Shannon entropy of an information reservoir which is in contact with a physical system. We extend Mandal and Jarzynski’s main findings in several directions: first, we allow sequences of correlated bits rather than just independent bits. Secondly, at least for the case of binary information, we show that, in fact, the Shannon entropy is only one measure of complexity of the information that must increase in order for work to be extracted. The extracted work can also be upper bounded in terms of the increase in other quantities that measure complexity, like the predictability of future bits from past ones. Third, we provide an extension to the case of non-binary information (i.e. a larger alphabet), and finally, we extend the scope to the case where the incoming bits (before the interaction) form an individual sequence, rather than a random one. In this case, the entropy before the interaction can be replaced by the Lempel–Ziv (LZ) complexity of the incoming sequence, a fact that gives rise to an entropic meaning of the LZ complexity, not only in information theory, but also in physics. (paper)

  8. Ademe et Vous. Research Newsletter No. 11, July 2015. Urban planning and climate change: intertwined issues and practices we should reconsider

    International Nuclear Information System (INIS)

    Varet, Anne; Guignard, Stephanie

    2015-07-01

    This Research Newsletter, the first in a series of three dedicated to climate change, focuses on the climate change research undertaken with ADEME's support and its relation to urban management, and the results obtained. Content: - urban planning and climate change: intertwined issues and practices we should reconsider; - significant results: climate change adaptation and urban planning: what sorts of challenges should this obligation meet? - meeting: Jacques Comby, climatologist and president of the university Jean Moulin Lyon III, and Emmanuel Acchiardi, deputy director of Ademe's sustainable cities and regions department

  9. 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 ...

  10. Chaotic generation of PN sequences : a VLSI implementation

    NARCIS (Netherlands)

    Dornbusch, A.; Pineda de Gyvez, J.

    1999-01-01

    Generation of repeatable pseudo-random sequences with chaotic analog electronics is not feasible using standard circuit topologies. Component variation caused by imperfect fabrication causes the same divergence of output sequences as does varying initial conditions. By quantizing the output of a

  11. Complete genome sequences of six measles virus strains

    NARCIS (Netherlands)

    Phan, M.V.T. (My V.T.); C.M.E. Schapendonk (Claudia); B.B. Oude Munnink (Bas B.); M.P.G. Koopmans D.V.M. (Marion); R.L. de Swart (Rik); Cotten, M. (Matthew)

    2018-01-01

    textabstractGenetic characterization of wild-type measles virus (MV) strains is a critical component of measles surveillance and molecular epidemiology. We have obtained complete genome sequences of six MV strains belonging to different genotypes, using random-primed next generation sequencing.

  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. 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

  14. 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 ...

  15. 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.

  16. 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.

  17. Simulation of a directed random-walk model: the effect of pseudo-random-number correlations

    OpenAIRE

    Shchur, L. N.; Heringa, J. R.; Blöte, H. W. J.

    1996-01-01

    We investigate the mechanism that leads to systematic deviations in cluster Monte Carlo simulations when correlated pseudo-random numbers are used. We present a simple model, which enables an analysis of the effects due to correlations in several types of pseudo-random-number sequences. This model provides qualitative understanding of the bias mechanism in a class of cluster Monte Carlo algorithms.

  18. Experimental Rugged Fitness Landscape in Protein Sequence Space

    OpenAIRE

    HAYASHI, Yuuki; 相田, 拓洋; TOYOTA, Hitoshi; 伏見, 譲; URABE, Itaru; YOMO, Tetsuya

    2006-01-01

    The fitness landscape in sequence space determines the process of biomolecular evolution. To plot the fitness landscape of protein function, we carried out in vitro molecular evolution beginning with a defective fd phage carrying a random polypeptide of 139 amino acids in place of the g3p minor coat protein D2 domain, which is essential for phage infection. After 20 cycles of random substitution at sites 12-130 of the initial random polypeptide and selection for infectivity, the selected phag...

  19. CMOS Compressed Imaging by Random Convolution

    OpenAIRE

    Jacques, Laurent; Vandergheynst, Pierre; Bibet, Alexandre; Majidzadeh, Vahid; Schmid, Alexandre; Leblebici, Yusuf

    2009-01-01

    We present a CMOS imager with built-in capability to perform Compressed Sensing. The adopted sensing strategy is the random Convolution due to J. Romberg. It is achieved by a shift register set in a pseudo-random configuration. It acts as a convolutive filter on the imager focal plane, the current issued from each CMOS pixel undergoing a pseudo-random redirection controlled by each component of the filter sequence. A pseudo-random triggering of the ADC reading is finally applied to comp...

  20. 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.

  1. Electric dipole moments reconsidered

    International Nuclear Information System (INIS)

    Rupertsberger, H.

    1989-01-01

    The electric dipole moments of elementary particles, atoms, molecules and their connection to the electric susceptibility are discussed for stationary states. Assuming rotational invariance it is emphasized that for such states only in the case of a parity and time reversal violating interaction the considered particles can obtain a nonvanishing expectation value for the electric dipole moment. 1 fig., 13 refs. (Author)

  2. 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…

  3. 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...

  4. Reconsidering Formative Measurement

    Science.gov (United States)

    Howell, Roy D.; Breivik, Einar; Wilcox, James B.

    2007-01-01

    The relationship between observable responses and the latent constructs they are purported to measure has received considerable attention recently, with particular focus on what has become known as formative measurement. This alternative to reflective measurement in the area of theory-testing research is examined in the context of the potential…

  5. 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 d...

  6. Reconsidering formative measurement.

    Science.gov (United States)

    Howell, Roy D; Breivik, Einar; Wilcox, James B

    2007-06-01

    The relationship between observable responses and the latent constructs they are purported to measure has received considerable attention recently, with particular focus on what has become known as formative measurement. This alternative to reflective measurement in the area of theory-testing research is examined in the context of the potential for interpretational confounding and a construct's ability to function as a point variable within a larger model. Although these issues have been addressed in the traditional reflective measurement context, the authors suggest that they are particularly relevant in evaluating formative measurement models. On the basis of this analysis, the authors conclude that formative measurement is not an equally attractive alternative to reflective measurement and that whenever possible, in developing new measures or choosing among alternative existing measures, researchers should opt for reflective measurement. In addition, the authors provide guidelines for researchers dealing with existing formative measures. Copyright 2007 APA, all rights reserved.

  7. 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 .

  8. Approaching archetypes: reconsidering innateness.

    Science.gov (United States)

    Goodwyn, Erik

    2010-09-01

    The question of innateness has hounded Jungian psychology since Jung originally postulated the archetype as an a priori structure within the psyche. During his life and after his death he was continually accused of Lamarckianism and criticized for his theory that the archetypes existed as prior structures. More recently, with the advent of genetic research and the human genome project, the idea that psychological structures can be innate has come under even harsher criticism even within Jungian thought. There appears to be a growing consensus that Jung's idea of innate psychological structures was misguided, and that perhaps the archetype-as-such should be abandoned for more developmental and 'emergent' theories of the psyche. The purpose of this essay is to question this conclusion, and introduce some literature on psychological innateness that appears relevant to this discussion. © 2010, The Society of Analytical Psychology.

  9. 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...... area. But, so far, the success seems only to be related to informal learning through just-in-time and just-in-place short courses available on the Internet. In this article, I will focus on the development of virtual universities and discuss some reasons for the lack of success.  ...

  10. Reconsidering Written Language

    Directory of Open Access Journals (Sweden)

    Gopal P. Sarma

    2015-07-01

    Full Text Available A number of elite thinkers in Europe during the 16th and 17th centuries pursued an agenda which historian Paolo Rossi calls the “quest for a universal language,” a quest which was deeply interwoven with the emergence of the scientific method. From a modern perspective, one of the many surprising aspects of these efforts is that they relied on a diverse array of memorization techniques as foundational elements. In the case of Leibniz’s universal calculus, the ultimate vision was to create a pictorial language that could be learned by anyone in a matter of weeks and which would contain within it a symbolic representation of all domains of contemporary thought, ranging from the natural sciences, to theology, to law. In this brief article, I explore why this agenda might have been appealing to thinkers of this era by examining ancient and modern memory feats. As a thought experiment, I suggest that a society built entirely upon memorization might be less limited than we might otherwise imagine, and furthermore, that cultural norms discouraging the use of written language might have had implications for the development of scientific methodology. Viewed in this light, the efforts of Leibniz and others seem significantly less surprising. I close with some general observations about cross-cultural origins of scientific thought.

  11. Utility franchises reconsidered

    Energy Technology Data Exchange (ETDEWEB)

    Weidner, B.

    1981-11-01

    It is easier to obtain a public utility franchise than one for a fast food store because companies like Burger King value the profit share and control available with a franchise arrangement. The investor-owned utilities (IOUs) in Chicago and elsewhere gets little financial or regulatory benefit, although they do have an alternative because the franchise can be taken over by the city with a one-year notice. As IOUs evolved, the annual franchise fee has been incorporated into the rate in a move that taxes ratepayers and maximizes profits. Cities that found franchising unsatisfactory are looking for ways to terminate the franchise and finance a takeover, but limited-term and indeterminate franchises may offer a better mechanism when public needs and utility aims diverge. A directory lists franchised utilities by state and comments on their legal status. (DCK)

  12. Military Deception Reconsidered

    National Research Council Canada - National Science Library

    Martin, Charmaine L

    2008-01-01

    ...: focus, integration, timeliness, security, objective, and centralized control. However, I propose that operational advantage, consisting of surprise, information advantage and security, are essential elements of a successful military deception...

  13. Reconsidering Emotion Dysregulation.

    Science.gov (United States)

    D'Agostino, Alessandra; Covanti, Serena; Rossi Monti, Mario; Starcevic, Vladan

    2017-12-01

    This article aims to review the concept of emotion dysregulation, focusing on issues related to its definition, meanings and role in psychiatric disorders. Articles on emotion dysregulation published until May 2016 were identified through electronic database searches. Although there is no agreement about the definition of emotion dysregulation, the following five overlapping, not mutually exclusive dimensions of emotion dysregulation were identified: decreased emotional awareness, inadequate emotional reactivity, intense experience and expression of emotions, emotional rigidity and cognitive reappraisal difficulty. These dimensions characterise a number of psychiatric disorders in various proportions, with borderline personality disorder and eating disorders seemingly more affected than other conditions. The present review contributes to the literature by identifying the key components of emotion dysregulation and by showing how these permeate various forms of psychopathology. It also makes suggestions for improving research endeavours. Better understanding of the various dimensions of emotion dysregulation will have implications for clinical practice. Future research needs to address emotion dysregulation in all its multifaceted complexity so that it becomes clearer what the concept encompasses.

  14. Reconsidering solar grid parity

    International Nuclear Information System (INIS)

    Yang, C.-J.

    2010-01-01

    Grid parity-reducing the cost of solar energy to be competitive with conventional grid-supplied electricity-has long been hailed as the tipping point for solar dominance in the energy mix. Such expectations are likely to be overly optimistic. A realistic examination of grid parity suggests that the cost-effectiveness of distributed photovoltaic (PV) systems may be further away than many are hoping for. Furthermore, cost-effectiveness may not guarantee commercial competitiveness. Solar hot water technology is currently far more cost-effective than photovoltaic technology and has already reached grid parity in many places. Nevertheless, the market penetration of solar water heaters remains limited for reasons including unfamiliarity with the technologies and high upfront costs. These same barriers will likely hinder the adoption of distributed solar photovoltaic systems as well. The rapid growth in PV deployment in recent years is largely policy-driven and such rapid growth would not be sustainable unless governments continue to expand financial incentives and policy mandates, as well as address regulatory and market barriers.

  15. Climate science reconsidered

    OpenAIRE

    Rapley, C.; De Meyer, K.

    2014-01-01

    There is a gap between the current role of the climate science community and the needs of society. Closing this gap represents a necessary but insufficient step towards improved public discourse and more constructive policy formulation on climate change.

  16. Symbol Formation Reconsidered

    DEFF Research Database (Denmark)

    Wagoner, Brady

    2013-01-01

    them vis-à-vis other research at Clark and in American psychology more generally. The second two articles analyse Werner and Kaplan’s notions of ‘distancing’ and ‘physiognomic metaphor’, showing their roots in naturphilosophie and comparing them with contemporary theories. The last four articles apply......Werner and Kaplan’s Symbol formation was published 50 years ago but its insights have yet to be adequately explored by psychology and other social sciences. This special issue aims to revisit this seminal work in search of concepts to work on key issues facing us today. This introductory article...... begins with a brief outline and contextualization of the book as well as of the articles that this special issue comprises. The first two articles were written by contributors who were part of the Werner era at Clark University. They explore the key concepts of the organismic and development, and situate...

  17. 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.

  18. Reconsidering the unreliable narrator

    DEFF Research Database (Denmark)

    Hansen, Per Krogh

    2007-01-01

    to the position of A. Nünning. In the final section, a four-category taxonomy for the different textual strategies that establishes unreliable narration is suggested. The headlines for the taxonomy are intranarrational unreliability, internarrational unreliability, intertextual unreliability, and extratextual...

  19. Serious reactor accidents reconsidered

    International Nuclear Information System (INIS)

    1987-12-01

    The chance is determined for damage of the reactor core and that sequel events will cause excursion of radioactive materials into the environment. The gravity of such an accident is expressed by the source term. It appears that the chance for such an accident varies with the source term. In general it is valid that how larger the source term how smaller the chance is for it and vice versa. The chance for excursion is related to two complexes of events: serious damage (meltdown) of the reactor core, and the escape of the liberated radionuclides into the environment. The results are an order of magnitude consideration of the relation between the extent of the source term and the chance for it. From the spectrum of possible source terms three representative ones have been chosen: a large, a medium and a relative small source term. This choice is in accordance with international considerations. The hearth of this study is the estimation of the chance for occurrence of the three chosen source terms for new light-water reactors. refs.; figs.; tabs

  20. 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.

  1. Water Reuse Reconsidered

    Science.gov (United States)

    Environmental Science and Technology, 1975

    1975-01-01

    The Second National Conference on Complete WateReuse stressed better planning, management, and use of water. The sessions covered: water reuse and its problems; water's interface with air and land, and modification of these interactions by the imposition of energy; and heavy metals in the environment and methods for their removal. (BT)

  2. Reconsidering Division Cavalry Squadrons

    Science.gov (United States)

    2017-05-25

    starts with acknowledgement of relevant literature. The topic’s historiography, which has enjoyed modest academic and professional attention since its...August 1992): 6-11; for an example academic monograph see Peter Kindsvattor, “The Army-of Excellence Divisional Cavalry Squadron—A Doctrinal Step...Reconnaissance and Security Capability,” 16-1 Land Power Essay : Institute of Land Warfare Publication, Association of the United States Army, June 2016, 2-3

  3. Professional negligence reconsidered

    OpenAIRE

    DeVries, Ubaldus R M Th

    1996-01-01

    This thesis examines the concept of professional negligence. In doing so, it aims to find the distinguishing factors that characterize professional negligence as against other types of negligence. It seeks to emphasize the functions, duties and activities of professional people, rather than any examination of their status. The thesis demonstrates that this concept is based on a "broadspectrum" duty of care with specific obligations, particular to professional conduct. ...

  4. 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....

  5. Simulating efficiently the evolution of DNA sequences.

    Science.gov (United States)

    Schöniger, M; von Haeseler, A

    1995-02-01

    Two menu-driven FORTRAN programs are described that simulate the evolution of DNA sequences in accordance with a user-specified model. This general stochastic model allows for an arbitrary stationary nucleotide composition and any transition-transversion bias during the process of base substitution. In addition, the user may define any hypothetical model tree according to which a family of sequences evolves. The programs suggest the computationally most inexpensive approach to generate nucleotide substitutions. Either reproducible or non-repeatable simulations, depending on the method of initializing the pseudo-random number generator, can be performed. The corresponding options are offered by the interface menu.

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

    Indian Academy of Sciences (India)

    We analyse the problem with multiple values of initial conditions and perform statistical hypothesis testing for differences in means to determine the minimum ... the datasets showed a significant main effect (F3,196 = 77.04, P < 0.001). Post hoc.

  7. Sequences for Student Investigation

    Science.gov (United States)

    Barton, Jeffrey; Feil, David; Lartigue, David; Mullins, Bernadette

    2004-01-01

    We describe two classes of sequences that give rise to accessible problems for undergraduate research. These problems may be understood with virtually no prerequisites and are well suited for computer-aided investigation. The first sequence is a variation of one introduced by Stephen Wolfram in connection with his study of cellular automata. The…

  8. Sequence History Update Tool

    Science.gov (United States)

    Khanampompan, Teerapat; Gladden, Roy; Fisher, Forest; DelGuercio, Chris

    2008-01-01

    The Sequence History Update Tool performs Web-based sequence statistics archiving for Mars Reconnaissance Orbiter (MRO). Using a single UNIX command, the software takes advantage of sequencing conventions to automatically extract the needed statistics from multiple files. This information is then used to populate a PHP database, which is then seamlessly formatted into a dynamic Web page. This tool replaces a previous tedious and error-prone process of manually editing HTML code to construct a Web-based table. Because the tool manages all of the statistics gathering and file delivery to and from multiple data sources spread across multiple servers, there is also a considerable time and effort savings. With the use of The Sequence History Update Tool what previously took minutes is now done in less than 30 seconds, and now provides a more accurate archival record of the sequence commanding for MRO.

  9. The MIXMAX random number generator

    Science.gov (United States)

    Savvidy, Konstantin G.

    2015-11-01

    In this paper, we study the randomness properties of unimodular matrix random number generators. Under well-known conditions, these discrete-time dynamical systems have the highly desirable K-mixing properties which guarantee high quality random numbers. It is found that some widely used random number generators have poor Kolmogorov entropy and consequently fail in empirical tests of randomness. These tests show that the lowest acceptable value of the Kolmogorov entropy is around 50. Next, we provide a solution to the problem of determining the maximal period of unimodular matrix generators of pseudo-random numbers. We formulate the necessary and sufficient condition to attain the maximum period and present a family of specific generators in the MIXMAX family with superior performance and excellent statistical properties. Finally, we construct three efficient algorithms for operations with the MIXMAX matrix which is a multi-dimensional generalization of the famous cat-map. First, allowing to compute the multiplication by the MIXMAX matrix with O(N) operations. Second, to recursively compute its characteristic polynomial with O(N2) operations, and third, to apply skips of large number of steps S to the sequence in O(N2 log(S)) operations.

  10. 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.

  11. 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.

  12. The Colliding Beams Sequencer

    International Nuclear Information System (INIS)

    Johnson, D.E.; Johnson, R.P.

    1989-01-01

    The Colliding Beam Sequencer (CBS) is a computer program used to operate the pbar-p Collider by synchronizing the applications programs and simulating the activities of the accelerator operators during filling and storage. The Sequencer acts as a meta-program, running otherwise stand alone applications programs, to do the set-up, beam transfers, acceleration, low beta turn on, and diagnostics for the transfers and storage. The Sequencer and its operational performance will be described along with its special features which include a periodic scheduler and command logger. 14 refs., 3 figs

  13. Phylogenetic Trees From Sequences

    Science.gov (United States)

    Ryvkin, Paul; Wang, Li-San

    In this chapter, we review important concepts and approaches for phylogeny reconstruction from sequence data.We first cover some basic definitions and properties of phylogenetics, and briefly explain how scientists model sequence evolution and measure sequence divergence. We then discuss three major approaches for phylogenetic reconstruction: distance-based phylogenetic reconstruction, maximum parsimony, and maximum likelihood. In the third part of the chapter, we review how multiple phylogenies are compared by consensus methods and how to assess confidence using bootstrapping. At the end of the chapter are two sections that list popular software packages and additional reading.

  14. Multiple sequence alignment accuracy and phylogenetic inference.

    Science.gov (United States)

    Ogden, T Heath; Rosenberg, Michael S

    2006-04-01

    Phylogenies are often thought to be more dependent upon the specifics of the sequence alignment rather than on the method of reconstruction. Simulation of sequences containing insertion and deletion events was performed in order to determine the role that alignment accuracy plays during phylogenetic inference. Data sets were simulated for pectinate, balanced, and random tree shapes under different conditions (ultrametric equal branch length, ultrametric random branch length, nonultrametric random branch length). Comparisons between hypothesized alignments and true alignments enabled determination of two measures of alignment accuracy, that of the total data set and that of individual branches. In general, our results indicate that as alignment error increases, topological accuracy decreases. This trend was much more pronounced for data sets derived from more pectinate topologies. In contrast, for balanced, ultrametric, equal branch length tree shapes, alignment inaccuracy had little average effect on tree reconstruction. These conclusions are based on average trends of many analyses under different conditions, and any one specific analysis, independent of the alignment accuracy, may recover very accurate or inaccurate topologies. Maximum likelihood and Bayesian, in general, outperformed neighbor joining and maximum parsimony in terms of tree reconstruction accuracy. Results also indicated that as the length of the branch and of the neighboring branches increase, alignment accuracy decreases, and the length of the neighboring branches is the major factor in topological accuracy. Thus, multiple-sequence alignment can be an important factor in downstream effects on topological reconstruction.

  15. Random pulse generator

    International Nuclear Information System (INIS)

    Guo Ya'nan; Jin Dapeng; Zhao Dixin; Liu Zhen'an; Qiao Qiao; Chinese Academy of Sciences, Beijing

    2007-01-01

    Due to the randomness of radioactive decay and nuclear reaction, the signals from detectors are random in time. But normal pulse generator generates periodical pulses. To measure the performances of nuclear electronic devices under random inputs, a random generator is necessary. Types of random pulse generator are reviewed, 2 digital random pulse generators are introduced. (authors)

  16. Detecting change in stochastic sound sequences.

    Directory of Open Access Journals (Sweden)

    Benjamin Skerritt-Davis

    2018-05-01

    Full Text Available Our ability to parse our acoustic environment relies on the brain's capacity to extract statistical regularities from surrounding sounds. Previous work in regularity extraction has predominantly focused on the brain's sensitivity to predictable patterns in sound sequences. However, natural sound environments are rarely completely predictable, often containing some level of randomness, yet the brain is able to effectively interpret its surroundings by extracting useful information from stochastic sounds. It has been previously shown that the brain is sensitive to the marginal lower-order statistics of sound sequences (i.e., mean and variance. In this work, we investigate the brain's sensitivity to higher-order statistics describing temporal dependencies between sound events through a series of change detection experiments, where listeners are asked to detect changes in randomness in the pitch of tone sequences. Behavioral data indicate listeners collect statistical estimates to process incoming sounds, and a perceptual model based on Bayesian inference shows a capacity in the brain to track higher-order statistics. Further analysis of individual subjects' behavior indicates an important role of perceptual constraints in listeners' ability to track these sensory statistics with high fidelity. In addition, the inference model facilitates analysis of neural electroencephalography (EEG responses, anchoring the analysis relative to the statistics of each stochastic stimulus. This reveals both a deviance response and a change-related disruption in phase of the stimulus-locked response that follow the higher-order statistics. These results shed light on the brain's ability to process stochastic sound sequences.

  17. 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...

  18. Yeast genome sequencing:

    DEFF Research Database (Denmark)

    Piskur, Jure; Langkjær, Rikke Breinhold

    2004-01-01

    For decades, unicellular yeasts have been general models to help understand the eukaryotic cell and also our own biology. Recently, over a dozen yeast genomes have been sequenced, providing the basis to resolve several complex biological questions. Analysis of the novel sequence data has shown...... of closely related species helps in gene annotation and to answer how many genes there really are within the genomes. Analysis of non-coding regions among closely related species has provided an example of how to determine novel gene regulatory sequences, which were previously difficult to analyse because...... they are short and degenerate and occupy different positions. Comparative genomics helps to understand the origin of yeasts and points out crucial molecular events in yeast evolutionary history, such as whole-genome duplication and horizontal gene transfer(s). In addition, the accumulating sequence data provide...

  19. Dynamic Sequence Assignment.

    Science.gov (United States)

    1983-12-01

    D-136 548 DYNAMIIC SEQUENCE ASSIGNMENT(U) ADVANCED INFORMATION AND 1/2 DECISION SYSTEMS MOUNTAIN YIELW CA C A 0 REILLY ET AL. UNCLSSIIED DEC 83 AI/DS...I ADVANCED INFORMATION & DECISION SYSTEMS Mountain View. CA 94040 84 u ,53 V,..’. Unclassified _____ SCURITY CLASSIFICATION OF THIS PAGE REPORT...reviews some important heuristic algorithms developed for fas- ter solution of the sequence assignment problem. 3.1. DINAMIC MOGRAMUNIG FORMULATION FOR

  20. 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.

  1. General LTE Sequence

    OpenAIRE

    Billal, Masum

    2015-01-01

    In this paper,we have characterized sequences which maintain the same property described in Lifting the Exponent Lemma. Lifting the Exponent Lemma is a very powerful tool in olympiad number theory and recently it has become very popular. We generalize it to all sequences that maintain a property like it i.e. if p^{\\alpha}||a_k and p^\\b{eta}||n, then p^{{\\alpha}+\\b{eta}}||a_{nk}.

  2. Pairwise Sequence Alignment Library

    Energy Technology Data Exchange (ETDEWEB)

    2015-05-20

    Vector extensions, such as SSE, have been part of the x86 CPU since the 1990s, with applications in graphics, signal processing, and scientific applications. Although many algorithms and applications can naturally benefit from automatic vectorization techniques, there are still many that are difficult to vectorize due to their dependence on irregular data structures, dense branch operations, or data dependencies. Sequence alignment, one of the most widely used operations in bioinformatics workflows, has a computational footprint that features complex data dependencies. The trend of widening vector registers adversely affects the state-of-the-art sequence alignment algorithm based on striped data layouts. Therefore, a novel SIMD implementation of a parallel scan-based sequence alignment algorithm that can better exploit wider SIMD units was implemented as part of the Parallel Sequence Alignment Library (parasail). Parasail features: Reference implementations of all known vectorized sequence alignment approaches. Implementations of Smith Waterman (SW), semi-global (SG), and Needleman Wunsch (NW) sequence alignment algorithms. Implementations across all modern CPU instruction sets including AVX2 and KNC. Language interfaces for C/C++ and Python.

  3. Effects of changing the random number stride in Monte Carlo calculations

    International Nuclear Information System (INIS)

    Hendricks, J.S.

    1991-01-01

    This paper reports on a common practice in Monte Carlo radiation transport codes which is to start each random walk a specified number of steps up the random number sequence from the previous one. This is called the stride in the random number sequence between source particles. It is used for correlated sampling or to provide tree-structured random numbers. A new random number generator algorithm for the major Monte Carlo code MCNP has been written to allow adjustment of the random number stride. This random number generator is machine portable. The effects of varying the stride for several sample problems are examined

  4. Error Analysis of Deep Sequencing of Phage Libraries: Peptides Censored in Sequencing

    Directory of Open Access Journals (Sweden)

    Wadim L. Matochko

    2013-01-01

    Full Text Available Next-generation sequencing techniques empower selection of ligands from phage-display libraries because they can detect low abundant clones and quantify changes in the copy numbers of clones without excessive selection rounds. Identification of errors in deep sequencing data is the most critical step in this process because these techniques have error rates >1%. Mechanisms that yield errors in Illumina and other techniques have been proposed, but no reports to date describe error analysis in phage libraries. Our paper focuses on error analysis of 7-mer peptide libraries sequenced by Illumina method. Low theoretical complexity of this phage library, as compared to complexity of long genetic reads and genomes, allowed us to describe this library using convenient linear vector and operator framework. We describe a phage library as N×1 frequency vector n=ni, where ni is the copy number of the ith sequence and N is the theoretical diversity, that is, the total number of all possible sequences. Any manipulation to the library is an operator acting on n. Selection, amplification, or sequencing could be described as a product of a N×N matrix and a stochastic sampling operator (Sa. The latter is a random diagonal matrix that describes sampling of a library. In this paper, we focus on the properties of Sa and use them to define the sequencing operator (Seq. Sequencing without any bias and errors is Seq=Sa IN, where IN is a N×N unity matrix. Any bias in sequencing changes IN to a nonunity matrix. We identified a diagonal censorship matrix (CEN, which describes elimination or statistically significant downsampling, of specific reads during the sequencing process.

  5. Topics in random walks in random environment

    International Nuclear Information System (INIS)

    Sznitman, A.-S.

    2004-01-01

    Over the last twenty-five years random motions in random media have been intensively investigated and some new general methods and paradigms have by now emerged. Random walks in random environment constitute one of the canonical models of the field. However in dimension bigger than one they are still poorly understood and many of the basic issues remain to this day unresolved. The present series of lectures attempt to give an account of the progresses which have been made over the last few years, especially in the study of multi-dimensional random walks in random environment with ballistic behavior. (author)

  6. Fast physical random bit generation with chaotic semiconductor lasers

    Science.gov (United States)

    Uchida, Atsushi; Amano, Kazuya; Inoue, Masaki; Hirano, Kunihito; Naito, Sunao; Someya, Hiroyuki; Oowada, Isao; Kurashige, Takayuki; Shiki, Masaru; Yoshimori, Shigeru; Yoshimura, Kazuyuki; Davis, Peter

    2008-12-01

    Random number generators in digital information systems make use of physical entropy sources such as electronic and photonic noise to add unpredictability to deterministically generated pseudo-random sequences. However, there is a large gap between the generation rates achieved with existing physical sources and the high data rates of many computation and communication systems; this is a fundamental weakness of these systems. Here we show that good quality random bit sequences can be generated at very fast bit rates using physical chaos in semiconductor lasers. Streams of bits that pass standard statistical tests for randomness have been generated at rates of up to 1.7 Gbps by sampling the fluctuating optical output of two chaotic lasers. This rate is an order of magnitude faster than that of previously reported devices for physical random bit generators with verified randomness. This means that the performance of random number generators can be greatly improved by using chaotic laser devices as physical entropy sources.

  7. Waiting Time Distributions for Pattern Occurrence in a Constrained Sequence

    Directory of Open Access Journals (Sweden)

    Valeri Stefanov

    2007-01-01

    Full Text Available A binary sequence of zeros and ones is called a (d,k-sequence if it does not contain runs of zeros of length either less than d or greater than k, where d and k are arbitrary, but fixed, non-negative integers and d < k. Such sequences find an abundance of applications in communications, in particular for magnetic and optical recording. Occasionally, one requires that (d,k-sequences do not contain a specific pattern w. Therefore, distribution results concerning pattern occurrence in (d,k-sequences are of interest. In this paper we study the distribution of the waiting time until the r th occurrence of a pattern w in a random (d,k-sequence generated by a Markov source. Numerical examples are also provided.

  8. Adaptive Processing for Sequence Alignment

    KAUST Repository

    Zidan, Mohammed A.; Bonny, Talal; Salama, Khaled N.

    2012-01-01

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

  9. 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.

  10. Some limit theorems for negatively associated random variables

    Indian Academy of Sciences (India)

    random sampling without replacement, and (i) joint distribution of ranks. ... wide applications in multivariate statistical analysis and system reliability, the ... strong law of large numbers for negatively associated sequences under the case where.

  11. 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.

  12. Variable depth recursion algorithm for leaf sequencing

    International Nuclear Information System (INIS)

    Siochi, R. Alfredo C.

    2007-01-01

    The processes of extraction and sweep are basic segmentation steps that are used in leaf sequencing algorithms. A modified version of a commercial leaf sequencer changed the way that the extracts are selected and expanded the search space, but the modification maintained the basic search paradigm of evaluating multiple solutions, each one consisting of up to 12 extracts and a sweep sequence. While it generated the best solutions compared to other published algorithms, it used more computation time. A new, faster algorithm selects one extract at a time but calls itself as an evaluation function a user-specified number of times, after which it uses the bidirectional sweeping window algorithm as the final evaluation function. To achieve a performance comparable to that of the modified commercial leaf sequencer, 2-3 calls were needed, and in all test cases, there were only slight improvements beyond two calls. For the 13 clinical test maps, computation speeds improved by a factor between 12 and 43, depending on the constraints, namely the ability to interdigitate and the avoidance of the tongue-and-groove under dose. The new algorithm was compared to the original and modified versions of the commercial leaf sequencer. It was also compared to other published algorithms for 1400, random, 15x15, test maps with 3-16 intensity levels. In every single case the new algorithm provided the best solution

  13. Main sequence mass loss

    International Nuclear Information System (INIS)

    Brunish, W.M.; Guzik, J.A.; Willson, L.A.; Bowen, G.

    1987-01-01

    It has been hypothesized that variable stars may experience mass loss, driven, at least in part, by oscillations. The class of stars we are discussing here are the δ Scuti variables. These are variable stars with masses between about 1.2 and 2.25 M/sub θ/, lying on or very near the main sequence. According to this theory, high rotation rates enhance the rate of mass loss, so main sequence stars born in this mass range would have a range of mass loss rates, depending on their initial rotation velocity and the amplitude of the oscillations. The stars would evolve rapidly down the main sequence until (at about 1.25 M/sub θ/) a surface convection zone began to form. The presence of this convective region would slow the rotation, perhaps allowing magnetic braking to occur, and thus sharply reduce the mass loss rate. 7 refs

  14. Electricity sequence control

    International Nuclear Information System (INIS)

    Shin, Heung Ryeol

    2010-03-01

    The contents of the book are introduction of control system, like classification and control signal, introduction of electricity power switch, such as push-button and detection switch sensor for induction type and capacitance type machinery for control, solenoid valve, expression of sequence and type of electricity circuit about using diagram, time chart, marking and term, logic circuit like Yes, No, and, or and equivalence logic, basic electricity circuit, electricity sequence control, added condition, special program control about choice and jump of program, motor control, extra circuit on repeat circuit, pause circuit in a conveyer, safety regulations and rule about classification of electricity disaster and protective device for insulation.

  15. Next-generation sequencing

    DEFF Research Database (Denmark)

    Rieneck, Klaus; Bak, Mads; Jønson, Lars

    2013-01-01

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

  16. RDNAnalyzer: A tool for DNA secondary structure prediction and sequence analysis.

    Science.gov (United States)

    Afzal, Muhammad; Shahid, Ahmad Ali; Shehzadi, Abida; Nadeem, Shahid; Husnain, Tayyab

    2012-01-01

    RDNAnalyzer is an innovative computer based tool designed for DNA secondary structure prediction and sequence analysis. It can randomly generate the DNA sequence or user can upload the sequences of their own interest in RAW format. It uses and extends the Nussinov dynamic programming algorithm and has various application for the sequence analysis. It predicts the DNA secondary structure and base pairings. It also provides the tools for routinely performed sequence analysis by the biological scientists such as DNA replication, reverse compliment generation, transcription, translation, sequence specific information as total number of nucleotide bases, ATGC base contents along with their respective percentages and sequence cleaner. RDNAnalyzer is a unique tool developed in Microsoft Visual Studio 2008 using Microsoft Visual C# and Windows Presentation Foundation and provides user friendly environment for sequence analysis. It is freely available. http://www.cemb.edu.pk/sw.html RDNAnalyzer - Random DNA Analyser, GUI - Graphical user interface, XAML - Extensible Application Markup Language.

  17. 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...

  18. THE RHIC SEQUENCER

    International Nuclear Information System (INIS)

    VAN ZEIJTS, J.; DOTTAVIO, T.; FRAK, B.; MICHNOFF, R.

    2001-01-01

    The Relativistic Heavy Ion Collider (RHIC) has a high level asynchronous time-line driven by a controlling program called the ''Sequencer''. Most high-level magnet and beam related issues are orchestrated by this system. The system also plays an important task in coordinated data acquisition and saving. We present the program, operator interface, operational impact and experience

  19. 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

  20. simple sequence repeat (SSR)

    African Journals Online (AJOL)

    In the present study, 78 mapped simple sequence repeat (SSR) markers representing 11 linkage groups of adzuki bean were evaluated for transferability to mungbean and related Vigna spp. 41 markers amplified characteristic bands in at least one Vigna species. The transferability percentage across the genotypes ranged ...

  1. Random Generators and Normal Numbers

    OpenAIRE

    Bailey, David H.; Crandall, Richard E.

    2002-01-01

    Pursuant to the authors' previous chaotic-dynamical model for random digits of fundamental constants, we investigate a complementary, statistical picture in which pseudorandom number generators (PRNGs) are central. Some rigorous results are achieved: We establish b-normality for constants of the form $\\sum_i 1/(b^{m_i} c^{n_i})$ for certain sequences $(m_i), (n_i)$ of integers. This work unifies and extends previously known classes of explicit normals. We prove that for coprime $b,c>1$ the...

  2. 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-...

  3. Almost convergence of triple sequences

    OpenAIRE

    Ayhan Esi; M.Necdet Catalbas

    2013-01-01

    In this paper we introduce and study the concepts of almost convergence and almost Cauchy for triple sequences. Weshow that the set of almost convergent triple sequences of 0's and 1's is of the first category and also almost everytriple sequence of 0's and 1's is not almost convergent.Keywords: almost convergence, P-convergent, triple sequence.

  4. A few Smarandache Integer Sequences

    OpenAIRE

    Ibstedt, Henry

    2010-01-01

    This paper deals with the analysis of a few Smarandache Integer Sequences which first appeared in Properties or the Numbers, F. Smarandache, University or Craiova Archives, 1975. The first four sequences are recurrence generated sequences while the last three are concatenation sequences.

  5. Frequency characteristics of coordinate sequences of linear recurrences over Galois rings

    Science.gov (United States)

    Kamlovskii, O. V.

    2013-12-01

    We consider some properties of the coordinate sequences of linear recurrences over Galois rings which characterize the possibility of regarding them as pseudo-random sequences. We study the periodicity properties, linear complexity and frequency characteristics of these sequences. Up to now, these parameters have been studied mainly in the case when the linear recurring sequence has maximal possible period. We investigate the coordinate sequences of linear recurrences of not necessarily maximal period. We obtain sharpened and generalized estimates for the number of elements and r-patterns on the cycles and intervals of these sequences.

  6. Frequency characteristics of coordinate sequences of linear recurrences over Galois rings

    International Nuclear Information System (INIS)

    Certification Research Center, Moscow (Russian Federation))" data-affiliation=" (LLC Certification Research Center, Moscow (Russian Federation))" >Kamlovskii, O V

    2013-01-01

    We consider some properties of the coordinate sequences of linear recurrences over Galois rings which characterize the possibility of regarding them as pseudo-random sequences. We study the periodicity properties, linear complexity and frequency characteristics of these sequences. Up to now, these parameters have been studied mainly in the case when the linear recurring sequence has maximal possible period. We investigate the coordinate sequences of linear recurrences of not necessarily maximal period. We obtain sharpened and generalized estimates for the number of elements and r-patterns on the cycles and intervals of these sequences

  7. Allele Re-sequencing Technologies

    DEFF Research Database (Denmark)

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

    2013-01-01

    The development of next-generation sequencing technologies has made sequencing an affordable approach for detection of genetic variations associated with various traits. However, the cost of whole genome re-sequencing still remains too high to be feasible for many plant species with large...... alternative to whole genome re-sequencing to identify causative genetic variations in plants. One challenge, however, will be efficient bioinformatics strategies for data handling and analysis from the increasing amount of sequence information....

  8. How edge-reinforced random walk arises naturally

    NARCIS (Netherlands)

    Rolles, S.W.W.

    2003-01-01

    We give a characterization of a modified edge-reinforced random walk in terms of certain partially exchangeable sequences. In particular, we obtain a characterization of an edge-reinforced random walk (introduced by Coppersmith and Diaconis) on a 2-edge-connected graph. Modifying the notion of

  9. Multilocus Sequence Typing

    OpenAIRE

    Belén, Ana; Pavón, Ibarz; Maiden, Martin C.J.

    2009-01-01

    Multilocus sequence typing (MLST) was first proposed in 1998 as a typing approach that enables the unambiguous characterization of bacterial isolates in a standardized, reproducible, and portable manner using the human pathogen Neisseria meningitidis as the exemplar organism. Since then, the approach has been applied to a large and growing number of organisms by public health laboratories and research institutions. MLST data, shared by investigators over the world via the Internet, have been ...

  10. Achalasia Carcinoma Sequence

    OpenAIRE

    Makmun, Dadang

    2001-01-01

    We report a case of carcinoma of the esophagus in a 58 years old woman with achalasia, who has been diagnosed since 30 years ago, which initiated by surgical treatment (myotomy) and the symptoms recurred since 3 years ago. According to the progress of the disease, Malignancy was strongly suspected due to prolonged stasis and mucosal irritation caused by achalasia (achalasia carcinoma sequence). Because of these contributing factors for the development of serious complications such as Malignan...

  11. 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.

  12. Sequencing BPS spectra

    International Nuclear Information System (INIS)

    Gukov, Sergei; Nawata, Satoshi; Saberi, Ingmar; Stošić, Marko; Sułkowski, Piotr

    2016-01-01

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

  13. 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 ...

  14. PILOT DECONTAMINATION THROUGH PILOT SEQUENCE HOPPING IN MASSIVE MIMO SYSTEMS

    DEFF Research Database (Denmark)

    2015-01-01

    path between one of the users and one of the base stations define one of the channels. The system comprises a pilot generation unit configured to assign pilot sequences randomly among the users and a pilot processing unit configured to filter the pilot sequences received from a user of interest so...... that the channel coefficient of the channel of the user of interest is determined. The pilot sequences received from the user of interest are contaminated by other non-orthogonal or identical pilot sequences from other users of the cell of interest or other cells. The filter is configured so that the contamination...... caused by the other non-orthogonal or identical pilot sequences from the other users is reduced....

  15. Abstracting Sequences: Reasoning That Is a Key to Academic Achievement.

    Science.gov (United States)

    Pasnak, Robert; Kidd, Julie K; Gadzichowski, K Marinka; Gallington, Debbie A; Schmerold, Katrina Lea; West, Heather

    2015-01-01

    The ability to understand sequences of items may be an important cognitive ability. To test this proposition, 8 first-grade children from each of 36 classes were randomly assigned to four conditions. Some were taught sequences that represented increasing or decreasing values, or were symmetrical, or were rotations of an object through 6 or 8 positions. Control children received equal numbers of sessions on mathematics, reading, or social studies. Instruction was conducted three times weekly in 15-min sessions for seven months. In May, the children taught sequences applied their understanding to novel sequences, and scored as well or better on three standardized reading tests as the control children. They outscored all children on tests of mathematics concepts, and scored better than control children on some mathematics scales. These findings indicate that developing an understanding of sequences is a form of abstraction, probably involving fluid reasoning, that provides a foundation for academic achievement in early education.

  16. 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.

  17. Quantumness, Randomness and Computability

    International Nuclear Information System (INIS)

    Solis, Aldo; Hirsch, Jorge G

    2015-01-01

    Randomness plays a central role in the quantum mechanical description of our interactions. We review the relationship between the violation of Bell inequalities, non signaling and randomness. We discuss the challenge in defining a random string, and show that algorithmic information theory provides a necessary condition for randomness using Borel normality. We close with a view on incomputablity and its implications in physics. (paper)

  18. 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

    2018-01-01

    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 FRNAPH subgroup II (FRNAPH-II). These viral indicators have been neglected because their behavior is sometimes different 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. This bias is that, in the absence of routine culture methods, NoV is targeted by genome detection, while the presence of FRNAPH is usually investigated by isolation of infectious particles. In this study, by targeting both viruses using genome detection, a significant correlation between the presence of FRNAPH-II and that of NoV in shellfish collected from various European harvesting areas impacted by fecal pollution was observed. Moreover, during their depuration, while the long period of persistence of NoV was confirmed, a similar or even longer period of persistence of the FRNAPH-II genome, which was over 30 days, was observed. Such a striking genome persistence calls into question the relevance of molecular methods for assessing viral hazards. Targeting the same virus (i.e., FRNAPH-II) by culture and genome detection in specimens 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 use in assessing viral hazard needs to be investigated. IMPORTANCE This work brings new data about the behavior of viruses in shellfish, as well as about the relevance of molecular methods for their detection and evaluation of the viral hazard. First, a strong

  19. How random is a random vector?

    Science.gov (United States)

    Eliazar, Iddo

    2015-12-01

    Over 80 years ago Samuel Wilks proposed that the "generalized variance" of a random vector is the determinant of its covariance matrix. To date, the notion and use of the generalized variance is confined only to very specific niches in statistics. In this paper we establish that the "Wilks standard deviation" -the square root of the generalized variance-is indeed the standard deviation of a random vector. We further establish that the "uncorrelation index" -a derivative of the Wilks standard deviation-is a measure of the overall correlation between the components of a random vector. Both the Wilks standard deviation and the uncorrelation index are, respectively, special cases of two general notions that we introduce: "randomness measures" and "independence indices" of random vectors. In turn, these general notions give rise to "randomness diagrams"-tangible planar visualizations that answer the question: How random is a random vector? The notion of "independence indices" yields a novel measure of correlation for Lévy laws. In general, the concepts and results presented in this paper are applicable to any field of science and engineering with random-vectors empirical data.

  20. How random is a random vector?

    International Nuclear Information System (INIS)

    Eliazar, Iddo

    2015-01-01

    Over 80 years ago Samuel Wilks proposed that the “generalized variance” of a random vector is the determinant of its covariance matrix. To date, the notion and use of the generalized variance is confined only to very specific niches in statistics. In this paper we establish that the “Wilks standard deviation” –the square root of the generalized variance–is indeed the standard deviation of a random vector. We further establish that the “uncorrelation index” –a derivative of the Wilks standard deviation–is a measure of the overall correlation between the components of a random vector. Both the Wilks standard deviation and the uncorrelation index are, respectively, special cases of two general notions that we introduce: “randomness measures” and “independence indices” of random vectors. In turn, these general notions give rise to “randomness diagrams”—tangible planar visualizations that answer the question: How random is a random vector? The notion of “independence indices” yields a novel measure of correlation for Lévy laws. In general, the concepts and results presented in this paper are applicable to any field of science and engineering with random-vectors empirical data.

  1. Multiformity of inherent randomicity and visitation density in n symbolic dynamics

    International Nuclear Information System (INIS)

    Zhang Yagang; Wang Changjiang

    2007-01-01

    The multiformity of inherent randomicity and visitation density in n symbolic dynamics will be clarified in this paper. These stochastic symbolic sequences bear three features. The distribution of frequency, inter-occurrence times and the alignment of two random sequences are amplified in detail. The features of visitation density in surjective maps presents catholicity and the catholicity in n letters randomicity has the same measure foundation. We hope to offer a symbolic platform that satisfies these stochastic properties and to attempt to study certain properties of DNA base sequences, 20 amino acids symbolic sequences of proteid structure, and the time series that can be symbolic in finance market et al

  2. Foundations of Sequence-to-Sequence Modeling for Time Series

    OpenAIRE

    Kuznetsov, Vitaly; Mariet, Zelda

    2018-01-01

    The availability of large amounts of time series data, paired with the performance of deep-learning algorithms on a broad class of problems, has recently led to significant interest in the use of sequence-to-sequence models for time series forecasting. We provide the first theoretical analysis of this time series forecasting framework. We include a comparison of sequence-to-sequence modeling to classical time series models, and as such our theory can serve as a quantitative guide for practiti...

  3. Secure self-calibrating quantum random-bit generator

    International Nuclear Information System (INIS)

    Fiorentino, M.; Santori, C.; Spillane, S. M.; Beausoleil, R. G.; Munro, W. J.

    2007-01-01

    Random-bit generators (RBGs) are key components of a variety of information processing applications ranging from simulations to cryptography. In particular, cryptographic systems require 'strong' RBGs that produce high-entropy bit sequences, but traditional software pseudo-RBGs have very low entropy content and therefore are relatively weak for cryptography. Hardware RBGs yield entropy from chaotic or quantum physical systems and therefore are expected to exhibit high entropy, but in current implementations their exact entropy content is unknown. Here we report a quantum random-bit generator (QRBG) that harvests entropy by measuring single-photon and entangled two-photon polarization states. We introduce and implement a quantum tomographic method to measure a lower bound on the 'min-entropy' of the system, and we employ this value to distill a truly random-bit sequence. This approach is secure: even if an attacker takes control of the source of optical states, a secure random sequence can be distilled

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

    African Journals Online (AJOL)

    A study to compare the effectiveness of inter-simple sequence repeats (ISSR) and randomly amplified polymorphic DNA (RAPD) profiling was carried out with a total of 65 DNA samples using 12 species of Indian Garcinia. ISSR and RAPD profiling were performed with 19 and 12 primers, respectively. ISSR markers ...

  5. Novel expressed sequence tag- simple sequence repeats (EST ...

    African Journals Online (AJOL)

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

  6. 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.

  7. Reconsidering vocational interests for personnel selection: the validity of an interest-based selection test in relation to job knowledge, job performance, and continuance intentions.

    Science.gov (United States)

    Van Iddekinge, Chad H; Putka, Dan J; Campbell, John P

    2011-01-01

    Although vocational interests have a long history in vocational psychology, they have received extremely limited attention within the recent personnel selection literature. We reconsider some widely held beliefs concerning the (low) validity of interests for predicting criteria important to selection researchers, and we review theory and empirical evidence that challenge such beliefs. We then describe the development and validation of an interests-based selection measure. Results of a large validation study (N = 418) reveal that interests predicted a diverse set of criteria—including measures of job knowledge, job performance, and continuance intentions—with corrected, cross-validated Rs that ranged from .25 to .46 across the criteria (mean R = .31). Interests also provided incremental validity beyond measures of general cognitive aptitude and facets of the Big Five personality dimensions in relation to each criterion. Furthermore, with a couple exceptions, the interest scales were associated with small to medium subgroup differences, which in most cases favored women and racial minorities. Taken as a whole, these results appear to call into question the prevailing thought that vocational interests have limited usefulness for selection.

  8. "To serve the community best": reconsidering Black politics in the struggle to save Homer G. Phillips Hospital in St. Louis, 1976-1984.

    Science.gov (United States)

    Kirouac-Fram, Jaclyn

    2010-01-01

    The move to consolidate, and eventually to close, Homer G. Phillips Hospital sparked a major uprising in St. Louis, Missouri, during the years 1976 through 1984. This article explores the struggle in St. Louis’s black community to keep open, and later to reopen, Homer G. Phillips Hospital from a vantage point that demonstrates the diversity of opinion surrounding the struggle. For many black St. Louis residents, the physical space of Homer G. Phillips Hospital was a metaphor for identity, a manifestation of citizenship rights, and a means of delineating a territory of shared histories, understandings, and values. For others, it was a relic of segregation and racism. In seeking to understand the diversity of public reaction, this article addresses class antagonism, examines the varied and divergent motivations for eliminating or maintaining services at the hospital, and reconsiders the discourse of "black politics." It is a decisive illustration of how the national twin crises of deindustrialization and privatization affected a heterogeneous black community.

  9. Infinite sequences and series

    CERN Document Server

    Knopp, Konrad

    1956-01-01

    One of the finest expositors in the field of modern mathematics, Dr. Konrad Knopp here concentrates on a topic that is of particular interest to 20th-century mathematicians and students. He develops the theory of infinite sequences and series from its beginnings to a point where the reader will be in a position to investigate more advanced stages on his own. The foundations of the theory are therefore presented with special care, while the developmental aspects are limited by the scope and purpose of the book. All definitions are clearly stated; all theorems are proved with enough detail to ma

  10. Fast global sequence alignment technique

    KAUST Repository

    Bonny, Mohamed Talal; Salama, Khaled N.

    2011-01-01

    fast alignment algorithm, called 'Alignment By Scanning' (ABS), to provide an approximate alignment of two DNA sequences. We compare our algorithm with the wellknown sequence alignment algorithms, the 'GAP' (which is heuristic) and the 'Needleman

  11. Next-Generation Sequencing Platforms

    Science.gov (United States)

    Mardis, Elaine R.

    2013-06-01

    Automated DNA sequencing instruments embody an elegant interplay among chemistry, engineering, software, and molecular biology and have built upon Sanger's founding discovery of dideoxynucleotide sequencing to perform once-unfathomable tasks. Combined with innovative physical mapping approaches that helped to establish long-range relationships between cloned stretches of genomic DNA, fluorescent DNA sequencers produced reference genome sequences for model organisms and for the reference human genome. New types of sequencing instruments that permit amazing acceleration of data-collection rates for DNA sequencing have been developed. The ability to generate genome-scale data sets is now transforming the nature of biological inquiry. Here, I provide an historical perspective of the field, focusing on the fundamental developments that predated the advent of next-generation sequencing instruments and providing information about how these instruments work, their application to biological research, and the newest types of sequencers that can extract data from single DNA molecules.

  12. Network clustering coefficient approach to DNA sequence analysis

    Energy Technology Data Exchange (ETDEWEB)

    Gerhardt, Guenther J.L. [Universidade Federal do Rio Grande do Sul-Hospital de Clinicas de Porto Alegre, Rua Ramiro Barcelos 2350/sala 2040/90035-003 Porto Alegre (Brazil); Departamento de Fisica e Quimica da Universidade de Caxias do Sul, Rua Francisco Getulio Vargas 1130, 95001-970 Caxias do Sul (Brazil); Lemke, Ney [Programa Interdisciplinar em Computacao Aplicada, Unisinos, Av. Unisinos, 950, 93022-000 Sao Leopoldo, RS (Brazil); Corso, Gilberto [Departamento de Biofisica e Farmacologia, Centro de Biociencias, Universidade Federal do Rio Grande do Norte, Campus Universitario, 59072 970 Natal, RN (Brazil)]. E-mail: corso@dfte.ufrn.br

    2006-05-15

    In this work we propose an alternative DNA sequence analysis tool based on graph theoretical concepts. The methodology investigates the path topology of an organism genome through a triplet network. In this network, triplets in DNA sequence are vertices and two vertices are connected if they occur juxtaposed on the genome. We characterize this network topology by measuring the clustering coefficient. We test our methodology against two main bias: the guanine-cytosine (GC) content and 3-bp (base pairs) periodicity of DNA sequence. We perform the test constructing random networks with variable GC content and imposed 3-bp periodicity. A test group of some organisms is constructed and we investigate the methodology in the light of the constructed random networks. We conclude that the clustering coefficient is a valuable tool since it gives information that is not trivially contained in 3-bp periodicity neither in the variable GC content.

  13. 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.

  14. The advantages of SMRT sequencing

    OpenAIRE

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

    2013-01-01

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

  15. Putting instruction sequences into effect

    NARCIS (Netherlands)

    Bergstra, J.A.

    2011-01-01

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

  16. Region segmentation along image sequence

    International Nuclear Information System (INIS)

    Monchal, L.; Aubry, P.

    1995-01-01

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

  17. 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.

  18. 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

  19. Parallel random number generator for inexpensive configurable hardware cells

    Science.gov (United States)

    Ackermann, J.; Tangen, U.; Bödekker, B.; Breyer, J.; Stoll, E.; McCaskill, J. S.

    2001-11-01

    A new random number generator ( RNG) adapted to parallel processors has been created. This RNG can be implemented with inexpensive hardware cells. The correlation between neighboring cells is suppressed with smart connections. With such connection structures, sequences of pseudo-random numbers are produced. Numerical tests including a self-avoiding random walk test and the simulation of the order parameter and energy of the 2D Ising model give no evidence for correlation in the pseudo-random sequences. Because the new random number generator has suppressed the correlation between neighboring cells which is usually observed in cellular automaton implementations, it is applicable for extended time simulations. It gives an immense speed-up factor if implemented directly in configurable hardware, and has recently been used for long time simulations of spatially resolved molecular evolution.

  20. Log-balanced combinatorial sequences

    Directory of Open Access Journals (Sweden)

    Tomislav Došlic

    2005-01-01

    Full Text Available We consider log-convex sequences that satisfy an additional constraint imposed on their rate of growth. We call such sequences log-balanced. It is shown that all such sequences satisfy a pair of double inequalities. Sufficient conditions for log-balancedness are given for the case when the sequence satisfies a two- (or more- term linear recurrence. It is shown that many combinatorially interesting sequences belong to this class, and, as a consequence, that the above-mentioned double inequalities are valid for all of them.

  1. A unified approach for squeal instability analysis of disc brakes with two types of random-fuzzy uncertainties

    Science.gov (United States)

    Lü, Hui; Shangguan, Wen-Bin; Yu, Dejie

    2017-09-01

    Automotive brake systems are always subjected to various types of uncertainties and two types of random-fuzzy uncertainties may exist in the brakes. In this paper, a unified approach is proposed for squeal instability analysis of disc brakes with two types of random-fuzzy uncertainties. In the proposed approach, two uncertainty analysis models with mixed variables are introduced to model the random-fuzzy uncertainties. The first one is the random and fuzzy model, in which random variables and fuzzy variables exist simultaneously and independently. The second one is the fuzzy random model, in which uncertain parameters are all treated as random variables while their distribution parameters are expressed as fuzzy numbers. Firstly, the fuzziness is discretized by using α-cut technique and the two uncertainty analysis models are simplified into random-interval models. Afterwards, by temporarily neglecting interval uncertainties, the random-interval models are degraded into random models, in which the expectations, variances, reliability indexes and reliability probabilities of system stability functions are calculated. And then, by reconsidering the interval uncertainties, the bounds of the expectations, variances, reliability indexes and reliability probabilities are computed based on Taylor series expansion. Finally, by recomposing the analysis results at each α-cut level, the fuzzy reliability indexes and probabilities can be obtained, by which the brake squeal instability can be evaluated. The proposed approach gives a general framework to deal with both types of random-fuzzy uncertainties that may exist in the brakes and its effectiveness is demonstrated by numerical examples. It will be a valuable supplement to the systematic study of brake squeal considering uncertainty.

  2. New MR pulse sequence

    International Nuclear Information System (INIS)

    Harms, S.E.; Flamig, D.P.; Griffey, R.H.

    1990-01-01

    This paper describes a method for fat suppression for three-dimensional MR imaging. The FATS (fat-suppressed acquisition with echo time shortened) sequence employs a pair of opposing adiabatic half-passage RF pulses tuned on fat resonance. The imaging parameters are as follows: TR, 20 msec; TE, 21.7-3.2 msec; 1,024 x 128 x 128 acquired matrix; imaging time, approximately 11 minutes. A series of 54 examinations were performed. Excellent fat suppression with water excitation is achieved in all cases. The orbital images demonstrate superior resolution of small orbital lesions. The high signal-to-noise ratio (SNR) in cranial studies demonstrates excellent petrous bone and internal auditory canal anatomy

  3. Influence of Layup Sequence on the Surface Accuracy of Carbon Fiber Composite Space Mirrors

    Science.gov (United States)

    Yang, Zhiyong; Liu, Qingnian; Zhang, Boming; Xu, Liang; Tang, Zhanwen; Xie, Yongjie

    2018-04-01

    Layup sequence is directly related to stiffness and deformation resistance of the composite space mirror, and error caused by layup sequence can affect the surface precision of composite mirrors evidently. Variation of layup sequence with the same total thickness of composite space mirror changes surface form of the composite mirror, which is the focus of our study. In our research, the influence of varied quasi-isotropic stacking sequences and random angular deviation on the surface accuracy of composite space mirrors was investigated through finite element analyses (FEA). We established a simulation model for the studied concave mirror with 500 mm diameter, essential factors of layup sequences and random angular deviations on different plies were discussed. Five guiding findings were described in this study. Increasing total plies, optimizing stacking sequence and keeping consistency of ply alignment in ply placement are effective to improve surface accuracy of composite mirror.

  4. 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.

  5. 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.

  6. A Note on Sequence Prediction over Large Alphabets

    Directory of Open Access Journals (Sweden)

    Travis Gagie

    2012-02-01

    Full Text Available Building on results from data compression, we prove nearly tight bounds on how well sequences of length n can be predicted in terms of the size σ of the alphabet and the length k of the context considered when making predictions. We compare the performance achievable by an adaptive predictor with no advance knowledge of the sequence, to the performance achievable by the optimal static predictor using a table listing the frequency of each (k + 1-tuple in the sequence. We show that, if the elements of the sequence are chosen uniformly at random, then an adaptive predictor can compete in the expected case if k ≤ logσ n – 3 – ε, for a constant ε > 0, but not if k ≥ logσ n.

  7. Hybridization Capture Using Short PCR Products Enriches Small Genomes by Capturing Flanking Sequences (CapFlank)

    DEFF Research Database (Denmark)

    Tsangaras, Kyriakos; Wales, Nathan; Sicheritz-Pontén, Thomas

    2014-01-01

    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...

  8. 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.

  9. Universal sequence map (USM of arbitrary discrete sequences

    Directory of Open Access Journals (Sweden)

    Almeida Jonas S

    2002-02-01

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

  10. Are electrostatic potentials between regions of different chemical composition measurable? The Gibbs-Guggenheim Principle reconsidered, extended and its consequences revisited.

    Science.gov (United States)

    Pethica, Brian A

    2007-12-21

    As indicated by Gibbs and made explicit by Guggenheim, the electrical potential difference between two regions of different chemical composition cannot be measured. The Gibbs-Guggenheim Principle restricts the use of classical electrostatics in electrochemical theories as thermodynamically unsound with some few approximate exceptions, notably for dilute electrolyte solutions and concomitant low potentials where the linear limit for the exponential of the relevant Boltzmann distribution applies. The Principle invalidates the widespread use of forms of the Poisson-Boltzmann equation which do not include the non-electrostatic components of the chemical potentials of the ions. From a thermodynamic analysis of the parallel plate electrical condenser, employing only measurable electrical quantities and taking into account the chemical potentials of the components of the dielectric and their adsorption at the surfaces of the condenser plates, an experimental procedure to provide exceptions to the Principle has been proposed. This procedure is now reconsidered and rejected. No other related experimental procedures circumvent the Principle. Widely-used theoretical descriptions of electrolyte solutions, charged surfaces and colloid dispersions which neglect the Principle are briefly discussed. MD methods avoid the limitations of the Poisson-Bolzmann equation. Theoretical models which include the non-electrostatic components of the inter-ion and ion-surface interactions in solutions and colloid systems assume the additivity of dispersion and electrostatic forces. An experimental procedure to test this assumption is identified from the thermodynamics of condensers at microscopic plate separations. The available experimental data from Kelvin probe studies are preliminary, but tend against additivity. A corollary to the Gibbs-Guggenheim Principle is enunciated, and the Principle is restated that for any charged species, neither the difference in electrostatic potential nor the

  11. Non-pineal supratentorial primitive neuro-ectodermal tumors (sPNET) in teenagers and young adults: Time to reconsider cisplatin based chemotherapy after cranio-spinal irradiation?

    Science.gov (United States)

    Biswas, Swethajit; Burke, Amos; Cherian, Sheen; Williams, Denise; Nicholson, James; Horan, Gail; Jefferies, Sarah; Williams, Michael; Earl, Helena M; Burnet, Neil G; Hatcher, Helen

    2009-07-01

    Supratentorial PNET (sPNET) are rare CNS tumors of embryonal origin arising in children and adults. The treatment of sPNET for all age groups at our cancer center has been based on the management of medulloblastoma (MB), involving neurosurgical debulking followed by cranio-spinal irradiation (CSI) and systemic chemotherapy. Medical records were reviewed to gather demographic and clinical data about all embryonal CNS tumors in children and adults from 2001 to 2007. Tumor pathology, clinical management and survival data were also assessed, particularly as regards those patients who received the Packer chemotherapy regimen for either sPNET or MB. Eleven patients (five children and six adults) were identified with non-pineal sPNET, three children with pineal sPNET, and 19 patients (18 children and 1 adult) with MB. There was no difference in overall survival (OS) rates between pediatric and adult sPNET. When all sPNET were compared to all MB, 5-year OS was 14% versus 73%, respectively, but was only 9% for non-pineal sPNET. When only considering those patients treated with the Packer chemotherapy regimen, the 5-year OS was 12% for sPNET versus 79% for MB. This retrospective study demonstrates that non-pineal sPNET are clinically distinct from MB and are resistant to the Packer chemotherapy regimen. We suggest that it is time to reconsider the use of this regimen in teenage and young adult non-pineal sPNET and to investigate the utility of alternative approaches. (c) 2009 Wiley-Liss, Inc.

  12. 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.

  13. Augmented brain function by coordinated reset stimulation with slowly varying sequences

    Directory of Open Access Journals (Sweden)

    Magteld eZeitler

    2015-03-01

    Full Text Available Several brain disorders are characterized by abnormally strong neuronal synchrony. Coordinated Reset (CR stimulation was developed to selectively counteract abnormal neuronal synchrony by desynchronization. For this, phase resetting stimuli are delivered to different subpopulations in a timely coordinated way. In neural networks with spike timing-dependent plasticity CR stimulation may eventually lead to an anti-kindling, i.e. an unlearning of abnormal synaptic connectivity and abnormal synchrony. The spatiotemporal sequence by which all stimulation sites are stimulated exactly once is called the stimulation site sequence, or briefly sequence. So far, in simulations, pre-clinical and clinical applications CR was applied either with fixed sequences or rapidly varying sequences (RVS. In this computational study we show that appropriate repetition of the sequence with occasional random switching to the next sequence may significantly improve the anti-kindling effect of CR. To this end, a sequence is applied many times before randomly switching to the next sequence. This new method is called SVS CR stimulation, i.e. CR with slowly varying sequences. In a neuronal network with strong short-range excitatory and weak long-range inhibitory dynamic couplings SVS CR stimulation turns out to be superior to CR stimulation with fixed sequences or RVS.

  14. Augmented brain function by coordinated reset stimulation with slowly varying sequences.

    Science.gov (United States)

    Zeitler, Magteld; Tass, Peter A

    2015-01-01

    Several brain disorders are characterized by abnormally strong neuronal synchrony. Coordinated Reset (CR) stimulation was developed to selectively counteract abnormal neuronal synchrony by desynchronization. For this, phase resetting stimuli are delivered to different subpopulations in a timely coordinated way. In neural networks with spike timing-dependent plasticity CR stimulation may eventually lead to an anti-kindling, i.e., an unlearning of abnormal synaptic connectivity and abnormal synchrony. The spatiotemporal sequence by which all stimulation sites are stimulated exactly once is called the stimulation site sequence, or briefly sequence. So far, in simulations, pre-clinical and clinical applications CR was applied either with fixed sequences or rapidly varying sequences (RVS). In this computational study we show that appropriate repetition of the sequence with occasional random switching to the next sequence may significantly improve the anti-kindling effect of CR. To this end, a sequence is applied many times before randomly switching to the next sequence. This new method is called SVS CR stimulation, i.e., CR with slowly varying sequences. In a neuronal network with strong short-range excitatory and weak long-range inhibitory dynamic couplings SVS CR stimulation turns out to be superior to CR stimulation with fixed sequences or RVS.

  15. Differentiating Visual from Response Sequencing during Long-term Skill Learning.

    Science.gov (United States)

    Lynch, Brighid; Beukema, Patrick; Verstynen, Timothy

    2017-01-01

    The dual-system model of sequence learning posits that during early learning there is an advantage for encoding sequences in sensory frames; however, it remains unclear whether this advantage extends to long-term consolidation. Using the serial RT task, we set out to distinguish the dynamics of learning sequential orders of visual cues from learning sequential responses. On each day, most participants learned a new mapping between a set of symbolic cues and responses made with one of four fingers, after which they were exposed to trial blocks of either randomly ordered cues or deterministic ordered cues (12-item sequence). Participants were randomly assigned to one of four groups (n = 15 per group): Visual sequences (same sequence of visual cues across training days), Response sequences (same order of key presses across training days), Combined (same serial order of cues and responses on all training days), and a Control group (a novel sequence each training day). Across 5 days of training, sequence-specific measures of response speed and accuracy improved faster in the Visual group than any of the other three groups, despite no group differences in explicit awareness of the sequence. The two groups that were exposed to the same visual sequence across days showed a marginal improvement in response binding that was not found in the other groups. These results indicate that there is an advantage, in terms of rate of consolidation across multiple days of training, for learning sequences of actions in a sensory representational space, rather than as motoric representations.

  16. Cranial modularity and sequence heterochrony in mammals.

    Science.gov (United States)

    Goswami, Anjali

    2007-01-01

    Heterochrony, the temporal shifting of developmental events relative to each other, requires a degree of autonomy among those processes or structures. Modularity, the division of larger structures or processes into autonomous sets of internally integrated units, is often discussed in relation to the concept of heterochrony. However, the relationship between the developmental modules derived from studies of heterochrony and evolutionary modules, which should be of adaptive importance and relate to the genotype-phenotype map, has not been explicitly studied. I analyzed a series of sectioned and whole cleared-and-stained embryological and neonatal specimens, supplemented with published ontogenetic data, to test the hypothesis that bones within the same phenotypic modules, as determined by morphometric analysis, are developmentally integrated and will display coordinated heterochronic shifts across taxa. Modularity was analyzed in cranial bone ossification sequences of 12 therian mammals. A dataset of 12-18 developmental events was used to assess if modularity in developmental sequences corresponds to six phenotypic modules, derived from a recent morphometric analysis of cranial modularity in mammals. Kendall's tau was used to measure rank correlations, with randomization tests for significance. If modularity in developmental sequences corresponds to observed phenotypic modules, bones within a single phenotypic module should show integration of developmental timing, maintaining the same timing of ossification relative to each other, despite differences in overall ossification sequences across taxa. Analyses did not find any significant conservation of developmental timing within the six phenotypic modules, meaning that bones that are highly integrated in adult morphology are not significantly integrated in developmental timing.

  17. On a randomly imperfect spherical cap pressurized by a random ...

    African Journals Online (AJOL)

    On a randomly imperfect spherical cap pressurized by a random dynamic load. ... In this paper, we investigate a dynamical system in a random setting of dual ... characterization of the random process for determining the dynamic buckling load ...

  18. Intermittency as a universal characteristic of the complete chromosome DNA sequences of eukaryotes: From protozoa to human genomes

    Science.gov (United States)

    Rybalko, S.; Larionov, S.; Poptsova, M.; Loskutov, A.

    2011-10-01

    Large-scale dynamical properties of complete chromosome DNA sequences of eukaryotes are considered. Using the proposed deterministic models with intermittency and symbolic dynamics we describe a wide spectrum of large-scale patterns inherent in these sequences, such as segmental duplications, tandem repeats, and other complex sequence structures. It is shown that the recently discovered gene number balance on the strands is not of a random nature, and certain subsystems of a complete chromosome DNA sequence exhibit the properties of deterministic chaos.

  19. Genomic sequencing in clinical trials

    OpenAIRE

    Mestan, Karen K; Ilkhanoff, Leonard; Mouli, Samdeep; Lin, Simon

    2011-01-01

    Abstract Human genome sequencing is the process by which the exact order of nucleic acid base pairs in the 24 human chromosomes is determined. Since the completion of the Human Genome Project in 2003, genomic sequencing is rapidly becoming a major part of our translational research efforts to understand and improve human health and disease. This article reviews the current and future directions of clinical research with respect to genomic sequencing, a technology that is just beginning to fin...

  20. 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.

  1. 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.

  2. ABS: Sequence alignment by scanning

    KAUST Repository

    Bonny, Mohamed Talal; Salama, Khaled N.

    2011-01-01

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

  3. 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.

  4. Relative oral bioavailability of morphine and naltrexone derived from crushed morphine sulfate and naltrexone hydrochloride extended-release capsules versus intact product and versus naltrexone solution: a single-dose, randomized-sequence, open-label, three-way crossover trial in healthy volunteers.

    Science.gov (United States)

    Johnson, Franklin K; Stark, Jeffrey G; Bieberdorf, Frederick A; Stauffer, Joe

    2010-06-01

    Morphine sulfate/sequestered naltrexone hydrochloride (HCl) (MS-sNT) extended-release fixed-dose combination capsules, approved by the US Food and Drug Administration (FDA) in August 2009 for chronic moderate to severe pain, contain extended-release morphine pellets with a sequestered core of the opioid antagonist naltrexone. MS-sNT was designed so that if the product is tampered with by crushing, the naltrexone becomes bioavailable to mitigate morphine-induced subjective effects, rendering the product less attractive for tampering. The primary aim of this study was to compare the oral bioavailability of naltrexone and its metabolite 6-beta-naltrexol, derived from crushed pellets from MS-sNT capsules, to naltrexone solution. This study also assessed the relative bioavailability of morphine from crushed pellets from MS-sNT capsules and that from the whole, intact product. This single-dose, randomized-sequence, open-label, 3-period, 3-treatment crossover trial was conducted in healthy volunteers. Adults admitted to the study center underwent a 10-hour overnight fast before study drug administration. Each subject received all 3 of the following treatments, 1 per session, separated by a 14-day washout: tampered pellets (crushed for >or=2 minutes with a mortar and pestle) from a 60-mg MS-sNT capsule (60 mg morphine/2.4 mg naltrexone); 60-mg whole, intact MS-sNT capsule; and oral naltrexone HCl (2.4 mg) solution. Plasma concentrations of naltrexone and 6-beta-naltrexol were measured 0 to 168 hours after administration. Morphine pharmaco-kinetics of crushed and whole pellets were determined 0 to 72 hours after administration. The analysis of relative bioavailability was based on conventional FDA criteria for assuming bioequivalence; that is, 90% CIs for ratios of geometric means (natural logarithm [In]-transformed C(max) and AUC) fell within the range of 80% to 125%. Subjects underwent physical examinations, clinical laboratory tests, and ECG at screening and study

  5. Multilocus Sequence Typing of Total-Genome-Sequenced Bacteria

    DEFF Research Database (Denmark)

    Larsen, Mette Voldby; Cosentino, Salvatore; Rasmussen, Simon

    2012-01-01

    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...

  6. 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...

  7. 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

  8. SVX Sequencer Board

    International Nuclear Information System (INIS)

    Utes, M.

    1997-01-01

    The SVX Sequencer boards are 9U by 280mm circuit boards that reside in slots 2 through 21 of each of eight Eurocard crates in the D0 Detector Platform. The basic purpose is to control the SVX chips for data acquisition and when a trigger occurs, to gather the SVX data and relay the data to the VRB boards in the Movable Counting House. Functions and features are as follows: (1) Initialization of eight SVX chip strings using the MIL-STD-1553 data bus; (2) Real time manipulation of the SVX control lines to effect data acquisition, digitization, and readout based on the NRZ/Clock signals from the Controller; (3) Conversion of 8-bit electrical SVX readout data to an optical signal operating at 1.062 Gbit/sec, sent to the VRB. Eight HDIs will be serviced per board; (4) Built-in logic analyzer which can record the most important control and data lines during a data acquisition cycle and put this recorded information onto the 1553 bus; (5) Identification header and end of data trailer tacked onto data stream; (6) 1553 register which can read the current values of the control and data lines; (7) 1553 register which can test the optical link; (8) 1553 registers for crossing pulse width, calibration pulse voltage, and calibration pipeline select; (9) 1553 register for reading the optical drivers status link; (10) 1553 register for power control of SVX chips and ignoring bad SVX strings; (11) Front panel displays and LEDs show the board status at a glance; (12) In-system programmable EPLDs are programmed via 1553 or Altera's 'Bitblaster'; (13) Automatic readout abort after 45us; (14) Supplies BUSY signal back to Trigger Framework; (15) Supports a heartbeat system to prevent excessive SVX current draw; and (16) Supports a SVX power trip feature if heartbeat failure occurs.

  9. Sequence Algebra, Sequence Decision Diagrams and Dynamic Fault Trees

    International Nuclear Information System (INIS)

    Rauzy, Antoine B.

    2011-01-01

    A large attention has been focused on the Dynamic Fault Trees in the past few years. By adding new gates to static (regular) Fault Trees, Dynamic Fault Trees aim to take into account dependencies among events. Merle et al. proposed recently an algebraic framework to give a formal interpretation to these gates. In this article, we extend Merle et al.'s work by adopting a slightly different perspective. We introduce Sequence Algebras that can be seen as Algebras of Basic Events, representing failures of non-repairable components. We show how to interpret Dynamic Fault Trees within this framework. Finally, we propose a new data structure to encode sets of sequences of Basic Events: Sequence Decision Diagrams. Sequence Decision Diagrams are very much inspired from Minato's Zero-Suppressed Binary Decision Diagrams. We show that all operations of Sequence Algebras can be performed on this data structure.

  10. Predicting tissue-specific expressions based on sequence characteristics

    KAUST Repository

    Paik, Hyojung; Ryu, Tae Woo; Heo, Hyoungsam; Seo, Seungwon; Lee, Doheon; Hur, Cheolgoo

    2011-01-01

    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.

  11. A New Images Hiding Scheme Based on Chaotic Sequences

    Institute of Scientific and Technical Information of China (English)

    LIU Nian-sheng; GUO Dong-hui; WU Bo-xi; Parr G

    2005-01-01

    We propose a data hidding technique in a still image. This technique is based on chaotic sequence in the transform domain of covert image. We use different chaotic random sequences multiplied by multiple sensitive images, respectively, to spread the spectrum of sensitive images. Multiple sensitive images are hidden in a covert image as a form of noise. The results of theoretical analysis and computer simulation show the new hiding technique have better properties with high security, imperceptibility and capacity for hidden information in comparison with the conventional scheme such as LSB (Least Significance Bit).

  12. 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.

  13. 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.

  14. 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...... virus (HBV) infection were identified that tested Chinese medicinal herbs. They were published in 49 Chinese journals. Only 10% (18/176) of the studies reported the method by which they randomized patients. Only two reported allocation concealment and were considered as adequate. Twenty percent (30...

  15. A hybrid-type quantum random number generator

    Science.gov (United States)

    Hai-Qiang, Ma; Wu, Zhu; Ke-Jin, Wei; Rui-Xue, Li; Hong-Wei, Liu

    2016-05-01

    This paper proposes a well-performing hybrid-type truly quantum random number generator based on the time interval between two independent single-photon detection signals, which is practical and intuitive, and generates the initial random number sources from a combination of multiple existing random number sources. A time-to-amplitude converter and multichannel analyzer are used for qualitative analysis to demonstrate that each and every step is random. Furthermore, a carefully designed data acquisition system is used to obtain a high-quality random sequence. Our scheme is simple and proves that the random number bit rate can be dramatically increased to satisfy practical requirements. Project supported by the National Natural Science Foundation of China (Grant Nos. 61178010 and 11374042), the Fund of State Key Laboratory of Information Photonics and Optical Communications (Beijing University of Posts and Telecommunications), China, and the Fundamental Research Funds for the Central Universities of China (Grant No. bupt2014TS01).

  16. Chameleon sequences in neurodegenerative diseases

    International Nuclear Information System (INIS)

    Bahramali, Golnaz; Goliaei, Bahram; Minuchehr, Zarrin; Salari, Ali

    2016-01-01

    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. Direct, rapid RNA sequence analysis

    International Nuclear Information System (INIS)

    Peattie, D.A.

    1987-01-01

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

  18. 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.

  19. Farey sequences and resistor networks

    Indian Academy of Sciences (India)

    Green's function, while the perturbation of a network is investigated in [3]. ... In Theorem 1 below, we employ the Farey sequence to establish a strict .... We next show that the Farey sequence method is applicable for circuits with n or fewer.

  20. DNA Sequencing by Capillary Electrophoresis

    Science.gov (United States)

    Karger, Barry L.; Guttman, Andras

    2009-01-01

    Sequencing of human and other genomes has been at the center of interest in the biomedical field over the past several decades and is now leading toward an era of personalized medicine. During this time, DNA sequencing methods have evolved from the labor intensive slab gel electrophoresis, through automated multicapillary electrophoresis systems using fluorophore labeling with multispectral imaging, to the “next generation” technologies of cyclic array, hybridization based, nanopore and single molecule sequencing. Deciphering the genetic blueprint and follow-up confirmatory sequencing of Homo sapiens and other genomes was only possible by the advent of modern sequencing technologies that was a result of step by step advances with a contribution of academics, medical personnel and instrument companies. While next generation sequencing is moving ahead at break-neck speed, the multicapillary electrophoretic systems played an essential role in the sequencing of the Human Genome, the foundation of the field of genomics. In this prospective, we wish to overview the role of capillary electrophoresis in DNA sequencing based in part of several of our articles in this journal. PMID:19517496

  1. 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

  2. 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.

  3. Commercial Art: Scope and Sequence.

    Science.gov (United States)

    Nashville - Davidson County Metropolitan Public Schools, TN.

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

  4. Note on Marsaglia\\'s Xorshift Random Number Generators

    Directory of Open Access Journals (Sweden)

    Richard P. Brent

    2004-08-01

    Full Text Available Marsaglia (2003 has described a class of Xorshift random number generators (RNGs with periods 2n - 1 for n = 32, 64, etc. We show that the sequences generated by these RNGs are identical to the sequences generated by certain linear feedback shift register (LFSR generators using "exclusive or" (xor operations on n-bit words, with a recurrence defined by a primitive polynomial of degree n.

  5. 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.

  6. Quantitative measure of randomness and order for complete genomes

    Science.gov (United States)

    Kong, Sing-Guan; Fan, Wen-Lang; Chen, Hong-Da; Wigger, Jan; Torda, Andrew E.; Lee, H. C.

    2009-06-01

    We propose an order index, ϕ , which gives a quantitative measure of randomness and order of complete genomic sequences. It maps genomes to a number from 0 (random and of infinite length) to 1 (fully ordered) and applies regardless of sequence length. The 786 complete genomic sequences in GenBank were found to have ϕ values in a very narrow range, ϕg=0.031-0.015+0.028 . We show this implies that genomes are halfway toward being completely random, or, at the “edge of chaos.” We further show that artificial “genomes” converted from literary classics have ϕ ’s that almost exactly coincide with ϕg , but sequences of low information content do not. We infer that ϕg represents a high information-capacity “fixed point” in sequence space, and that genomes are driven to it by the dynamics of a robust growth and evolution process. We show that a growth process characterized by random segmental duplication can robustly drive genomes to the fixed point.

  7. Rapid Diagnostics of Onboard Sequences

    Science.gov (United States)

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

    2012-01-01

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

  8. 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.)

  9. Accident sequence quantification with KIRAP

    International Nuclear Information System (INIS)

    Kim, Tae Un; Han, Sang Hoon; Kim, Kil You; Yang, Jun Eon; Jeong, Won Dae; Chang, Seung Cheol; Sung, Tae Yong; Kang, Dae Il; Park, Jin Hee; Lee, Yoon Hwan; Hwang, Mi Jeong.

    1997-01-01

    The tasks of probabilistic safety assessment(PSA) consists of the identification of initiating events, the construction of event tree for each initiating event, construction of fault trees for event tree logics, the analysis of reliability data and finally the accident sequence quantification. In the PSA, the accident sequence quantification is to calculate the core damage frequency, importance analysis and uncertainty analysis. Accident sequence quantification requires to understand the whole model of the PSA because it has to combine all event tree and fault tree models, and requires the excellent computer code because it takes long computation time. Advanced Research Group of Korea Atomic Energy Research Institute(KAERI) has developed PSA workstation KIRAP(Korea Integrated Reliability Analysis Code Package) for the PSA work. This report describes the procedures to perform accident sequence quantification, the method to use KIRAP's cut set generator, and method to perform the accident sequence quantification with KIRAP. (author). 6 refs

  10. Accident sequence quantification with KIRAP

    Energy Technology Data Exchange (ETDEWEB)

    Kim, Tae Un; Han, Sang Hoon; Kim, Kil You; Yang, Jun Eon; Jeong, Won Dae; Chang, Seung Cheol; Sung, Tae Yong; Kang, Dae Il; Park, Jin Hee; Lee, Yoon Hwan; Hwang, Mi Jeong

    1997-01-01

    The tasks of probabilistic safety assessment(PSA) consists of the identification of initiating events, the construction of event tree for each initiating event, construction of fault trees for event tree logics, the analysis of reliability data and finally the accident sequence quantification. In the PSA, the accident sequence quantification is to calculate the core damage frequency, importance analysis and uncertainty analysis. Accident sequence quantification requires to understand the whole model of the PSA because it has to combine all event tree and fault tree models, and requires the excellent computer code because it takes long computation time. Advanced Research Group of Korea Atomic Energy Research Institute(KAERI) has developed PSA workstation KIRAP(Korea Integrated Reliability Analysis Code Package) for the PSA work. This report describes the procedures to perform accident sequence quantification, the method to use KIRAP`s cut set generator, and method to perform the accident sequence quantification with KIRAP. (author). 6 refs.

  11. 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)

  12. [Complete genome sequencing and sequence analysis of BCG Tice].

    Science.gov (United States)

    Wang, Zhiming; Pan, Yuanlong; Wu, Jun; Zhu, Baoli

    2012-10-04

    The objective of this study is to obtain the complete genome sequence of Bacillus Calmette-Guerin Tice (BCG Tice), in order to provide more information about the molecular biology of BCG Tice and design more reasonable vaccines to prevent tuberculosis. We assembled the data from high-throughput sequencing with SOAPdenovo software, with many contigs and scaffolds obtained. There are many sequence gaps and physical gaps remained as a result of regional low coverage and low quality. We designed primers at the end of contigs and performed PCR amplification in order to link these contigs and scaffolds. With various enzymes to perform PCR amplification, adjustment of PCR reaction conditions, and combined with clone construction to sequence, all the gaps were finished. We obtained the complete genome sequence of BCG Tice and submitted it to GenBank of National Center for Biotechnology Information (NCBI). The genome of BCG Tice is 4334064 base pairs in length, with GC content 65.65%. The problems and strategies during the finishing step of BCG Tice sequencing are illuminated here, with the hope of affording some experience to those who are involved in the finishing step of genome sequencing. The microarray data were verified by our results.

  13. An extended sequence specificity for UV-induced DNA damage.

    Science.gov (United States)

    Chung, Long H; Murray, Vincent

    2018-01-01

    The sequence specificity of UV-induced DNA damage was determined with a higher precision and accuracy than previously reported. UV light induces two major damage adducts: cyclobutane pyrimidine dimers (CPDs) and pyrimidine(6-4)pyrimidone photoproducts (6-4PPs). Employing capillary electrophoresis with laser-induced fluorescence and taking advantages of the distinct properties of the CPDs and 6-4PPs, we studied the sequence specificity of UV-induced DNA damage in a purified DNA sequence using two approaches: end-labelling and a polymerase stop/linear amplification assay. A mitochondrial DNA sequence that contained a random nucleotide composition was employed as the target DNA sequence. With previous methodology, the UV sequence specificity was determined at a dinucleotide or trinucleotide level; however, in this paper, we have extended the UV sequence specificity to a hexanucleotide level. With the end-labelling technique (for 6-4PPs), the consensus sequence was found to be 5'-GCTC*AC (where C* is the breakage site); while with the linear amplification procedure, it was 5'-TCTT*AC. With end-labelling, the dinucleotide frequency of occurrence was highest for 5'-TC*, 5'-TT* and 5'-CC*; whereas it was 5'-TT* for linear amplification. The influence of neighbouring nucleotides on the degree of UV-induced DNA damage was also examined. The core sequences consisted of pyrimidine nucleotides 5'-CTC* and 5'-CTT* while an A at position "1" and C at position "2" enhanced UV-induced DNA damage. Crown Copyright © 2017. Published by Elsevier B.V. All rights reserved.

  14. High-Throughput Next-Generation Sequencing of Polioviruses

    Science.gov (United States)

    Montmayeur, Anna M.; Schmidt, Alexander; Zhao, Kun; Magaña, Laura; Iber, Jane; Castro, Christina J.; Chen, Qi; Henderson, Elizabeth; Ramos, Edward; Shaw, Jing; Tatusov, Roman L.; Dybdahl-Sissoko, Naomi; Endegue-Zanga, Marie Claire; Adeniji, Johnson A.; Oberste, M. Steven; Burns, Cara C.

    2016-01-01

    ABSTRACT The poliovirus (PV) is currently targeted for worldwide eradication and containment. Sanger-based sequencing of the viral protein 1 (VP1) capsid region is currently the standard method for PV surveillance. However, the whole-genome sequence is sometimes needed for higher resolution global surveillance. In this study, we optimized whole-genome sequencing protocols for poliovirus isolates and FTA cards using next-generation sequencing (NGS), aiming for high sequence coverage, efficiency, and throughput. We found that DNase treatment of poliovirus RNA followed by random reverse transcription (RT), amplification, and the use of the Nextera XT DNA library preparation kit produced significantly better results than other preparations. The average viral reads per total reads, a measurement of efficiency, was as high as 84.2% ± 15.6%. PV genomes covering >99 to 100% of the reference length were obtained and validated with Sanger sequencing. A total of 52 PV genomes were generated, multiplexing as many as 64 samples in a single Illumina MiSeq run. This high-throughput, sequence-independent NGS approach facilitated the detection of a diverse range of PVs, especially for those in vaccine-derived polioviruses (VDPV), circulating VDPV, or immunodeficiency-related VDPV. In contrast to results from previous studies on other viruses, our results showed that filtration and nuclease treatment did not discernibly increase the sequencing efficiency of PV isolates. However, DNase treatment after nucleic acid extraction to remove host DNA significantly improved the sequencing results. This NGS method has been successfully implemented to generate PV genomes for molecular epidemiology of the most recent PV isolates. Additionally, the ability to obtain full PV genomes from FTA cards will aid in facilitating global poliovirus surveillance. PMID:27927929

  15. The Matrix Method of Representation, Analysis and Classification of Long Genetic Sequences

    Directory of Open Access Journals (Sweden)

    Ivan V. Stepanyan

    2017-01-01

    Full Text Available The article is devoted to a matrix method of comparative analysis of long nucleotide sequences by means of presenting each sequence in the form of three digital binary sequences. This method uses a set of symmetries of biochemical attributes of nucleotides. It also uses the possibility of presentation of every whole set of N-mers as one of the members of a Kronecker family of genetic matrices. With this method, a long nucleotide sequence can be visually represented as an individual fractal-like mosaic or another regular mosaic of binary type. In contrast to natural nucleotide sequences, artificial random sequences give non-regular patterns. Examples of binary mosaics of long nucleotide sequences are shown, including cases of human chromosomes and penicillins. The obtained results are then discussed.

  16. A Repetition Test for Pseudo-Random Number Generators

    OpenAIRE

    Gil, Manuel; Gonnet, Gaston H.; Petersen, Wesley P.

    2017-01-01

    A new statistical test for uniform pseudo-random number generators (PRNGs) is presented. The idea is that a sequence of pseudo-random numbers should have numbers reappear with a certain probability. The expectation time that a repetition occurs provides the metric for the test. For linear congruential generators (LCGs) failure can be shown theoretically. Empirical test results for a number of commonly used PRNGs are reported, showing that some PRNGs considered to have good statistical propert...

  17. Return probabilities for the reflected random walk on N_0

    NARCIS (Netherlands)

    Essifi, R.; Peigné, M.

    2015-01-01

    Let \\((Y_n)\\) be a sequence of i.i.d. \\(\\mathbb{Z }\\)-valued random variables with law \\(\\mu \\). The reflected random walk \\((X_n)\\) is defined recursively by \\(X_0=x \\in \\mathbb{N }_0, X_{n+1}=\\vert X_n+Y_{n+1}\\vert \\). Under mild hypotheses on the law \\(\\mu \\), it is proved that, for any \\( y \\in

  18. Metaheuristic approaches to order sequencing on a unidirectional picking line

    Directory of Open Access Journals (Sweden)

    AP de Villiers

    2013-06-01

    Full Text Available 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 local search are presented as possible solution approaches. Computational results based on real life data instances are presented for these metaheuristics and compared to the performance of a lower bound and the solutions used in practise. The random local search exhibits the best overall solution quality, however, the generalised extremal optimisation approach delivers comparable results in considerably shorter computational times.

  19. 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.

  20. PuLSE: Quality control and quantification of peptide sequences explored by phage display libraries.

    Science.gov (United States)

    Shave, Steven; Mann, Stefan; Koszela, Joanna; Kerr, Alastair; Auer, Manfred

    2018-01-01

    The design of highly diverse phage display libraries is based on assumption that DNA bases are incorporated at similar rates within the randomized sequence. As library complexity increases and expected copy numbers of unique sequences decrease, the exploration of library space becomes sparser and the presence of truly random sequences becomes critical. We present the program PuLSE (Phage Library Sequence Evaluation) as a tool for assessing randomness and therefore diversity of phage display libraries. PuLSE runs on a collection of sequence reads in the fastq file format and generates tables profiling the library in terms of unique DNA sequence counts and positions, translated peptide sequences, and normalized 'expected' occurrences from base to residue codon frequencies. The output allows at-a-glance quantitative quality control of a phage library in terms of sequence coverage both at the DNA base and translated protein residue level, which has been missing from toolsets and literature. The open source program PuLSE is available in two formats, a C++ source code package for compilation and integration into existing bioinformatics pipelines and precompiled binaries for ease of use.

  1. Random surfaces and strings

    International Nuclear Information System (INIS)

    Ambjoern, J.

    1987-08-01

    The theory of strings is the theory of random surfaces. I review the present attempts to regularize the world sheet of the string by triangulation. The corresponding statistical theory of triangulated random surfaces has a surprising rich structure, but the connection to conventional string theory seems non-trivial. (orig.)

  2. Derandomizing from random strings

    NARCIS (Netherlands)

    Buhrman, H.; Fortnow, L.; Koucký, M.; Loff, B.

    2010-01-01

    In this paper we show that BPP is truth-table reducible to the set of Kolmogorov random strings R(K). It was previously known that PSPACE, and hence BPP is Turing-reducible to R(K). The earlier proof relied on the adaptivity of the Turing-reduction to find a Kolmogorov-random string of polynomial

  3. Quantum random number generator

    Science.gov (United States)

    Soubusta, Jan; Haderka, Ondrej; Hendrych, Martin

    2001-03-01

    Since reflection or transmission of a quantum particle on a beamsplitter is inherently random quantum process, a device built on this principle does not suffer from drawbacks of neither pseudo-random computer generators or classical noise sources. Nevertheless, a number of physical conditions necessary for high quality random numbers generation must be satisfied. Luckily, in quantum optics realization they can be well controlled. We present an easy random number generator based on the division of weak light pulses on a beamsplitter. The randomness of the generated bit stream is supported by passing the data through series of 15 statistical test. The device generates at a rate of 109.7 kbit/s.

  4. Quantum random number generator

    Science.gov (United States)

    Pooser, Raphael C.

    2016-05-10

    A quantum random number generator (QRNG) and a photon generator for a QRNG are provided. The photon generator may be operated in a spontaneous mode below a lasing threshold to emit photons. Photons emitted from the photon generator may have at least one random characteristic, which may be monitored by the QRNG to generate a random number. In one embodiment, the photon generator may include a photon emitter and an amplifier coupled to the photon emitter. The amplifier may enable the photon generator to be used in the QRNG without introducing significant bias in the random number and may enable multiplexing of multiple random numbers. The amplifier may also desensitize the photon generator to fluctuations in power supplied thereto while operating in the spontaneous mode. In one embodiment, the photon emitter and amplifier may be a tapered diode amplifier.

  5. 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.

  6. Musical Scales in Tone Sequences Improve Temporal Accuracy.

    Science.gov (United States)

    Li, Min S; Di Luca, Massimiliano

    2018-01-01

    Predicting the time of stimulus onset is a key component in perception. Previous investigations of perceived timing have focused on the effect of stimulus properties such as rhythm and temporal irregularity, but the influence of non-temporal properties and their role in predicting stimulus timing has not been exhaustively considered. The present study aims to understand how a non-temporal pattern in a sequence of regularly timed stimuli could improve or bias the detection of temporal deviations. We presented interspersed sequences of 3, 4, 5, and 6 auditory tones where only the timing of the last stimulus could slightly deviate from isochrony. Participants reported whether the last tone was 'earlier' or 'later' relative to the expected regular timing. In two conditions, the tones composing the sequence were either organized into musical scales or they were random tones. In one experiment, all sequences ended with the same tone; in the other experiment, each sequence ended with a different tone. Results indicate higher discriminability of anisochrony with musical scales and with longer sequences, irrespective of the knowledge of the final tone. Such an outcome suggests that the predictability of non-temporal properties, as enabled by the musical scale pattern, can be a factor in determining the sensitivity of time judgments.

  7. 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.

  8. GROUPING WEB ACCESS SEQUENCES uSING SEQUENCE ALIGNMENT METHOD

    OpenAIRE

    BHUPENDRA S CHORDIA; KRISHNAKANT P ADHIYA

    2011-01-01

    In web usage mining grouping of web access sequences can be used to determine the behavior or intent of a set of users. Grouping websessions is how to measure the similarity between web sessions. There are many shortcomings in traditional measurement methods. The taskof grouping web sessions based on similarity and consists of maximizing the intra-group similarity while minimizing the inter-groupsimilarity is done using sequence alignment method. This paper introduces a new method to group we...

  9. Hybridization Capture Using Short PCR Products Enriches Small Genomes by Capturing Flanking Sequences (CapFlank)

    DEFF Research Database (Denmark)

    Tsangaras, Kyriakos; Wales, Nathan; Sicheritz-Pontén, Thomas

    2014-01-01

    , 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...

  10. 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

  11. Nonlinear analysis of sequence symmetry of beta-trefoil family proteins

    Energy Technology Data Exchange (ETDEWEB)

    Li Mingfeng [Biomolecular Physics and Modeling Group, Department of Physics, Huazhong University of Science and Technology, Wuhan 430074, Hubei (China); Huang Yanzhao [Biomolecular Physics and Modeling Group, Department of Physics, Huazhong University of Science and Technology, Wuhan 430074, Hubei (China); Xu Ruizhen [Biomolecular Physics and Modeling Group, Department of Physics, Huazhong University of Science and Technology, Wuhan 430074, Hubei (China); Xiao Yi [Biomolecular Physics and Modeling Group, Department of Physics, Huazhong University of Science and Technology, Wuhan 430074, Hubei (China)]. E-mail: yxiao@mail.hust.edu.cn

    2005-07-01

    The tertiary structures of proteins of beta-trefoil family have three-fold quasi-symmetry while their amino acid sequences appear almost at random. In the present paper we show that these amino acid sequences have hidden symmetries in fact and furthermore the degrees of these hidden symmetries are the same as those of their tertiary structures. We shall present a modified recurrence plot to reveal hidden symmetries in protein sequences. Our results can explain the contradiction in sequence-structure relations of proteins of beta-trefoil family.

  12. Random walk centrality for temporal networks

    International Nuclear Information System (INIS)

    Rocha, Luis E C; Masuda, Naoki

    2014-01-01

    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. (paper)

  13. 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.

  14. Sampling problems for randomly broken sticks

    Energy Technology Data Exchange (ETDEWEB)

    Huillet, Thierry [Laboratoire de Physique Theorique et Modelisation, CNRS-UMR 8089 et Universite de Cergy-Pontoise, 5 mail Gay-Lussac, 95031, Neuville sur Oise (France)

    2003-04-11

    Consider the random partitioning model of a population (represented by a stick of length 1) into n species (fragments) with identically distributed random weights (sizes). Upon ranking the fragments' weights according to ascending sizes, let S{sub m:n} be the size of the mth smallest fragment. Assume that some observer is sampling such populations as follows: drop at random k points (the sample size) onto this stick and record the corresponding numbers of visited fragments. We shall investigate the following sampling problems: (1) what is the sample size if the sampling is carried out until the first visit of the smallest fragment (size S{sub 1:n})? (2) For a given sample size, have all the fragments of the stick been visited at least once or not? This question is related to Feller's random coupon collector problem. (3) In what order are new fragments being discovered and what is the random number of samples separating the discovery of consecutive new fragments until exhaustion of the list? For this problem, the distribution of the size-biased permutation of the species' weights, as the sequence of their weights in their order of appearance is needed and studied.

  15. Weak disorder in Fibonacci sequences

    Energy Technology Data Exchange (ETDEWEB)

    Ben-Naim, E [Theoretical Division and Center for Nonlinear Studies, Los Alamos National Laboratory, Los Alamos, NM 87545 (United States); Krapivsky, P L [Department of Physics and Center for Molecular Cybernetics, Boston University, Boston, MA 02215 (United States)

    2006-05-19

    We study how weak disorder affects the growth of the Fibonacci series. We introduce a family of stochastic sequences that grow by the normal Fibonacci recursion with probability 1 - {epsilon}, but follow a different recursion rule with a small probability {epsilon}. We focus on the weak disorder limit and obtain the Lyapunov exponent that characterizes the typical growth of the sequence elements, using perturbation theory. The limiting distribution for the ratio of consecutive sequence elements is obtained as well. A number of variations to the basic Fibonacci recursion including shift, doubling and copying are considered. (letter to the editor)

  16. Thermoresponsive Poly(2-Oxazoline) Molecular Brushes by Living Ionic Polymerization: Modulation of the Cloud Point by Random and Block Copolymer Pendant Chains

    KAUST Repository

    Zhang, Ning; Luxenhofer, Robert; Jordan, Rainer

    2012-01-01

    random and block copolymers. Their aqueous solutions displayed a distinct thermoresponsive behavior as a function of the side-chain composition and sequence. The cloud point (CP) of MBs with random copolymer side chains is a linear function

  17. ADHD Psychosocial Treatments: Generalization Reconsidered

    Science.gov (United States)

    Abikoff, Howard

    2009-01-01

    Behavioral interventions have demonstrated clinical utility in improving the behavior of children with ADHD, especially in specialized therapeutic milieus (Pelham et al., 2000). Improvements in children's target behaviors often occur in the treatment settings where contingencies are in place and delivered consistently. However, generalization of…

  18. 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.

  19. The Principles of War Reconsidered

    Science.gov (United States)

    2009-06-01

    and technological innovation that affected all military capabilities” (Williamson Murray, “Armored Warfare,” W. Murray, A.R. Millet (Eds), Military...Richard M. Muller, “Close Air Support,” W. Murray, A.R. Millet (ed.), Military Innovation in the Interwar Period, Cambridge: University Press, 1996...dispersed battle-groups – making sharp ‘ finger -thrust’ … On the Russian Front the defensive 44 capacity of small mobile forces, distributed in battle

  20. Reconsidering Subextraction: Evidence from Spanish

    Directory of Open Access Journals (Sweden)

    Ignacio Bosque

    2014-11-01

    Full Text Available This paper argues that so-called subextraction (e.g., Whoi has John seen a picture of ti ?; cf. Corver 2006 for recent discussion does not involve movement of a wh-phrase to a DP internal escape hatch position before reaching the CP layer. Instead, we claim that apparently subextracted wh-phrases are actually direct dependents of the verb after a process of reanalysis (or readjustment; cf. Chomsky 1977, Kayne 2002 applies. Our proposal rethinks an old (Bach & Horn 1976 idea, reframes it in modern terms and argues against the cyclic status of DPs (cf. Bruening 2009, Leu 2008, Ott 2008, and references therein, by leaning on new evidence from Spanish. The non-cyclic status of DPs is a fairly standard idea ever since clausal properties were assumed to hold for nominal domains (cf. Chomsky 1970, Brame 1982, Abney 1987, and much subsequent literature.

  1. 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.

  2. Reconsidering the extinction of ichthyosaurs

    OpenAIRE

    Fischer, Valentin

    2010-01-01

    Despite their extreme adaptation to life in open sea, ichthyosaurs were one of the first major groups of post-Triassic marine reptiles to disappear, at the end of Cenomanian, whereas plesiosaurs, mosasaurs and numerous families of marine crocodiles and sea turtles disappeared during the Cretaceous/Paleocene Extinction Event. It has been proposed that unique biological factors drove ichthyosaurs to extinction, namely a break in the food chain at the level of belemnites or a progressive ecologi...

  3. The relativistic harmonic oscillator reconsidered

    International Nuclear Information System (INIS)

    Hofsaess, T.

    1978-01-01

    The bound states of scalar quarks interacting through a scalar harmonic oscillator are investigated. In the presence of this interaction the dressed quark propagator differs substantially from the free one. This leads to a Bethe Salpeter equation which does not allow for any stable bound states of positive mass. (orig.) [de

  4. 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

  5. The Areopagus Oval Building Reconsidered

    NARCIS (Netherlands)

    van den Eijnde, F.; Laughy, Michael H.

    2017-01-01

    The Areopagus Oval Building (AOB) provides a rare insight into Athenian architecture during the Geometric period, a time in which the archaeological record is mostly confined to graves. Dorothy Burr’s original 1933 publication of the building remains an exemplary and exhaustive presentation of the

  6. 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…

  7. Reconsidering Asian American Student Development

    Science.gov (United States)

    Kodama, Corinne M.; Maramba, Dina C.

    2017-01-01

    This chapter addresses the applicability of student development theories in light of empirical research on Asian American college students through a twofold approach: (a) revisiting the relevance of Kodama, McEwen, Liang, and Lee's (2001, 2002) theoretical work on Asian American student development; and (b) using Jones' and Stewart's (2016)…

  8. 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.…

  9. 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.

  10. Reconsidering Community-based Retailing

    OpenAIRE

    Maughan, Rebecca; O'Driscoll, Aidan

    2012-01-01

    One of the areas with great potential for economic, social and environmental benefit is community-based retailing. The concept of community based retailing can incorporate a number of different tenets. We suggest that it is retailing that is based close to the community it serves, usually within the town or village centre rather than out-of-town locations, and which is composed of a diverse range of small and medium sized business that are often independently or co-operatively owned. These co...

  11. Experimental Rugged Fitness Landscape in Protein Sequence Space

    Science.gov (United States)

    Hayashi, Yuuki; Aita, Takuyo; Toyota, Hitoshi; Husimi, Yuzuru; Urabe, Itaru; Yomo, Tetsuya

    2006-01-01

    The fitness landscape in sequence space determines the process of biomolecular evolution. To plot the fitness landscape of protein function, we carried out in vitro molecular evolution beginning with a defective fd phage carrying a random polypeptide of 139 amino acids in place of the g3p minor coat protein D2 domain, which is essential for phage infection. After 20 cycles of random substitution at sites 12–130 of the initial random polypeptide and selection for infectivity, the selected phage showed a 1.7×104-fold increase in infectivity, defined as the number of infected cells per ml of phage suspension. Fitness was defined as the logarithm of infectivity, and we analyzed (1) the dependence of stationary fitness on library size, which increased gradually, and (2) the time course of changes in fitness in transitional phases, based on an original theory regarding the evolutionary dynamics in Kauffman's n-k fitness landscape model. In the landscape model, single mutations at single sites among n sites affect the contribution of k other sites to fitness. Based on the results of these analyses, k was estimated to be 18–24. According to the estimated parameters, the landscape was plotted as a smooth surface up to a relative fitness of 0.4 of the global peak, whereas the landscape had a highly rugged surface with many local peaks above this relative fitness value. Based on the landscapes of these two different surfaces, it appears possible for adaptive walks with only random substitutions to climb with relative ease up to the middle region of the fitness landscape from any primordial or random sequence, whereas an enormous range of sequence diversity is required to climb further up the rugged surface above the middle region. PMID:17183728

  12. Experimental rugged fitness landscape in protein sequence space.

    Science.gov (United States)

    Hayashi, Yuuki; Aita, Takuyo; Toyota, Hitoshi; Husimi, Yuzuru; Urabe, Itaru; Yomo, Tetsuya

    2006-12-20

    The fitness landscape in sequence space determines the process of biomolecular evolution. To plot the fitness landscape of protein function, we carried out in vitro molecular evolution beginning with a defective fd phage carrying a random polypeptide of 139 amino acids in place of the g3p minor coat protein D2 domain, which is essential for phage infection. After 20 cycles of random substitution at sites 12-130 of the initial random polypeptide and selection for infectivity, the selected phage showed a 1.7x10(4)-fold increase in infectivity, defined as the number of infected cells per ml of phage suspension. Fitness was defined as the logarithm of infectivity, and we analyzed (1) the dependence of stationary fitness on library size, which increased gradually, and (2) the time course of changes in fitness in transitional phases, based on an original theory regarding the evolutionary dynamics in Kauffman's n-k fitness landscape model. In the landscape model, single mutations at single sites among n sites affect the contribution of k other sites to fitness. Based on the results of these analyses, k was estimated to be 18-24. According to the estimated parameters, the landscape was plotted as a smooth surface up to a relative fitness of 0.4 of the global peak, whereas the landscape had a highly rugged surface with many local peaks above this relative fitness value. Based on the landscapes of these two different surfaces, it appears possible for adaptive walks with only random substitutions to climb with relative ease up to the middle region of the fitness landscape from any primordial or random sequence, whereas an enormous range of sequence diversity is required to climb further up the rugged surface above the middle region.

  13. Experimental rugged fitness landscape in protein sequence space.

    Directory of Open Access Journals (Sweden)

    Yuuki Hayashi

    Full Text Available The fitness landscape in sequence space determines the process of biomolecular evolution. To plot the fitness landscape of protein function, we carried out in vitro molecular evolution beginning with a defective fd phage carrying a random polypeptide of 139 amino acids in place of the g3p minor coat protein D2 domain, which is essential for phage infection. After 20 cycles of random substitution at sites 12-130 of the initial random polypeptide and selection for infectivity, the selected phage showed a 1.7x10(4-fold increase in infectivity, defined as the number of infected cells per ml of phage suspension. Fitness was defined as the logarithm of infectivity, and we analyzed (1 the dependence of stationary fitness on library size, which increased gradually, and (2 the time course of changes in fitness in transitional phases, based on an original theory regarding the evolutionary dynamics in Kauffman's n-k fitness landscape model. In the landscape model, single mutations at single sites among n sites affect the contribution of k other sites to fitness. Based on the results of these analyses, k was estimated to be 18-24. According to the estimated parameters, the landscape was plotted as a smooth surface up to a relative fitness of 0.4 of the global peak, whereas the landscape had a highly rugged surface with many local peaks above this relative fitness value. Based on the landscapes of these two different surfaces, it appears possible for adaptive walks with only random substitutions to climb with relative ease up to the middle region of the fitness landscape from any primordial or random sequence, whereas an enormous range of sequence diversity is required to climb further up the rugged surface above the middle region.

  14. The span of correlations in dolphin whistle sequences

    International Nuclear Information System (INIS)

    Ferrer-i-Cancho, Ramon; McCowan, Brenda

    2012-01-01

    Long-range correlations are found in symbolic sequences from human language, music and DNA. Determining the span of correlations in dolphin whistle sequences is crucial for shedding light on their communicative complexity. Dolphin whistles share various statistical properties with human words, i.e. Zipf's law for word frequencies (namely that the probability of the ith most frequent word of a text is about i −α ) and a parallel of the tendency of more frequent words to have more meanings. The finding of Zipf's law for word frequencies in dolphin whistles has been the topic of an intense debate on its implications. One of the major arguments against the relevance of Zipf's law in dolphin whistles is that it is not possible to distinguish the outcome of a die-rolling experiment from that of a linguistic or communicative source producing Zipf's law for word frequencies. Here we show that statistically significant whistle–whistle correlations extend back to the second previous whistle in the sequence, using a global randomization test, and to the fourth previous whistle, using a local randomization test. None of these correlations are expected by a die-rolling experiment and other simple explanations of Zipf's law for word frequencies, such as Simon's model, that produce sequences of unpredictable elements

  15. Noisy: Identification of problematic columns in multiple sequence alignments

    Directory of Open Access Journals (Sweden)

    Grünewald Stefan

    2008-06-01

    Full Text Available Abstract Motivation Sequence-based methods for phylogenetic reconstruction from (nucleic acid sequence data are notoriously plagued by two effects: homoplasies and alignment errors. Large evolutionary distances imply a large number of homoplastic sites. As most protein-coding genes show dramatic variations in substitution rates that are not uncorrelated across the sequence, this often leads to a patchwork pattern of (i phylogenetically informative and (ii effectively randomized regions. In highly variable regions, furthermore, alignment errors accumulate resulting in sometimes misleading signals in phylogenetic reconstruction. Results We present here a method that, based on assessing the distribution of character states along a cyclic ordering of the taxa, allows the identification of phylogenetically uninformative homoplastic sites in a multiple sequence alignment. Removal of these sites appears to improve the performance of phylogenetic reconstruction algorithms as measured by various indices of "tree quality". In particular, we obtain more stable trees due to the exclusion of phylogenetically incompatible sites that most likely represent strongly randomized characters. Software The computer program noisy implements this approach. It can be employed to improving phylogenetic reconstruction capability with quite a considerable success rate whenever (1 the average bootstrap support obtained from the original alignment is low, and (2 there are sufficiently many taxa in the data set – at least, say, 12 to 15 taxa. The software can be obtained under the GNU Public License from http://www.bioinf.uni-leipzig.de/Software/noisy/.

  16. Spectral sum rules and search for periodicities in DNA sequences

    International Nuclear Information System (INIS)

    Chechetkin, V.R.

    2011-01-01

    Periodic patterns play the important regulatory and structural roles in genomic DNA sequences. Commonly, the underlying periodicities should be understood in a broad statistical sense, since the corresponding periodic patterns have been strongly distorted by the random point mutations and insertions/deletions during molecular evolution. The latent periodicities in DNA sequences can be efficiently displayed by Fourier transform. The criteria of significance for observed periodicities are obtained via the comparison versus the counterpart characteristics of the reference random sequences. We show that the restrictions imposed on the significance criteria by the rigorous spectral sum rules can be rationally described with De Finetti distribution. This distribution provides the convenient intermediate asymptotic form between Rayleigh distribution and exact combinatoric theory. - Highlights: → We study the significance criteria for latent periodicities in DNA sequences. → The constraints imposed by sum rules can be described with De Finetti distribution. → It is intermediate between Rayleigh distribution and exact combinatoric theory. → Theory is applicable to the study of correlations between different periodicities. → The approach can be generalized to the arbitrary discrete Fourier transform.

  17. Random numbers spring from alpha decay

    International Nuclear Information System (INIS)

    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 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

  18. Sequence analysis of Leukemia DNA

    Science.gov (United States)

    Nacong, Nasria; Lusiyanti, Desy; Irawan, Muhammad. Isa

    2018-03-01

    Cancer is a very deadly disease, one of which is leukemia disease or better known as blood cancer. The cancer cell can be detected by taking DNA in laboratory test. This study focused on local alignment of leukemia and non leukemia data resulting from NCBI in the form of DNA sequences by using Smith-Waterman algorithm. SmithWaterman algorithm was invented by TF Smith and MS Waterman in 1981. These algorithms try to find as much as possible similarity of a pair of sequences, by giving a negative value to the unequal base pair (mismatch), and positive values on the same base pair (match). So that will obtain the maximum positive value as the end of the alignment, and the minimum value as the initial alignment. This study will use sequences of leukemia and 3 sequences of non leukemia.

  19. 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

  20. Random number generation

    International Nuclear Information System (INIS)

    Coveyou, R.R.

    1974-01-01

    The subject of random number generation is currently controversial. Differing opinions on this subject seem to stem from implicit or explicit differences in philosophy; in particular, from differing ideas concerning the role of probability in the real world of physical processes, electronic computers, and Monte Carlo calculations. An attempt is made here to reconcile these views. The role of stochastic ideas in mathematical models is discussed. In illustration of these ideas, a mathematical model of the use of random number generators in Monte Carlo calculations is constructed. This model is used to set up criteria for the comparison and evaluation of random number generators. (U.S.)

  1. Quantum random access memory

    OpenAIRE

    Giovannetti, Vittorio; Lloyd, Seth; Maccone, Lorenzo

    2007-01-01

    A random access memory (RAM) uses n bits to randomly address N=2^n distinct memory cells. A quantum random access memory (qRAM) uses n qubits to address any quantum superposition of N memory cells. We present an architecture that exponentially reduces the requirements for a memory call: O(log N) switches need be thrown instead of the N used in conventional (classical or quantum) RAM designs. This yields a more robust qRAM algorithm, as it in general requires entanglement among exponentially l...

  2. Randomization of inspections

    International Nuclear Information System (INIS)

    Markin, J.T.

    1989-01-01

    As the numbers and complexity of nuclear facilities increase, limitations on resources for international safeguards may restrict attainment of safeguards goals. One option for improving the efficiency of limited resources is to expand the current inspection regime to include random allocation of the amount and frequency of inspection effort to material strata or to facilities. This paper identifies the changes in safeguards policy, administrative procedures, and operational procedures that would be necessary to accommodate randomized inspections and identifies those situations where randomization can improve inspection efficiency and those situations where the current nonrandom inspections should be maintained. 9 refs., 1 tab

  3. Random phenomena; Phenomenes aleatoires

    Energy Technology Data Exchange (ETDEWEB)

    Bonnet, G. [Commissariat a l' energie atomique et aux energies alternatives - CEA, C.E.N.G., Service d' Electronique, Section d' Electronique, Grenoble (France)

    1963-07-01

    This document gathers a set of conferences presented in 1962. A first one proposes a mathematical introduction to the analysis of random phenomena. The second one presents an axiomatic of probability calculation. The third one proposes an overview of one-dimensional random variables. The fourth one addresses random pairs, and presents basic theorems regarding the algebra of mathematical expectations. The fifth conference discusses some probability laws: binomial distribution, the Poisson distribution, and the Laplace-Gauss distribution. The last one deals with the issues of stochastic convergence and asymptotic distributions.

  4. Integrated sequence analysis. Final report

    International Nuclear Information System (INIS)

    Andersson, K.; Pyy, P.

    1998-02-01

    The NKS/RAK subprojet 3 'integrated sequence analysis' (ISA) was formulated with the overall objective to develop and to test integrated methodologies in order to evaluate event sequences with significant human action contribution. The term 'methodology' denotes not only technical tools but also methods for integration of different scientific disciplines. In this report, we first discuss the background of ISA and the surveys made to map methods in different application fields, such as man machine system simulation software, human reliability analysis (HRA) and expert judgement. Specific event sequences were, after the surveys, selected for application and testing of a number of ISA methods. The event sequences discussed in the report were cold overpressure of BWR, shutdown LOCA of BWR, steam generator tube rupture of a PWR and BWR disturbed signal view in the control room after an external event. Different teams analysed these sequences by using different ISA and HRA methods. Two kinds of results were obtained from the ISA project: sequence specific and more general findings. The sequence specific results are discussed together with each sequence description. The general lessons are discussed under a separate chapter by using comparisons of different case studies. These lessons include areas ranging from plant safety management (design, procedures, instrumentation, operations, maintenance and safety practices) to methodological findings (ISA methodology, PSA,HRA, physical analyses, behavioural analyses and uncertainty assessment). Finally follows a discussion about the project and conclusions are presented. An interdisciplinary study of complex phenomena is a natural way to produce valuable and innovative results. This project came up with structured ways to perform ISA and managed to apply the in practice. The project also highlighted some areas where more work is needed. In the HRA work, development is required for the use of simulators and expert judgement as

  5. Pseudo-random bit generator based on lag time series

    Science.gov (United States)

    García-Martínez, M.; Campos-Cantón, E.

    2014-12-01

    In this paper, we present a pseudo-random bit generator (PRBG) based on two lag time series of the logistic map using positive and negative values in the bifurcation parameter. In order to hidden the map used to build the pseudo-random series we have used a delay in the generation of time series. These new series when they are mapped xn against xn+1 present a cloud of points unrelated to the logistic map. Finally, the pseudo-random sequences have been tested with the suite of NIST giving satisfactory results for use in stream ciphers.

  6. 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

  7. Hedysarum L. (Fabaceae: Hedysareae) Is Not Monophyletic - Evidence from Phylogenetic Analyses Based on Five Nuclear and Five Plastid Sequences.

    Science.gov (United States)

    Liu, Pei-Liang; Wen, Jun; Duan, Lei; Arslan, Emine; Ertuğrul, Kuddisi; Chang, Zhao-Yang

    2017-01-01

    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.

  8. Hedysarum L. (Fabaceae: Hedysareae) Is Not Monophyletic – Evidence from Phylogenetic Analyses Based on Five Nuclear and Five Plastid Sequences

    Science.gov (United States)

    Liu, Pei-Liang; Wen, Jun; Duan, Lei; Arslan, Emine; Ertuğrul, Kuddisi; Chang, Zhao-Yang

    2017-01-01

    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. PMID:28122062

  9. 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

  10. 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.

  11. ADDRESS SEQUENCES FOR MULTI RUN RAM TESTING

    Directory of Open Access Journals (Sweden)

    V. N. Yarmolik

    2014-01-01

    Full Text Available A universal approach for generation of address sequences with specified properties is proposed and analyzed. A modified version of the Antonov and Saleev algorithm for Sobol sequences genera-tion is chosen as a mathematical description of the proposed method. Within the framework of the proposed universal approach, the Sobol sequences form a subset of the address sequences. Other sub-sets are also formed, which are Gray sequences, anti-Gray sequences, counter sequences and sequenc-es with specified properties.

  12. Fast and secure retrieval of DNA sequences

    NARCIS (Netherlands)

    2014-01-01

    Sequence models are retrieved from a sequences index. The sequence models model DNA or RNA sequences stored in a database, and each comprises a finite memory tree source model and parameters for the finite memory tree source model. One or more DNA or RNA sequences stored in the database are

  13. Decidability of uniform recurrence of morphic sequences

    OpenAIRE

    Durand , Fabien

    2012-01-01

    We prove that the uniform recurrence of morphic sequences is decidable. For this we show that the number of derived sequences of uniformly recurrent morphic sequences is bounded. As a corollary we obtain that uniformly recurrent morphic sequences are primitive substitutive sequences.

  14. [Influence of "prehistory" of sequential movements of the right and the left hand on reproduction: coding of positions, movements and sequence structure].

    Science.gov (United States)

    Bobrova, E V; Liakhovetskiĭ, V A; Borshchevskaia, E R

    2011-01-01

    The dependence of errors during reproduction of a sequence of hand movements without visual feedback on the previous right- and left-hand performance ("prehistory") and on positions in space of sequence elements (random or ordered by the explicit rule) was analyzed. It was shown that the preceding information about the ordered positions of the sequence elements was used during right-hand movements, whereas left-hand movements were performed with involvement of the information about the random sequence. The data testify to a central mechanism of the analysis of spatial structure of sequence elements. This mechanism activates movement coding specific for the left hemisphere (vector coding) in case of an ordered sequence structure and positional coding specific for the right hemisphere in case of a random sequence structure.

  15. Tunable random packings

    International Nuclear Information System (INIS)

    Lumay, G; Vandewalle, N

    2007-01-01

    We present an experimental protocol that allows one to tune the packing fraction η of a random pile of ferromagnetic spheres from a value close to the lower limit of random loose packing η RLP ≅0.56 to the upper limit of random close packing η RCP ≅0.64. This broad range of packing fraction values is obtained under normal gravity in air, by adjusting a magnetic cohesion between the grains during the formation of the pile. Attractive and repulsive magnetic interactions are found to affect stongly the internal structure and the stability of sphere packing. After the formation of the pile, the induced cohesion is decreased continuously along a linear decreasing ramp. The controlled collapse of the pile is found to generate various and reproducible values of the random packing fraction η

  16. 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...

  17. 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...

  18. 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

  19. Efficiency of random amplified polymorphic DNA (RAPD) and inter ...

    African Journals Online (AJOL)

    Efficiency of random amplified polymorphic DNA (RAPD) and inter-simple sequence repeats (ISSR) markers for genotype fingerprinting and genetic diversity studies in canola ( ) ... The number of amplified fragments with RAPD primers ranged from 8 to 21, with the size of amplicons ranging from 162 to 3154 bp.

  20. 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)

  1. 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.

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

    Science.gov (United States)

    Tan, M K

    1991-08-01

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

  3. Comparative genome sequencing of Drosophila pseudoobscura: Chromosomal, gene, and cis-element evolution

    DEFF Research Database (Denmark)

    Richards, Stephen; Liu, Yue; Bettencourt, Brian R.

    2005-01-01

    years (Myr) since the pseudoobscura/melanogaster divergence. Genes expressed in the testes had higher amino acid sequence divergence than the genome-wide average, consistent with the rapid evolution of sex-specific proteins. Cis-regulatory sequences are more conserved than random and nearby sequences......We have sequenced the genome of a second Drosophila species, Drosophila pseudoobscura, and compared this to the genome sequence of Drosophila melanogaster, a primary model organism. Throughout evolution the vast majority of Drosophila genes have remained on the same chromosome arm, but within each...... between the species-but the difference is slight, suggesting that the evolution of cis-regulatory elements is flexible. Overall, a pattern of repeat-mediated chromosomal rearrangement, and high coadaptation of both male genes and cis-regulatory sequences emerges as important themes of genome divergence...

  4. DNA-based random number generation in security circuitry.

    Science.gov (United States)

    Gearheart, Christy M; Arazi, Benjamin; Rouchka, Eric C

    2010-06-01

    DNA-based circuit design is an area of research in which traditional silicon-based technologies are replaced by naturally occurring phenomena taken from biochemistry and molecular biology. This research focuses on further developing DNA-based methodologies to mimic digital data manipulation. While exhibiting fundamental principles, this work was done in conjunction with the vision that DNA-based circuitry, when the technology matures, will form the basis for a tamper-proof security module, revolutionizing the meaning and concept of tamper-proofing and possibly preventing it altogether based on accurate scientific observations. A paramount part of such a solution would be self-generation of random numbers. A novel prototype schema employs solid phase synthesis of oligonucleotides for random construction of DNA sequences; temporary storage and retrieval is achieved through plasmid vectors. A discussion of how to evaluate sequence randomness is included, as well as how these techniques are applied to a simulation of the random number generation circuitry. Simulation results show generated sequences successfully pass three selected NIST random number generation tests specified for security applications.

  5. 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.

  6. Genome Sequences of Oryza Species

    KAUST Repository

    Kumagai, Masahiko; Tanaka, Tsuyoshi; Ohyanagi, Hajime; Hsing, Yue-Ie C.; Itoh, Takeshi

    2018-01-01

    This chapter summarizes recent data obtained from genome sequencing, annotation projects, and studies on the genome diversity of Oryza sativa and related Oryza species. O. sativa, commonly known as Asian rice, is the first monocot species whose complete genome sequence was deciphered based on physical mapping by an international collaborative effort. This genome, along with its accurate and comprehensive annotation, has become an indispensable foundation for crop genomics and breeding. With the development of innovative sequencing technologies, genomic studies of O. sativa have dramatically increased; in particular, a large number of cultivars and wild accessions have been sequenced and compared with the reference rice genome. Since de novo genome sequencing has become cost-effective, the genome of African cultivated rice, O. glaberrima, has also been determined. Comparative genomic studies have highlighted the independent domestication processes of different rice species, but it also turned out that Asian and African rice share a common gene set that has experienced similar artificial selection. An international project aimed at constructing reference genomes and examining the genome diversity of wild Oryza species is currently underway, and the genomes of some species are publicly available. This project provides a platform for investigations such as the evolution, development, polyploidization, and improvement of crops. Studies on the genomic diversity of Oryza species, including wild species, should provide new insights to solve the problem of growing food demands in the face of rapid climatic changes.

  7. Genome Sequences of Oryza Species

    KAUST Repository

    Kumagai, Masahiko

    2018-02-14

    This chapter summarizes recent data obtained from genome sequencing, annotation projects, and studies on the genome diversity of Oryza sativa and related Oryza species. O. sativa, commonly known as Asian rice, is the first monocot species whose complete genome sequence was deciphered based on physical mapping by an international collaborative effort. This genome, along with its accurate and comprehensive annotation, has become an indispensable foundation for crop genomics and breeding. With the development of innovative sequencing technologies, genomic studies of O. sativa have dramatically increased; in particular, a large number of cultivars and wild accessions have been sequenced and compared with the reference rice genome. Since de novo genome sequencing has become cost-effective, the genome of African cultivated rice, O. glaberrima, has also been determined. Comparative genomic studies have highlighted the independent domestication processes of different rice species, but it also turned out that Asian and African rice share a common gene set that has experienced similar artificial selection. An international project aimed at constructing reference genomes and examining the genome diversity of wild Oryza species is currently underway, and the genomes of some species are publicly available. This project provides a platform for investigations such as the evolution, development, polyploidization, and improvement of crops. Studies on the genomic diversity of Oryza species, including wild species, should provide new insights to solve the problem of growing food demands in the face of rapid climatic changes.

  8. Transformed composite sequences for improved qubit addressing

    Science.gov (United States)

    Merrill, J. True; Doret, S. Charles; Vittorini, Grahame; Addison, J. P.; Brown, Kenneth R.

    2014-10-01

    Selective laser addressing of a single atom or atomic ion qubit can be improved using narrow-band composite pulse sequences. We describe a Lie-algebraic technique to generalize known narrow-band sequences and introduce sequences related by dilation and rotation of sequence generators. Our method improves known narrow-band sequences by decreasing both the pulse time and the residual error. Finally, we experimentally demonstrate these composite sequences using 40Ca+ ions trapped in a surface-electrode ion trap.

  9. On the expected duration of a search for a fixed pattern in random data

    DEFF Research Database (Denmark)

    Nielsen, Peter Tolstrup

    1973-01-01

    An expression is obtained for the expected duration of a search to find a givenL-ary sequence in a semi-infinite stream of randomL-ary data. The search time is found to be an increasing function of the lengths of the "bifices" of the pattern, where the term bifix denotes a sequence which is both...

  10. On Sequence Lengths of Some Special External Exclusive OR Type LFSR Structures – Study and Analysis

    Directory of Open Access Journals (Sweden)

    A Ahmad

    2014-12-01

    Full Text Available The study of the length of pseudo-random binary sequences generated by Linear- Feedback Shift Registers (LFSRs plays an important role in the design approaches of built-in selftest, cryptosystems, and other applications. However, certain LFSR structures might not be appropriate in some situations. Given that determining the length of generated pseudo-random binary sequence is a complex task, therefore, before using an LFSR structure, it is essential to investigate the length and the properties of the sequence. This paper investigates some conditions and LFSR’s structures, which restrict the pseudo-random binary sequences’ generation to a certain fixed length. The outcomes of this paper are presented in the form of theorems, simulations, and analyses. We believe that these outcomes are of great importance to the designers of built-in self-test equipment, cryptosystems, and other applications such as radar, CDMA, error correction, and Monte Carlo simulation.

  11. Sequences, groups, and number theory

    CERN Document Server

    Rigo, Michel

    2018-01-01

    This collaborative book presents recent trends on the study of sequences, including combinatorics on words and symbolic dynamics, and new interdisciplinary links to group theory and number theory. Other chapters branch out from those areas into subfields of theoretical computer science, such as complexity theory and theory of automata. The book is built around four general themes: number theory and sequences, word combinatorics, normal numbers, and group theory. Those topics are rounded out by investigations into automatic and regular sequences, tilings and theory of computation, discrete dynamical systems, ergodic theory, numeration systems, automaton semigroups, and amenable groups.  This volume is intended for use by graduate students or research mathematicians, as well as computer scientists who are working in automata theory and formal language theory. With its organization around unified themes, it would also be appropriate as a supplemental text for graduate level courses.

  12. Explaining the harmonic sequence paradox.

    Science.gov (United States)

    Schmidt, Ulrich; Zimper, Alexander

    2012-05-01

    According to the harmonic sequence paradox, an expected utility decision maker's willingness to pay for a gamble whose expected payoffs evolve according to the harmonic series is finite if and only if his marginal utility of additional income becomes zero for rather low payoff levels. Since the assumption of zero marginal utility is implausible for finite payoff levels, expected utility theory - as well as its standard generalizations such as cumulative prospect theory - are apparently unable to explain a finite willingness to pay. This paper presents first an experimental study of the harmonic sequence paradox. Additionally, it demonstrates that the theoretical argument of the harmonic sequence paradox only applies to time-patient decision makers, whereas the paradox is easily avoided if time-impatience is introduced. ©2011 The British Psychological Society.

  13. Does consolidation of visuospatial sequence knowledge depend on eye movements?

    Directory of Open Access Journals (Sweden)

    Daphné Coomans

    Full Text Available In the current study, we assessed whether visuospatial sequence knowledge is retained over 24 hours and whether this retention is dependent on the occurrence of eye movements. Participants performed two sessions of a serial reaction time (SRT task in which they had to manually react to the identity of a target letter pair presented in one of four locations around a fixation cross. When the letter pair 'XO' was presented, a left response had to be given, when the letter pair 'OX' was presented, a right response was required. In the Eye Movements (EM condition, eye movements were necessary to perform the task since the fixation cross and the target were separated by at least 9° visual angle. In the No Eye Movements (NEM condition, on the other hand, eye movements were minimized by keeping the distance from the fixation cross to the target below 1° visual angle and by limiting the stimulus presentation to 100 ms. Since the target identity changed randomly in both conditions, no manual response sequence was present in the task. However, target location was structured according to a deterministic sequence in both the EM and NEM condition. Learning of the target location sequence was determined at the end of the first session and 24 hours after initial learning. Results indicated that the sequence learning effect in the SRT task diminished, yet remained significant, over the 24 hour interval in both conditions. Importantly, the difference in eye movements had no impact on the transfer of sequence knowledge. These results suggest that the retention of visuospatial sequence knowledge occurs alike, irrespective of whether this knowledge is supported by eye movements or not.

  14. Integrated sequence analysis. Final report

    Energy Technology Data Exchange (ETDEWEB)

    Andersson, K.; Pyy, P

    1998-02-01

    The NKS/RAK subprojet 3 `integrated sequence analysis` (ISA) was formulated with the overall objective to develop and to test integrated methodologies in order to evaluate event sequences with significant human action contribution. The term `methodology` denotes not only technical tools but also methods for integration of different scientific disciplines. In this report, we first discuss the background of ISA and the surveys made to map methods in different application fields, such as man machine system simulation software, human reliability analysis (HRA) and expert judgement. Specific event sequences were, after the surveys, selected for application and testing of a number of ISA methods. The event sequences discussed in the report were cold overpressure of BWR, shutdown LOCA of BWR, steam generator tube rupture of a PWR and BWR disturbed signal view in the control room after an external event. Different teams analysed these sequences by using different ISA and HRA methods. Two kinds of results were obtained from the ISA project: sequence specific and more general findings. The sequence specific results are discussed together with each sequence description. The general lessons are discussed under a separate chapter by using comparisons of different case studies. These lessons include areas ranging from plant safety management (design, procedures, instrumentation, operations, maintenance and safety practices) to methodological findings (ISA methodology, PSA,HRA, physical analyses, behavioural analyses and uncertainty assessment). Finally follows a discussion about the project and conclusions are presented. An interdisciplinary study of complex phenomena is a natural way to produce valuable and innovative results. This project came up with structured ways to perform ISA and managed to apply the in practice. The project also highlighted some areas where more work is needed. In the HRA work, development is required for the use of simulators and expert judgement as

  15. Matrix transformations and sequence spaces

    International Nuclear Information System (INIS)

    Nanda, S.

    1983-06-01

    In most cases the most general linear operator from one sequence space into another is actually given by an infinite matrix and therefore the theory of matrix transformations has always been of great interest in the study of sequence spaces. The study of general theory of matrix transformations was motivated by the special results in summability theory. This paper is a review article which gives almost all known results on matrix transformations. This also suggests a number of open problems for further study and will be very useful for research workers. (author)

  16. Green's theorem and Gorenstein sequences

    OpenAIRE

    Ahn, Jeaman; Migliore, Juan C.; Shin, Yong-Su

    2016-01-01

    We study consequences, for a standard graded algebra, of extremal behavior in Green's Hyperplane Restriction Theorem. First, we extend his Theorem 4 from the case of a plane curve to the case of a hypersurface in a linear space. Second, assuming a certain Lefschetz condition, we give a connection to extremal behavior in Macaulay's theorem. We apply these results to show that $(1,19,17,19,1)$ is not a Gorenstein sequence, and as a result we classify the sequences of the form $(1,a,a-2,a,1)$ th...

  17. Distribution and sequence homogeneity of an abundant satellite DNA in the beetle, Tenebrio molitor.

    Science.gov (United States)

    Davis, C A; Wyatt, G R

    1989-01-01

    The mealworm beetle, Tenebrio molitor, contains an unusually abundant and homogeneous satellite DNA which constitutes up to 60% of its genome. The satellite DNA is shown to be present in all of the chromosomes by in situ hybridization. 18 dimers of the repeat unit were cloned and sequenced. The consensus sequence is 142 nt long and lacks any internal repeat structure. Monomers of the sequence are very similar, showing on average a 2% divergence from the calculated consensus. Variant nucleotides are scattered randomly throughout the sequence although some variants are more common than others. Neighboring repeat units are no more alike than randomly chosen ones. The results suggest that some mechanism, perhaps gene conversion, is acting to maintain the homogeneity of the satellite DNA despite its abundance and distribution on all of the chromosomes. Images PMID:2762148

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

    Science.gov (United States)

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

    2011-04-01

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

  19. Time fluctuation analysis of forest fire sequences

    Science.gov (United States)

    Vega Orozco, Carmen D.; Kanevski, Mikhaïl; Tonini, Marj; Golay, Jean; Pereira, Mário J. G.

    2013-04-01

    Forest fires are complex events involving both space and time fluctuations. Understanding of their dynamics and pattern distribution is of great importance in order to improve the resource allocation and support fire management actions at local and global levels. This study aims at characterizing the temporal fluctuations of forest fire sequences observed in Portugal, which is the country that holds the largest wildfire land dataset in Europe. This research applies several exploratory data analysis measures to 302,000 forest fires occurred from 1980 to 2007. The applied clustering measures are: Morisita clustering index, fractal and multifractal dimensions (box-counting), Ripley's K-function, Allan Factor, and variography. These algorithms enable a global time structural analysis describing the degree of clustering of a point pattern and defining whether the observed events occur randomly, in clusters or in a regular pattern. The considered methods are of general importance and can be used for other spatio-temporal events (i.e. crime, epidemiology, biodiversity, geomarketing, etc.). An important contribution of this research deals with the analysis and estimation of local measures of clustering that helps understanding their temporal structure. Each measure is described and executed for the raw data (forest fires geo-database) and results are compared to reference patterns generated under the null hypothesis of randomness (Poisson processes) embedded in the same time period of the raw data. This comparison enables estimating the degree of the deviation of the real data from a Poisson process. Generalizations to functional measures of these clustering methods, taking into account the phenomena, were also applied and adapted to detect time dependences in a measured variable (i.e. burned area). The time clustering of the raw data is compared several times with the Poisson processes at different thresholds of the measured function. Then, the clustering measure value

  20. Problems with the random number generator RANF implemented on the CDC cyber 205

    Science.gov (United States)

    Kalle, Claus; Wansleben, Stephan

    1984-10-01

    We show that using RANF may lead to wrong results when lattice models are simulated by Monte Carlo methods. We present a shift-register sequence random number generator which generates two random numbers per cycle on a two pipe CDC Cyber 205.