Long period pseudo random number sequence generator
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).
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
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
ACORN—A new method for generating sequences of uniformly distributed Pseudo-random Numbers
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.
A Repetition Test for Pseudo-Random Number Generators
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...
Pseudo-Random Number Generators
Howell, L. W.; Rheinfurth, M. H.
1984-01-01
Package features comprehensive selection of probabilistic distributions. Monte Carlo simulations resorted to whenever systems studied not amenable to deterministic analyses or when direct experimentation not feasible. Random numbers having certain specified distribution characteristic integral part of simulations. Package consists of collector of "pseudorandom" number generators for use in Monte Carlo simulations.
Properties making a chaotic system a good Pseudo Random Number Generator
Falcioni, Massimo; Palatella, Luigi; Pigolotti, Simone; Vulpiani, Angelo
2005-01-01
We discuss two properties making a deterministic algorithm suitable to generate a pseudo random sequence of numbers: high value of Kolmogorov-Sinai entropy and high-dimensionality. We propose the multi dimensional Anosov symplectic (cat) map as a Pseudo Random Number Generator. We show what chaotic features of this map are useful for generating Pseudo Random Numbers and investigate numerically which of them survive in the discrete version of the map. Testing and comparisons with other generat...
a Pseudo-Random Number Generator Employing Multiple RÉNYI Maps
Lui, Oi-Yan; Yuen, Ching-Hung; Wong, Kwok-Wo
2013-11-01
The increasing risk along with the drastic development of multimedia data transmission has raised a big concern on data security. A good pseudo-random number generator is an essential tool in cryptography. In this paper, we propose a novel pseudo-random number generator based on the controlled combination of the outputs of several digitized chaotic Rényi maps. The generated pseudo-random sequences have passed both the NIST 800-22 Revision 1a and the DIEHARD tests. Moreover, simulation results show that the proposed pseudo-random number generator requires less operation time than existing generators and is highly sensitive to the seed.
Simulation of a directed random-walk model: the effect of pseudo-random-number correlations
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.
Graphical analysis of some pseudo-random number generators
Lewis, Peter A. W.
1986-01-01
There exist today many 'good' pseudo-random number generators; the problem is to retrieve them. This document discusses three commonly used pseudo- random number generators, the first being RANDU, a notoriously bad generator, but one which is still occasionally used. The next is the widely used prime modulus, multiplicative congruential generator used in LL-RANDOMII, the Naval Postgraduate School random number package, and the last is the random number generator provided for microcomputers wi...
A pseudo-random number generator and its spectral test
International Nuclear Information System (INIS)
Wang Lai
1998-01-01
The author introduces a pseudo-random number generator and describes its algorithm and C language implementation. The performance of the generator is tested and compared with some well known LCG generators
Hardware implementation of a GFSR pseudo-random number generator
Aiello, G. R.; Budinich, M.; Milotti, E.
1989-12-01
We describe the hardware implementation of a pseudo-random number generator of the "Generalized Feedback Shift Register" (GFSR) type. After brief theoretical considerations we describe two versions of the hardware, the tests done and the performances achieved.
Generation of pseudo-random sequences for spread spectrum systems
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.
Pseudo random number generator based on quantum chaotic map
Akhshani, A.; Akhavan, A.; Mobaraki, A.; Lim, S.-C.; Hassan, Z.
2014-01-01
For many years dissipative quantum maps were widely used as informative models of quantum chaos. In this paper, a new scheme for generating good pseudo-random numbers (PRNG), based on quantum logistic map is proposed. Note that the PRNG merely relies on the equations used in the quantum chaotic map. The algorithm is not complex, which does not impose high requirement on computer hardware and thus computation speed is fast. In order to face the challenge of using the proposed PRNG in quantum cryptography and other practical applications, the proposed PRNG is subjected to statistical tests using well-known test suites such as NIST, DIEHARD, ENT and TestU01. The results of the statistical tests were promising, as the proposed PRNG successfully passed all these tests. Moreover, the degree of non-periodicity of the chaotic sequences of the quantum map is investigated through the Scale index technique. The obtained result shows that, the sequence is more non-periodic. From these results it can be concluded that, the new scheme can generate a high percentage of usable pseudo-random numbers for simulation and other applications in scientific computing.
Primitive polynomials selection method for pseudo-random number generator
Anikin, I. V.; Alnajjar, Kh
2018-01-01
In this paper we suggested the method for primitive polynomials selection of special type. This kind of polynomials can be efficiently used as a characteristic polynomials for linear feedback shift registers in pseudo-random number generators. The proposed method consists of two basic steps: finding minimum-cost irreducible polynomials of the desired degree and applying primitivity tests to get the primitive ones. Finally two primitive polynomials, which was found by the proposed method, used in pseudorandom number generator based on fuzzy logic (FRNG) which had been suggested before by the authors. The sequences generated by new version of FRNG have low correlation magnitude, high linear complexity, less power consumption, is more balanced and have better statistical properties.
Pseudo-Random Number Generator Based on Coupled Map Lattices
Lü, Huaping; Wang, Shihong; Hu, Gang
A one-way coupled chaotic map lattice is used for generating pseudo-random numbers. It is shown that with suitable cooperative applications of both chaotic and conventional approaches, the output of the spatiotemporally chaotic system can easily meet the practical requirements of random numbers, i.e., excellent random statistical properties, long periodicity of computer realizations, and fast speed of random number generations. This pseudo-random number generator system can be used as ideal synchronous and self-synchronizing stream cipher systems for secure communications.
Generation of pseudo-random numbers
Howell, L. W.; Rheinfurth, M. H.
1982-01-01
Practical methods for generating acceptable random numbers from a variety of probability distributions which are frequently encountered in engineering applications are described. The speed, accuracy, and guarantee of statistical randomness of the various methods are discussed.
Chaos-based Pseudo-random Number Generation
Barakat, Mohamed L.
2014-04-10
Various methods and systems related to chaos-based pseudo-random number generation are presented. In one example, among others, a system includes a pseudo-random number generator (PRNG) to generate a series of digital outputs and a nonlinear post processing circuit to perform an exclusive OR (XOR) operation on a first portion of a current digital output of the PRNG and a permutated version of a corresponding first portion of a previous post processed output to generate a corresponding first portion of a current post processed output. In another example, a method includes receiving at least a first portion of a current output from a PRNG and performing an XOR operation on the first portion of the current PRNG output with a permutated version of a corresponding first portion of a previous post processed output to generate a corresponding first portion of a current post processed output.
Chaos-based Pseudo-random Number Generation
Barakat, Mohamed L.; Mansingka, Abhinav S.; Radwan, Ahmed Gomaa Ahmed; Salama, Khaled N.
2014-01-01
Various methods and systems related to chaos-based pseudo-random number generation are presented. In one example, among others, a system includes a pseudo-random number generator (PRNG) to generate a series of digital outputs and a nonlinear post processing circuit to perform an exclusive OR (XOR) operation on a first portion of a current digital output of the PRNG and a permutated version of a corresponding first portion of a previous post processed output to generate a corresponding first portion of a current post processed output. In another example, a method includes receiving at least a first portion of a current output from a PRNG and performing an XOR operation on the first portion of the current PRNG output with a permutated version of a corresponding first portion of a previous post processed output to generate a corresponding first portion of a current post processed output.
A universal algorithm to generate pseudo-random numbers based on uniform mapping as homeomorphism
International Nuclear Information System (INIS)
Fu-Lai, Wang
2010-01-01
A specific uniform map is constructed as a homeomorphism mapping chaotic time series into [0,1] to obtain sequences of standard uniform distribution. With the uniform map, a chaotic orbit and a sequence orbit obtained are topologically equivalent to each other so the map can preserve the most dynamic properties of chaotic systems such as permutation entropy. Based on the uniform map, a universal algorithm to generate pseudo random numbers is proposed and the pseudo random series is tested to follow the standard 0–1 random distribution both theoretically and experimentally. The algorithm is not complex, which does not impose high requirement on computer hard ware and thus computation speed is fast. The method not only extends the parameter spaces but also avoids the drawback of small function space caused by constraints on chaotic maps used to generate pseudo random numbers. The algorithm can be applied to any chaotic system and can produce pseudo random sequence of high quality, thus can be a good universal pseudo random number generator. (general)
A universal algorithm to generate pseudo-random numbers based on uniform mapping as homeomorphism
Wang, Fu-Lai
2010-09-01
A specific uniform map is constructed as a homeomorphism mapping chaotic time series into [0,1] to obtain sequences of standard uniform distribution. With the uniform map, a chaotic orbit and a sequence orbit obtained are topologically equivalent to each other so the map can preserve the most dynamic properties of chaotic systems such as permutation entropy. Based on the uniform map, a universal algorithm to generate pseudo random numbers is proposed and the pseudo random series is tested to follow the standard 0-1 random distribution both theoretically and experimentally. The algorithm is not complex, which does not impose high requirement on computer hard ware and thus computation speed is fast. The method not only extends the parameter spaces but also avoids the drawback of small function space caused by constraints on chaotic maps used to generate pseudo random numbers. The algorithm can be applied to any chaotic system and can produce pseudo random sequence of high quality, thus can be a good universal pseudo random number generator.
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.
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.
Program pseudo-random number generator for microcomputers
International Nuclear Information System (INIS)
Ososkov, G.A.
1980-01-01
Program pseudo-random number generators (PNG) intended for the test of control equipment and communication channels are considered. In the case of 8-bit microcomputers it is necessary to assign 4 words of storage to allocate one random number. The proposed economical algorithms of the random number generation are based on the idea of the ''mixing'' of such quarters of the preceeding random number to obtain the next one. Test results of the PNG are displayed for two such generators. A FORTRAN variant of the PNG is presented along with a program realizing the PNG made on the base of the INTEL-8080 autocode
Accelerating Pseudo-Random Number Generator for MCNP on GPU
Gong, Chunye; Liu, Jie; Chi, Lihua; Hu, Qingfeng; Deng, Li; Gong, Zhenghu
2010-09-01
Pseudo-random number generators (PRNG) are intensively used in many stochastic algorithms in particle simulations, artificial neural networks and other scientific computation. The PRNG in Monte Carlo N-Particle Transport Code (MCNP) requires long period, high quality, flexible jump and fast enough. In this paper, we implement such a PRNG for MCNP on NVIDIA's GTX200 Graphics Processor Units (GPU) using CUDA programming model. Results shows that 3.80 to 8.10 times speedup are achieved compared with 4 to 6 cores CPUs and more than 679.18 million double precision random numbers can be generated per second on GPU.
New Trends in Pseudo-Random Number Generation
Gutbrod, F.
Properties of pseudo-random number generators are reviewed. The emphasis is on correlations between successive random numbers and their suppression by improvement steps. The generators under discussion are the linear congruential generators, lagged Fibonacci generators with various operations, and the improvement techniques combination, shuffling and decimation. The properties of the RANSHI generator are reviewed somewhat more extensively. The transition to 64-bit technology is discussed in several cases. The generators are subject to several tests, which look both for short range and for long range correlations. Some performance figures are given for a Pentium Pro PC. Recommendations are presented in the final chapter.
Pseudo-random number generator for the Sigma 5 computer
Carroll, S. N.
1983-01-01
A technique is presented for developing a pseudo-random number generator based on the linear congruential form. The two numbers used for the generator are a prime number and a corresponding primitive root, where the prime is the largest prime number that can be accurately represented on a particular computer. The primitive root is selected by applying Marsaglia's lattice test. The technique presented was applied to write a random number program for the Sigma 5 computer. The new program, named S:RANDOM1, is judged to be superior to the older program named S:RANDOM. For applications requiring several independent random number generators, a table is included showing several acceptable primitive roots. The technique and programs described can be applied to any computer having word length different from that of the Sigma 5.
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.
Fully Digital Chaotic Oscillators Applied to Pseudo Random Number Generation
Mansingka, Abhinav S.
2012-05-01
adapted for pseudo random number generation by truncating statistically defective bits. Finally, a novel post-processing technique using the Fibonacci series is proposed and implemented with a non-autonomous driven hyperchaotic system to provide pseudo random number generators with high nonlinear complexity and controllable period length that enables full utilization of all branches of the chaotic output as statistically secure pseudo random output.
Quantifiers for randomness of chaotic pseudo-random number generators.
De Micco, L; Larrondo, H A; Plastino, A; Rosso, O A
2009-08-28
We deal with randomness quantifiers and concentrate on their ability to discern the hallmark of chaos in time series used in connection with pseudo-random number generators (PRNGs). Workers in the field are motivated to use chaotic maps for generating PRNGs because of the simplicity of their implementation. Although there exist very efficient general-purpose benchmarks for testing PRNGs, we feel that the analysis provided here sheds additional didactic light on the importance of the main statistical characteristics of a chaotic map, namely (i) its invariant measure and (ii) the mixing constant. This is of help in answering two questions that arise in applications: (i) which is the best PRNG among the available ones? and (ii) if a given PRNG turns out not to be good enough and a randomization procedure must still be applied to it, which is the best applicable randomization procedure? Our answer provides a comparative analysis of several quantifiers advanced in the extant literature.
Very high performance pseudo-random number generation on DAP
Smith, K. A.; Reddaway, S. F.; Scott, D. M.
1985-07-01
Since the National DAP Service began at QMC in 1980, extensive use has been made of pseudo-random numbers in Monte Carlo simulation. Matrices of uniform numbers have been produced by various generators: (a) multiplicative ( x+ 1 = 13 13xn mod 2 59); (b) very long period shift register ( x4423 + x271 + 1); (c) multiple shorter period ( x127 + x7 + 1) shift registers generating several matrices per iteration. The above uniform generators can also feed a normal distribution generator that uses the Box-Muller transformation. This paper describes briefly the generators, their implementation and speed. Generator (b) has been greatly speeded-up by re-implementation, and now produces more than 100 × 10 6 high quality 16-bit numbers/s. Generator (c) is under development and will achieve even higher performance, mainly due to producing data in greater bulk. High quality numbers are expected, and performance will range from 400 to 800 × 10 6 numbers/s, depending on how the generator is used.
An empirical test of pseudo random number generators by means of an exponential decaying process
International Nuclear Information System (INIS)
Coronel B, H.F.; Hernandez M, A.R.; Jimenez M, M.A.; Mora F, L.E.
2007-01-01
Empirical tests for pseudo random number generators based on the use of processes or physical models have been successfully used and are considered as complementary to theoretical tests of randomness. In this work a statistical methodology for evaluating the quality of pseudo random number generators is presented. The method is illustrated in the context of the so-called exponential decay process, using some pseudo random number generators commonly used in physics. (Author)
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.
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
Pseudo-random number generation using a 3-state cellular automaton
Bhattacharjee, Kamalika; Paul, Dipanjyoti; Das, Sukanta
This paper investigates the potentiality of pseudo-random number generation of a 3-neighborhood 3-state cellular automaton (CA) under periodic boundary condition. Theoretical and empirical tests are performed on the numbers, generated by the CA, to observe the quality of it as pseudo-random number generator (PRNG). We analyze the strength and weakness of the proposed PRNG and conclude that the selected CA is a good random number generator.
Three-dimensional pseudo-random number generator for implementing in hybrid computer systems
International Nuclear Information System (INIS)
Ivanov, M.A.; Vasil'ev, N.P.; Voronin, A.V.; Kravtsov, M.Yu.; Maksutov, A.A.; Spiridonov, A.A.; Khudyakova, V.I.; Chugunkov, I.V.
2012-01-01
The algorithm for generating pseudo-random numbers oriented to implementation by using hybrid computer systems is considered. The proposed solution is characterized by a high degree of parallel computing [ru
Pseudo-Random Sequences Generated by a Class of One-Dimensional Smooth Map
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.
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)
Using pseudo-random number generator for making iterative algorithms of hashing data
International Nuclear Information System (INIS)
Ivanov, M.A.; Vasil'ev, N.P.; Kozyrskij, B.L.
2014-01-01
The method of stochastic data transformation made for usage in cryptographic methods of information protection has been analyzed. The authors prove the usage of cryptographically strong pseudo-random number generators as a basis for Sponge construction. This means that the analysis of the quality of the known methods and tools for assessing the statistical security of pseudo-random number generators can be used effectively [ru
High-Performance Pseudo-Random Number Generation on Graphics Processing Units
Nandapalan, Nimalan; Brent, Richard P.; Murray, Lawrence M.; Rendell, Alistair
2011-01-01
This work considers the deployment of pseudo-random number generators (PRNGs) on graphics processing units (GPUs), developing an approach based on the xorgens generator to rapidly produce pseudo-random numbers of high statistical quality. The chosen algorithm has configurable state size and period, making it ideal for tuning to the GPU architecture. We present a comparison of both speed and statistical quality with other common parallel, GPU-based PRNGs, demonstrating favourable performance o...
Directory of Open Access Journals (Sweden)
Bilan Stepan
2017-01-01
Full Text Available To date, there are many tasks that are aimed at studying the dynamic changes in physical processes. These tasks do not give advance known result. The solution of such problems is based on the construction of a dynamic model of the object. Successful structural and functional implementation of the object model can give a positive result in time. This approach uses the task of constructing artificial biological objects. To solve such problems, pseudo-random number generators are used, which also find wide application for information protection tasks. Such generators should have good statistical properties and give a long repetition period of the generated pseudo-random bit sequence. This work is aimed at improving these characteristics. The paper considers the method of forming pseudo-random sequences of numbers on the basis of aperiodic cellular automata with two active cells. A pseudo-random number generator is proposed that generates three bit sequences. The first two bit sequences are formed by the corresponding two active cells in the cellular automaton. The third bit sequence is the result of executing the XOR function over the bits of the first two sequences and it has better characteristics compared to them. The use of cellular automata with two active cells allowed to improve the statistical properties of the formed bit sequence, as well as its repetition period. This is proved by using graphical tests for generators built based on cellular automata using the neighborhoods of von Neumann and Moore. The tests showed high efficiency of the generator based on an asynchronous cellular automaton with the neighborhood of Moore. The proposed pseudo-random number generators have good statistical properties, which makes it possible to use them in information security systems, as well as for simulation tasks of various dynamic processes.
A Bidirectional Generalized Synchronization Theorem-Based Chaotic Pseudo-random Number Generator
Directory of Open Access Journals (Sweden)
Han Shuangshuang
2013-07-01
Full Text Available Based on a bidirectional generalized synchronization theorem for discrete chaos system, this paper introduces a new 5-dimensional bidirectional generalized chaos synchronization system (BGCSDS, whose prototype is a novel chaotic system introduced in [12]. Numerical simulation showed that two pair variables of the BGCSDS achieve generalized chaos synchronization via a transform H.A chaos-based pseudo-random number generator (CPNG was designed by the new BGCSDS. Using the FIPS-140-2 tests issued by the National Institute of Standard and Technology (NIST verified the randomness of the 1000 binary number sequences generated via the CPNG and the RC4 algorithm respectively. The results showed that all the tested sequences passed the FIPS-140-2 tests. The confidence interval analysis showed the statistical properties of the randomness of the sequences generated via the CPNG and the RC4 algorithm do not have significant differences.
Non-periodic pseudo-random numbers used in Monte Carlo calculations
Barberis, Gaston E.
2007-09-01
The generation of pseudo-random numbers is one of the interesting problems in Monte Carlo simulations, mostly because the common computer generators produce periodic numbers. We used simple pseudo-random numbers generated with the simplest chaotic system, the logistic map, with excellent results. The numbers generated in this way are non-periodic, which we demonstrated for 1013 numbers, and they are obtained in a deterministic way, which allows to repeat systematically any calculation. The Monte Carlo calculations are the ideal field to apply these numbers, and we did it for simple and more elaborated cases. Chemistry and Information Technology use this kind of simulations, and the application of this numbers to quantum Monte Carlo and cryptography is immediate. I present here the techniques to calculate, analyze and use these pseudo-random numbers, show that they lack periodicity up to 1013 numbers and that they are not correlated.
Non-periodic pseudo-random numbers used in Monte Carlo calculations
International Nuclear Information System (INIS)
Barberis, Gaston E.
2007-01-01
The generation of pseudo-random numbers is one of the interesting problems in Monte Carlo simulations, mostly because the common computer generators produce periodic numbers. We used simple pseudo-random numbers generated with the simplest chaotic system, the logistic map, with excellent results. The numbers generated in this way are non-periodic, which we demonstrated for 10 13 numbers, and they are obtained in a deterministic way, which allows to repeat systematically any calculation. The Monte Carlo calculations are the ideal field to apply these numbers, and we did it for simple and more elaborated cases. Chemistry and Information Technology use this kind of simulations, and the application of this numbers to quantum Monte Carlo and cryptography is immediate. I present here the techniques to calculate, analyze and use these pseudo-random numbers, show that they lack periodicity up to 10 13 numbers and that they are not correlated
Security Flaws in an Efficient Pseudo-Random Number Generator for Low-Power Environments
Peris-Lopez, Pedro; Hernandez-Castro, Julio C.; Tapiador, Juan M. E.; Millán, Enrique San; van der Lubbe, Jan C. A.
In 2004, Settharam and Rhee tackled the design of a lightweight Pseudo-Random Number Generator (PRNG) suitable for low-power environments (e.g. sensor networks, low-cost RFID tags). First, they explicitly fixed a set of requirements for this primitive. Then, they proposed a PRNG conforming to these requirements and using a free-running timer [9]. We analyze this primitive discovering important security faults. The proposed algorithm fails to pass even relatively non-stringent batteries of randomness such as ENT (i.e. a pseudorandom number sequence test program). We prove that their recommended PRNG has a very short period due to the flawed design of its core. The internal state can be easily revealed, compromising its backward and forward security. Additionally, the rekeying algorithm is defectively designed mainly related to the unpractical value proposed for this purpose.
Pseudo-random number generators for Monte Carlo simulations on ATI Graphics Processing Units
Demchik, Vadim
2011-03-01
Basic uniform pseudo-random number generators are implemented on ATI Graphics Processing Units (GPU). The performance results of the realized generators (multiplicative linear congruential (GGL), XOR-shift (XOR128), RANECU, RANMAR, RANLUX and Mersenne Twister (MT19937)) on CPU and GPU are discussed. The obtained speed up factor is hundreds of times in comparison with CPU. RANLUX generator is found to be the most appropriate for using on GPU in Monte Carlo simulations. The brief review of the pseudo-random number generators used in modern software packages for Monte Carlo simulations in high-energy physics is presented.
Pseudo-random number generator based on asymptotic deterministic randomness
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.
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
Pseudo-Random Number Generators for Vector Processors and Multicore Processors
DEFF Research Database (Denmark)
Fog, Agner
2015-01-01
Large scale Monte Carlo applications need a good pseudo-random number generator capable of utilizing both the vector processing capabilities and multiprocessing capabilities of modern computers in order to get the maximum performance. The requirements for such a generator are discussed. New ways...
Pseudo-random-number generators and the square site percolation threshold.
Lee, Michael J
2008-09-01
Selected pseudo-random-number generators are applied to a Monte Carlo study of the two-dimensional square-lattice site percolation model. A generator suitable for high precision calculations is identified from an application specific test of randomness. After extended computation and analysis, an ostensibly reliable value of p_{c}=0.59274598(4) is obtained for the percolation threshold.
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.
Modular Transformations, Order-Chaos Transitions and Pseudo-Random Number Generation
Bonelli, Antonio; Ruffo, Stefano
Successive pairs of pseudo-random numbers generated by standard linear congruential transformations display ordered patterns of parallel lines. We study the "ordered" and "chaotic" distribution of such pairs by solving the eigenvalue problem for two-dimensional modular transformations over integers. We conjecture that the optimal uniformity for pair distribution is obtained when the slope of linear modular eigenspaces takes the value n opt =maxint (p/√ {p-1}), where p is a prime number. We then propose a new generator of pairs of independent pseudo-random numbers, which realizes an optimal uniform distribution (in the "statistical" sense) of points on the unit square (0, 1] × (0, 1]. The method can be easily generalized to the generation of k-tuples of random numbers (with k>2).
Novel pseudo-random number generator based on quantum random walks
Yang, Yu-Guang; Zhao, Qian-Qian
2016-02-01
In this paper, we investigate the potential application of quantum computation for constructing pseudo-random number generators (PRNGs) and further construct a novel PRNG based on quantum random walks (QRWs), a famous quantum computation model. The PRNG merely relies on the equations used in the QRWs, and thus the generation algorithm is simple and the computation speed is fast. The proposed PRNG is subjected to statistical tests such as NIST and successfully passed the test. Compared with the representative PRNG based on quantum chaotic maps (QCM), the present QRWs-based PRNG has some advantages such as better statistical complexity and recurrence. For example, the normalized Shannon entropy and the statistical complexity of the QRWs-based PRNG are 0.999699456771172 and 1.799961178212329e-04 respectively given the number of 8 bits-words, say, 16Mbits. By contrast, the corresponding values of the QCM-based PRNG are 0.999448131481064 and 3.701210794388818e-04 respectively. Thus the statistical complexity and the normalized entropy of the QRWs-based PRNG are closer to 0 and 1 respectively than those of the QCM-based PRNG when the number of words of the analyzed sequence increases. It provides a new clue to construct PRNGs and also extends the applications of quantum computation.
Novel pseudo-random number generator based on quantum random walks.
Yang, Yu-Guang; Zhao, Qian-Qian
2016-02-04
In this paper, we investigate the potential application of quantum computation for constructing pseudo-random number generators (PRNGs) and further construct a novel PRNG based on quantum random walks (QRWs), a famous quantum computation model. The PRNG merely relies on the equations used in the QRWs, and thus the generation algorithm is simple and the computation speed is fast. The proposed PRNG is subjected to statistical tests such as NIST and successfully passed the test. Compared with the representative PRNG based on quantum chaotic maps (QCM), the present QRWs-based PRNG has some advantages such as better statistical complexity and recurrence. For example, the normalized Shannon entropy and the statistical complexity of the QRWs-based PRNG are 0.999699456771172 and 1.799961178212329e-04 respectively given the number of 8 bits-words, say, 16Mbits. By contrast, the corresponding values of the QCM-based PRNG are 0.999448131481064 and 3.701210794388818e-04 respectively. Thus the statistical complexity and the normalized entropy of the QRWs-based PRNG are closer to 0 and 1 respectively than those of the QCM-based PRNG when the number of words of the analyzed sequence increases. It provides a new clue to construct PRNGs and also extends the applications of quantum computation.
Distributed Pseudo-Random Number Generation and Its Application to Cloud Database
Chen, Jiageng; Miyaji, Atsuko; Su, Chunhua
2014-01-01
Cloud database is now a rapidly growing trend in cloud computing market recently. It enables the clients run their computation on out-sourcing databases or access to some distributed database service on the cloud. At the same time, the security and privacy concerns is major challenge for cloud database to continue growing. To enhance the security and privacy of the cloud database technology, the pseudo-random number generation (PRNG) plays an important roles in data encryptions and privacy-pr...
Pseudo-random number generator based on mixing of three chaotic maps
François, M.; Grosges, T.; Barchiesi, D.; Erra, R.
2014-04-01
A secure pseudo-random number generator three-mixer is proposed. The principle of the method consists in mixing three chaotic maps produced from an input initial vector. The algorithm uses permutations whose positions are computed and indexed by a standard chaotic function and a linear congruence. The performance of that scheme is evaluated through statistical analysis. Such a cryptosystem lets appear significant cryptographic qualities for a high security level.
Lawnik, Marcin
2018-01-01
The scope of the paper is the presentation of a new method of generating numbers from a given distribution. The method uses the inverse cumulative distribution function and a method of flattening of probabilistic distributions. On the grounds of these methods, a new construction of chaotic maps was derived, which generates values from a given distribution. The analysis of the new method was conducted on the example of a newly constructed chaotic recurrences, based on the Box-Muller transformation and the quantile function of the exponential distribution. The obtained results certify that the proposed method may be successively applicable for the construction of generators of pseudo-random numbers.
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.
Efficient pseudo-random number generation for monte-carlo simulations using graphic processors
Mohanty, Siddhant; Mohanty, A. K.; Carminati, F.
2012-06-01
A hybrid approach based on the combination of three Tausworthe generators and one linear congruential generator for pseudo random number generation for GPU programing as suggested in NVIDIA-CUDA library has been used for MONTE-CARLO sampling. On each GPU thread, a random seed is generated on fly in a simple way using the quick and dirty algorithm where mod operation is not performed explicitly due to unsigned integer overflow. Using this hybrid generator, multivariate correlated sampling based on alias technique has been carried out using both CUDA and OpenCL languages.
Efficient pseudo-random number generation for Monte-Carlo simulations using graphic processors
International Nuclear Information System (INIS)
Mohanty, Siddhant; Mohanty, A K; Carminati, F
2012-01-01
A hybrid approach based on the combination of three Tausworthe generators and one linear congruential generator for pseudo random number generation for GPU programing as suggested in NVIDIA-CUDA library has been used for MONTE-CARLO sampling. On each GPU thread, a random seed is generated on fly in a simple way using the quick and dirty algorithm where mod operation is not performed explicitly due to unsigned integer overflow. Using this hybrid generator, multivariate correlated sampling based on alias technique has been carried out using both CUDA and OpenCL languages.
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.
Generation of pseudo-random numbers with the use of inverse chaotic transformation
Directory of Open Access Journals (Sweden)
Lawnik Marcin
2018-02-01
Full Text Available In (Lawnik M., Generation of numbers with the distribution close to uniform with the use of chaotic maps, In: Obaidat M.S., Kacprzyk J., Ören T. (Ed., International Conference on Simulation and Modeling Methodologies, Technologies and Applications (SIMULTECH (28-30 August 2014, Vienna, Austria, SCITEPRESS, 2014 Lawnik discussed a method of generating pseudo-random numbers from uniform distribution with the use of adequate chaotic transformation. The method enables the “flattening” of continuous distributions to uniform one. In this paper a inverse process to the above-mentioned method is presented, and, in consequence, a new manner of generating pseudo-random numbers from a given continuous distribution. The method utilizes the frequency of the occurrence of successive branches of chaotic transformation in the process of “flattening”. To generate the values from the given distribution one discrete and one continuous value of a random variable are required. The presented method does not directly involve the knowledge of the density function or the cumulative distribution function, which is, undoubtedly, a great advantage in comparison with other well-known methods. The described method was analysed on the example of the standard normal distribution.
Phillips, Carolyn L.; Anderson, Joshua A.; Glotzer, Sharon C.
2011-08-01
Brownian Dynamics (BD), also known as Langevin Dynamics, and Dissipative Particle Dynamics (DPD) are implicit solvent methods commonly used in models of soft matter and biomolecular systems. The interaction of the numerous solvent particles with larger particles is coarse-grained as a Langevin thermostat is applied to individual particles or to particle pairs. The Langevin thermostat requires a pseudo-random number generator (PRNG) to generate the stochastic force applied to each particle or pair of neighboring particles during each time step in the integration of Newton's equations of motion. In a Single-Instruction-Multiple-Thread (SIMT) GPU parallel computing environment, small batches of random numbers must be generated over thousands of threads and millions of kernel calls. In this communication we introduce a one-PRNG-per-kernel-call-per-thread scheme, in which a micro-stream of pseudorandom numbers is generated in each thread and kernel call. These high quality, statistically robust micro-streams require no global memory for state storage, are more computationally efficient than other PRNG schemes in memory-bound kernels, and uniquely enable the DPD simulation method without requiring communication between threads.
International Nuclear Information System (INIS)
Phillips, Carolyn L.; Anderson, Joshua A.; Glotzer, Sharon C.
2011-01-01
Highlights: → Molecular Dynamics codes implemented on GPUs have achieved two-order of magnitude computational accelerations. → Brownian Dynamics and Dissipative Particle Dynamics simulations require a large number of random numbers per time step. → We introduce a method for generating small batches of pseudorandom numbers distributed over many threads of calculations. → With this method, Dissipative Particle Dynamics is implemented on a GPU device without requiring thread-to-thread communication. - Abstract: Brownian Dynamics (BD), also known as Langevin Dynamics, and Dissipative Particle Dynamics (DPD) are implicit solvent methods commonly used in models of soft matter and biomolecular systems. The interaction of the numerous solvent particles with larger particles is coarse-grained as a Langevin thermostat is applied to individual particles or to particle pairs. The Langevin thermostat requires a pseudo-random number generator (PRNG) to generate the stochastic force applied to each particle or pair of neighboring particles during each time step in the integration of Newton's equations of motion. In a Single-Instruction-Multiple-Thread (SIMT) GPU parallel computing environment, small batches of random numbers must be generated over thousands of threads and millions of kernel calls. In this communication we introduce a one-PRNG-per-kernel-call-per-thread scheme, in which a micro-stream of pseudorandom numbers is generated in each thread and kernel call. These high quality, statistically robust micro-streams require no global memory for state storage, are more computationally efficient than other PRNG schemes in memory-bound kernels, and uniquely enable the DPD simulation method without requiring communication between threads.
Least squares deconvolution for leak detection with a pseudo random binary sequence excitation
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.
Beliakov, G.; Creighton, D.; Johnstone, M.; Wilkin, T.
2013-08-01
This paper describes an implementation of a Linear Congruential Generator (LCG) based on the binary representation of the normal number α, and of a combined generator based on that LCG. The base LCG with the modulus 333 provides a quality sequence with the period ≈3.7ṡ1015, which passes all but two statistical tests from BigCrush test suite. We improved on the original implementation by adapting Barrett's modular reduction method, which resulted in four-fold increase in efficiency. The combined generator has the period of ≈1023 and passes all tests from BigCrush suite.
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.
A high-speed on-chip pseudo-random binary sequence generator for multi-tone phase calibration
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.
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
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)
International Nuclear Information System (INIS)
Chakraborty, Brahmananda
2009-01-01
Random number plays an important role in any Monte Carlo simulation. The accuracy of the results depends on the quality of the sequence of random numbers employed in the simulation. These include randomness of the random numbers, uniformity of their distribution, absence of correlation and long period. In a typical Monte Carlo simulation of particle transport in a nuclear reactor core, the history of a particle from its birth in a fission event until its death by an absorption or leakage event is tracked. The geometry of the core and the surrounding materials are exactly modeled in the simulation. To track a neutron history one needs random numbers for determining inter collision distance, nature of the collision, the direction of the scattered neutron etc. Neutrons are tracked in batches. In one batch approximately 2000-5000 neutrons are tracked. The statistical accuracy of the results of the simulation depends on the total number of particles (number of particles in one batch multiplied by the number of batches) tracked. The number of histories to be generated is usually large for a typical radiation transport problem. To track a very large number of histories one needs to generate a long sequence of independent random numbers. In other words the cycle length of the random number generator (RNG) should be more than the total number of random numbers required for simulating the given transport problem. The number of bits of the machine generally limits the cycle length. For a binary machine of p bits the maximum cycle length is 2 p . To achieve higher cycle length in the same machine one has to use either register arithmetic or bit manipulation technique
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 ...
Energy Technology Data Exchange (ETDEWEB)
Coronel B, H.F.; Hernandez M, A.R.; Jimenez M, M.A. [Facultad de Fisica e Inteligencia Artificial, Universidad Veracruzana, A.P. 475, Xalapa, Veracruz (Mexico); Mora F, L.E. [CIMAT, A.P. 402, 36000 Guanajuato (Mexico)]. e-mail: hcoronel@uv.mx
2007-07-01
Empirical tests for pseudo random number generators based on the use of processes or physical models have been successfully used and are considered as complementary to theoretical tests of randomness. In this work a statistical methodology for evaluating the quality of pseudo random number generators is presented. The method is illustrated in the context of the so-called exponential decay process, using some pseudo random number generators commonly used in physics. (Author)
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.
Rinehart, Nicole J.; Bradshaw, John L.; Moss, Simon A.; Brereton, Avril V.; Tonge, Bruce J.
2006-01-01
The repetitive, stereotyped and obsessive behaviours, which are core diagnostic features of autism, are thought to be underpinned by executive dysfunction. This study examined executive impairment in individuals with autism and Asperger's disorder using a verbal equivalent of an established pseudo-random number generating task. Different patterns…
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.
Yang, Yu-Guang; Xu, Peng; Yang, Rui; Zhou, Yi-Hua; Shi, Wei-Min
2016-01-01
Quantum information and quantum computation have achieved a huge success during the last years. In this paper, we investigate the capability of quantum Hash function, which can be constructed by subtly modifying quantum walks, a famous quantum computation model. It is found that quantum Hash function can act as a hash function for the privacy amplification process of quantum key distribution systems with higher security. As a byproduct, quantum Hash function can also be used for pseudo-random number generation due to its inherent chaotic dynamics. Further we discuss the application of quantum Hash function to image encryption and propose a novel image encryption algorithm. Numerical simulations and performance comparisons show that quantum Hash function is eligible for privacy amplification in quantum key distribution, pseudo-random number generation and image encryption in terms of various hash tests and randomness tests. It extends the scope of application of quantum computation and quantum information.
Yang, Yu-Guang; Xu, Peng; Yang, Rui; Zhou, Yi-Hua; Shi, Wei-Min
2016-01-01
Quantum information and quantum computation have achieved a huge success during the last years. In this paper, we investigate the capability of quantum Hash function, which can be constructed by subtly modifying quantum walks, a famous quantum computation model. It is found that quantum Hash function can act as a hash function for the privacy amplification process of quantum key distribution systems with higher security. As a byproduct, quantum Hash function can also be used for pseudo-random number generation due to its inherent chaotic dynamics. Further we discuss the application of quantum Hash function to image encryption and propose a novel image encryption algorithm. Numerical simulations and performance comparisons show that quantum Hash function is eligible for privacy amplification in quantum key distribution, pseudo-random number generation and image encryption in terms of various hash tests and randomness tests. It extends the scope of application of quantum computation and quantum information. PMID:26823196
Cryptography, statistics and pseudo-randomness (Part 1)
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
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)
Mansingka, Abhinav S.
2014-06-18
This paper introduces fully digital implementations of four di erent systems in the 3rd order jerk-equation based chaotic family using the Euler approximation. The digitization approach enables controllable chaotic systems that reliably provide sinusoidal or chaotic output based on a selection input. New systems are introduced, derived using logical and arithmetic operations between two system implementations of different bus widths, with up to 100x higher maximum Lyapunov exponent than the original jerkequation based chaotic systems. The resulting chaotic output is shown to pass the NIST sp. 800-22 statistical test suite for pseudorandom number generators without post-processing by only eliminating the statistically defective bits. The systems are designed in Verilog HDL and experimentally verified on a Xilinx Virtex 4 FPGA for a maximum throughput of 15.59 Gbits/s for the native chaotic output and 8.77 Gbits/s for the resulting pseudo-random number generators.
Implementation of a RANLUX Based Pseudo-Random Number Generator in FPGA Using VHDL and Impulse C
Agnieszka Dąbrowska-Boruch; Grzegorz Gancarczyk; Kazimierz Wiatr
2014-01-01
Monte Carlo simulations are widely used e.g. in the field of physics and molecular modelling. The main role played in these is by the high performance random number generators, such as RANLUX or MERSSENE TWISTER. In this paper the authors introduce the world's first implementation of the RANLUX algorithm on an FPGA platform for high performance computing purposes. A significant speed-up of one generator instance over 60 times, compared with a graphic card based solution, can be noticed. Compa...
Radwan, Ahmed Gomaa
2014-06-18
This paper presents a digital implementation of a 3rd order chaotic system using the Euler approximation. Short-term predictability is studied in relation to system precision, Euler step size and attractor size and optimal parameters for maximum performance are derived. Defective bits from the native chaotic output are neglected and the remaining pass the NIST SP. 800-22 tests without post-processing. The resulting optimized pseudorandom number generator has throughput up to 17.60 Gbits/s for a 64-bit design experimentally verified on a Xilinx Virtex 4 FPGA with logic utilization less than 1.85%.
Radwan, Ahmed Gomaa; Mansingka, Abhinav S.; Salama, Khaled N.; Zidan, Mohammed A.
2014-01-01
This paper presents a digital implementation of a 3rd order chaotic system using the Euler approximation. Short-term predictability is studied in relation to system precision, Euler step size and attractor size and optimal parameters for maximum performance are derived. Defective bits from the native chaotic output are neglected and the remaining pass the NIST SP. 800-22 tests without post-processing. The resulting optimized pseudorandom number generator has throughput up to 17.60 Gbits/s for a 64-bit design experimentally verified on a Xilinx Virtex 4 FPGA with logic utilization less than 1.85%.
Fully digital 1-D, 2-D and 3-D multiscroll chaos as hardware pseudo random number generators
Mansingka, Abhinav S.
2012-10-07
This paper introduces the first fully digital implementation of 1-D, 2-D and 3-D multiscroll chaos using the sawtooth nonlinearity in a 3rd order ODE with the Euler approximation. Systems indicate chaotic behaviour through phase space boundedness and positive Lyapunov exponent. Low-significance bits form a PRNG and pass all tests in the NIST SP. 800-22 suite without post-processing. Real-time control of the number of scrolls allows distinct output streams with 2-D and 3-D multiscroll chaos enabling greater controllability. The proposed PRNGs are experimentally verified on a Xilinx Virtex 4 FPGA with logic utilization less than 1.25%, throughput up to 5.25 Gbits/s and up to 512 distinct output streams with low cross-correlation.
International Nuclear Information System (INIS)
Rotzoll, G.
1982-01-01
After a brief summary of the pseudo-random time-of-flight (TOF) method, the design criteria for construction of a pseudo-random TOF disc are considered and complemented by computer simulations. The question of resolution and the choice of the sequence length and number of time channels per element are discussed. Moreover, the stability requirements of the chopper motor frequency are investigated. (author)
Pseudo-random bit generator based on lag time series
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.
Kucukgoz, Mehmet; Harmanci, Oztan; Mihcak, Mehmet K.; Venkatesan, Ramarathnam
2005-03-01
In this paper, we propose a novel semi-blind video watermarking scheme, where we use pseudo-random robust semi-global features of video in the three dimensional wavelet transform domain. We design the watermark sequence via solving an optimization problem, such that the features of the mark-embedded video are the quantized versions of the features of the original video. The exact realizations of the algorithmic parameters are chosen pseudo-randomly via a secure pseudo-random number generator, whose seed is the secret key, that is known (resp. unknown) by the embedder and the receiver (resp. by the public). We experimentally show the robustness of our algorithm against several attacks, such as conventional signal processing modifications and adversarial estimation attacks.
Pseudo-random bit generator based on Chebyshev map
Stoyanov, B. P.
2013-10-01
In this paper, we study a pseudo-random bit generator based on two Chebyshev polynomial maps. The novel derivative algorithm shows perfect statistical properties established by number of statistical tests.
Pseudo random signal processing theory and application
Zepernick, Hans-Jurgen
2013-01-01
In recent years, pseudo random signal processing has proven to be a critical enabler of modern communication, information, security and measurement systems. The signal's pseudo random, noise-like properties make it vitally important as a tool for protecting against interference, alleviating multipath propagation and allowing the potential of sharing bandwidth with other users. Taking a practical approach to the topic, this text provides a comprehensive and systematic guide to understanding and using pseudo random signals. Covering theoretical principles, design methodologies and applications
Pseudo Random Coins Show More Heads Than Tails
Bauke, Heiko; Mertens, Stephan
2003-01-01
Tossing a coin is the most elementary Monte Carlo experiment. In a computer the coin is replaced by a pseudo random number generator. It can be shown analytically and by exact enumerations that popular random number generators are not capable of imitating a fair coin: pseudo random coins show more heads than tails. This bias explains the empirically observed failure of some random number generators in random walk experiments. It can be traced down to the special role of the value zero in the ...
Targeted reduction of highly abundant transcripts using pseudo-random primers.
Arnaud, Ophélie; Kato, Sachi; Poulain, Stéphane; Plessy, Charles
2016-04-01
Transcriptome studies based on quantitative sequencing can estimate levels of gene expression by measuring target RNA abundance in sequencing libraries. Sequencing costs are proportional to the total number of sequenced reads, and in order to cover rare RNAs, considerable quantities of abundant and identical reads are needed. This major limitation can be addressed by depleting a proportion of the most abundant sequences from the library. However, such depletion strategies involve either extra handling of the input RNA sample or use of a large number of reverse transcription primers, termed not-so-random (NSR) primers, which are costly to synthesize. Taking advantage of the high tolerance of reverse transcriptase to mis-prime, we found that it is possible to use as few as 40 pseudo-random (PS) reverse transcription primers to decrease the rate of undesirable abundant sequences within a library without affecting the overall transcriptome diversity. PS primers are simple to design and can be used to deplete several undesirable RNAs simultaneously, thus creating a flexible tool for enriching transcriptome libraries for rare transcript sequences.
International Nuclear Information System (INIS)
Kostic, Lj.
1973-01-01
Specially constructed fast reactivity oscillator was stimulating the zero power reactor by a stimulus which caused pseudo-random reactivity changes. Measuring system included stochastic oscillator BCR-1 supplied by pseudo-random pulses from noise generator GBS-16, instrumental tape-recorder, system for data acquisition and digital computer ZUSE-Z-23. For measuring the spatially dependent transfer function, reactor response was measured at a number of different positions of stochastic oscillator and ionization chamber. In order to keep the reactor system linear, experiment was limited to small reactivity fluctuations. Experimental results were compared to theoretical ones
Calibration of Correlation Radiometers Using Pseudo-Random Noise Signals
Directory of Open Access Journals (Sweden)
Sebastián Pantoja
2009-08-01
Full Text Available The calibration of correlation radiometers, and particularly aperture synthesis interferometric radiometers, is a critical issue to ensure their performance. Current calibration techniques are based on the measurement of the cross-correlation of receivers’ outputs when injecting noise from a common noise source requiring a very stable distribution network. For large interferometric radiometers this centralized noise injection approach is very complex from the point of view of mass, volume and phase/amplitude equalization. Distributed noise injection techniques have been proposed as a feasible alternative, but are unable to correct for the so-called “baseline errors” associated with the particular pair of receivers forming the baseline. In this work it is proposed the use of centralized Pseudo-Random Noise (PRN signals to calibrate correlation radiometers. PRNs are sequences of symbols with a long repetition period that have a flat spectrum over a bandwidth which is determined by the symbol rate. Since their spectrum resembles that of thermal noise, they can be used to calibrate correlation radiometers. At the same time, since these sequences are deterministic, new calibration schemes can be envisaged, such as the correlation of each receiver’s output with a baseband local replica of the PRN sequence, as well as new distribution schemes of calibration signals. This work analyzes the general requirements and performance of using PRN sequences for the calibration of microwave correlation radiometers, and particularizes the study to a potential implementation in a large aperture synthesis radiometer using an optical distribution network.
About the problem of generating three-dimensional pseudo-random points.
Carpintero, D. D.
The author demonstrates that a popular pseudo-random number generator is not adequate in some circumstances to generate n-dimensional random points, n > 2. This problem is particularly noxious when direction cosines are generated. He proposes several soultions, among them a good generator that satisfies all statistical criteria.
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
Protocols for data hiding in pseudo-random state
Craver, Scott; Li, Enping; Yu, Jun
2009-02-01
An emerging form of steganographic communication uses ciphertext to replace the output of a random or strong pseudo-random number generator. PRNG-driven media, for example computer animated backdrops in video-conferencing channels, can then be used as a covert channel, if the PRNG bits that generated a piece of content can be estimated by the recipient. However, all bits sent over such a channel must be computationally indistinguishable from i.i.d. coin flips. Ciphertext messages and even key exchange datagrams are easily shaped to match this distribution; however, when placing these messages into a continous stream of PRNG bits, the sender is unable to provide synchronization markers, metadata, or error correction to ensure the message's location and proper decoding. In this paper we explore methods for message transmission and steganographic key exchange in such a "coin flip" channel. We establish that key exchange is generally not possible in this channel if an adversary possesses even a modest noise budget. If the warden is not vigilant in adding noise, however, communication is very simple.
Hirst, Keith
1994-01-01
Number and geometry are the foundations upon which mathematics has been built over some 3000 years. This book is concerned with the logical foundations of number systems from integers to complex numbers. The author has chosen to develop the ideas by illustrating the techniques used throughout mathematics rather than using a self-contained logical treatise. The idea of proof has been emphasised, as has the illustration of concepts from a graphical, numerical and algebraic point of view. Having laid the foundations of the number system, the author has then turned to the analysis of infinite proc
Characterization of electron microscopes with binary pseudo-random multilayer test samples
Yashchuk, Valeriy V.; Conley, Raymond; Anderson, Erik H.; Barber, Samuel K.; Bouet, Nathalie; McKinney, Wayne R.; Takacs, Peter Z.; Voronov, Dmitriy L.
2011-09-01
Verification of the reliability of metrology data from high quality X-ray optics requires that adequate methods for test and calibration of the instruments be developed. For such verification for optical surface profilometers in the spatial frequency domain, a modulation transfer function (MTF) calibration method based on binary pseudo-random (BPR) gratings and arrays has been suggested [1,2] and proven to be an effective calibration method for a number of interferometric microscopes, a phase shifting Fizeau interferometer, and a scatterometer [5]. Here we describe the details of development of binary pseudo-random multilayer (BPRML) test samples suitable for characterization of scanning (SEM) and transmission (TEM) electron microscopes. We discuss the results of TEM measurements with the BPRML test samples fabricated from a WiSi 2/Si multilayer coating with pseudo-randomly distributed layers. In particular, we demonstrate that significant information about the metrological reliability of the TEM measurements can be extracted even when the fundamental frequency of the BPRML sample is smaller than the Nyquist frequency of the measurements. The measurements demonstrate a number of problems related to the interpretation of the SEM and TEM data. Note that similar BPRML test samples can be used to characterize X-ray microscopes. Corresponding work with X-ray microscopes is in progress.
Characterization of electron microscopes with binary pseudo-random multilayer test samples
International Nuclear Information System (INIS)
Yashchuk, Valeriy V.; Conley, Raymond; Anderson, Erik H.; Barber, Samuel K.; Bouet, Nathalie; McKinney, Wayne R.; Takacs, Peter Z.; Voronov, Dmitriy L.
2011-01-01
Verification of the reliability of metrology data from high quality X-ray optics requires that adequate methods for test and calibration of the instruments be developed. For such verification for optical surface profilometers in the spatial frequency domain, a modulation transfer function (MTF) calibration method based on binary pseudo-random (BPR) gratings and arrays has been suggested and proven to be an effective calibration method for a number of interferometric microscopes, a phase shifting Fizeau interferometer, and a scatterometer [5]. Here we describe the details of development of binary pseudo-random multilayer (BPRML) test samples suitable for characterization of scanning (SEM) and transmission (TEM) electron microscopes. We discuss the results of TEM measurements with the BPRML test samples fabricated from a WiSi 2 /Si multilayer coating with pseudo-randomly distributed layers. In particular, we demonstrate that significant information about the metrological reliability of the TEM measurements can be extracted even when the fundamental frequency of the BPRML sample is smaller than the Nyquist frequency of the measurements. The measurements demonstrate a number of problems related to the interpretation of the SEM and TEM data. Note that similar BPRML test samples can be used to characterize X-ray microscopes. Corresponding work with X-ray microscopes is in progress.
Sequences, groups, and number theory
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.
Programmable pseudo-random detector-pulse-pattern generator
International Nuclear Information System (INIS)
Putten, R. van der; Nationaal Inst. voor Kernfysica en Hoge-Energiefysica
1990-01-01
This report discusses the design and realization of the digital part of the programmable pseudo-random detector pulse-pattern generator. For the design and realization use has been made of F-TTL and high speed special purpose ic's, in particular FAL's (15 ns). The design possibilities offered by the software for pro-gramming of the FAL's have been utilized as much as possible. In this way counters, registers and a state machine with extended control possibilities have been designed and an advanced 8 channel pulse generator has been developed which is controlled via the VME system bus. the generator possesses an internal clock oscillator of 16 MHZ. The moment when a pulse is generated can be adjusted with a step size of 250 ps. 2000 different periods (time windows) can be stored for generating a pattern. (author). 37 refs.; 6 figs
Improving the pseudo-randomness properties of chaotic maps using deep-zoom
Machicao, Jeaneth; Bruno, Odemir M.
2017-05-01
A generalized method is proposed to compose new orbits from a given chaotic map. The method provides an approach to examine discrete-time chaotic maps in a "deep-zoom" manner by using k-digits to the right from the decimal separator of a given point from the underlying chaotic map. Interesting phenomena have been identified. Rapid randomization was observed, i.e., chaotic patterns tend to become indistinguishable when compared to the original orbits of the underlying chaotic map. Our results were presented using different graphical analyses (i.e., time-evolution, bifurcation diagram, Lyapunov exponent, Poincaré diagram, and frequency distribution). Moreover, taking advantage of this randomization improvement, we propose a Pseudo-Random Number Generator (PRNG) based on the k-logistic map. The pseudo-random qualities of the proposed PRNG passed both tests successfully, i.e., DIEHARD and NIST, and were comparable with other traditional PRNGs such as the Mersenne Twister. The results suggest that simple maps such as the logistic map can be considered as good PRNG methods.
International Nuclear Information System (INIS)
Hayashi, Koji; Shimazaki, Junya; Nabeshima, Kunihiko; Ochiai, Masaaki; Shinohara, Yoshikuni; Inoue, Kimihiko.
1995-01-01
In order to investigate dynamics of the reactor plant of the nuclear ship Mutsu, the second reactor noise experiment using pseudo random binary sequences (PRBS) was performed on August 30, 1991 in the third experimental navigation. The experiments using both reactivity and load disturbances were performed at 50% of reactor power and under a quiet sea condition. Each PRBS was applied by manual operation of the control rod or the main steam valve. Various signals of the plant responses and of the acceleration of ship motion were measured. Furthermore, natural reactor noise signals were measured after each PRBS experiment in order to evaluate the effects of the PRBS disturbances. This paper summarizes the planning of the experiment, the instruction for the experiment and logs, the data recording conditions, recorded signal wave forms and the results of power spectral analysis. (author)
Covert Communication in MIMO-OFDM System Using Pseudo Random Location of Fake Subcarriers
Directory of Open Access Journals (Sweden)
Rizky Pratama Hudhajanto
2016-08-01
Full Text Available Multiple-Input Multiple-Output Orthogonal Frequency Division Multiplexing (MIMO-OFDM is the most used wireless transmission scheme in the world. However, its security is the interesting problem to discuss if we want to use this scheme to transmit a sensitive data, such as in the military and commercial communication systems. In this paper, we propose a new method to increase the security of MIMO-OFDM system using the change of location of fake subcarrier. The fake subcarriers’ location is generated per packet of data using Pseudo Random sequence generator. The simulation results show that the proposed scheme does not decrease the performance of conventional MIMO-OFDM. The attacker or eavesdropper gets worse Bit Error Rate (BER than the legal receiver compared to the conventional MIMO-OFDM system.
International Nuclear Information System (INIS)
Hayashi, Koji; Shimazaki, Junya; Nabeshima, Kunihiko; Ochiai, Masaaki; Shinohara, Yoshikuni; Inoue, Kimihiko.
1995-03-01
In order to investigate dynamics of the reactor plant of the nuclear ship Mutsu, the third reactor noise experiment using pseudo random binary sequences (PRBS) was performed on September 16, 1991 in the third experimental navigation. The experiments using both reactivity and load disturbances were performed at 70% of reactor power and under a normal sea condition. Each PRBS was applied by manual operation of the control rod or the main steam valve. Various signals of the plant responses and of the acceleration of ship motion were measured. Furthermore, natural reactor noise signals were measured after each PRBS experiment in order to evaluate the effects of the PRBS disturbances. This paper summarizes the planning of the experiment, the instruction for the experiment and logs, the data recording conditions, recorded signal wave forms and the results of power spectral analysis. (author)
International Nuclear Information System (INIS)
Yashchuk, Valeriy V.; Anderson, Erik H.; Barber, Samuel K.; Bouet, Nathalie; Cambie, Rossana; Conley, Raymond; McKinney, Wayne R.; Takacs, Peter Z.; Voronov, Dmitriy L.
2011-01-01
A modulation transfer function (MTF) calibration method based on binary pseudo-random (BPR) gratings and arrays (Proc. SPIE 7077-7 (2007), Opt. Eng. 47, 073602 (2008)) has been proven to be an effective MTF calibration method for a number of interferometric microscopes and a scatterometer (Nucl. Instr. and Meth. A616, 172 (2010)). Here we report on a further expansion of the application range of the method. We describe the MTF calibration of a 6 inch phase shifting Fizeau interferometer. Beyond providing a direct measurement of the interferometer's MTF, tests with a BPR array surface have revealed an asymmetry in the instrument's data processing algorithm that fundamentally limits its bandwidth. Moreover, the tests have illustrated the effects of the instrument's detrending and filtering procedures on power spectral density measurements. The details of the development of a BPR test sample suitable for calibration of scanning and transmission electron microscopes are also presented. Such a test sample is realized as a multilayer structure with the layer thicknesses of two materials corresponding to BPR sequence. The investigations confirm the universal character of the method that makes it applicable to a large variety of metrology instrumentation with spatial wavelength bandwidths from a few nanometers to hundreds of millimeters.
Pseudo-random arranged color filter array for controlling moiré patterns in display.
Zhou, Yangui; Fan, Hang; An, Sengzhong; Li, Juntao; Wang, Jiahui; Zhou, Jianying; Liu, Yikun
2015-11-16
Optical display quality can be degraded by the appearance of moiré pattern occurring in a display system consisting of a basic matrix superimposed with a functional structured optical layer. We propose in this paper a novel pseudo-random arranged color filter array with the table number arranged with an optimal design scenario. We show that the moiré pattern can be significantly reduced with the introduction of the special color filter array. The idea is tested with an experiment that gives rise to a substantially reduced moiré pattern in a display system. It is believed that the novel functional optical structures have significant impact to complex structured display system in general and to the autostereoscopic and integrated display systems in particular.
Design of a Handheld Pseudo Random Coded UWB Radar for Human Sensing
Directory of Open Access Journals (Sweden)
Xia Zheng-huan
2015-10-01
Full Text Available This paper presents the design of a handheld pseudo random coded Ultra-WideBand (UWB radar for human sensing. The main tasks of the radar are to track the moving human object and extract the human respiratory frequency. In order to achieve perfect penetrability and good range resolution, m sequence with a carrier of 800 MHz is chosen as the transmitting signal. The modulated m-sequence can be generated directly by the high-speed DAC and FPGA to reduce the size of the radar system, and the mean power of the transmitting signal is 5 dBm. The receiver has two receiving channels based on hybrid sampling, the first receiving channel is to sample the reference signal and the second receiving channel is to obtain the radar echo. The real-time pulse compression is computed in parallel with a group of on-chip DSP48E slices in FPGA to improve the scanning rate of the radar system. Additionally, the algorithms of moving target tracking and life detection are implemented using Intel’s micro-processor, and the detection results are sent to the micro displayer fixed on the helmet. The experimental results show that the moving target located at less than 16 m far away from the wall can be tracked, and the respiratory frequency of the static human at less than 14 m far away from the wall can be extracted.
International Nuclear Information System (INIS)
Nasserzadeh, V.; Swithenbank, J.; Jones, B.
1995-01-01
The problem of measuring gas-residence time in large incinerators was studied by the pseudo-random binary sequence (PRBS) stimulus tracer response technique at the Sheffield municipal solid-waste incinerator (35 MW plant). The steady-state system was disturbed by the superimposition of small fluctuations in the form of a pseudo-random binary sequence of methane pulses, and the response of the incinerator was determined from the CO 2 concentration in flue gases at the boiler exit, measured with a specially developed optical gas analyser with a high-frequency response. For data acquisition, an on-line PC computer was used together with the LAB Windows software system; the output response was then cross-correlated with the perturbation signal to give the impulse response of the incinerator. There was very good agreement between the gas-residence time for the Sheffield MSW incinerator as calculated by computational fluid dynamics (FLUENT Model) and gas-residence time at the plant as measured by the PRBS tracer technique. The results obtained from this research programme clearly demonstrate that the PRBS stimulus tracer response technique can be successfully and economically used to measure gas-residence times in large incinerator plants. It also suggests that the common commercial practice of characterising the incinerator operation by a single-residence-time parameter may lead to a misrepresentation of the complexities involved in describing the operation of the incineration system. (author)
Reactor dynamics experiment of N.S. Mutsu using pseudo random signal. 1
International Nuclear Information System (INIS)
Hayashi, Koji; Nabeshima, Kunihiko; Shinohara, Yoshikuni; Shimazaki, Junya; Inoue, Kimihiko; Ochiai, Masaaki.
1993-10-01
In order to investigate dynamics of the reactor plant of the nuclear ship Mutsu, reactor noise experiments using pseudo random binary sequences (PRBS) have been planned, and a preliminary experiment was performed on March 4, 1991 in the first experimental navigation with the aim of checking the experimental procedures and conditions. The experiments using both reactivity and load disturbances were performed at 70 % of reactor power and under a quiet sea condition. Each PRBS was applied by manual operation of the control rod or the main steam valve. Various signals of the plant responses and of the acceleration of ship motion were measured. From the results obtained, we confirmed that (1) the procedures and experimental conditions determined prior to the experiment were suitable for performing the PRBS experiments, (2) when the PRBS disturbances were applied, the plant state remained quite stable, and (3) the quality of the measured data is adequate for the purpose of dynamics analysis. This paper summarizes the planning and preparation of the experiment, the instruction for the experiment and logs, the data recording conditions, recorded signal wave forms and the results of power spectral analysis. (author)
Range walk error correction and modeling on Pseudo-random photon counting system
Shen, Shanshan; Chen, Qian; He, Weiji
2017-08-01
Signal to noise ratio and depth accuracy are modeled for the pseudo-random ranging system with two random processes. The theoretical results, developed herein, capture the effects of code length and signal energy fluctuation are shown to agree with Monte Carlo simulation measurements. First, the SNR is developed as a function of the code length. Using Geiger-mode avalanche photodiodes (GMAPDs), longer code length is proven to reduce the noise effect and improve SNR. Second, the Cramer-Rao lower bound on range accuracy is derived to justify that longer code length can bring better range accuracy. Combined with the SNR model and CRLB model, it is manifested that the range accuracy can be improved by increasing the code length to reduce the noise-induced error. Third, the Cramer-Rao lower bound on range accuracy is shown to converge to the previously published theories and introduce the Gauss range walk model to range accuracy. Experimental tests also converge to the presented boundary model in this paper. It has been proven that depth error caused by the fluctuation of the number of detected photon counts in the laser echo pulse leads to the depth drift of Time Point Spread Function (TPSF). Finally, numerical fitting function is used to determine the relationship between the depth error and the photon counting ratio. Depth error due to different echo energy is calibrated so that the corrected depth accuracy is improved to 1cm.
Surface detection performance evaluation of pseudo-random noise continuous wave laser radar
Mitev, Valentin; Matthey, Renaud; Pereira do Carmo, Joao
2017-11-01
A number of space missions (including in the ESA Exploration Programme) foreseen a use of laser radar sensor (or lidar) for determination of range between spacecrafts or between spacecraft and ground surface (altimetry). Such sensors need to be compact, robust and power efficient, at the same time with high detection performance. These requirements can be achieved with a Pseudo-Random Noise continuous wave lidar (PRN cw lidar). Previous studies have pointed to the advantages of this lidar with respect to space missions, but they also identified its limitations in high optical background. The progress of the lasers and the detectors in the near IR spectral range requires a re-evaluation of the PRN cw lidar potential. Here we address the performances of this lidar for surface detection (altimetry) in planetary missions. The evaluation is based on the following system configuration: (i) A cw fiber amplifier as lidar transmitter. The seeding laser exhibits a single-frequency spectral line, with subsequent amplitude modulation. The fiber amplifier allows high output power level, keeping the spectral characteristics and the modulation of the seeding light input. (ii) An avalanche photodiode in photon counting detection; (iii) Measurement scenarios representative for Earth, Mercury and Mars.
Energy Technology Data Exchange (ETDEWEB)
Barber, Samuel K.; Anderson, Erik D.; Cambie, Rossana; McKinney, Wayne R.; Takacs, Peter Z.; Stover, John C.; Voronov, Dmitriy L.; Yashchuk, Valeriy V.
2009-09-11
A technique for precise measurement of the modulation transfer function (MTF), suitable for characterization of a broad class of surface profilometers, is investigated in detail. The technique suggested in [Proc. SPIE 7077-7, (2007), Opt. Eng. 47(7), 073602-1-5 (2008)]is based on use of binary pseudo-random (BPR) gratings and arrays as standard MTF test surfaces. Unlike most conventional test surfaces, BPR gratings and arrays possess white-noise-like inherent power spectral densities (PSD), allowing the direct determination of the one- and two-dimensional MTF, respectively, with a sensitivity uniform over the entire spatial frequency range of a profiler. In the cited work, a one dimensional realization of the suggested method based on use of BPR gratings has been demonstrated. Here, a high-confidence of the MTF calibration technique is demonstrated via cross comparison measurements of a number of two dimensional BPR arrays using two different interferometric microscopes and a scatterometer. We also present the results of application of the experimentally determined MTF correction to the measurement taken with the MicromapTM-570 interferometric microscope of the surface roughness of a super-polished test mirror. In this particular case, without accounting for the instrumental MTF, the surface rms roughness over half of the instrumental spatial frequency bandwidth would be underestimated by a factor of approximately 1.4.
Stream cipher based on pseudorandom number generation using optical affine transformation
Sasaki, Toru; Togo, Hiroyuki; Tanida, Jun; Ichioka, Yoshiki
2000-07-01
We propose a new stream cipher technique for 2D image data which can be implemented by iterative optical transformation. The stream cipher uses a pseudo-random number generator (PRNG) to generate pseudo-random bit sequence. The proposed method for the PRNG is composed of iterative operation of 2D affine transformation achieved by optical components, and modulo-n addition of the transformed images. The method is expected to be executed efficiently by optical parallel processing. We verify performance of the proposed method in terms of security strength and clarify problems on optical implementation by the optical fractal synthesizer.
Lensless digital holography with diffuse illumination through a pseudo-random phase mask.
Bernet, Stefan; Harm, Walter; Jesacher, Alexander; Ritsch-Marte, Monika
2011-12-05
Microscopic imaging with a setup consisting of a pseudo-random phase mask, and an open CMOS camera, without an imaging objective, is demonstrated. The pseudo random phase mask acts as a diffuser for an incoming laser beam, scattering a speckle pattern to a CMOS chip, which is recorded once as a reference. A sample which is afterwards inserted somewhere in the optical beam path changes the speckle pattern. A single (non-iterative) image processing step, comparing the modified speckle pattern with the previously recorded one, generates a sharp image of the sample. After a first calibration the method works in real-time and allows quantitative imaging of complex (amplitude and phase) samples in an extended three-dimensional volume. Since no lenses are used, the method is free from lens abberations. Compared to standard inline holography the diffuse sample illumination improves the axial sectioning capability by increasing the effective numerical aperture in the illumination path, and it suppresses the undesired so-called twin images. For demonstration, a high resolution spatial light modulator (SLM) is programmed to act as the pseudo-random phase mask. We show experimental results, imaging microscopic biological samples, e.g. insects, within an extended volume at a distance of 15 cm with a transverse and longitudinal resolution of about 60 μm and 400 μm, respectively.
International Nuclear Information System (INIS)
Yashchuk, Valeriy V.; McKinney, Wayne R.; Takacs, Peter Z.
2008-01-01
We suggest and describe the use of a binary pseudo-random grating as a standard test surface for calibration of the modulation transfer function of microscopes. Results from calibration of a MicromapTM-570 interferometric microscope are presented.
Pseudo-random Aloha for inter-frame soft combining in RFID systems
DEFF Research Database (Denmark)
Castiglione, Paolo; Ricciato, Fabio; Popovski, Petar
2013-01-01
In this work we consider a recently proposed variant of the classical Framed Slotted-ALOHA where slot selection is based on a pseudo-random function of the message to be transmitted and of the frame index. We couple this feature with convolutional encoding, that allows to perform Inter-frame Soft...... cancellation (instead of combining). Numerical simulation results show that the ISoC scheme brings a noticeable throughput gain over traditional schemes in a dense RFID scenario with multiple concurrent Tag transmissions....
Pseudo-random tool paths for CNC sub-aperture polishing and other applications.
Dunn, Christina R; Walker, David D
2008-11-10
In this paper we first contrast classical and CNC polishing techniques in regard to the repetitiveness of the machine motions. We then present a pseudo-random tool path for use with CNC sub-aperture polishing techniques and report polishing results from equivalent random and raster tool-paths. The random tool-path used - the unicursal random tool-path - employs a random seed to generate a pattern which never crosses itself. Because of this property, this tool-path is directly compatible with dwell time maps for corrective polishing. The tool-path can be used to polish any continuous area of any boundary shape, including surfaces with interior perforations.
On a direct algorithm for the generation of log-normal pseudo-random numbers
Chamayou, J M F
1976-01-01
The random variable ( Pi /sub i=1//sup n/X/sub i//X/sub i+n/)/sup 1/ square root 2n/ is used to generate standard log normal variables Lambda (0, 1), where the X/sub i/ are independent uniform variables on (0, 1). (8 refs).
Parallel random number generator for inexpensive configurable hardware cells
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.
Design of an Ultra-wideband Pseudo Random Coded MIMO Radar Based on Radio Frequency Switches
Directory of Open Access Journals (Sweden)
Su Hai
2017-02-01
Full Text Available A Multiple-Input Multiple-Output (MIMO ultra-wideband radar can detect the range and azimuth information of targets in real time. It is widely used for geological surveys, life rescue, through-wall tracking, and other military or civil fields. This paper presents the design of an ultra-wideband pseudo random coded MIMO radar that is based on Radio Frequency (RF switches and implements a MIMO radar system. RF switches are employed to reduce cost and complexity of the system. As the switch pressure value is limited, the peak power of the transmitting signal is 18 dBm. The ultra-wideband radar echo is obtained by hybrid sampling, and pulse compression is computed by Digital Signal Processors (DSPs embedded in an Field-Programmable Gate Array (FPGA to simplify the signal process. The experiment illustrates that the radar system can detect the range and azimuth information of targets in real time.
Spreading Sequences Generated Using Asymmetrical Integer-Number Maps
Directory of Open Access Journals (Sweden)
V. Sebesta
2007-09-01
Full Text Available Chaotic sequences produced by piecewise linear maps can be transformed to binary sequences. The binary sequences are optimal for the asynchronous DS/CDMA systems in case of certain shapes of the maps. This paper is devoted to the one-to-one integer-number maps derived from the suitable asymmetrical piecewise linear maps. Such maps give periodic integer-number sequences, which can be transformed to the binary sequences. The binary sequences produced via proposed modified integer-number maps are perfectly balanced and embody good autocorrelation and crosscorrelation properties. The number of different binary sequences is sizable. The sequences are suitable as spreading sequences in DS/CDMA systems.
Generalized catalan numbers, sequences and polynomials
KOÇ, Cemal; GÜLOĞLU, İsmail; ESİN, Songül
2010-01-01
In this paper we present an algebraic interpretation for generalized Catalan numbers. We describe them as dimensions of certain subspaces of multilinear polynomials. This description is of utmost importance in the investigation of annihilators in exterior algebras.
Liu, Xiaoyong; Lu, Pei; Shao, Jianxin; Cao, Haibin; Zhu, Zhenmin
2017-10-01
In this paper, an information hiding method using decimal expansion of irrational numbers to generate random phase mask is proposed. Firstly, the decimal expansion parts of irrational numbers generate pseudo-random sequences using a new coding schemed, the irrational number and start and end bit numbers were used as keys in image information hiding. Secondly, we apply the coding schemed to the double phase encoding system, the pseudo-random sequences are taken to generate random phase masks. The mean square error is used to calculate the quality of the recovered image information. Finally, two tests had been carried out to verify the security of our method; the experimental results demonstrate that the cipher image has such features, strong robustness, key sensitivity, and resistance to brute force attack.
Tauberian theorems for Abel summability of sequences of fuzzy numbers
Yavuz, Enes; ćoşkun, Hüsamettin
2015-09-01
We give some conditions under which Abel summable sequences of fuzzy numbers are convergent. As corollaries we obtain the results given in [E. Yavuz, Ö. Talo, Abel summability of sequences of fuzzy numbers, Soft computing 2014, doi: 10.1007/s00500-014-1563-7].
Multi-kW coherent combining of fiber lasers seeded with pseudo random phase modulated light
Flores, Angel; Ehrehreich, Thomas; Holten, Roger; Anderson, Brian; Dajani, Iyad
2016-03-01
We report efficient coherent beam combining of five kilowatt-class fiber amplifiers with a diffractive optical element (DOE). Based on a master oscillator power amplifier (MOPA) configuration, the amplifiers were seeded with pseudo random phase modulated light. Each non-polarization maintaining fiber amplifier was optically path length matched and provides approximately 1.2 kW of near diffraction-limited output power (measured M2polarization control. A low power sample of the combined beam after the DOE provided an error signal for active phase locking which was performed via Locking of Optical Coherence by Single-Detector Electronic-Frequency Tagging (LOCSET). After phase stabilization, the beams were coherently combined via the 1x5 DOE. A total combined output power of 4.9 kW was achieved with 82% combining efficiency and excellent beam quality (M2splitter loss was 5%. Similarly, losses due in part to non-ideal polarization, ASE content, uncorrelated wavefront errors, and misalignment errors contributed to the efficiency reduction.
International Nuclear Information System (INIS)
Lucianna F A; Carrillo M A; Mangussi M J
2012-01-01
The present work describes the development of a pseudo-random system to provide to a simulator pulse of radiation detectors the ability to emit pulses patterns similar to those recorded when measuring actual radioisotope. The idea is that the system can emulate characteristic spectral distributions of known radioisotopes, as well as creating individual spectra for specific purposes. This design is based on an improvement in terms of software from earlier development that only supplied predefined amplitude pulses at constant intervals (author)
Frequency characteristics of coordinate sequences of linear recurrences over Galois rings
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.
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
Simulating efficiently the evolution of DNA sequences.
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.
Energy Technology Data Exchange (ETDEWEB)
Yashchuk, V. V., E-mail: VVYashchuk@lbl.gov; Chan, E. R.; Lacey, I. [Advanced Light Source, Lawrence Berkeley National Laboratory, Berkeley, California 94720 (United States); Fischer, P. J. [Center for X-Ray Optics, Lawrence Berkeley National Laboratory, Berkeley, California 94720 (United States); Physics Department, University of California Santa Cruz, Santa Cruz, California 94056 (United States); Conley, R. [Advance Photon Source, Argonne National Laboratory, Argonne, Illinois 60439 (United States); National Synchrotron Light Source II, Brookhaven National Laboratory, Upton, New York 11973 (United States); McKinney, W. R. [Diablo Valley College, 321 Golf Club Road, Pleasant Hill, California 94523 (United States); Artemiev, N. A. [KLA-Tencor Corp., 1 Technology Drive, Milpitas, California 95035 (United States); Bouet, N. [National Synchrotron Light Source II, Brookhaven National Laboratory, Upton, New York 11973 (United States); Cabrini, S. [Molecular Foundry, Lawrence Berkeley National Laboratory, Berkeley, California 94720 (United States); Calafiore, G.; Peroz, C.; Babin, S. [aBeam Technologies, Inc., Hayward, California 94541 (United States)
2015-12-15
We present a modulation transfer function (MTF) calibration method based on binary pseudo-random (BPR) one-dimensional sequences and two-dimensional arrays as an effective method for spectral characterization in the spatial frequency domain of a broad variety of metrology instrumentation, including interferometric microscopes, scatterometers, phase shifting Fizeau interferometers, scanning and transmission electron microscopes, and at this time, x-ray microscopes. The inherent power spectral density of BPR gratings and arrays, which has a deterministic white-noise-like character, allows a direct determination of the MTF with a uniform sensitivity over the entire spatial frequency range and field of view of an instrument. We demonstrate the MTF calibration and resolution characterization over the full field of a transmission soft x-ray microscope using a BPR multilayer (ML) test sample with 2.8 nm fundamental layer thickness. We show that beyond providing a direct measurement of the microscope’s MTF, tests with the BPRML sample can be used to fine tune the instrument’s focal distance. Our results confirm the universality of the method that makes it applicable to a large variety of metrology instrumentation with spatial wavelength bandwidths from a few nanometers to hundreds of millimeters.
International Nuclear Information System (INIS)
Yashchuk, V. V.; Chan, E. R.; Lacey, I.; Fischer, P. J.; Conley, R.; McKinney, W. R.; Artemiev, N. A.; Bouet, N.; Cabrini, S.; Calafiore, G.; Peroz, C.; Babin, S.
2015-01-01
We present a modulation transfer function (MTF) calibration method based on binary pseudo-random (BPR) one-dimensional sequences and two-dimensional arrays as an effective method for spectral characterization in the spatial frequency domain of a broad variety of metrology instrumentation, including interferometric microscopes, scatterometers, phase shifting Fizeau interferometers, scanning and transmission electron microscopes, and at this time, x-ray microscopes. The inherent power spectral density of BPR gratings and arrays, which has a deterministic white-noise-like character, allows a direct determination of the MTF with a uniform sensitivity over the entire spatial frequency range and field of view of an instrument. We demonstrate the MTF calibration and resolution characterization over the full field of a transmission soft x-ray microscope using a BPR multilayer (ML) test sample with 2.8 nm fundamental layer thickness. We show that beyond providing a direct measurement of the microscope’s MTF, tests with the BPRML sample can be used to fine tune the instrument’s focal distance. Our results confirm the universality of the method that makes it applicable to a large variety of metrology instrumentation with spatial wavelength bandwidths from a few nanometers to hundreds of millimeters
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
Energy Technology Data Exchange (ETDEWEB)
Minegishi, M; Tsuburaya, Y [Japan National Oil Corp., Tokyo (Japan). Technology Research Center
1996-10-01
Influence of pseudo-random geometry on the imaging for 3D seismic exploration data acquisition has been investigate using a simple model by comparing with the regular geometry. When constituting wave front by the interference of elemental waves, pseudo-random geometry data did not always provide good results. In the case of a point diffractor, the imaging operation, where the constituted wave front was returned to the point diffractor by the interference of elemental waves for the spatial alias records, did not always give clear images. In the case of multi point diffractor, good images were obtained with less noise generation in spite of alias records. There are a lot of diffractors in the actual geological structures, which corresponds to the case of multi point diffractors. Finally, better images could be obtained by inputting records acquired using the pseudo-random geometry rather than by inputting spatial alias records acquired using the regular geometry. 7 refs., 6 figs.
Cluster growing process and a sequence of magic numbers
DEFF Research Database (Denmark)
Solov'yov, Ilia; Solov'yov, Andrey V.; Greiner, Walter
2003-01-01
demonstrate that in this way all known global minimum structures of the Lennard-Jones (LJ) clusters can be found. Our method provides an efficient tool for the calculation and analysis of atomic cluster structure. With its use we justify the magic number sequence for the clusters of noble gas atoms......We present a new theoretical framework for modeling the cluster growing process. Starting from the initial tetrahedral cluster configuration, adding new atoms to the system, and absorbing its energy at each step, we find cluster growing paths up to the cluster sizes of more than 100 atoms. We...
Mapping copy number variation by population-scale genome sequencing
DEFF Research Database (Denmark)
Mills, Ryan E.; Walter, Klaudia; Stewart, Chip
2011-01-01
Genomic structural variants (SVs) are abundant in humans, differing from other forms of variation in extent, origin and functional impact. Despite progress in SV characterization, the nucleotide resolution architecture of most SVs remains unknown. We constructed a map of unbalanced SVs (that is......, copy number variants) based on whole genome DNA sequencing data from 185 human genomes, integrating evidence from complementary SV discovery approaches with extensive experimental validations. Our map encompassed 22,025 deletions and 6,000 additional SVs, including insertions and tandem duplications...
Directory of Open Access Journals (Sweden)
Lara Ortiz-Martin
2018-01-01
Full Text Available The proliferation of wearable and implantable medical devices has given rise to an interest in developing security schemes suitable for these systems and the environment in which they operate. One area that has received much attention lately is the use of (human biological signals as the basis for biometric authentication, identification and the generation of cryptographic keys. The heart signal (e.g., as recorded in an electrocardiogram has been used by several researchers in the last few years. Specifically, the so-called Inter-Pulse Intervals (IPIs, which is the time between two consecutive heartbeats, have been repeatedly pointed out as a potentially good source of entropy and are at the core of various recent authentication protocols. In this work, we report the results of a large-scale statistical study to determine whether such an assumption is (or not upheld. For this, we have analyzed 19 public datasets of heart signals from the Physionet repository, spanning electrocardiograms from 1353 subjects sampled at different frequencies and with lengths that vary between a few minutes and several hours. We believe this is the largest dataset on this topic analyzed in the literature. We have then applied a standard battery of randomness tests to the extracted IPIs. Under the algorithms described in this paper and after analyzing these 19 public ECG datasets, our results raise doubts about the use of IPI values as a good source of randomness for cryptographic purposes. This has repercussions both in the security of some of the protocols proposed up to now and also in the design of future IPI-based schemes.
Fully digital 1-D, 2-D and 3-D multiscroll chaos as hardware pseudo random number generators
Mansingka, Abhinav S.; Radwan, Ahmed Gomaa; Salama, Khaled N.
2012-01-01
This paper introduces the first fully digital implementation of 1-D, 2-D and 3-D multiscroll chaos using the sawtooth nonlinearity in a 3rd order ODE with the Euler approximation. Systems indicate chaotic behaviour through phase space boundedness
Pseudo-random properties of a linear congruential generator investigated by b-adic diaphony
Stoev, Peter; Stoilova, Stanislava
2017-12-01
In the proposed paper we continue the study of the diaphony, defined in b-adic number system, and we extend it in different directions. We investigate this diaphony as a tool for estimation of the pseudorandom properties of some of the most used random number generators. This is done by evaluating the distribution of specially constructed two-dimensional nets on the base of the obtained random numbers. The aim is to see how the generated numbers are suitable for calculations in some numerical methods (Monte Carlo etc.).
Cooperative multi-user detection and ranging based on pseudo-random codes
Directory of Open Access Journals (Sweden)
C. Morhart
2009-05-01
Full Text Available We present an improved approach for a Round Trip Time of Flight distance measurement system. The system is intended for the usage in a cooperative localisation system for automotive applications. Therefore, it is designed to address a large number of communication partners per measurement cycle. By using coded signals in a time divison multiple access order, we can detect a large number of pedestrian sensors with just one car sensor. We achieve this by using very short transmit bursts in combination with a real time correlation algorithm. Futhermore, the correlation approach offers real time data, concerning the time of arrival, that can serve as a trigger impulse for other comunication systems. The distance accuracy of the correlation result was further increased by adding a fourier interpolation filter. The system performance was checked with a prototype at 2.4 GHz. We reached a distance measurement accuracy of 12 cm at a range up to 450 m.
Characterization of electron microscopes with binary pseudo-random multilayer test samples
International Nuclear Information System (INIS)
Yashchuk, Valeriy V.; Conley, Raymond; Anderson, Erik H.; Barber, Samuel K.; Bouet, Nathalie; McKinney, Wayne R.; Takacs, Peter Z.; Voronov, Dmitriy L.
2010-01-01
We discuss the results of SEM and TEM measurements with the BPRML test samples fabricated from a BPRML (WSi2/Si with fundamental layer thickness of 3 nm) with a Dual Beam FIB (focused ion beam)/SEM technique. In particular, we demonstrate that significant information about the metrological reliability of the TEM measurements can be extracted even when the fundamental frequency of the BPRML sample is smaller than the Nyquist frequency of the measurements. The measurements demonstrate a number of problems related to the interpretation of the SEM and TEM data. Note that similar BPRML test samples can be used to characterize x-ray microscopes. Corresponding work with x-ray microscopes is in progress.
Energy Technology Data Exchange (ETDEWEB)
Barber, Samuel K.; Soldate, Paul; Anderson, Erik H.; Cambie, Rossana; Marchesini, Stefano; McKinney, Wanye R.; Takacs, Peter Z.; Voronov, Dmitry L.; Yashchuk, Valeriy V.
2009-07-07
The major problem of measurement of a power spectral density (PSD) distribution of the surface heights with surface profilometers arises due to the unknown Modulation Transfer Function (MTF) of the instruments. The MTF tends to distort the PSD at higher spatial frequencies. It has been suggested [Proc. SPIE 7077-7, (2007), Opt. Eng. 47 (7), 073602-1-5 (2008)] that the instrumental MTF of a surface profiler can be precisely measured using standard test surfaces based on binary pseudo-random (BPR) patterns. In the cited work, a one dimensional (1D) realization of the suggested method based on use of BPR gratings has been demonstrated. Here, we present recent achievements made in fabricating and using two-dimensional (2D) BPR arrays that allow for a direct 2D calibration of the instrumental MTF. The 2D BPRAs were used as standard test surfaces for 2D MTF calibration of the MicromapTM-570 interferometric microscope with all available objectives. The effects of fabrication imperfections on the efficiency of calibration are also discussed.
International Nuclear Information System (INIS)
Luna, M.; Chavez, I.; Cajas, D.; Santos, R.
2015-01-01
The study of thermal-hydraulic performance of a fixed bed nuclear reactor (FBNR) core and the effect of the porosity was studied by the CFD method with 'SolidWorks' software. The representative sections of three different packed beds arrangements were analyzed: face-centered cubic (FCC), body-centered cubic (BCC), and a pseudo-random, with values of porosity of 0.28, 0.33 and 0.53 respectively. The minimum coolant flow required to avoid the phase change for each one of the configurations was determined. The results show that the heat transfer rate increases when the porosity value decreases, and consequently the minimum coolant flow in each configuration. The results of minimum coolant flow were: 728.51 kg/s for the FCC structure, 372.72 kg/s for the BCC, and 304.96 kg/s for the pseudo-random. Meanwhile, the heat transfer coefficients in each packed bed were 6480 W/m 2 *K, 3718 W/m 2 *K and 3042 W/m 2 *K respectively. Finally the pressure drop was calculated, and the results were 0.588 MPa for FCC configuration, 0.033 MPa for BCC and 0.017 MPa for the pseudo-random one. This means that with a higher porosity, the fluid can circulate easier because there are fewer obstacles to cross, so there are fewer energy losses. (authors)
Random Numbers and Quantum Computers
McCartney, Mark; Glass, David
2002-01-01
The topic of random numbers is investigated in such a way as to illustrate links between mathematics, physics and computer science. First, the generation of random numbers by a classical computer using the linear congruential generator and logistic map is considered. It is noted that these procedures yield only pseudo-random numbers since…
Study on random number generator in Monte Carlo code
International Nuclear Information System (INIS)
Oya, Kentaro; Kitada, Takanori; Tanaka, Shinichi
2011-01-01
The Monte Carlo code uses a sequence of pseudo-random numbers with a random number generator (RNG) to simulate particle histories. A pseudo-random number has its own period depending on its generation method and the period is desired to be long enough not to exceed the period during one Monte Carlo calculation to ensure the correctness especially for a standard deviation of results. The linear congruential generator (LCG) is widely used as Monte Carlo RNG and the period of LCG is not so long by considering the increasing rate of simulation histories in a Monte Carlo calculation according to the remarkable enhancement of computer performance. Recently, many kinds of RNG have been developed and some of their features are better than those of LCG. In this study, we investigate the appropriate RNG in a Monte Carlo code as an alternative to LCG especially for the case of enormous histories. It is found that xorshift has desirable features compared with LCG, and xorshift has a larger period, a comparable speed to generate random numbers, a better randomness, and good applicability to parallel calculation. (author)
Some Double Sequence Spaces of Fuzzy Real Numbers of Paranormed Type
Directory of Open Access Journals (Sweden)
Bipul Sarma
2013-01-01
Full Text Available We study different properties of convergent, null, and bounded double sequence spaces of fuzzy real numbers like completeness, solidness, sequence algebra, symmetricity, convergence-free, and so forth. We prove some inclusion results too.
Directory of Open Access Journals (Sweden)
Fred Lunnon
2009-06-01
Full Text Available We review the concept of the number wall as an alternative to the traditional linear complexity profile (LCP, and sketch the relationship to other topics such as linear feedback shift-register (LFSR and context-free Lindenmayer (D0L sequences. A remarkable ternary analogue of the Thue-Morse sequence is introduced having deficiency 2 modulo 3, and this property verified via the re-interpretation of the number wall as an aperiodic plane tiling.
Takizawa, Ken; Beaucamp, Anthony
2017-09-18
A new category of circular pseudo-random paths is proposed in order to suppress repetitive patterns and improve surface waviness on ultra-precision polished surfaces. Random paths in prior research had many corners, therefore deceleration of the polishing tool affected the surface waviness. The new random path can suppress velocity changes of the polishing tool and thus restrict degradation of the surface waviness, making it suitable for applications with stringent mid-spatial-frequency requirements such as photomask blanks for EUV lithography.
Some double sequence spaces of interval numbers defined by Orlicz function
Directory of Open Access Journals (Sweden)
Ayhan Esi
2014-10-01
Full Text Available In this paper we introduce some interval valued double sequence spaces defined by Orlicz function and study different properties of these spaces like inclusion relations, solidity, etc. We establish some inclusion relations among them. Also we introduce the concept of double statistical convergence for interval number sequences and give an inclusion relation between interval valued double sequence spaces.
RANDNA: a random DNA sequence generator.
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.
Generalized statistical convergence of order β for sequences of fuzzy numbers
Altınok, Hıfsı; Karakaş, Abdulkadir; Altın, Yavuz
2018-01-01
In the present paper, we introduce the concepts of Δm-statistical convergence of order β for sequences of fuzzy numbers and strongly Δm-summable of order β for sequences of fuzzy numbers by using a modulus function f and taking supremum on metric d for 0 < β ≤ 1 and give some inclusion relations between them.
An Investigation of the Sequence of Catalan Numbers with Activities for Prospective Teachers.
Koker, John; Kuenzi, Norbert J.; Oktac, Asuman; Carmony, Lowell; Leibowitz, Rochelle
1998-01-01
Investigates several problems with the sequences of numbers known as the Catalan numbers and the Bell numbers. Finds that the problems are appropriate for both pre- and in-service teachers, as well as students studying discrete mathematics. (Author/CCM)
Droit-Volet, Sylvie; Clement, Angelique; Fayol, Michel
2003-01-01
This study tested 5- and 8-year-olds and adults in a bisection task with a sequence of stimuli in which time and number co-varied. Findings indicated that the number of stimuli interfered with 5-year-olds' performance on the temporal bisection task. Number interference decreased both with age and counting strategy. In the numerical bisection task,…
Effective Normalization for Copy Number Variation Detection from Whole Genome Sequencing
Janevski, A.; Varadan, V.; Kamalakaran, S.; Banerjee, N.; Dimitrova, D.
2012-01-01
Background Whole genome sequencing enables a high resolution view ofthe human genome and provides unique insights into genome structureat an unprecedented scale. There have been a number of tools to infer copy number variation in the genome. These tools while validatedalso include a number of
EPCGen2 Pseudorandom Number Generators: Analysis of J3Gen
Directory of Open Access Journals (Sweden)
Alberto Peinado
2014-04-01
Full Text Available This paper analyzes the cryptographic security of J3Gen, a promising pseudo random number generator for low-cost passive Radio Frequency Identification (RFID tags. Although J3Gen has been shown to fulfill the randomness criteria set by the EPCglobal Gen2 standard and is intended for security applications, we describe here two cryptanalytic attacks that question its security claims: (i a probabilistic attack based on solving linear equation systems; and (ii a deterministic attack based on the decimation of the output sequence. Numerical results, supported by simulations, show that for the specific recommended values of the configurable parameters, a low number of intercepted output bits are enough to break J3Gen. We then make some recommendations that address these issues.
Directory of Open Access Journals (Sweden)
Romer C. Castillo
2015-11-01
Full Text Available This study established some recurrence relations and exponential generating functions of the sequence of factoriangular numbers. A factoriangular number is defined as a sum of corresponding factorial and triangular number. The proofs utilize algebraic manipulations with some known results from calculus, particularly on power series and Maclaurin’s series. The recurrence relations were found by manipulating the formula defining a factoringular number while the ascertained exponential generating functions were in the closed form.
Evidence of significant bias in an elementary random number generator
International Nuclear Information System (INIS)
Borgwaldt, H.; Brandl, V.
1981-03-01
An elementary pseudo random number generator for isotropically distributed unit vectors in 3-dimensional space has ben tested for bias. This generator uses the IBM-suplied routine RANDU and a transparent rejection technique. The tests show clearly that non-randomness in the pseudo random numbers generated by the primary IBM generator leads to bias in the order of 1 percent in estimates obtained from the secondary random number generator. FORTRAN listings of 4 variants of the random number generator called by a simple test programme and output listings are included for direct reference. (orig.) [de
The MIXMAX random number generator
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.
Chaotic generation of PN sequences : a VLSI implementation
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
On Sequences of Numbers and Polynomials Defined by Linear Recurrence Relations of Order 2
Directory of Open Access Journals (Sweden)
Tian-Xiao He
2009-01-01
Full Text Available Here we present a new method to construct the explicit formula of a sequence of numbers and polynomials generated by a linear recurrence relation of order 2. The applications of the method to the Fibonacci and Lucas numbers, Chebyshev polynomials, the generalized Gegenbauer-Humbert polynomials are also discussed. The derived idea provides a general method to construct identities of number or polynomial sequences defined by linear recurrence relations. The applications using the method to solve some algebraic and ordinary differential equations are presented.
Theoretical and empirical convergence results for additive congruential random number generators
Wikramaratna, Roy S.
2010-03-01
Additive Congruential Random Number (ACORN) generators represent an approach to generating uniformly distributed pseudo-random numbers that is straightforward to implement efficiently for arbitrarily large order and modulus; if it is implemented using integer arithmetic, it becomes possible to generate identical sequences on any machine. This paper briefly reviews existing results concerning ACORN generators and relevant theory concerning sequences that are well distributed mod 1 in k dimensions. It then demonstrates some new theoretical results for ACORN generators implemented in integer arithmetic with modulus M=2[mu] showing that they are a family of generators that converge (in a sense that is defined in the paper) to being well distributed mod 1 in k dimensions, as [mu]=log2M tends to infinity. By increasing k, it is possible to increase without limit the number of dimensions in which the resulting sequences approximate to well distributed. The paper concludes by applying the standard TestU01 test suite to ACORN generators for selected values of the modulus (between 260 and 2150), the order (between 4 and 30) and various odd seed values. On the basis of these and earlier results, it is recommended that an order of at least 9 be used together with an odd seed and modulus equal to 230p, for a small integer value of p. While a choice of p=2 should be adequate for most typical applications, increasing p to 3 or 4 gives a sequence that will consistently pass all the tests in the TestU01 test suite, giving additional confidence in more demanding applications. The results demonstrate that the ACORN generators are a reliable source of uniformly distributed pseudo-random numbers, and that in practice (as suggested by the theoretical convergence results) the quality of the ACORN sequences increases with increasing modulus and order.
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.
DNA copy number, including telomeres and mitochondria, assayed using next-generation sequencing
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Jackson Stuart
2010-04-01
Full Text Available Abstract Background DNA copy number variations occur within populations and aberrations can cause disease. We sought to develop an improved lab-automatable, cost-efficient, accurate platform to profile DNA copy number. Results We developed a sequencing-based assay of nuclear, mitochondrial, and telomeric DNA copy number that draws on the unbiased nature of next-generation sequencing and incorporates techniques developed for RNA expression profiling. To demonstrate this platform, we assayed UMC-11 cells using 5 million 33 nt reads and found tremendous copy number variation, including regions of single and homogeneous deletions and amplifications to 29 copies; 5 times more mitochondria and 4 times less telomeric sequence than a pool of non-diseased, blood-derived DNA; and that UMC-11 was derived from a male individual. Conclusion The described assay outputs absolute copy number, outputs an error estimate (p-value, and is more accurate than array-based platforms at high copy number. The platform enables profiling of mitochondrial levels and telomeric length. The assay is lab-automatable and has a genomic resolution and cost that are tunable based on the number of sequence reads.
International Nuclear Information System (INIS)
Procassini, R J; Beck, B R
2004-01-01
It might be assumed that use of a ''high-quality'' random number generator (RNG), producing a sequence of ''pseudo random'' numbers with a ''long'' repetition period, is crucial for producing unbiased results in Monte Carlo particle transport simulations. While several theoretical and empirical tests have been devised to check the quality (randomness and period) of an RNG, for many applications it is not clear what level of RNG quality is required to produce unbiased results. This paper explores the issue of RNG quality in the context of parallel, Monte Carlo transport simulations in order to determine how ''good'' is ''good enough''. This study employs the MERCURY Monte Carlo code, which incorporates the CNPRNG library for the generation of pseudo-random numbers via linear congruential generator (LCG) algorithms. The paper outlines the usage of random numbers during parallel MERCURY simulations, and then describes the source and criticality transport simulations which comprise the empirical basis of this study. A series of calculations for each test problem in which the quality of the RNG (period of the LCG) is varied provides the empirical basis for determining the minimum repetition period which may be employed without producing a bias in the mean integrated results
Sep?lveda, Nuno; Campino, Susana G; Assefa, Samuel A; Sutherland, Colin J; Pain5, Arnab; Clark, Taane G
2013-01-01
BACKGROUND: The advent of next generation sequencing technology has accelerated efforts to map and catalogue copy number variation (CNV) in genomes of important micro-organisms for public health. A typical analysis of the sequence data involves mapping reads onto a reference genome, calculating the respective coverage, and detecting regions with too-low or too-high coverage (deletions and amplifications, respectively). Current CNV detection methods rely on statistical assumptions (e.g., a Poi...
Random number generators in support of Monte Carlo problems in physics
International Nuclear Information System (INIS)
Dyadkin, I.G.
1993-01-01
The ability to support a modern users' expectations of random number generators to solve problems in physics is analyzed. The capabilities of the newest concepts and the old pseudo-random algorithms are compared. The author is in favor of multiplicative generators. Due to the 64-bit arithmetic of a modern PC, multiplicative generators have a sufficient number of periods (up to 2 62 ) and are quicker to generate and to govern independent sequences for parallel processing. In addition they are able to replicate sub-sequences (without storing their seeds) for each standard trial in any code and to simulate spatial and planar directions and EXP(-x) distributions often needed as ''bricks'' for simulating events in physics. Hundreds of multipliers for multiplicative generators have been tabulated and tested, and the required speeds have been obtained. (author)
Random number generators tested on quantum Monte Carlo simulations.
Hongo, Kenta; Maezono, Ryo; Miura, Kenichi
2010-08-01
We have tested and compared several (pseudo) random number generators (RNGs) applied to a practical application, ground state energy calculations of molecules using variational and diffusion Monte Carlo metheds. A new multiple recursive generator with 8th-order recursion (MRG8) and the Mersenne twister generator (MT19937) are tested and compared with the RANLUX generator with five luxury levels (RANLUX-[0-4]). Both MRG8 and MT19937 are proven to give the same total energy as that evaluated with RANLUX-4 (highest luxury level) within the statistical error bars with less computational cost to generate the sequence. We also tested the notorious implementation of linear congruential generator (LCG), RANDU, for comparison. (c) 2010 Wiley Periodicals, Inc.
ReadDepth: a parallel R package for detecting copy number alterations from short sequencing reads.
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Christopher A Miller
2011-01-01
Full Text Available Copy number alterations are important contributors to many genetic diseases, including cancer. We present the readDepth package for R, which can detect these aberrations by measuring the depth of coverage obtained by massively parallel sequencing of the genome. In addition to achieving higher accuracy than existing packages, our tool runs much faster by utilizing multi-core architectures to parallelize the processing of these large data sets. In contrast to other published methods, readDepth does not require the sequencing of a reference sample, and uses a robust statistical model that accounts for overdispersed data. It includes a method for effectively increasing the resolution obtained from low-coverage experiments by utilizing breakpoint information from paired end sequencing to do positional refinement. We also demonstrate a method for inferring copy number using reads generated by whole-genome bisulfite sequencing, thus enabling integrative study of epigenomic and copy number alterations. Finally, we apply this tool to two genomes, showing that it performs well on genomes sequenced to both low and high coverage. The readDepth package runs on Linux and MacOSX, is released under the Apache 2.0 license, and is available at http://code.google.com/p/readdepth/.
International Nuclear Information System (INIS)
Chugunkov, I.V.
2014-01-01
The report contains the description of an approach based on calculation of missing sets quantity, which allows to reduce memory usage needed for implementation of statistical tests. Information about estimation procedure of test statistics derived as a result of using this approach is also provided [ru
Sequence diversity and copy number variation of Mutator-like transposases in wheat
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Nobuaki Asakura
2008-01-01
Full Text Available Partial transposase-coding sequences of Mutator-like elements (MULEs were isolated from a wild einkorn wheat, Triticum urartu, by degenerate PCR. The isolated sequences were classified into a MuDR or Class I clade and divided into two distinct subclasses (subclass I and subclass II. The average pair-wise identity between members of both subclasses was 58.8% at the nucleotide sequence level. Sequence diversity of subclass I was larger than that of subclass II. DNA gel blot analysis showed that subclass I was present as low copy number elements in the genomes of all Triticum and Aegilops accessions surveyed, while subclass II was present as high copy number elements. These two subclasses seemed uncapable of recognizing each other for transposition. The number of copies of subclass II elements was much higher in Aegilops with the S, Sl and D genomes and polyploid Triticum species than in diploid Triticum with the A genome, indicating that active transposition occurred in S, Sl and D genomes before polyploidization. DNA gel blot analysis of six species selected from three subfamilies of Poaceae demonstrated that only the tribe Triticeae possessed both subclasses. These results suggest that the differentiation of these two subclasses occurred before or immediately after the establishment of the tribe Triticeae.
On Sequence Lengths of Some Special External Exclusive OR Type LFSR Structures – Study and Analysis
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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.
Fast integration using quasi-random numbers
International Nuclear Information System (INIS)
Bossert, J.; Feindt, M.; Kerzel, U.
2006-01-01
Quasi-random numbers are specially constructed series of numbers optimised to evenly sample a given s-dimensional volume. Using quasi-random numbers in numerical integration converges faster with a higher accuracy compared to the case of pseudo-random numbers. The basic properties of quasi-random numbers are introduced, various generators are discussed and the achieved gain is illustrated by examples
Fast integration using quasi-random numbers
Bossert, J.; Feindt, M.; Kerzel, U.
2006-04-01
Quasi-random numbers are specially constructed series of numbers optimised to evenly sample a given s-dimensional volume. Using quasi-random numbers in numerical integration converges faster with a higher accuracy compared to the case of pseudo-random numbers. The basic properties of quasi-random numbers are introduced, various generators are discussed and the achieved gain is illustrated by examples.
Inferring Variation in Copy Number Using High Throughput Sequencing Data in R.
Knaus, Brian J; Grünwald, Niklaus J
2018-01-01
Inference of copy number variation presents a technical challenge because variant callers typically require the copy number of a genome or genomic region to be known a priori . Here we present a method to infer copy number that uses variant call format (VCF) data as input and is implemented in the R package vcfR . This method is based on the relative frequency of each allele (in both genic and non-genic regions) sequenced at heterozygous positions throughout a genome. These heterozygous positions are summarized by using arbitrarily sized windows of heterozygous positions, binning the allele frequencies, and selecting the bin with the greatest abundance of positions. This provides a non-parametric summary of the frequency that alleles were sequenced at. The method is applicable to organisms that have reference genomes that consist of full chromosomes or sub-chromosomal contigs. In contrast to other software designed to detect copy number variation, our method does not rely on an assumption of base ploidy, but instead infers it. We validated these approaches with the model system of Saccharomyces cerevisiae and applied it to the oomycete Phytophthora infestans , both known to vary in copy number. This functionality has been incorporated into the current release of the R package vcfR to provide modular and flexible methods to investigate copy number variation in genomic projects.
An On-Demand Optical Quantum Random Number Generator with In-Future Action and Ultra-Fast Response.
Stipčević, Mario; Ursin, Rupert
2015-06-09
Random numbers are essential for our modern information based society e.g. in cryptography. Unlike frequently used pseudo-random generators, physical random number generators do not depend on complex algorithms but rather on a physical process to provide true randomness. Quantum random number generators (QRNG) do rely on a process, which can be described by a probabilistic theory only, even in principle. Here we present a conceptually simple implementation, which offers a 100% efficiency of producing a random bit upon a request and simultaneously exhibits an ultra low latency. A careful technical and statistical analysis demonstrates its robustness against imperfections of the actual implemented technology and enables to quickly estimate randomness of very long sequences. Generated random numbers pass standard statistical tests without any post-processing. The setup described, as well as the theory presented here, demonstrate the maturity and overall understanding of the technology.
[Influence of PCR cycle number on microbial diversity analysis through next generation sequencing].
An, Yunhe; Gao, Lijuan; Li, Junbo; Tian, Yanjie; Wang, Jinlong; Zheng, Xuejuan; Wu, Huijuan
2016-08-25
Using of high throughput sequencing technology to study the microbial diversity in complex samples has become one of the hottest issues in the field of microbial diversity research. In this study, the soil and sheep rumen chyme samples were used to extract DNA, respectively. Then the 25 ng total DNA was used to amplify the 16S rRNA V3 region with 20, 25, 30 PCR cycles, and the final sequencing library was constructed by mixing equal amounts of purified PCR products. Finally, the operational taxonomic unit (OUT) amount, rarefaction curve, microbial number and species were compared through data analysis. It was found that at the same amount of DNA template, the proportion of the community composition was not the best with more numbers of PCR cycle, although the species number was much more. In all, when the PCR cycle number is 25, the number of species and proportion of the community composition were the most optimal both in soil or chyme samples.
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Brian B Tuch
Full Text Available Due to growing throughput and shrinking cost, massively parallel sequencing is rapidly becoming an attractive alternative to microarrays for the genome-wide study of gene expression and copy number alterations in primary tumors. The sequencing of transcripts (RNA-Seq should offer several advantages over microarray-based methods, including the ability to detect somatic mutations and accurately measure allele-specific expression. To investigate these advantages we have applied a novel, strand-specific RNA-Seq method to tumors and matched normal tissue from three patients with oral squamous cell carcinomas. Additionally, to better understand the genomic determinants of the gene expression changes observed, we have sequenced the tumor and normal genomes of one of these patients. We demonstrate here that our RNA-Seq method accurately measures allelic imbalance and that measurement on the genome-wide scale yields novel insights into cancer etiology. As expected, the set of genes differentially expressed in the tumors is enriched for cell adhesion and differentiation functions, but, unexpectedly, the set of allelically imbalanced genes is also enriched for these same cancer-related functions. By comparing the transcriptomic perturbations observed in one patient to his underlying normal and tumor genomes, we find that allelic imbalance in the tumor is associated with copy number mutations and that copy number mutations are, in turn, strongly associated with changes in transcript abundance. These results support a model in which allele-specific deletions and duplications drive allele-specific changes in gene expression in the developing tumor.
Human Y chromosome copy number variation in the next generation sequencing era and beyond.
Massaia, Andrea; Xue, Yali
2017-05-01
The human Y chromosome provides a fertile ground for structural rearrangements owing to its haploidy and high content of repeated sequences. The methodologies used for copy number variation (CNV) studies have developed over the years. Low-throughput techniques based on direct observation of rearrangements were developed early on, and are still used, often to complement array-based or sequencing approaches which have limited power in regions with high repeat content and specifically in the presence of long, identical repeats, such as those found in human sex chromosomes. Some specific rearrangements have been investigated for decades; because of their effects on fertility, or their outstanding evolutionary features, the interest in these has not diminished. However, following the flourishing of large-scale genomics, several studies have investigated CNVs across the whole chromosome. These studies sometimes employ data generated within large genomic projects such as the DDD study or the 1000 Genomes Project, and often survey large samples of healthy individuals without any prior selection. Novel technologies based on sequencing long molecules and combinations of technologies, promise to stimulate the study of Y-CNVs in the immediate future.
Sepú lveda, Nuno; Campino, Susana G; Assefa, Samuel A; Sutherland, Colin J; Pain, Arnab; Clark, Taane G
2013-01-01
Background: The advent of next generation sequencing technology has accelerated efforts to map and catalogue copy number variation (CNV) in genomes of important micro-organisms for public health. A typical analysis of the sequence data involves mapping reads onto a reference genome, calculating the respective coverage, and detecting regions with too-low or too-high coverage (deletions and amplifications, respectively). Current CNV detection methods rely on statistical assumptions (e.g., a Poisson model) that may not hold in general, or require fine-tuning the underlying algorithms to detect known hits. We propose a new CNV detection methodology based on two Poisson hierarchical models, the Poisson-Gamma and Poisson-Lognormal, with the advantage of being sufficiently flexible to describe different data patterns, whilst robust against deviations from the often assumed Poisson model.Results: Using sequence coverage data of 7 Plasmodium falciparum malaria genomes (3D7 reference strain, HB3, DD2, 7G8, GB4, OX005, and OX006), we showed that empirical coverage distributions are intrinsically asymmetric and overdispersed in relation to the Poisson model. We also demonstrated a low baseline false positive rate for the proposed methodology using 3D7 resequencing data and simulation. When applied to the non-reference isolate data, our approach detected known CNV hits, including an amplification of the PfMDR1 locus in DD2 and a large deletion in the CLAG3.2 gene in GB4, and putative novel CNV regions. When compared to the recently available FREEC and cn.MOPS approaches, our findings were more concordant with putative hits from the highest quality array data for the 7G8 and GB4 isolates.Conclusions: In summary, the proposed methodology brings an increase in flexibility, robustness, accuracy and statistical rigour to CNV detection using sequence coverage data. 2013 Seplveda et al.; licensee BioMed Central Ltd.
Sepúlveda, Nuno; Campino, Susana G; Assefa, Samuel A; Sutherland, Colin J; Pain, Arnab; Clark, Taane G
2013-02-26
The advent of next generation sequencing technology has accelerated efforts to map and catalogue copy number variation (CNV) in genomes of important micro-organisms for public health. A typical analysis of the sequence data involves mapping reads onto a reference genome, calculating the respective coverage, and detecting regions with too-low or too-high coverage (deletions and amplifications, respectively). Current CNV detection methods rely on statistical assumptions (e.g., a Poisson model) that may not hold in general, or require fine-tuning the underlying algorithms to detect known hits. We propose a new CNV detection methodology based on two Poisson hierarchical models, the Poisson-Gamma and Poisson-Lognormal, with the advantage of being sufficiently flexible to describe different data patterns, whilst robust against deviations from the often assumed Poisson model. Using sequence coverage data of 7 Plasmodium falciparum malaria genomes (3D7 reference strain, HB3, DD2, 7G8, GB4, OX005, and OX006), we showed that empirical coverage distributions are intrinsically asymmetric and overdispersed in relation to the Poisson model. We also demonstrated a low baseline false positive rate for the proposed methodology using 3D7 resequencing data and simulation. When applied to the non-reference isolate data, our approach detected known CNV hits, including an amplification of the PfMDR1 locus in DD2 and a large deletion in the CLAG3.2 gene in GB4, and putative novel CNV regions. When compared to the recently available FREEC and cn.MOPS approaches, our findings were more concordant with putative hits from the highest quality array data for the 7G8 and GB4 isolates. In summary, the proposed methodology brings an increase in flexibility, robustness, accuracy and statistical rigour to CNV detection using sequence coverage data.
Sepúlveda, Nuno
2013-02-26
Background: The advent of next generation sequencing technology has accelerated efforts to map and catalogue copy number variation (CNV) in genomes of important micro-organisms for public health. A typical analysis of the sequence data involves mapping reads onto a reference genome, calculating the respective coverage, and detecting regions with too-low or too-high coverage (deletions and amplifications, respectively). Current CNV detection methods rely on statistical assumptions (e.g., a Poisson model) that may not hold in general, or require fine-tuning the underlying algorithms to detect known hits. We propose a new CNV detection methodology based on two Poisson hierarchical models, the Poisson-Gamma and Poisson-Lognormal, with the advantage of being sufficiently flexible to describe different data patterns, whilst robust against deviations from the often assumed Poisson model.Results: Using sequence coverage data of 7 Plasmodium falciparum malaria genomes (3D7 reference strain, HB3, DD2, 7G8, GB4, OX005, and OX006), we showed that empirical coverage distributions are intrinsically asymmetric and overdispersed in relation to the Poisson model. We also demonstrated a low baseline false positive rate for the proposed methodology using 3D7 resequencing data and simulation. When applied to the non-reference isolate data, our approach detected known CNV hits, including an amplification of the PfMDR1 locus in DD2 and a large deletion in the CLAG3.2 gene in GB4, and putative novel CNV regions. When compared to the recently available FREEC and cn.MOPS approaches, our findings were more concordant with putative hits from the highest quality array data for the 7G8 and GB4 isolates.Conclusions: In summary, the proposed methodology brings an increase in flexibility, robustness, accuracy and statistical rigour to CNV detection using sequence coverage data. 2013 Seplveda et al.; licensee BioMed Central Ltd.
Variations in CCL3L gene cluster sequence and non-specific gene copy numbers
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Edberg Jeffrey C
2010-03-01
Full Text Available Abstract Background Copy number variations (CNVs of the gene CC chemokine ligand 3-like1 (CCL3L1 have been implicated in HIV-1 susceptibility, but the association has been inconsistent. CCL3L1 shares homology with a cluster of genes localized to chromosome 17q12, namely CCL3, CCL3L2, and, CCL3L3. These genes are involved in host defense and inflammatory processes. Several CNV assays have been developed for the CCL3L1 gene. Findings Through pairwise and multiple alignments of these genes, we have shown that the homology between these genes ranges from 50% to 99% in complete gene sequences and from 70-100% in the exonic regions, with CCL3L1 and CCL3L3 being identical. By use of MEGA 4 and BioEdit, we aligned sense primers, anti-sense primers, and probes used in several previously described assays against pre-multiple alignments of all four chemokine genes. Each set of probes and primers aligned and matched with overlapping sequences in at least two of the four genes, indicating that previously utilized RT-PCR based CNV assays are not specific for only CCL3L1. The four available assays measured median copies of 2 and 3-4 in European and African American, respectively. The concordance between the assays ranged from 0.44-0.83 suggesting individual discordant calls and inconsistencies with the assays from the expected gene coverage from the known sequence. Conclusions This indicates that some of the inconsistencies in the association studies could be due to assays that provide heterogenous results. Sequence information to determine CNV of the three genes separately would allow to test whether their association with the pathogenesis of a human disease or phenotype is affected by an individual gene or by a combination of these genes.
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.
Galustov, G. G.; Voronin, V. V.
2017-05-01
The sequence generator generates a sequence of pseudorandom binary numbers using a linear-feedback shift register (LFSR). This block implements LFSR using a simple shift register generator (SSRG, or Fibonacci) configuration. In this article we introduce the concept of probabilistic binary element provides requirements, which ensure compliance with the criterion of "uniformity" in the implementation of the basic physical generators uniformly distributed random number sequences. Based on these studies, we obtained an analytic relation between the parameters of the binary sequence and parameters of a numerical sequence with the shift register output. The received analytical dependencies can help in evaluating the statistical characteristics of the processes in solving problems of statistical modeling. It is supposed that the formation of the binary sequence output from the binary probabilistic element is produced using a physical noise process. It is shown that the observed errors in statistical modeling using pseudo-random numbers do not occur if the model examines linear systems with constant parameters, but in case models of nonlinear systems, higher order moments can have a Gaussian distribution.
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Jo Nishino
2013-01-01
Full Text Available There has been recent success in identifying disease-causing variants in Mendelian disorders by exome sequencing followed by simple filtering techniques. Studies generally assume complete or high penetrance. However, there are likely many failed and unpublished studies due in part to incomplete penetrance or phenocopy. In this study, the expected number of candidate single-nucleotide variants (SNVs in exome data for autosomal dominant or recessive Mendelian disorders was investigated under the assumption of “no genetic heterogeneity.” All variants were assumed to be under the “null model,” and sample allele frequencies were modeled using a standard population genetics theory. To investigate the properties of pedigree data, full-sibs were considered in addition to unrelated individuals. In both cases, particularly regarding full-sibs, the number of SNVs remained very high without controls. The high efficacy of controls was also confirmed. When controls were used with a relatively large total sample size (e.g., N=20, 50, filtering incorporating of incomplete penetrance and phenocopy efficiently reduced the number of candidate SNVs. This suggests that filtering is useful when an assumption of no “genetic heterogeneity” is appropriate and could provide general guidelines for sample size determination.
DEEPre: sequence-based enzyme EC number prediction by deep learning
Li, Yu
2017-10-20
Annotation of enzyme function has a broad range of applications, such as metagenomics, industrial biotechnology, and diagnosis of enzyme deficiency-caused diseases. However, the time and resource required make it prohibitively expensive to experimentally determine the function of every enzyme. Therefore, computational enzyme function prediction has become increasingly important. In this paper, we develop such an approach, determining the enzyme function by predicting the Enzyme Commission number.We propose an end-to-end feature selection and classification model training approach, as well as an automatic and robust feature dimensionality uniformization method, DEEPre, in the field of enzyme function prediction. Instead of extracting manuallycrafted features from enzyme sequences, our model takes the raw sequence encoding as inputs, extracting convolutional and sequential features from the raw encoding based on the classification result to directly improve the prediction performance. The thorough cross-fold validation experiments conducted on two large-scale datasets show that DEEPre improves the prediction performance over the previous state-of-the-art methods. In addition, our server outperforms five other servers in determining the main class of enzymes on a separate low-homology dataset. Two case studies demonstrate DEEPre\\'s ability to capture the functional difference of enzyme isoforms.The server could be accessed freely at http://www.cbrc.kaust.edu.sa/DEEPre.
DEEPre: sequence-based enzyme EC number prediction by deep learning
Li, Yu; Wang, Sheng; Umarov, Ramzan; Xie, Bingqing; Fan, Ming; Li, Lihua; Gao, Xin
2017-01-01
Annotation of enzyme function has a broad range of applications, such as metagenomics, industrial biotechnology, and diagnosis of enzyme deficiency-caused diseases. However, the time and resource required make it prohibitively expensive to experimentally determine the function of every enzyme. Therefore, computational enzyme function prediction has become increasingly important. In this paper, we develop such an approach, determining the enzyme function by predicting the Enzyme Commission number.We propose an end-to-end feature selection and classification model training approach, as well as an automatic and robust feature dimensionality uniformization method, DEEPre, in the field of enzyme function prediction. Instead of extracting manuallycrafted features from enzyme sequences, our model takes the raw sequence encoding as inputs, extracting convolutional and sequential features from the raw encoding based on the classification result to directly improve the prediction performance. The thorough cross-fold validation experiments conducted on two large-scale datasets show that DEEPre improves the prediction performance over the previous state-of-the-art methods. In addition, our server outperforms five other servers in determining the main class of enzymes on a separate low-homology dataset. Two case studies demonstrate DEEPre's ability to capture the functional difference of enzyme isoforms.The server could be accessed freely at http://www.cbrc.kaust.edu.sa/DEEPre.
Gromko, Joyce Eastlund; Hansen, Dee; Tortora, Anne Halloran; Higgins, Daniel; Boccia, Eric
2009-01-01
The purpose of this study was to determine whether children's recall of tones, numbers, and words was supported by a common temporal sequencing mechanism; whether children's patterns of memory for tones, numbers, and nonsense words were the same despite differences in symbol systems; and whether children's recall of tones, numbers, and nonsense…
Golden Ratio Versus Pi as Random Sequence Sources for Monte Carlo Integration
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.
Human PTCHD3 nulls: rare copy number and sequence variants suggest a non-essential gene
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Lionel Anath C
2011-03-01
Full Text Available Abstract Background Copy number variations (CNVs can contribute to variable degrees of fitness and/or disease predisposition. Recent studies show that at least 1% of any given genome is copy number variable when compared to the human reference sequence assembly. Homozygous deletions (or CNV nulls that are found in the normal population are of particular interest because they may serve to define non-essential genes in human biology. Results In a genomic screen investigating CNV in Autism Spectrum Disorders (ASDs we detected a heterozygous deletion on chromosome 10p12.1, spanning the Patched-domain containing 3 (PTCHD3 gene, at a frequency of ~1.4% (6/427. This finding seemed interesting, given recent discoveries on the role of another Patched-domain containing gene (PTCHD1 in ASD. Screening of another 177 ASD probands yielded two additional heterozygous deletions bringing the frequency to 1.3% (8/604. The deletion was found at a frequency of ~0.73% (27/3,695 in combined control population from North America and Northern Europe predominately of European ancestry. Screening of the human genome diversity panel (HGDP-CEPH covering worldwide populations yielded deletions in 7/1,043 unrelated individuals and those detected were confined to individuals of European/Mediterranean/Middle Eastern ancestry. Breakpoint mapping yielded an identical 102,624 bp deletion in all cases and controls tested, suggesting a common ancestral event. Interestingly, this CNV occurs at a break of synteny between humans and mouse. Considering all data, however, no significant association of these rare PTCHD3 deletions with ASD was observed. Notwithstanding, our RNA expression studies detected PTCHD3 in several tissues, and a novel shorter isoform for PTCHD3 was characterized. Expression in transfected COS-7 cells showed PTCHD3 isoforms colocalize with calnexin in the endoplasmic reticulum. The presence of a patched (Ptc domain suggested a role for PTCHD3 in various biological
Novitsky, Vlad; Moyo, Sikhulile; Lei, Quanhong; DeGruttola, Victor; Essex, M
2015-05-01
To improve the methodology of HIV cluster analysis, we addressed how analysis of HIV clustering is associated with parameters that can affect the outcome of viral clustering. The extent of HIV clustering and tree certainty was compared between 401 HIV-1C near full-length genome sequences and subgenomic regions retrieved from the LANL HIV Database. Sliding window analysis was based on 99 windows of 1,000 bp and 45 windows of 2,000 bp. Potential associations between the extent of HIV clustering and sequence length and the number of variable and informative sites were evaluated. The near full-length genome HIV sequences showed the highest extent of HIV clustering and the highest tree certainty. At the bootstrap threshold of 0.80 in maximum likelihood (ML) analysis, 58.9% of near full-length HIV-1C sequences but only 15.5% of partial pol sequences (ViroSeq) were found in clusters. Among HIV-1 structural genes, pol showed the highest extent of clustering (38.9% at a bootstrap threshold of 0.80), although it was significantly lower than in the near full-length genome sequences. The extent of HIV clustering was significantly higher for sliding windows of 2,000 bp than 1,000 bp. We found a strong association between the sequence length and proportion of HIV sequences in clusters, and a moderate association between the number of variable and informative sites and the proportion of HIV sequences in clusters. In HIV cluster analysis, the extent of detectable HIV clustering is directly associated with the length of viral sequences used, as well as the number of variable and informative sites. Near full-length genome sequences could provide the most informative HIV cluster analysis. Selected subgenomic regions with a high extent of HIV clustering and high tree certainty could also be considered as a second choice.
Population clustering based on copy number variations detected from next generation sequencing data.
Duan, Junbo; Zhang, Ji-Gang; Wan, Mingxi; Deng, Hong-Wen; Wang, Yu-Ping
2014-08-01
Copy number variations (CNVs) can be used as significant bio-markers and next generation sequencing (NGS) provides a high resolution detection of these CNVs. But how to extract features from CNVs and further apply them to genomic studies such as population clustering have become a big challenge. In this paper, we propose a novel method for population clustering based on CNVs from NGS. First, CNVs are extracted from each sample to form a feature matrix. Then, this feature matrix is decomposed into the source matrix and weight matrix with non-negative matrix factorization (NMF). The source matrix consists of common CNVs that are shared by all the samples from the same group, and the weight matrix indicates the corresponding level of CNVs from each sample. Therefore, using NMF of CNVs one can differentiate samples from different ethnic groups, i.e. population clustering. To validate the approach, we applied it to the analysis of both simulation data and two real data set from the 1000 Genomes Project. The results on simulation data demonstrate that the proposed method can recover the true common CNVs with high quality. The results on the first real data analysis show that the proposed method can cluster two family trio with different ancestries into two ethnic groups and the results on the second real data analysis show that the proposed method can be applied to the whole-genome with large sample size consisting of multiple groups. Both results demonstrate the potential of the proposed method for population clustering.
Iacocca, Michael A; Wang, Jian; Dron, Jacqueline S; Robinson, John F; McIntyre, Adam D; Cao, Henian; Hegele, Robert A
2017-11-01
Familial hypercholesterolemia (FH) is a heritable condition of severely elevated LDL cholesterol, caused predominantly by autosomal codominant mutations in the LDL receptor gene ( LDLR ). In providing a molecular diagnosis for FH, the current procedure often includes targeted next-generation sequencing (NGS) panels for the detection of small-scale DNA variants, followed by multiplex ligation-dependent probe amplification (MLPA) in LDLR for the detection of whole-exon copy number variants (CNVs). The latter is essential because ∼10% of FH cases are attributed to CNVs in LDLR ; accounting for them decreases false negative findings. Here, we determined the potential of replacing MLPA with bioinformatic analysis applied to NGS data, which uses depth-of-coverage analysis as its principal method to identify whole-exon CNV events. In analysis of 388 FH patient samples, there was 100% concordance in LDLR CNV detection between these two methods: 38 reported CNVs identified by MLPA were also successfully detected by our NGS method, while 350 samples negative for CNVs by MLPA were also negative by NGS. This result suggests that MLPA can be removed from the routine diagnostic screening for FH, significantly reducing associated costs, resources, and analysis time, while promoting more widespread assessment of this important class of mutations across diagnostic laboratories. Copyright © 2017 by the American Society for Biochemistry and Molecular Biology, Inc.
Shah, Nameeta; Lankerovich, Michael; Lee, Hwahyung; Yoon, Jae-Geun; Schroeder, Brett; Foltz, Greg
2013-11-22
RNA-seq has spurred important gene fusion discoveries in a number of different cancers, including lung, prostate, breast, brain, thyroid and bladder carcinomas. Gene fusion discovery can potentially lead to the development of novel treatments that target the underlying genetic abnormalities. In this study, we provide comprehensive view of gene fusion landscape in 185 glioblastoma multiforme patients from two independent cohorts. Fusions occur in approximately 30-50% of GBM patient samples. In the Ivy Center cohort of 24 patients, 33% of samples harbored fusions that were validated by qPCR and Sanger sequencing. We were able to identify high-confidence gene fusions from RNA-seq data in 53% of the samples in a TCGA cohort of 161 patients. We identified 13 cases (8%) with fusions retaining a tyrosine kinase domain in the TCGA cohort and one case in the Ivy Center cohort. Ours is the first study to describe recurrent fusions involving non-coding genes. Genomic locations 7p11 and 12q14-15 harbor majority of the fusions. Fusions on 7p11 are formed in focally amplified EGFR locus whereas 12q14-15 fusions are formed by complex genomic rearrangements. All the fusions detected in this study can be further visualized and analyzed using our website: http://ivygap.swedish.org/fusions. Our study highlights the prevalence of gene fusions as one of the major genomic abnormalities in GBM. The majority of the fusions are private fusions, and a minority of these recur with low frequency. A small subset of patients with fusions of receptor tyrosine kinases can benefit from existing FDA approved drugs and drugs available in various clinical trials. Due to the low frequency and rarity of clinically relevant fusions, RNA-seq of GBM patient samples will be a vital tool for the identification of patient-specific fusions that can drive personalized therapy.
Bruce, Jeff; Pugh, Trevor; Samadian, Soroush
2017-01-01
Somatic copy number variations (CNVs) play a crucial role in development of many human cancers. The broad availability of next-generation sequencing data has enabled the development of algorithms to computationally infer CNV profiles from a variety of data types including exome and targeted sequence data; currently the most prevalent types of cancer genomics data. However, systemic evaluation and comparison of these tools remains challenging due to a lack of ground truth reference sets. To ad...
Directory of Open Access Journals (Sweden)
Jun Ding
2015-07-01
Full Text Available DNA sequencing identifies common and rare genetic variants for association studies, but studies typically focus on variants in nuclear DNA and ignore the mitochondrial genome. In fact, analyzing variants in mitochondrial DNA (mtDNA sequences presents special problems, which we resolve here with a general solution for the analysis of mtDNA in next-generation sequencing studies. The new program package comprises 1 an algorithm designed to identify mtDNA variants (i.e., homoplasmies and heteroplasmies, incorporating sequencing error rates at each base in a likelihood calculation and allowing allele fractions at a variant site to differ across individuals; and 2 an estimation of mtDNA copy number in a cell directly from whole-genome sequencing data. We also apply the methods to DNA sequence from lymphocytes of ~2,000 SardiNIA Project participants. As expected, mothers and offspring share all homoplasmies but a lesser proportion of heteroplasmies. Both homoplasmies and heteroplasmies show 5-fold higher transition/transversion ratios than variants in nuclear DNA. Also, heteroplasmy increases with age, though on average only ~1 heteroplasmy reaches the 4% level between ages 20 and 90. In addition, we find that mtDNA copy number averages ~110 copies/lymphocyte and is ~54% heritable, implying substantial genetic regulation of the level of mtDNA. Copy numbers also decrease modestly but significantly with age, and females on average have significantly more copies than males. The mtDNA copy numbers are significantly associated with waist circumference (p-value = 0.0031 and waist-hip ratio (p-value = 2.4×10-5, but not with body mass index, indicating an association with central fat distribution. To our knowledge, this is the largest population analysis to date of mtDNA dynamics, revealing the age-imposed increase in heteroplasmy, the relatively high heritability of copy number, and the association of copy number with metabolic traits.
Search for a perfect generator of random numbers
International Nuclear Information System (INIS)
Musyck, E.
1977-01-01
Theoretical tests have been carried out by COVEYOU and MAC PHERSON to verify the applications of the LEHMER algorithm. In a similar way, a theoretical method is proposed to evaluate in a rigorous way the random character of numbers generated by a shift register. This theory introduces the concept of ''degree of randomness'' of the elements, taken in a definite order, of a shift register. It permits making the judicious choice of the elements of the shift register which will produce the bits of the random numbers. On the other hand, a calculation method is developed in order to verify the primitive character of any shift register of high complexity. A new test, called ''slice test'', of empirical and theoretical use is also described; it constitutes a significant contribution to the understanding of certain properties of pseudo-random sequences. As a practical example, a random number generator structure formed with 32 bits, built out of a shift register with 61 elements and 60 modulo-2 adder circuits was made. The author is convinced that this generator can be considered to be practically perfect for all empirical applications of random numbers, particularly for the solution of Monte-Carlo problems. (author)
Jang, Su; Lee, Yunjoo; Lee, Gileung; Seo, Jeonghwan; Lee, Dongryung; Yu, Yoye; Chin, Joong Hyoun; Koh, Hee-Jong
2018-01-15
Balancing panicle-related traits such as panicle length and the numbers of primary and secondary branches per panicle, is key to improving the number of spikelets per panicle in rice. Identifying genetic information contributes to a broader understanding of the roles of gene and provides candidate alleles for use as DNA markers. Discovering relations between panicle-related traits and sequence variants allows opportunity for molecular application in rice breeding to improve the number of spikelets per panicle. In total, 142 polymorphic sites, which constructed 58 haplotypes, were detected in coding regions of ten panicle development gene and 35 sequence variants in six genes were significantly associated with panicle-related traits. Rice cultivars were clustered according to their sequence variant profiles. One of the four resultant clusters, which contained only indica and tong-il varieties, exhibited the largest average number of favorable alleles and highest average number of spikelets per panicle, suggesting that the favorable allele combination found in this cluster was beneficial in increasing the number of spikelets per panicle. Favorable alleles identified in this study can be used to develop functional markers for rice breeding programs. Furthermore, stacking several favorable alleles has the potential to substantially improve the number of spikelets per panicle in rice.
Directory of Open Access Journals (Sweden)
Zhang Xinmin
2011-05-01
Full Text Available Abstract Background In highly copy number variable (CNV regions such as the human defensin gene locus, comprehensive assessment of sequence variations is challenging. PCR approaches are practically restricted to tiny fractions, and next-generation sequencing (NGS approaches of whole individual genomes e.g. by the 1000 Genomes Project is confined by an affordable sequence depth. Combining target enrichment with NGS may represent a feasible approach. Results As a proof of principle, we enriched a ~850 kb section comprising the CNV defensin gene cluster DEFB, the invariable DEFA part and 11 control regions from two genomes by sequence capture and sequenced it by 454 technology. 6,651 differences to the human reference genome were found. Comparison to HapMap genotypes revealed sensitivities and specificities in the range of 94% to 99% for the identification of variations. Using error probabilities for rigorous filtering revealed 2,886 unique single nucleotide variations (SNVs including 358 putative novel ones. DEFB CN determinations by haplotype ratios were in agreement with alternative methods. Conclusion Although currently labor extensive and having high costs, target enriched NGS provides a powerful tool for the comprehensive assessment of SNVs in highly polymorphic CNV regions of individual genomes. Furthermore, it reveals considerable amounts of putative novel variations and simultaneously allows CN estimation.
Directory of Open Access Journals (Sweden)
Mindaugas Liogys
2013-08-01
Full Text Available Purpose—is to investigate a shift sequence-based approach efficiency then problem consisting of a high number of shifts.Research objectives:• Solve health care workers rostering problem using a shift sequence based method.• Measure its efficiency then number of shifts increases.Design/methodology/approach—Usually rostering problems are highly constrained. Constraints are classified to soft and hard constraints. Soft and hard constraints of the problem are additionally classified to: sequence constraints, schedule constraints and roster constraints. Sequence constraints are considered when constructing shift sequences. Schedule constraints are considered when constructing a schedule. Roster constraints are applied, then constructing overall solution, i.e. combining all schedules.Shift sequence based approach consists of two stages:• Shift sequences construction,• The construction of schedules.In the shift sequences construction stage, the shift sequences are constructed for each set of health care workers of different skill, considering sequence constraints. Shifts sequences are ranked by their penalties for easier retrieval in later stage.In schedules construction stage, schedules for each health care worker are constructed iteratively, using the shift sequences produced in stage 1.Shift sequence based method is an adaptive iterative method where health care workers who received the highest schedule penalties in the last iteration are scheduled first at the current iteration.During the roster construction, and after a schedule has been generated for the current health care worker, an improvement method based on an efficient greedy local search is carried out on the partial roster. It simply swaps any pair of shifts between two health care workers in the (partial roster, as long as the swaps satisfy hard constraints and decrease the roster penalty.Findings—Using shift sequence method for solving health care workers rostering problem
Directory of Open Access Journals (Sweden)
Mindaugas Liogys
2011-08-01
Full Text Available Purpose—is to investigate a shift sequence-based approach efficiency then problem consisting of a high number of shifts. Research objectives:• Solve health care workers rostering problem using a shift sequence based method.• Measure its efficiency then number of shifts increases. Design/methodology/approach—Usually rostering problems are highly constrained.Constraints are classified to soft and hard constraints. Soft and hard constraints of the problem are additionally classified to: sequence constraints, schedule constraints and roster constraints. Sequence constraints are considered when constructing shift sequences. Schedule constraints are considered when constructing a schedule. Roster constraints are applied, then constructing overall solution, i.e. combining all schedules.Shift sequence based approach consists of two stages:• Shift sequences construction,• The construction of schedules.In the shift sequences construction stage, the shift sequences are constructed for each set of health care workers of different skill, considering sequence constraints. Shifts sequences are ranked by their penalties for easier retrieval in later stage.In schedules construction stage, schedules for each health care worker are constructed iteratively, using the shift sequences produced in stage 1. Shift sequence based method is an adaptive iterative method where health care workers who received the highest schedule penalties in the last iteration are scheduled first at the current iteration. During the roster construction, and after a schedule has been generated for the current health care worker, an improvement method based on an efficient greedy local search is carried out on the partial roster. It simply swaps any pair of shifts between two health care workers in the (partial roster, as long as the swaps satisfy hard constraints and decrease the roster penalty.Findings—Using shift sequence method for solving health care workers rostering
Boogaard, E. van den; Cohn, D.M.; Korevaar, J.C.; Dawood, F.; Vissenberg, R.; Middeldorp, S.; Goddijn, M.; Farquharson, R.G.
2013-01-01
Objective: To investigate the relationship between the number and sequence of preceding miscarriages and antiphospholipid syndrome (APS). Design: Retrospective cohort study. Setting: Recurrent miscarriage (RM) clinic. Patient(s): Women who attended the RM clinic from 1988 to 2006. Intervention(s):
Cellular Automata-Based Parallel Random Number Generators Using FPGAs
Directory of Open Access Journals (Sweden)
David H. K. Hoe
2012-01-01
Full Text Available Cellular computing represents a new paradigm for implementing high-speed massively parallel machines. Cellular automata (CA, which consist of an array of locally connected processing elements, are a basic form of a cellular-based architecture. The use of field programmable gate arrays (FPGAs for implementing CA accelerators has shown promising results. This paper investigates the design of CA-based pseudo-random number generators (PRNGs using an FPGA platform. To improve the quality of the random numbers that are generated, the basic CA structure is enhanced in two ways. First, the addition of a superrule to each CA cell is considered. The resulting self-programmable CA (SPCA uses the superrule to determine when to make a dynamic rule change in each CA cell. The superrule takes its inputs from neighboring cells and can be considered itself a second CA working in parallel with the main CA. When implemented on an FPGA, the use of lookup tables in each logic cell removes any restrictions on how the super-rules should be defined. Second, a hybrid configuration is formed by combining a CA with a linear feedback shift register (LFSR. This is advantageous for FPGA designs due to the compactness of the LFSR implementations. A standard software package for statistically evaluating the quality of random number sequences known as Diehard is used to validate the results. Both the SPCA and the hybrid CA/LFSR were found to pass all the Diehard tests.
Quantum random number generator
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.
International Nuclear Information System (INIS)
Calvayrac, Florent
2005-01-01
We present known and new applications of pseudo random numbers and of the Metropolis algorithm to phenomena of physical and mechanical interest, such as the search of simple clusters isomers with interactive visualization, or vehicle motion planning. The progression towards complicated problems was used with first-year graduate students who wrote most of the programs presented here. We argue that the use of pseudo random numbers in simulation and extrema research programs in teaching numerical methods in physics allows one to get quick programs and physically meaningful and demonstrative results without recurring to the advanced numerical analysis methods
Gog, Julia R; Lever, Andrew M L; Skittrall, Jordan P
2018-01-01
We present a fast, robust and parsimonious approach to detecting signals in an ordered sequence of numbers. Our motivation is in seeking a suitable method to take a sequence of scores corresponding to properties of positions in virus genomes, and find outlying regions of low scores. Suitable statistical methods without using complex models or making many assumptions are surprisingly lacking. We resolve this by developing a method that detects regions of low score within sequences of real numbers. The method makes no assumptions a priori about the length of such a region; it gives the explicit location of the region and scores it statistically. It does not use detailed mechanistic models so the method is fast and will be useful in a wide range of applications. We present our approach in detail, and test it on simulated sequences. We show that it is robust to a wide range of signal morphologies, and that it is able to capture multiple signals in the same sequence. Finally we apply it to viral genomic data to identify regions of evolutionary conservation within influenza and rotavirus.
Gilbert, Jack A; Field, Dawn; Huang, Ying; Edwards, Rob; Li, Weizhong; Gilna, Paul; Joint, Ian
2008-08-22
Sequencing the expressed genetic information of an ecosystem (metatranscriptome) can provide information about the response of organisms to varying environmental conditions. Until recently, metatranscriptomics has been limited to microarray technology and random cloning methodologies. The application of high-throughput sequencing technology is now enabling access to both known and previously unknown transcripts in natural communities. We present a study of a complex marine metatranscriptome obtained from random whole-community mRNA using the GS-FLX Pyrosequencing technology. Eight samples, four DNA and four mRNA, were processed from two time points in a controlled coastal ocean mesocosm study (Bergen, Norway) involving an induced phytoplankton bloom producing a total of 323,161,989 base pairs. Our study confirms the finding of the first published metatranscriptomic studies of marine and soil environments that metatranscriptomics targets highly expressed sequences which are frequently novel. Our alternative methodology increases the range of experimental options available for conducting such studies and is characterized by an exceptional enrichment of mRNA (99.92%) versus ribosomal RNA. Analysis of corresponding metagenomes confirms much higher levels of assembly in the metatranscriptomic samples and a far higher yield of large gene families with >100 members, approximately 91% of which were novel. This study provides further evidence that metatranscriptomic studies of natural microbial communities are not only feasible, but when paired with metagenomic data sets, offer an unprecedented opportunity to explore both structure and function of microbial communities--if we can overcome the challenges of elucidating the functions of so many never-seen-before gene families.
Sequence variants affecting eosinophil numbers associate with asthma and myocardial infarction
DEFF Research Database (Denmark)
Gudbjartsson, Daniel F; Bjornsdottir, Unnur S; Halapi, Eva
2009-01-01
Eosinophils are pleiotropic multifunctional leukocytes involved in initiation and propagation of inflammatory responses and thus have important roles in the pathogenesis of inflammatory diseases. Here we describe a genome-wide association scan for sequence variants affecting eosinophil counts.......2 x 10(-10) and 6.5 x 10(-19), respectively). A SNP at IL1RL1 associated with asthma (P = 5.5 x 10(-12)) in a collection of ten different populations (7,996 cases and 44,890 controls). SNPs at WDR36, IL33 and MYB that showed suggestive association with eosinophil counts were also associated...
Samadian, Soroush; Bruce, Jeff P; Pugh, Trevor J
2018-03-01
Somatic copy number variations (CNVs) play a crucial role in development of many human cancers. The broad availability of next-generation sequencing data has enabled the development of algorithms to computationally infer CNV profiles from a variety of data types including exome and targeted sequence data; currently the most prevalent types of cancer genomics data. However, systemic evaluation and comparison of these tools remains challenging due to a lack of ground truth reference sets. To address this need, we have developed Bamgineer, a tool written in Python to introduce user-defined haplotype-phased allele-specific copy number events into an existing Binary Alignment Mapping (BAM) file, with a focus on targeted and exome sequencing experiments. As input, this tool requires a read alignment file (BAM format), lists of non-overlapping genome coordinates for introduction of gains and losses (bed file), and an optional file defining known haplotypes (vcf format). To improve runtime performance, Bamgineer introduces the desired CNVs in parallel using queuing and parallel processing on a local machine or on a high-performance computing cluster. As proof-of-principle, we applied Bamgineer to a single high-coverage (mean: 220X) exome sequence file from a blood sample to simulate copy number profiles of 3 exemplar tumors from each of 10 tumor types at 5 tumor cellularity levels (20-100%, 150 BAM files in total). To demonstrate feasibility beyond exome data, we introduced read alignments to a targeted 5-gene cell-free DNA sequencing library to simulate EGFR amplifications at frequencies consistent with circulating tumor DNA (10, 1, 0.1 and 0.01%) while retaining the multimodal insert size distribution of the original data. We expect Bamgineer to be of use for development and systematic benchmarking of CNV calling algorithms by users using locally-generated data for a variety of applications. The source code is freely available at http://github.com/pughlab/bamgineer.
International Nuclear Information System (INIS)
Dai Jianrong; Zhu Yunping
2001-01-01
This paper proposes a sequencing algorithm for intensity-modulated radiation therapy with a multileaf collimator in the static mode. The algorithm aims to minimize the number of segments in a delivery sequence. For a machine with a long verification and recording overhead time (e.g., 15 s per segment), minimizing the number of segments is equivalent to minimizing the delivery time. The proposed new algorithm is based on checking numerous candidates for a segment and selecting the candidate that results in a residual intensity matrix with the least complexity. When there is more than one candidate resulting in the same complexity, the candidate with the largest size is selected. The complexity of an intensity matrix is measured in the new algorithm in terms of the number of segments in the delivery sequence obtained by using a published algorithm. The beam delivery efficiency of the proposed algorithm and the influence of different published algorithms used to calculate the complexity of an intensity matrix were tested with clinical intensity-modulated beams. The results show that no matter which published algorithm is used to calculate the complexity of an intensity matrix, the sequence generated by the algorithm proposed here is always more efficient than that generated by the published algorithm itself. The results also show that the algorithm used to calculate the complexity of an intensity matrix affects the efficiency of beam delivery. The delivery sequences are frequently most efficient when the algorithm of Bortfeld et al. is used to calculate the complexity of an intensity matrix. Because no single variation is most efficient for all beams tested, we suggest implementing multiple variations of our algorithm
Directory of Open Access Journals (Sweden)
Soroush Samadian
2018-03-01
Full Text Available Somatic copy number variations (CNVs play a crucial role in development of many human cancers. The broad availability of next-generation sequencing data has enabled the development of algorithms to computationally infer CNV profiles from a variety of data types including exome and targeted sequence data; currently the most prevalent types of cancer genomics data. However, systemic evaluation and comparison of these tools remains challenging due to a lack of ground truth reference sets. To address this need, we have developed Bamgineer, a tool written in Python to introduce user-defined haplotype-phased allele-specific copy number events into an existing Binary Alignment Mapping (BAM file, with a focus on targeted and exome sequencing experiments. As input, this tool requires a read alignment file (BAM format, lists of non-overlapping genome coordinates for introduction of gains and losses (bed file, and an optional file defining known haplotypes (vcf format. To improve runtime performance, Bamgineer introduces the desired CNVs in parallel using queuing and parallel processing on a local machine or on a high-performance computing cluster. As proof-of-principle, we applied Bamgineer to a single high-coverage (mean: 220X exome sequence file from a blood sample to simulate copy number profiles of 3 exemplar tumors from each of 10 tumor types at 5 tumor cellularity levels (20-100%, 150 BAM files in total. To demonstrate feasibility beyond exome data, we introduced read alignments to a targeted 5-gene cell-free DNA sequencing library to simulate EGFR amplifications at frequencies consistent with circulating tumor DNA (10, 1, 0.1 and 0.01% while retaining the multimodal insert size distribution of the original data. We expect Bamgineer to be of use for development and systematic benchmarking of CNV calling algorithms by users using locally-generated data for a variety of applications. The source code is freely available at http://github.com/pughlab/bamgineer.
On the Periods of the {ranshi} Random Number Generator
Gutbrod, F.
The stochastic properties of the pseudo-random number generator {ranshi} are discussed, with emphasis on the average period. Within a factor 2 this turns out to be the root of the maximally possible period. The actual set of periods depends on minor details of the algorithm, and the system settles down in one of only a few different cycles. These features are in perfect agreement with absolute random motion in phase space, to the extent allowed by deterministic dynamics.
The square root of 2 a dialogue concerning a number and a sequence
Flannery, David
2006-01-01
Using no more than the most basic algebra and geometry, Flannery (Cork Institute of Technology, Ireland) manages to convey not only why irrational numbers are fascinating, but how the whole enterprise of mathematical thinking is imaginative, intriguing, and engaging. A startlingly original and informative dialog, this book is a one-of-a-kind introduction to the pleasure and playful beauty of mathematical thinking.
The additive congruential random number generator--A special case of a multiple recursive generator
Wikramaratna, Roy S.
2008-07-01
This paper considers an approach to generating uniformly distributed pseudo-random numbers which works well in serial applications but which also appears particularly well-suited for application on parallel processing systems. Additive Congruential Random Number (ACORN) generators are straightforward to implement for arbitrarily large order and modulus; if implemented using integer arithmetic, it becomes possible to generate identical sequences on any machine. Previously published theoretical analysis has demonstrated that a kth order ACORN sequence approximates to being uniformly distributed in up to k dimensions, for any given k. ACORN generators can be constructed to give period lengths exceeding any given number (for example, with period length in excess of 230p, for any given p). Results of empirical tests have demonstrated that, if p is greater than or equal to 2, then the ACORN generator can be used successfully for generating double precision uniform random variates. This paper demonstrates that an ACORN generator is a particular case of a multiple recursive generator (and, therefore, also a special case of a matrix generator). Both these latter approaches have been widely studied, and it is to be hoped that the results given in the present paper will lead to greater confidence in using the ACORN generators.
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Hyun-Kyoung Kim
Full Text Available BACKGROUND: The concept of the utilization of rearranged ends for development of personalized biomarkers has attracted much attention owing to its clinical applicability. Although targeted next-generation sequencing (NGS for recurrent rearrangements has been successful in hematologic malignancies, its application to solid tumors is problematic due to the paucity of recurrent translocations. However, copy-number breakpoints (CNBs, which are abundant in solid tumors, can be utilized for identification of rearranged ends. METHOD: As a proof of concept, we performed targeted next-generation sequencing at copy-number breakpoints (TNGS-CNB in nine colon cancer cases including seven primary cancers and two cell lines, COLO205 and SW620. For deduction of CNBs, we developed a novel competitive single-nucleotide polymorphism (cSNP microarray method entailing CNB-region refinement by competitor DNA. RESULT: Using TNGS-CNB, 19 specific rearrangements out of 91 CNBs (20.9% were identified, and two polymerase chain reaction (PCR-amplifiable rearrangements were obtained in six cases (66.7%. And significantly, TNGS-CNB, with its high positive identification rate (82.6% of PCR-amplifiable rearrangements at candidate sites (19/23, just from filtering of aligned sequences, requires little effort for validation. CONCLUSION: Our results indicate that TNGS-CNB, with its utility for identification of rearrangements in solid tumors, can be successfully applied in the clinical laboratory for cancer-relapse and therapy-response monitoring.
Kim, Hyun-Kyoung; Park, Won Cheol; Lee, Kwang Man; Hwang, Hai-Li; Park, Seong-Yeol; Sorn, Sungbin; Chandra, Vishal; Kim, Kwang Gi; Yoon, Woong-Bae; Bae, Joon Seol; Shin, Hyoung Doo; Shin, Jong-Yeon; Seoh, Ju-Young; Kim, Jong-Il; Hong, Kyeong-Man
2014-01-01
The concept of the utilization of rearranged ends for development of personalized biomarkers has attracted much attention owing to its clinical applicability. Although targeted next-generation sequencing (NGS) for recurrent rearrangements has been successful in hematologic malignancies, its application to solid tumors is problematic due to the paucity of recurrent translocations. However, copy-number breakpoints (CNBs), which are abundant in solid tumors, can be utilized for identification of rearranged ends. As a proof of concept, we performed targeted next-generation sequencing at copy-number breakpoints (TNGS-CNB) in nine colon cancer cases including seven primary cancers and two cell lines, COLO205 and SW620. For deduction of CNBs, we developed a novel competitive single-nucleotide polymorphism (cSNP) microarray method entailing CNB-region refinement by competitor DNA. Using TNGS-CNB, 19 specific rearrangements out of 91 CNBs (20.9%) were identified, and two polymerase chain reaction (PCR)-amplifiable rearrangements were obtained in six cases (66.7%). And significantly, TNGS-CNB, with its high positive identification rate (82.6%) of PCR-amplifiable rearrangements at candidate sites (19/23), just from filtering of aligned sequences, requires little effort for validation. Our results indicate that TNGS-CNB, with its utility for identification of rearrangements in solid tumors, can be successfully applied in the clinical laboratory for cancer-relapse and therapy-response monitoring.
Yi, Guoqiang; Qu, Lujiang; Liu, Jianfeng; Yan, Yiyuan; Xu, Guiyun; Yang, Ning
2014-11-07
Copy number variation (CNV) is important and widespread in the genome, and is a major cause of disease and phenotypic diversity. Herein, we performed a genome-wide CNV analysis in 12 diversified chicken genomes based on whole genome sequencing. A total of 8,840 CNV regions (CNVRs) covering 98.2 Mb and representing 9.4% of the chicken genome were identified, ranging in size from 1.1 to 268.8 kb with an average of 11.1 kb. Sequencing-based predictions were confirmed at a high validation rate by two independent approaches, including array comparative genomic hybridization (aCGH) and quantitative PCR (qPCR). The Pearson's correlation coefficients between sequencing and aCGH results ranged from 0.435 to 0.755, and qPCR experiments revealed a positive validation rate of 91.71% and a false negative rate of 22.43%. In total, 2,214 (25.0%) predicted CNVRs span 2,216 (36.4%) RefSeq genes associated with specific biological functions. Besides two previously reported copy number variable genes EDN3 and PRLR, we also found some promising genes with potential in phenotypic variation. Two genes, FZD6 and LIMS1, related to disease susceptibility/resistance are covered by CNVRs. The highly duplicated SOCS2 may lead to higher bone mineral density. Entire or partial duplication of some genes like POPDC3 may have great economic importance in poultry breeding. Our results based on extensive genetic diversity provide a more refined chicken CNV map and genome-wide gene copy number estimates, and warrant future CNV association studies for important traits in chickens.
Epelboym, Irene; Zenati, Mazen S; Hamad, Ahmad; Steve, Jennifer; Lee, Kenneth K; Bahary, Nathan; Hogg, Melissa E; Zeh, Herbert J; Zureikat, Amer H
2017-09-01
Receipt of 6 cycles of adjuvant chemotherapy (AC) is standard of care in pancreatic cancer (PC). Neoadjuvant chemotherapy (NAC) is increasingly utilized; however, optimal number of cycles needed alone or in combination with AC remains unknown. We sought to determine the optimal number and sequence of perioperative chemotherapy cycles in PC. Single institutional review of all resected PCs from 2008 to 2015. The impact of cumulative number of chemotherapy cycles received (0, 1-5, and ≥6 cycles) and their sequence (NAC, AC, or NAC + AC) on overall survival was evaluated Cox-proportional hazard modeling, using 6 cycles of AC as reference. A total of 522 patients were analyzed. Based on sample size distribution, four combinations were evaluated: 0 cycles = 12.1%, 1-5 cycles of combined NAC + AC = 29%, 6 cycles of AC = 25%, and ≥6 cycles of combined NAC + AC = 34%, with corresponding survival. 13.1, 18.5, 37, and 36.8 months. On MVA (P cycles AC, receipt of 0 cycles [HR 3.57, confidence interval (CI) 2.47-5.18] or 1-5 cycles in any combination (HR 2.37, CI 1.73-3.23) was associated with increased hazard of death, whereas receipt of ≥6 cycles in any sequence was associated with optimal and comparable survival (HR 1.07, CI 0.78-1.47). Receipt of 6 or more perioperative cycles of chemotherapy either as combined neoadjuvant and adjuvant or adjuvant alone may be associated with optimal and comparable survival in resected PC.
Directory of Open Access Journals (Sweden)
Varala Kranthi
2007-05-01
Full Text Available Abstract Background Extensive computational and database tools are available to mine genomic and genetic databases for model organisms, but little genomic data is available for many species of ecological or agricultural significance, especially those with large genomes. Genome surveys using conventional sequencing techniques are powerful, particularly for detecting sequences present in many copies per genome. However these methods are time-consuming and have potential drawbacks. High throughput 454 sequencing provides an alternative method by which much information can be gained quickly and cheaply from high-coverage surveys of genomic DNA. Results We sequenced 78 million base-pairs of randomly sheared soybean DNA which passed our quality criteria. Computational analysis of the survey sequences provided global information on the abundant repetitive sequences in soybean. The sequence was used to determine the copy number across regions of large genomic clones or contigs and discover higher-order structures within satellite repeats. We have created an annotated, online database of sequences present in multiple copies in the soybean genome. The low bias of pyrosequencing against repeat sequences is demonstrated by the overall composition of the survey data, which matches well with past estimates of repetitive DNA content obtained by DNA re-association kinetics (Cot analysis. Conclusion This approach provides a potential aid to conventional or shotgun genome assembly, by allowing rapid assessment of copy number in any clone or clone-end sequence. In addition, we show that partial sequencing can provide access to partial protein-coding sequences.
Directory of Open Access Journals (Sweden)
Niedzica Camacho
2017-09-01
Full Text Available A variety of models have been proposed to explain regions of recurrent somatic copy number alteration (SCNA in human cancer. Our study employs Whole Genome DNA Sequence (WGS data from tumor samples (n = 103 to comprehensively assess the role of the Knudson two hit genetic model in SCNA generation in prostate cancer. 64 recurrent regions of loss and gain were detected, of which 28 were novel, including regions of loss with more than 15% frequency at Chr4p15.2-p15.1 (15.53%, Chr6q27 (16.50% and Chr18q12.3 (17.48%. Comprehensive mutation screens of genes, lincRNA encoding sequences, control regions and conserved domains within SCNAs demonstrated that a two-hit genetic model was supported in only a minor proportion of recurrent SCNA losses examined (15/40. We found that recurrent breakpoints and regions of inversion often occur within Knudson model SCNAs, leading to the identification of ZNF292 as a target gene for the deletion at 6q14.3-q15 and NKX3.1 as a two-hit target at 8p21.3-p21.2. The importance of alterations of lincRNA sequences was illustrated by the identification of a novel mutational hotspot at the KCCAT42, FENDRR, CAT1886 and STCAT2 loci at the 16q23.1-q24.3 loss. Our data confirm that the burden of SCNAs is predictive of biochemical recurrence, define nine individual regions that are associated with relapse, and highlight the possible importance of ion channel and G-protein coupled-receptor (GPCR pathways in cancer development. We concluded that a two-hit genetic model accounts for about one third of SCNA indicating that mechanisms, such haploinsufficiency and epigenetic inactivation, account for the remaining SCNA losses.
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.
Energy Technology Data Exchange (ETDEWEB)
Stern, T E; Cazemajou, J; Macherez, B; Valat, J; Vignon, A
1964-07-01
We summarize here the theoretical basis for the production of square wave having the values '1' or '0', the switching times being 'pseudo-random'. More precisely, the square-wave may or may not change value at regular time intervals of length {delta}, with probability approximately. 5 for each alternative. The wave-form is obtained by means of a shift-register having modulo-2 feedback. If the interval {delta} and the feedback connections are well chosen, it is possible to produce a waveform whose autocorrelation function is very close to a Dirac delta function. The square-wave therefore behaves like a quantized white noise, which has very interesting properties in cross-correlation techniques. (authors) [French] On resume ici les bases theoriques permettant d'obtenir un creneau prenant les valeurs '1' ou '0', les instants de commutation etant pseudo-aleatoires. Plus exactement, le creneau a la possibilite de changer (ou de ne pas changer) d'etat a intervalles de temps reguliers, separes par intervalle elementaire {delta}, chacune des deux possibilites possedant une probabilite d'apparition tres voisine de 0,5. Le creneau est obtenu par un registre a decalage (shift register) a contre-reactions logiques modulo-2. Si l'intervalle {delta} et les contre-reactions sont judicieusement choisis, il est possible d'obtenir pour le creneau une fonction d'autocorrelation triangulaire tres voisine d'une impulsion de Dirac. Par suite le creneau se comporte comme un bruit blanc quantifie possedant de tres interessantes proprietes pour les techniques statistiques d'intercorrelation. (auteurs)
An integrable low-cost hardware random number generator
Ranasinghe, Damith C.; Lim, Daihyun; Devadas, Srinivas; Jamali, Behnam; Zhu, Zheng; Cole, Peter H.
2005-02-01
A hardware random number generator is different from a pseudo-random number generator; a pseudo-random number generator approximates the assumed behavior of a real hardware random number generator. Simple pseudo random number generators suffices for most applications, however for demanding situations such as the generation of cryptographic keys, requires an efficient and a cost effective source of random numbers. Arbiter-based Physical Unclonable Functions (PUFs) proposed for physical authentication of ICs exploits statistical delay variation of wires and transistors across integrated circuits, as a result of process variations, to build a secret key unique to each IC. Experimental results and theoretical studies show that a sufficient amount of variation exits across IC"s. This variation enables each IC to be identified securely. It is possible to exploit the unreliability of these PUF responses to build a physical random number generator. There exists measurement noise, which comes from the instability of an arbiter when it is in a racing condition. There exist challenges whose responses are unpredictable. Without environmental variations, the responses of these challenges are random in repeated measurements. Compared to other physical random number generators, the PUF-based random number generators can be a compact and a low-power solution since the generator need only be turned on when required. A 64-stage PUF circuit costs less than 1000 gates and the circuit can be implemented using a standard IC manufacturing processes. In this paper we have presented a fast and an efficient random number generator, and analysed the quality of random numbers produced using an array of tests used by the National Institute of Standards and Technology to evaluate the randomness of random number generators designed for cryptographic applications.
International Nuclear Information System (INIS)
Bixler, N.E.; Schaperow, J.H.
1998-06-01
VICTORIA is a mechanistic computer code designed to analyze fission product behavior within a nuclear reactor coolant system (RCS) during a severe accident. It provides detailed predictions of the release of radioactive and nonradioactive materials from the reactor core and transport and deposition of these materials within the RCS. A recently completed independent peer review of VICTORIA, while confirming the overall adequacy of the code, recommended a number of modeling improvements. One of these recommendations, to model three rather than a single condensed phase, is the focus of the work reported here. The recommendation has been implemented as an option so that either a single or three condensed phases can be treated. Both options have been employed in the study of fission product behavior during an induced steam generator tube rupture sequence. Differences in deposition patterns and mechanisms predicted using these two options are discussed
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Seokhwi Kim
Full Text Available In the era of targeted therapy, mutation profiling of cancer is a crucial aspect of making therapeutic decisions. To characterize cancer at a molecular level, the use of formalin-fixed paraffin-embedded tissue is important. We tested the Ion AmpliSeq Cancer Hotspot Panel v2 and nCounter Copy Number Variation Assay in 89 formalin-fixed paraffin-embedded gastric cancer samples to determine whether they are applicable in archival clinical samples for personalized targeted therapies. We validated the results with Sanger sequencing, real-time quantitative PCR, fluorescence in situ hybridization and immunohistochemistry. Frequently detected somatic mutations included TP53 (28.17%, APC (10.1%, PIK3CA (5.6%, KRAS (4.5%, SMO (3.4%, STK11 (3.4%, CDKN2A (3.4% and SMAD4 (3.4%. Amplifications of HER2, CCNE1, MYC, KRAS and EGFR genes were observed in 8 (8.9%, 4 (4.5%, 2 (2.2%, 1 (1.1% and 1 (1.1% cases, respectively. In the cases with amplification, fluorescence in situ hybridization for HER2 verified gene amplification and immunohistochemistry for HER2, EGFR and CCNE1 verified the overexpression of proteins in tumor cells. In conclusion, we successfully performed semiconductor-based sequencing and nCounter copy number variation analyses in formalin-fixed paraffin-embedded gastric cancer samples. High-throughput screening in archival clinical samples enables faster, more accurate and cost-effective detection of hotspot mutations or amplification in genes.
Next-Generation Sequencing-Based Detection of Germline Copy Number Variations in BRCA1/BRCA2
DEFF Research Database (Denmark)
Schmidt, Ane Y; Hansen, Thomas V O; Ahlborn, Lise B
2017-01-01
Genetic testing of BRCA1/2 includes screening for single nucleotide variants and small insertions/deletions and for larger copy number variations (CNVs), primarily by Sanger sequencing and multiplex ligation-dependent probe amplification (MLPA). With the advent of next-generation sequencing (NGS)...
DEFF Research Database (Denmark)
Liu, Hongtai; Gao, Ya; Hu, Zhiyang
2016-01-01
, including 33 CNVs samples and 886 normal samples from September 1, 2011 to May 31, 2013, were enrolled in this study. The samples were randomly rearranged and blindly sequenced by low-coverage (about 7M reads) whole-genome sequencing of plasma DNA. Fetal CNVs were detected by Fetal Copy-number Analysis...
Wu, Ren-Chin; Chao, An-Shine; Lee, Li-Yu; Lin, Gigin; Chen, Shu-Jen; Lu, Yen-Jung; Huang, Huei-Jean; Yen, Chi-Feng; Han, Chien Min; Lee, Yun-Shien; Wang, Tzu-Hao; Chao, Angel
2017-07-18
Benign metastasizing leiomyoma (BML) is a rare disease entity typically presenting as multiple extrauterine leiomyomas associated with a uterine leiomyoma. It has been hypothesized that the extrauterine leiomyomata represent distant metastasis of the uterine leiomyoma. To date, the only molecular evidence supporting this hypothesis was derived from clonality analyses based on X-chromosome inactivation assays. Here, we sought to address this issue by examining paired specimens of synchronous pulmonary and uterine leiomyomata from three patients using targeted massively parallel sequencing and molecular inversion probe array analysis for detecting somatic mutations and copy number aberrations. We detected identical non-hot-spot somatic mutations and similar patterns of copy number aberrations (CNAs) in paired pulmonary and uterine leiomyomata from two patients, indicating the clonal relationship between pulmonary and uterine leiomyomata. In addition to loss of chromosome 22q found in the literature, we identified additional recurrent CNAs including losses of chromosome 3q and 11q. In conclusion, our findings of the clonal relationship between synchronous pulmonary and uterine leiomyomas support the hypothesis that BML represents a condition wherein a uterine leiomyoma disseminates to distant extrauterine locations.
Lee, Li-Yu; Lin, Gigin; Chen, Shu-Jen; Lu, Yen-Jung; Huang, Huei-Jean; Yen, Chi-Feng; Han, Chien Min; Lee, Yun-Shien; Wang, Tzu-Hao; Chao, Angel
2017-01-01
Benign metastasizing leiomyoma (BML) is a rare disease entity typically presenting as multiple extrauterine leiomyomas associated with a uterine leiomyoma. It has been hypothesized that the extrauterine leiomyomata represent distant metastasis of the uterine leiomyoma. To date, the only molecular evidence supporting this hypothesis was derived from clonality analyses based on X-chromosome inactivation assays. Here, we sought to address this issue by examining paired specimens of synchronous pulmonary and uterine leiomyomata from three patients using targeted massively parallel sequencing and molecular inversion probe array analysis for detecting somatic mutations and copy number aberrations. We detected identical non-hot-spot somatic mutations and similar patterns of copy number aberrations (CNAs) in paired pulmonary and uterine leiomyomata from two patients, indicating the clonal relationship between pulmonary and uterine leiomyomata. In addition to loss of chromosome 22q found in the literature, we identified additional recurrent CNAs including losses of chromosome 3q and 11q. In conclusion, our findings of the clonal relationship between synchronous pulmonary and uterine leiomyomas support the hypothesis that BML represents a condition wherein a uterine leiomyoma disseminates to distant extrauterine locations. PMID:28533481
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Kei-ichi Morita
Full Text Available Gorlin syndrome (GS is an autosomal dominant disorder that predisposes affected individuals to developmental defects and tumorigenesis, and caused mainly by heterozygous germline PTCH1 mutations. Despite exhaustive analysis, PTCH1 mutations are often unidentifiable in some patients; the failure to detect mutations is presumably because of mutations occurred in other causative genes or outside of analyzed regions of PTCH1, or copy number alterations (CNAs. In this study, we subjected a cohort of GS-affected individuals from six unrelated families to next-generation sequencing (NGS analysis for the combined screening of causative alterations in Hedgehog signaling pathway-related genes. Specific single nucleotide variations (SNVs of PTCH1 causing inferred amino acid changes were identified in four families (seven affected individuals, whereas CNAs within or around PTCH1 were found in two families in whom possible causative SNVs were not detected. Through a targeted resequencing of all coding exons, as well as simultaneous evaluation of copy number status using the alignment map files obtained via NGS, we found that GS phenotypes could be explained by PTCH1 mutations or deletions in all affected patients. Because it is advisable to evaluate CNAs of candidate causative genes in point mutation-negative cases, NGS methodology appears to be useful for improving molecular diagnosis through the simultaneous detection of both SNVs and CNAs in the targeted genes/regions.
Morita, Kei-ichi; Naruto, Takuya; Tanimoto, Kousuke; Yasukawa, Chisato; Oikawa, Yu; Masuda, Kiyoshi; Imoto, Issei; Inazawa, Johji; Omura, Ken; Harada, Hiroyuki
2015-01-01
Gorlin syndrome (GS) is an autosomal dominant disorder that predisposes affected individuals to developmental defects and tumorigenesis, and caused mainly by heterozygous germline PTCH1 mutations. Despite exhaustive analysis, PTCH1 mutations are often unidentifiable in some patients; the failure to detect mutations is presumably because of mutations occurred in other causative genes or outside of analyzed regions of PTCH1, or copy number alterations (CNAs). In this study, we subjected a cohort of GS-affected individuals from six unrelated families to next-generation sequencing (NGS) analysis for the combined screening of causative alterations in Hedgehog signaling pathway-related genes. Specific single nucleotide variations (SNVs) of PTCH1 causing inferred amino acid changes were identified in four families (seven affected individuals), whereas CNAs within or around PTCH1 were found in two families in whom possible causative SNVs were not detected. Through a targeted resequencing of all coding exons, as well as simultaneous evaluation of copy number status using the alignment map files obtained via NGS, we found that GS phenotypes could be explained by PTCH1 mutations or deletions in all affected patients. Because it is advisable to evaluate CNAs of candidate causative genes in point mutation-negative cases, NGS methodology appears to be useful for improving molecular diagnosis through the simultaneous detection of both SNVs and CNAs in the targeted genes/regions.
A fast random number generator for the Intel Paragon supercomputer
Gutbrod, F.
1995-06-01
A pseudo-random number generator is presented which makes optimal use of the architecture of the i860-microprocessor and which is expected to have a very long period. It is therefore a good candidate for use on the parallel supercomputer Paragon XP. In the assembler version, it needs 6.4 cycles for a real∗4 random number. There is a FORTRAN routine which yields identical numbers up to rare and minor rounding discrepancies, and it needs 28 cycles. The FORTRAN performance on other microprocessors is somewhat better. Arguments for the quality of the generator and some numerical tests are given.
Iacocca, Michael A.; Wang, Jian; Dron, Jacqueline S.; Robinson, John F.; McIntyre, Adam D.; Cao, Henian
2017-01-01
Familial hypercholesterolemia (FH) is a heritable condition of severely elevated LDL cholesterol, caused predominantly by autosomal codominant mutations in the LDL receptor gene (LDLR). In providing a molecular diagnosis for FH, the current procedure often includes targeted next-generation sequencing (NGS) panels for the detection of small-scale DNA variants, followed by multiplex ligation-dependent probe amplification (MLPA) in LDLR for the detection of whole-exon copy number variants (CNVs). The latter is essential because ∼10% of FH cases are attributed to CNVs in LDLR; accounting for them decreases false negative findings. Here, we determined the potential of replacing MLPA with bioinformatic analysis applied to NGS data, which uses depth-of-coverage analysis as its principal method to identify whole-exon CNV events. In analysis of 388 FH patient samples, there was 100% concordance in LDLR CNV detection between these two methods: 38 reported CNVs identified by MLPA were also successfully detected by our NGS method, while 350 samples negative for CNVs by MLPA were also negative by NGS. This result suggests that MLPA can be removed from the routine diagnostic screening for FH, significantly reducing associated costs, resources, and analysis time, while promoting more widespread assessment of this important class of mutations across diagnostic laboratories. PMID:28874442
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.
Teichmann, A Lina; Nieuwenstein, Mark R; Rich, Anina N
2015-01-01
Digit-color synesthetes report experiencing colors when perceiving letters and digits. The conscious experience is typically unidirectional (e.g., digits elicit colors but not vice versa) but recent evidence shows subtle bidirectional effects. We examined whether short-term memory for colors could be affected by the order of presentation reflecting more or less structure in the associated digits. We presented a stream of colored squares and asked participants to report the colors in order. The colors matched each synesthete's colors for digits 1-9 and the order of the colors corresponded either to a sequence of numbers (e.g., [red, green, blue] if 1 = red, 2 = green, 3 = blue) or no systematic sequence. The results showed that synesthetes recalled sequential color sequences more accurately than pseudo-randomized colors, whereas no such effect was found for the non-synesthetic controls. Synesthetes did not differ from non-synesthetic controls in recall of color sequences overall, providing no evidence of a general advantage in memory for serial recall of colors.
Directory of Open Access Journals (Sweden)
Ali M. Sajjad
2016-12-01
Full Text Available The present study was designed to establish a qualitative detection method based on conventional and real time PCR assay to screen the commonly grown rice varieties for the presence of the cry1Ac gene. The detection of genetically modified rice in the screening process would necessitate accurate assay development and precise qualitative PCR tests complying with established procedures for the detection and characterization of transgenes in food grains. Such assay would not only enable the monitoring of transgene flow in local agricultural environment but also the characterization of different plant species produced with this transgene and its regulatory components. Thus, a reliable and quick screening assay was established for the qualitative detection of the transgene along with the promoter and selectable marker gene in genetically modified rice. By conventional PCR, a fragment of 215 bp was amplified with gene specific primers of cry1Ac. Primers for other transgenes such as gna and bar were also employed; however, no amplification was detected. The presence of the p35s, sps, and nptII genes was confirmed by qualitative real-time PCR. The specificity of the respective PCR products was checked through melt peak curve analysis. Sharp and precise melting temperatures indicated the presence of a single kind of PCR product in correspondence to each of the primers used. Moreover, the copy number of cry1Ac was estimated by ∆∆CT method. It is proposed that the primer sets and experimental conditions used in this study will be sufficient to meet the requirements for molecular detection and characterization of the cry1Ac transgene and affiliated sequences in sorting out conventional rice varieties from the ones which are genetically modified. It will also help to monitor the ecological flow of these transgenes and other biosafety factors.
Do, Hongdo; Dobrovic, Alexander
2009-10-08
Mutation detection in clinical tumour samples is challenging when the proportion of tumour cells, and thus mutant alleles, is low. The limited sensitivity of conventional sequencing necessitates the adoption of more sensitive approaches. High resolution melting (HRM) is more sensitive than sequencing but identification of the mutation is desirable, particularly when it is important to discriminate false positives due to PCR errors or template degradation from true mutations.We thus developed limited copy number - high resolution melting (LCN-HRM) which applies limiting dilution to HRM. Multiple replicate reactions with a limited number of target sequences per reaction allow low level mutations to be detected. The dilutions used (based on Ct values) are chosen such that mutations, if present, can be detected by the direct sequencing of amplicons with aberrant melting patterns. Using cell lines heterozygous for mutations, we found that the mutations were not readily detected when they comprised 10% of total alleles (20% tumour cells) by sequencing, whereas they were readily detectable at 5% total alleles by standard HRM. LCN-HRM allowed these mutations to be identified by direct sequencing of those positive reactions.LCN-HRM was then used to review formalin-fixed paraffin-embedded (FFPE) clinical samples showing discordant findings between sequencing and HRM for KRAS exon 2 and EGFR exons 19 and 21. Both true mutations present at low levels and sequence changes due to artefacts were detected by LCN-HRM. The use of high fidelity polymerases showed that the majority of the artefacts were derived from the damaged template rather than replication errors during amplification. LCN-HRM bridges the sensitivity gap between HRM and sequencing and is effective in distinguishing between artefacts and true mutations.
International Nuclear Information System (INIS)
Cornejo Diaz, N.; Vergara Gil, A.; Jurado Vargas, M.
2010-01-01
The Monte Carlo method has become a valuable numerical laboratory framework in which to simulate complex physical systems. It is based on the generation of pseudo-random number sequences by numerical algorithms called random generators. In this work we assessed the suitability of different well-known random number generators for the simulation of gamma-ray spectrometry systems during efficiency calibrations. The assessment was carried out in two stages. The generators considered (Delphi's linear congruential, mersenne twister, XorShift, multiplier with carry, universal virtual array, and non-periodic logistic map based generator) were first evaluated with different statistical empirical tests, including moments, correlations, uniformity, independence of terms and the DIEHARD battery of tests. In a second step, an application-specific test was conducted by implementing the generators in our Monte Carlo program DETEFF and comparing the results obtained with them. The calculations were performed with two different CPUs, for a typical HpGe detector and a water sample in Marinelli geometry, with gamma-rays between 59 and 1800 keV. For the Non-periodic Logistic Map based generator, dependence of the most significant bits was evident. This explains the bias, in excess of 5%, of the efficiency values obtained with this generator. The results of the application-specific assessment and the statistical performance of the other algorithms studied indicate their suitability for the Monte Carlo simulation of gamma-ray spectrometry systems for efficiency calculations.
Díaz, N Cornejo; Gil, A Vergara; Vargas, M Jurado
2010-03-01
The Monte Carlo method has become a valuable numerical laboratory framework in which to simulate complex physical systems. It is based on the generation of pseudo-random number sequences by numerical algorithms called random generators. In this work we assessed the suitability of different well-known random number generators for the simulation of gamma-ray spectrometry systems during efficiency calibrations. The assessment was carried out in two stages. The generators considered (Delphi's linear congruential, mersenne twister, XorShift, multiplier with carry, universal virtual array, and non-periodic logistic map based generator) were first evaluated with different statistical empirical tests, including moments, correlations, uniformity, independence of terms and the DIEHARD battery of tests. In a second step, an application-specific test was conducted by implementing the generators in our Monte Carlo program DETEFF and comparing the results obtained with them. The calculations were performed with two different CPUs, for a typical HpGe detector and a water sample in Marinelli geometry, with gamma-rays between 59 and 1800 keV. For the Non-periodic Logistic Map based generator, dependence of the most significant bits was evident. This explains the bias, in excess of 5%, of the efficiency values obtained with this generator. The results of the application-specific assessment and the statistical performance of the other algorithms studied indicate their suitability for the Monte Carlo simulation of gamma-ray spectrometry systems for efficiency calculations. Copyright 2009 Elsevier Ltd. All rights reserved.
Van Lent, Sarah; Creasy, Heather Huot; Myers, Garry S A; Vanrompay, Daisy
2016-01-01
Variation is a central trait of the polymorphic membrane protein (Pmp) family. The number of pmp coding sequences differs between Chlamydia species, but it is unknown whether the number of pmp coding sequences is constant within a Chlamydia species. The level of conservation of the Pmp proteins has previously only been determined for Chlamydia trachomatis. As different Pmp proteins might be indispensible for the pathogenesis of different Chlamydia species, this study investigated the conservation of Pmp proteins both within and across C. trachomatis,C. pneumoniae,C. abortus, and C. psittaci. The pmp coding sequences were annotated in 16 C. trachomatis, 6 C. pneumoniae, 2 C. abortus, and 16 C. psittaci genomes. The number and organization of polymorphic membrane coding sequences differed within and across the analyzed Chlamydia species. The length of coding sequences of pmpA,pmpB, and pmpH was conserved among all analyzed genomes, while the length of pmpE/F and pmpG, and remarkably also of the subtype pmpD, differed among the analyzed genomes. PmpD, PmpA, PmpH, and PmpA were the most conserved Pmp in C. trachomatis,C. pneumoniae,C. abortus, and C. psittaci, respectively. PmpB was the most conserved Pmp across the 4 analyzed Chlamydia species. © 2016 S. Karger AG, Basel.
Hilton, Annette; Hilton, Geoff
2018-01-01
This article describes part of a study in which researchers designed lesson sequences based around using a string number line to help teachers support children's development of relative thinking and understanding of linear scale. In the first year of the study, eight teachers of Years 3-5 participated in four one-day professional development…
S. Zaccaria (Simone); M. El-Kebir (Mohammed); G.W. Klau (Gunnar); B.J. Raphael (Benjamin)
2017-01-01
textabstractCancer is an evolutionary process driven by somatic mutation. This process can be represented as a phylogenetic tree. Constructing such a phylogenetic tree from genome sequencing data is a challenging task due to the mutational complexity of cancer and the fact that nearly all cancer
Testing random number generators for Monte Carlo applications
International Nuclear Information System (INIS)
Sim, L.H.
1992-01-01
Central to any system for modelling radiation transport phenomena using Monte Carlo techniques is the method by which pseudo random numbers are generated. This method is commonly referred to as the Random Number Generator (RNG). It is usually a computer implemented mathematical algorithm which produces a series of numbers uniformly distributed on the interval [0,1]. If this series satisfies certain statistical tests for randomness, then for practical purposes the pseudo random numbers in the series can be considered to be random. Tests of this nature are important not only for new RNGs but also to test the implementation of known RNG algorithms in different computer environments. Six RNGs have been tested using six statistical tests and one visual test. The statistical tests are the moments, frequency (digit and number), serial, gap, and poker tests. The visual test is a simple two dimensional ordered pair display. In addition the RNGs have been tested in a specific Monte Carlo application. This type of test is often overlooked, however it is important that in addition to satisfactory performance in statistical tests, the RNG be able to perform effectively in the applications of interest. The RNGs tested here are based on a variety of algorithms, including multiplicative and linear congruential, lagged Fibonacci, and combination arithmetic and lagged Fibonacci. The effect of the Bays-Durham shuffling algorithm on the output of a known bad RNG has also been investigated. 18 refs., 11 tabs., 4 figs. of
Ramsey, Andrew J; Russell, Lance C; Chinkers, Michael
2009-10-12
Steroid-hormone-receptor maturation is a multi-step process that involves several TPR (tetratricopeptide repeat) proteins that bind to the maturation complex via the C-termini of hsp70 (heat-shock protein 70) and hsp90 (heat-shock protein 90). We produced a random T7 peptide library to investigate the roles played by the C-termini of the two heat-shock proteins in the TPR-hsp interactions. Surprisingly, phages with the MEEVD sequence, found at the C-terminus of hsp90, were not recovered from our biopanning experiments. However, two groups of phages were isolated that bound relatively tightly to HsPP5 (Homo sapiens protein phosphatase 5) TPR. Multiple copies of phages with a C-terminal sequence of LFG were isolated. These phages bound specifically to the TPR domain of HsPP5, although mutation studies produced no evidence that they bound to the domain's hsp90-binding groove. However, the most abundant family obtained in the initial screen had an aspartate residue at the C-terminus. Two members of this family with a C-terminal sequence of VD appeared to bind with approximately the same affinity as the hsp90 C-12 control. A second generation pseudo-random phage library produced a large number of phages with an LD C-terminus. These sequences acted as hsp70 analogues and had relatively low affinities for hsp90-specific TPR domains. Unfortunately, we failed to identify residues near hsp90's C-terminus that impart binding specificity to individual hsp90-TPR interactions. The results suggest that the C-terminal sequences of hsp70 and hsp90 act primarily as non-specific anchors for TPR proteins.
Bormann, Tobias; Seyboth, Margret; Umarova, Roza; Weiller, Cornelius
2015-06-01
Studies on verbal learning in patients with impaired verbal short-term memory (vSTM) have revealed dissociations among types of verbal information. Patients with impaired vSTM are able to learn lists of known words but fail to acquire new word forms. This suggests that vSTM is involved in new word learning. The present study assessed both new word learning and the learning of digit sequences in two patients with impaired vSTM. In two experiments, participants were required to learn people's names, ages and professions, or their four digit 'phone numbers'. The STM patients were impaired on learning unknown family names and phone numbers, but managed to acquire other verbal information. In contrast, a patient with a severe verbal episodic memory impairment was impaired across information types. These results indicate verbal STM involvement in the learning of digit sequences. Copyright © 2015 Elsevier Ltd. All rights reserved.
Castro, E.
2018-02-01
From the perturbative expansion of the exact Green function, an exact counting formula is derived to determine the number of different types of connected Feynman diagrams. This formula coincides with the Arquès-Walsh sequence formula in the rooted map theory, supporting the topological connection between Feynman diagrams and rooted maps. A classificatory summing-terms approach is used, in connection to discrete mathematical theory.
Zhang, Zhongyang; Hao, Ke
2015-11-01
Cancer genomes exhibit profound somatic copy number alterations (SCNAs). Studying tumor SCNAs using massively parallel sequencing provides unprecedented resolution and meanwhile gives rise to new challenges in data analysis, complicated by tumor aneuploidy and heterogeneity as well as normal cell contamination. While the majority of read depth based methods utilize total sequencing depth alone for SCNA inference, the allele specific signals are undervalued. We proposed a joint segmentation and inference approach using both signals to meet some of the challenges. Our method consists of four major steps: 1) extracting read depth supporting reference and alternative alleles at each SNP/Indel locus and comparing the total read depth and alternative allele proportion between tumor and matched normal sample; 2) performing joint segmentation on the two signal dimensions; 3) correcting the copy number baseline from which the SCNA state is determined; 4) calling SCNA state for each segment based on both signal dimensions. The method is applicable to whole exome/genome sequencing (WES/WGS) as well as SNP array data in a tumor-control study. We applied the method to a dataset containing no SCNAs to test the specificity, created by pairing sequencing replicates of a single HapMap sample as normal/tumor pairs, as well as a large-scale WGS dataset consisting of 88 liver tumors along with adjacent normal tissues. Compared with representative methods, our method demonstrated improved accuracy, scalability to large cancer studies, capability in handling both sequencing and SNP array data, and the potential to improve the estimation of tumor ploidy and purity.
Directory of Open Access Journals (Sweden)
Zhifu Sun
Full Text Available We used deep sequencing technology to profile the transcriptome, gene copy number, and CpG island methylation status simultaneously in eight commonly used breast cell lines to develop a model for how these genomic features are integrated in estrogen receptor positive (ER+ and negative breast cancer. Total mRNA sequence, gene copy number, and genomic CpG island methylation were carried out using the Illumina Genome Analyzer. Sequences were mapped to the human genome to obtain digitized gene expression data, DNA copy number in reference to the non-tumor cell line (MCF10A, and methylation status of 21,570 CpG islands to identify differentially expressed genes that were correlated with methylation or copy number changes. These were evaluated in a dataset from 129 primary breast tumors. Gene expression in cell lines was dominated by ER-associated genes. ER+ and ER- cell lines formed two distinct, stable clusters, and 1,873 genes were differentially expressed in the two groups. Part of chromosome 8 was deleted in all ER- cells and part of chromosome 17 amplified in all ER+ cells. These loci encoded 30 genes that were overexpressed in ER+ cells; 9 of these genes were overexpressed in ER+ tumors. We identified 149 differentially expressed genes that exhibited differential methylation of one or more CpG islands within 5 kb of the 5' end of the gene and for which mRNA abundance was inversely correlated with CpG island methylation status. In primary tumors we identified 84 genes that appear to be robust components of the methylation signature that we identified in ER+ cell lines. Our analyses reveal a global pattern of differential CpG island methylation that contributes to the transcriptome landscape of ER+ and ER- breast cancer cells and tumors. The role of gene amplification/deletion appears to more modest, although several potentially significant genes appear to be regulated by copy number aberrations.
Atibalentja, N; Noel, G R; Ciancio, A
2004-03-01
For many years the taxonomy of the genus Pasteuria has been marred with confusion because the bacterium could not be cultured in vitro and, therefore, descriptions were based solely on morphological, developmental, and pathological characteristics. The current study sought to devise a simple method for PCR-amplification, cloning, and sequencing of Pasteuria 16S rDNA from small numbers of endospores, with no need for prior DNA purification. Results show that DNA extracts from plain glass bead-beating of crude suspensions containing 10,000 endospores at 0.2 x 10 endospores ml(-1) were sufficient for PCR-amplification of Pasteuria 16S rDNA, when used in conjunction with specific primers. These results imply that for P. penetrans and P. nishizawae only one parasitized female of Meloidogyne spp. and Heterodera glycines, respectively, should be sufficient, and as few as eight cadavers of Belonolaimus longicaudatus with an average number of 1,250 endospores of "Candidatus Pasteuria usgae" are needed for PCR-amplification of Pasteuria 16S rDNA. The method described in this paper should facilitate the sequencing of the 16S rDNA of the many Pasteuria isolates that have been reported on nematodes and, consequently, expedite the classification of those isolates through comparative sequence analysis.
Random Numbers and Monte Carlo Methods
Scherer, Philipp O. J.
Many-body problems often involve the calculation of integrals of very high dimension which cannot be treated by standard methods. For the calculation of thermodynamic averages Monte Carlo methods are very useful which sample the integration volume at randomly chosen points. After summarizing some basic statistics, we discuss algorithms for the generation of pseudo-random numbers with given probability distribution which are essential for all Monte Carlo methods. We show how the efficiency of Monte Carlo integration can be improved by sampling preferentially the important configurations. Finally the famous Metropolis algorithm is applied to classical many-particle systems. Computer experiments visualize the central limit theorem and apply the Metropolis method to the traveling salesman problem.
Directory of Open Access Journals (Sweden)
Michal R Schweiger
Full Text Available BACKGROUND: Cancer re-sequencing programs rely on DNA isolated from fresh snap frozen tissues, the preparation of which is combined with additional preservation efforts. Tissue samples at pathology departments are routinely stored as formalin-fixed and paraffin-embedded (FFPE samples and their use would open up access to a variety of clinical trials. However, FFPE preparation is incompatible with many down-stream molecular biology techniques such as PCR based amplification methods and gene expression studies. METHODOLOGY/PRINCIPAL FINDINGS: Here we investigated the sample quality requirements of FFPE tissues for massively parallel short-read sequencing approaches. We evaluated key variables of pre-fixation, fixation related and post-fixation processes that occur in routine medical service (e.g. degree of autolysis, duration of fixation and of storage. We also investigated the influence of tissue storage time on sequencing quality by using material that was up to 18 years old. Finally, we analyzed normal and tumor breast tissues using the Sequencing by Synthesis technique (Illumina Genome Analyzer, Solexa to simultaneously localize genome-wide copy number alterations and to detect genomic variations such as substitutions and point-deletions and/or insertions in FFPE tissue samples. CONCLUSIONS/SIGNIFICANCE: The application of second generation sequencing techniques on small amounts of FFPE material opens up the possibility to analyze tissue samples which have been collected during routine clinical work as well as in the context of clinical trials. This is in particular important since FFPE samples are amply available from surgical tumor resections and histopathological diagnosis, and comprise tissue from precursor lesions, primary tumors, lymphogenic and/or hematogenic metastases. Large-scale studies using this tissue material will result in a better prediction of the prognosis of cancer patients and the early identification of patients which
Extracting random numbers from quantum tunnelling through a single diode.
Bernardo-Gavito, Ramón; Bagci, Ibrahim Ethem; Roberts, Jonathan; Sexton, James; Astbury, Benjamin; Shokeir, Hamzah; McGrath, Thomas; Noori, Yasir J; Woodhead, Christopher S; Missous, Mohamed; Roedig, Utz; Young, Robert J
2017-12-19
Random number generation is crucial in many aspects of everyday life, as online security and privacy depend ultimately on the quality of random numbers. Many current implementations are based on pseudo-random number generators, but information security requires true random numbers for sensitive applications like key generation in banking, defence or even social media. True random number generators are systems whose outputs cannot be determined, even if their internal structure and response history are known. Sources of quantum noise are thus ideal for this application due to their intrinsic uncertainty. In this work, we propose using resonant tunnelling diodes as practical true random number generators based on a quantum mechanical effect. The output of the proposed devices can be directly used as a random stream of bits or can be further distilled using randomness extraction algorithms, depending on the application.
Pittet, Vanessa; Phister, Trevor G.; Ziola, Barry
2013-01-01
Growth of specific lactic acid bacteria in beer leads to spoiled product and economic loss for the brewing industry. Microbial growth is typically inhibited by the combined stresses found in beer (e.g., ethanol, hops, low pH, minimal nutrients); however, certain bacteria have adapted to grow in this harsh environment. Considering little is known about the mechanisms used by bacteria to grow in and spoil beer, transcriptome sequencing was performed on a variant of the beer-spoilage organism Pediococcus claussenii ATCC BAA-344T (Pc344-358). Illumina sequencing was used to compare the transcript levels in Pc344-358 growing mid-exponentially in beer to those in nutrient-rich MRS broth. Various operons demonstrated high gene expression in beer, several of which are involved in nutrient acquisition and overcoming the inhibitory effects of hop compounds. As well, genes functioning in cell membrane modification and biosynthesis demonstrated significantly higher transcript levels in Pc344-358 growing in beer. Three plasmids had the majority of their genes showing increased transcript levels in beer, whereas the two cryptic plasmids showed slightly decreased gene expression. Follow-up analysis of plasmid copy number in both growth environments revealed similar trends, where more copies of the three non-cryptic plasmids were found in Pc344-358 growing in beer. Transcriptome sequencing also enabled the addition of several genes to the P . claussenii ATCC BAA-344T genome annotation, some of which are putatively transcribed as non-coding RNAs. The sequencing results not only provide the first transcriptome description of a beer-spoilage organism while growing in beer, but they also highlight several targets for future exploration, including genes that may have a role in the general stress response of lactic acid bacteria. PMID:24040005
Boivin, Vincent; Deschamps-Francoeur, Gabrielle; Couture, Sonia; Nottingham, Ryan M; Bouchard-Bourelle, Philia; Lambowitz, Alan M; Scott, Michelle S; Abou-Elela, Sherif
2018-07-01
Comparing the abundance of one RNA molecule to another is crucial for understanding cellular functions but most sequencing techniques can target only specific subsets of RNA. In this study, we used a new fragmented ribodepleted TGIRT sequencing method that uses a thermostable group II intron reverse transcriptase (TGIRT) to generate a portrait of the human transcriptome depicting the quantitative relationship of all classes of nonribosomal RNA longer than 60 nt. Comparison between different sequencing methods indicated that FRT is more accurate in ranking both mRNA and noncoding RNA than viral reverse transcriptase-based sequencing methods, even those that specifically target these species. Measurements of RNA abundance in different cell lines using this method correlate with biochemical estimates, confirming tRNA as the most abundant nonribosomal RNA biotype. However, the single most abundant transcript is 7SL RNA, a component of the signal recognition particle. S tructured n on c oding RNAs (sncRNAs) associated with the same biological process are expressed at similar levels, with the exception of RNAs with multiple functions like U1 snRNA. In general, sncRNAs forming RNPs are hundreds to thousands of times more abundant than their mRNA counterparts. Surprisingly, only 50 sncRNA genes produce half of the non-rRNA transcripts detected in two different cell lines. Together the results indicate that the human transcriptome is dominated by a small number of highly expressed sncRNAs specializing in functions related to translation and splicing. © 2018 Boivin et al.; Published by Cold Spring Harbor Laboratory Press for the RNA Society.
Pourcel, Christine; Minandri, Fabrizia; Hauck, Yolande; D'Arezzo, Silvia; Imperi, Francesco; Vergnaud, Gilles; Visca, Paolo
2011-01-01
Acinetobacter baumannii is an important opportunistic pathogen responsible for nosocomial outbreaks, mostly occurring in intensive care units. Due to the multiplicity of infection sources, reliable molecular fingerprinting techniques are needed to establish epidemiological correlations among A. baumannii isolates. Multiple-locus variable-number tandem-repeat analysis (MLVA) has proven to be a fast, reliable, and cost-effective typing method for several bacterial species. In this study, an MLVA assay compatible with simple PCR- and agarose gel-based electrophoresis steps as well as with high-throughput automated methods was developed for A. baumannii typing. Preliminarily, 10 potential polymorphic variable-number tandem repeats (VNTRs) were identified upon bioinformatic screening of six annotated genome sequences of A. baumannii. A collection of 7 reference strains plus 18 well-characterized isolates, including unique types and representatives of the three international A. baumannii lineages, was then evaluated in a two-center study aimed at validating the MLVA assay and comparing it with other genotyping assays, namely, macrorestriction analysis with pulsed-field gel electrophoresis (PFGE) and PCR-based sequence group (SG) profiling. The results showed that MLVA can discriminate between isolates with identical PFGE types and SG profiles. A panel of eight VNTR markers was selected, all showing the ability to be amplified and good amounts of polymorphism in the majority of strains. Independently generated MLVA profiles, composed of an ordered string of allele numbers corresponding to the number of repeats at each VNTR locus, were concordant between centers. Typeability, reproducibility, stability, discriminatory power, and epidemiological concordance were excellent. A database containing information and MLVA profiles for several A. baumannii strains is available from http://mlva.u-psud.fr/. PMID:21147956
Egeland, Jens
2015-01-01
The Wechsler Adult Intelligence Scale (WAIS) is one of the most frequently used tests among psychologists. In the fourth edition of the test (WAIS-IV), the subtests Digit Span and Letter-Number Sequencing are expanded for better measurement of working memory (WM). However, it is not clear whether the new extended tasks contribute sufficient complexity to be sensitive measures of manipulation WM, nor do we know to what degree WM capacity differs between the visual and the auditory modality because the WAIS-IV only tests the auditory modality. Performance by a mixed sample of 226 patients referred for neuropsychological examination on the Digit Span and Letter-Number Sequencing subtests from the WAIS-IV and on Spatial Span from the Wechsler Memory Scale-Third Edition was analyzed in two confirmatory factor analyses to investigate whether a unitary WM model or divisions based on modality or level/complexity best fit the data. The modality model showed the best fit when analyzing summed scores for each task as well as scores for the longest span. The clinician is advised to apply tests with higher manipulation load and to consider testing visual span as well before drawing conclusions about impaired WM from the WAIS-IV.
Directory of Open Access Journals (Sweden)
Scott Christopher J
2010-04-01
Full Text Available Abstract Background The DUB/USP17 subfamily of deubiquitinating enzymes were originally identified as immediate early genes induced in response to cytokine stimulation in mice (DUB-1, DUB-1A, DUB-2, DUB-2A. Subsequently we have identified a number of human family members and shown that one of these (DUB-3 is also cytokine inducible. We originally showed that constitutive expression of DUB-3 can block cell proliferation and more recently we have demonstrated that this is due to its regulation of the ubiquitination and activity of the 'CAAX' box protease RCE1. Results Here we demonstrate that the human DUB/USP17 family members are found on both chromosome 4p16.1, within a block of tandem repeats, and on chromosome 8p23.1, embedded within the copy number variable beta-defensin cluster. In addition, we show that the multiple genes observed in humans and other distantly related mammals have arisen due to the independent expansion of an ancestral sequence within each species. However, it is also apparent when sequences from humans and the more closely related chimpanzee are compared, that duplication events have taken place prior to these species separating. Conclusions The observation that the DUB/USP17 genes, which can influence cell growth and survival, have evolved from an unstable ancestral sequence which has undergone multiple and varied duplications in the species examined marks this as a unique family. In addition, their presence within the beta-defensin repeat raises the question whether they may contribute to the influence of this repeat on immune related conditions.
Scope of Various Random Number Generators in ant System Approach for TSP
Sen, S. K.; Shaykhian, Gholam Ali
2007-01-01
Experimented on heuristic, based on an ant system approach for traveling salesman problem, are several quasi- and pseudo-random number generators. This experiment is to explore if any particular generator is most desirable. Such an experiment on large samples has the potential to rank the performance of the generators for the foregoing heuristic. This is mainly to seek an answer to the controversial issue "which generator is the best in terms of quality of the result (accuracy) as well as cost of producing the result (time/computational complexity) in a probabilistic/statistical sense."
Garcia, S A L; Van der Lee, T A J; Ferreira, C F; Te Lintel Hekkert, B; Zapater, M-F; Goodwin, S B; Guzmán, M; Kema, G H J; Souza, M T
2010-11-09
We searched the genome of Mycosphaerella fijiensis for molecular markers that would allow population genetics analysis of this plant pathogen. M. fijiensis, the causal agent of banana leaf streak disease, also known as black Sigatoka, is the most devastating pathogen attacking bananas (Musa spp). Recently, the entire genome sequence of M. fijiensis became available. We screened this database for VNTR markers. Forty-two primer pairs were selected for validation, based on repeat type and length and the number of repeat units. Five VNTR markers showing multiple alleles were validated with a reference set of isolates from different parts of the world and a population from a banana plantation in Costa Rica. Polymorphism information content values varied from 0.6414 to 0.7544 for the reference set and from 0.0400 and 0.7373 for the population set. Eighty percent of the polymorphism information content values were above 0.60, indicating that the markers are highly informative. These markers allowed robust scoring of agarose gels and proved to be useful for variability and population genetics studies. In conclusion, the strategy we developed to identify and validate VNTR markers is an efficient means to incorporate markers that can be used for fungicide resistance management and to develop breeding strategies to control banana black leaf streak disease. This is the first report of VNTR-minisatellites from the M. fijiensis genome sequence.
Ossola, Giovanni; Sokal, Alan D
2004-08-01
We show that linear congruential pseudo-random-number generators can cause systematic errors in Monte Carlo simulations using the Swendsen-Wang algorithm, if the lattice size is a multiple of a very large power of 2 and one random number is used per bond. These systematic errors arise from correlations within a single bond-update half-sweep. The errors can be eliminated (or at least radically reduced) by updating the bonds in a random order or in an aperiodic manner. It also helps to use a generator of large modulus (e.g., 60 or more bits).
Klambauer, Günter; Schwarzbauer, Karin; Mayr, Andreas; Clevert, Djork-Arné; Mitterecker, Andreas; Bodenhofer, Ulrich; Hochreiter, Sepp
2012-05-01
Quantitative analyses of next-generation sequencing (NGS) data, such as the detection of copy number variations (CNVs), remain challenging. Current methods detect CNVs as changes in the depth of coverage along chromosomes. Technological or genomic variations in the depth of coverage thus lead to a high false discovery rate (FDR), even upon correction for GC content. In the context of association studies between CNVs and disease, a high FDR means many false CNVs, thereby decreasing the discovery power of the study after correction for multiple testing. We propose 'Copy Number estimation by a Mixture Of PoissonS' (cn.MOPS), a data processing pipeline for CNV detection in NGS data. In contrast to previous approaches, cn.MOPS incorporates modeling of depths of coverage across samples at each genomic position. Therefore, cn.MOPS is not affected by read count variations along chromosomes. Using a Bayesian approach, cn.MOPS decomposes variations in the depth of coverage across samples into integer copy numbers and noise by means of its mixture components and Poisson distributions, respectively. The noise estimate allows for reducing the FDR by filtering out detections having high noise that are likely to be false detections. We compared cn.MOPS with the five most popular methods for CNV detection in NGS data using four benchmark datasets: (i) simulated data, (ii) NGS data from a male HapMap individual with implanted CNVs from the X chromosome, (iii) data from HapMap individuals with known CNVs, (iv) high coverage data from the 1000 Genomes Project. cn.MOPS outperformed its five competitors in terms of precision (1-FDR) and recall for both gains and losses in all benchmark data sets. The software cn.MOPS is publicly available as an R package at http://www.bioinf.jku.at/software/cnmops/ and at Bioconductor.
Generating random numbers by means of nonlinear dynamic systems
Zang, Jiaqi; Hu, Haojie; Zhong, Juhua; Luo, Duanbin; Fang, Yi
2018-07-01
To introduce the randomness of a physical process to students, a chaotic pendulum experiment was opened in East China University of Science and Technology (ECUST) on the undergraduate level in the physics department. It was shown chaotic motion could be initiated through adjusting the operation of a chaotic pendulum. By using the data of the angular displacements of chaotic motion, random binary numerical arrays can be generated. To check the randomness of generated numerical arrays, the NIST Special Publication 800-20 method was adopted. As a result, it was found that all the random arrays which were generated by the chaotic motion could pass the validity criteria and some of them were even better than the quality of pseudo-random numbers generated by a computer. Through the experiments, it is demonstrated that chaotic pendulum can be used as an efficient mechanical facility in generating random numbers, and can be applied in teaching random motion to the students.
International Nuclear Information System (INIS)
Olivari, D.
1984-01-01
An attempt is made at identifying the most important factors which introduce difficulties in the analysis of results from tests on pollutant dispersal: the unsteadiness of the phenomenon, the effect of external uncontrollable parameters, and the inherent complexity of the problem itself. The basic models for prediction of dispersion of passive contaminants are discussed, and in particular a Lagrangian approach which seems to provide accurate results. For the analysis of results many problems arise. First the need of computing for the results the statistical quantities which describe them: the mean, the variance and higher order moments are important. It is shown that there is no easy solution if the duration and/or the number of independent ''events'' to be analyzed are too limited. The probability density function provides the most useful information, but is not easy to measure. A family of functions is recalled which predict reasonably well the trend of the pdf. Then the role of intermittency is shown in some detail. Its importance cannot be underestimated and its relationship to pdf and the effects on measurements are shown to be rather complex. Finally, an example is made to show the effects of the variance of external factors
International Nuclear Information System (INIS)
Myre, Michael A.; O'Day, Danton H.
2005-01-01
Nucleomorphin is a novel nuclear calmodulin (CaM)-binding protein (CaMBP) containing an extensive DEED (glu/asp repeat) domain that regulates nuclear number. GFP-constructs of the 38 kDa NumA1 isoform localize as intranuclear patches adjacent to the inner nuclear membrane. The translocation of CaMBPs into nuclei has previously been shown by others to be mediated by both classic nuclear localization sequences (NLSs) and CaM-binding domains (CaMBDs). Here we show that NumA1 possesses a CaMBD ( 171 EDVSRFIKGKLLQKQQKIYKDLERF 195 ) containing both calcium-dependent-binding motifs and an IQ-like motif for calcium-independent binding. GFP-constructs containing only NumA1 residues 1-129, lacking the DEED and CaMBDs, still localized as patches at the internal periphery of nuclei thus ruling out a direct role for the CaMBD in nuclear import. These constructs contained the amino acid residues 48 KKSYQDPEIIAHSRPRK 64 that include both a putative bipartite and classical NLS. GFP-bipartite NLS constructs localized uniformly within nuclei but not as patches. As with previous work, removal of the DEED domain resulted in highly multinucleate cells. However as shown here, multinuclearity only occurred when the NLS was present allowing the protein to enter nuclei. Site-directed mutation analysis in which the NLS was changed to 48 EF 49 abolished the stability of the GFP fusion at the protein but not RNA level preventing subcellular analyses. Cells transfected with the 48 EF 49 construct exhibited slowed growth when compared to parental AX3 cells and other GFP-NumA1 deletion mutants. In addition to identifying an NLS that is sufficient for nuclear translocation of nucleomorphin and ruling out CaM-binding in this event, this work shows that the nuclear localization of NumA1 is crucial to its ability to regulate nuclear number in Dictyostelium
Fast random-number generation using a diode laser's frequency noise characteristic
Takamori, Hiroki; Doi, Kohei; Maehara, Shinya; Kawakami, Kohei; Sato, Takashi; Ohkawa, Masashi; Ohdaira, Yasuo
2012-02-01
Random numbers can be classified as either pseudo- or physical-random, in character. Pseudo-random numbers are generated by definite periodicity, so, their usefulness in cryptographic applications is somewhat limited. On the other hand, naturally-generated physical-random numbers have no calculable periodicity, thereby making them ideal for the task. Diode lasers' considerable wideband noise gives them tremendous capacity for generating physical-random numbers, at a high rate of speed. We measured a diode laser's output with a fast photo detector, and evaluated the binary-numbers from the diode laser's frequency noise characteristics. We then identified and evaluated the binary-number-line's statistical properties. We also investigate the possibility that much faster physical-random number parallel-generation is possible, using separate outputs of different optical-path length and character, which we refer to as "coherence collapse".
Super fast physical-random number generation using laser diode frequency noises
Ushiki, Tetsuro; Doi, Kohei; Maehara, Shinya; Sato, Takashi; Ohkawa, Masashi; Ohdaira, Yasuo
2011-02-01
Random numbers can be classified as either pseudo- or physical-random in character. Pseudo-random numbers' periodicity renders them inappropriate for use in cryptographic applications, but naturally-generated physical-random numbers have no calculable periodicity, thereby making them ideally-suited to the task. The laser diode naturally produces a wideband "noise" signal that is believed to have tremendous capacity and great promise, for the rapid generation of physical-random numbers for use in cryptographic applications. We measured a laser diode's output, at a fast photo detector and generated physical-random numbers from frequency noises. We then identified and evaluated the binary-number-line's statistical properties. The result shows that physical-random number generation, at speeds as high as 40Gbps, is obtainable, using the laser diode's frequency noise characteristic.
True random numbers from amplified quantum vacuum.
Jofre, M; Curty, M; Steinlechner, F; Anzolin, G; Torres, J P; Mitchell, M W; Pruneri, V
2011-10-10
Random numbers are essential for applications ranging from secure communications to numerical simulation and quantitative finance. Algorithms can rapidly produce pseudo-random outcomes, series of numbers that mimic most properties of true random numbers while quantum random number generators (QRNGs) exploit intrinsic quantum randomness to produce true random numbers. Single-photon QRNGs are conceptually simple but produce few random bits per detection. In contrast, vacuum fluctuations are a vast resource for QRNGs: they are broad-band and thus can encode many random bits per second. Direct recording of vacuum fluctuations is possible, but requires shot-noise-limited detectors, at the cost of bandwidth. We demonstrate efficient conversion of vacuum fluctuations to true random bits using optical amplification of vacuum and interferometry. Using commercially-available optical components we demonstrate a QRNG at a bit rate of 1.11 Gbps. The proposed scheme has the potential to be extended to 10 Gbps and even up to 100 Gbps by taking advantage of high speed modulation sources and detectors for optical fiber telecommunication devices.
Mycosphaerella fijiensis, the causal agent of banana leaf streak disease (commonly known as black Sigatoka), is the most devastating pathogen attacking bananas (Musa spp). Recently the whole genome sequence of M. fijiensis became available. This sequence was screened for the presence of Variable Num...
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....
Ji, Caleb; Khovanova, Tanya; Park, Robin; Song, Angela
2015-01-01
In this paper, we consider a game played on a rectangular $m \\times n$ gridded chocolate bar. Each move, a player breaks the bar along a grid line. Each move after that consists of taking any piece of chocolate and breaking it again along existing grid lines, until just $mn$ individual squares remain. This paper enumerates the number of ways to break an $m \\times n$ bar, which we call chocolate numbers, and introduces four new sequences related to these numbers. Using various techniques, we p...
Ahlstrom, Christina; Barkema, Herman W; Stevenson, Karen; Zadoks, Ruth N; Biek, Roman; Kao, Rowland; Trewby, Hannah; Haupstein, Deb; Kelton, David F; Fecteau, Gilles; Labrecque, Olivia; Keefe, Greg P; McKenna, Shawn L B; De Buck, Jeroen
2015-03-08
Mycobacterium avium subsp. paratuberculosis (MAP), the causative bacterium of Johne's disease in dairy cattle, is widespread in the Canadian dairy industry and has significant economic and animal welfare implications. An understanding of the population dynamics of MAP can be used to identify introduction events, improve control efforts and target transmission pathways, although this requires an adequate understanding of MAP diversity and distribution between herds and across the country. Whole genome sequencing (WGS) offers a detailed assessment of the SNP-level diversity and genetic relationship of isolates, whereas several molecular typing techniques used to investigate the molecular epidemiology of MAP, such as variable number of tandem repeat (VNTR) typing, target relatively unstable repetitive elements in the genome that may be too unpredictable to draw accurate conclusions. The objective of this study was to evaluate the diversity of bovine MAP isolates in Canadian dairy herds using WGS and then determine if VNTR typing can distinguish truly related and unrelated isolates. Phylogenetic analysis based on 3,039 SNPs identified through WGS of 124 MAP isolates identified eight genetically distinct subtypes in dairy herds from seven Canadian provinces, with the dominant type including over 80% of MAP isolates. VNTR typing of 527 MAP isolates identified 12 types, including "bison type" isolates, from seven different herds. At a national level, MAP isolates differed from each other by 1-2 to 239-240 SNPs, regardless of whether they belonged to the same or different VNTR types. A herd-level analysis of MAP isolates demonstrated that VNTR typing may both over-estimate and under-estimate the relatedness of MAP isolates found within a single herd. The presence of multiple MAP subtypes in Canada suggests multiple introductions into the country including what has now become one dominant type, an important finding for Johne's disease control. VNTR typing often failed to
Saranathan, Manojkumar; Rettmann, Dan W; Hargreaves, Brian A; Clarke, Sharon E; Vasanawala, Shreyas S
2012-06-01
To develop and evaluate a multiphasic contrast-enhanced MRI method called DIfferential Sub-sampling with Cartesian Ordering (DISCO) for abdominal imaging. A three-dimensional, variable density pseudo-random k-space segmentation scheme was developed and combined with a Dixon-based fat-water separation algorithm to generate high temporal resolution images with robust fat suppression and without compromise in spatial resolution or coverage. With institutional review board approval and informed consent, 11 consecutive patients referred for abdominal MRI at 3 Tesla (T) were imaged with both DISCO and a routine clinical three-dimensional SPGR-Dixon (LAVA FLEX) sequence. All images were graded by two radiologists using quality of fat suppression, severity of artifacts, and overall image quality as scoring criteria. For assessment of arterial phase capture efficiency, the number of temporal phases with angiographic phase and hepatic arterial phase was recorded. There were no significant differences in quality of fat suppression, artifact severity or overall image quality between DISCO and LAVA FLEX images (P > 0.05, Wilcoxon signed rank test). The angiographic and arterial phases were captured in all 11 patients scanned using the DISCO acquisition (mean number of phases were two and three, respectively). DISCO effectively captures the fast dynamics of abdominal pathology such as hyperenhancing hepatic lesions with a high spatio-temporal resolution. Typically, 1.1 × 1.5 × 3 mm spatial resolution over 60 slices was achieved with a temporal resolution of 4-5 s. Copyright © 2012 Wiley Periodicals, Inc.
A true random number generator based on mouse movement and chaotic cryptography
International Nuclear Information System (INIS)
Hu Yue; Liao Xiaofeng; Wong, Kwok-wo; Zhou Qing
2009-01-01
True random number generators are in general more secure than pseudo random number generators. In this paper, we propose a novel true random number generator which generates a 256-bit random number by computer mouse movement. It is cheap, convenient and universal for personal computers. To eliminate the effect of similar movement patterns generated by the same user, three chaos-based approaches, namely, discretized 2D chaotic map permutation, spatiotemporal chaos and 'MASK' algorithm, are adopted to post-process the captured mouse movements. Random bits generated by three users are tested using NIST statistical tests. Both the spatiotemporal chaos approach and the 'MASK' algorithm pass the tests successfully. However, the latter has a better performance in terms of efficiency and effectiveness and so is more practical for common personal computer applications.
Private random numbers produced by entangled ions and certified by Bell's theorem
Hayes, David; Matsukevich, Dzmitry; Maunz, Peter; Monroe, Chris; Olmschenk, Steven
2010-03-01
It has been shown that entangled particles can be used to generate numbers whose privacy and randomness are guaranteed by the violation of a Bell inequality [1,2]. The authenticity of the bit stream produced is guaranteed when the system used can close the detection loophole and when the entangled particles are non-interacting. We report the use of remotely located trapped ions with near perfect state detection efficiency as a private random number generator. By entangling the ions through photon interference and choosing the measurement settings using a pseudo-random number generator, we measure a CHSH correlation function that is more than seven standard deviations above the classical limit. With a total of 3016 events, we are able to certify the generation of 42 new random numbers with 99% confidence. [1] S. Pironio et al.(submitted to Nature, arXiv:0911.3427) [2] Colbeck, R. PhD Dissertation (2007)
Schouls, Leo M; Ende, Arie van der; Damen, Marjolein; Pol, Ingrid van de
2006-01-01
We identified many variable-number tandem repeat (VNTR) loci in the genomes of Neisseria meningitidis serogroups A, B, and C and utilized a number of these loci to develop a multiple-locus variable-number tandem repeat analysis (MLVA). Eighty-five N. meningitidis serogroup B and C isolates obtained
Chelomina, Galina N; Rozhkovan, Konstantin V; Voronova, Anastasia N; Burundukova, Olga L; Muzarok, Tamara I; Zhuravlev, Yuri N
2016-04-01
Wild ginseng, Panax ginseng Meyer, is an endangered species of medicinal plants. In the present study, we analyzed variations within the ribosomal DNA (rDNA) cluster to gain insight into the genetic diversity of the Oriental ginseng, P. ginseng, at artificial plant cultivation. The roots of wild P. ginseng plants were sampled from a nonprotected natural population of the Russian Far East. The slides were prepared from leaf tissues using the squash technique for cytogenetic analysis. The 18S rDNA sequences were cloned and sequenced. The distribution of nucleotide diversity, recombination events, and interspecific phylogenies for the total 18S rDNA sequence data set was also examined. In mesophyll cells, mononucleolar nuclei were estimated to be dominant (75.7%), while the remaining nuclei contained two to four nucleoli. Among the analyzed 18S rDNA clones, 20% were identical to the 18S rDNA sequence of P. ginseng from Japan, and other clones differed in one to six substitutions. The nucleotide polymorphism was more expressed at the positions 440-640 bp, and distributed in variable regions, expansion segments, and conservative elements of core structure. The phylogenetic analysis confirmed conspecificity of ginseng plants cultivated in different regions, with two fixed mutations between P. ginseng and other species. This study identified the evidences of the intragenomic nucleotide polymorphism in the 18S rDNA sequences of P. ginseng. These data suggest that, in cultivated plants, the observed genome instability may influence the synthesis of biologically active compounds, which are widely used in traditional medicine.
International Nuclear Information System (INIS)
Tsuchihashi, Toshio; Maki, Toshio; Kitagawa, Matsuo; Suzuki, Takeshi; Fujita, Isao
1999-01-01
The T 2 relaxation effect of the fast spin echo sequence (FSE) was investigated using superparamagnetic iron oxide (SPIO) particles. When even echoes were used as the effective TE of FSE, the signal intensity ratio [signal intensity of FSE/signal intensity of conventional spin echo sequence (CSE)] of FSE and CSE increased, whereas the T 2 relaxation effect of SPIO with FSE was reduced. However, when odd echoes were used, neither signal intensity changed, and weakening of the T 2 relaxation effect, considered a problem with FSE, was reduced. This phenomenon was not observed when the refocusing flip angle was changed to 30 and 60 degrees. However, it was observed when the refocusing flip angle was 120 and 150 degrees. Thus, this phenomenon can be considered to be related to oscillation in longitudinal magnetization when using the Carr-Purcell-Meiboom-Gill (CPMG) technique. (author)
Number Sense on the Number Line
Woods, Dawn Marie; Ketterlin Geller, Leanne; Basaraba, Deni
2018-01-01
A strong foundation in early number concepts is critical for students' future success in mathematics. Research suggests that visual representations, like a number line, support students' development of number sense by helping them create a mental representation of the order and magnitude of numbers. In addition, explicitly sequencing instruction…
Digital chaotic sequence generator based on coupled chaotic systems
International Nuclear Information System (INIS)
Shu-Bo, Liu; Jing, Sun; Jin-Shuo, Liu; Zheng-Quan, Xu
2009-01-01
Chaotic systems perform well as a new rich source of cryptography and pseudo-random coding. Unfortunately their digital dynamical properties would degrade due to the finite computing precision. Proposed in this paper is a modified digital chaotic sequence generator based on chaotic logistic systems with a coupling structure where one chaotic subsystem generates perturbation signals to disturb the control parameter of the other one. The numerical simulations show that the length of chaotic orbits, the output distribution of chaotic system, and the security of chaotic sequences have been greatly improved. Moreover the chaotic sequence period can be extended at least by one order of magnitude longer than that of the uncoupled logistic system and the difficulty in decrypting increases 2 128 *2 128 times indicating that the dynamical degradation of digital chaos is effectively improved. A field programmable gate array (FPGA) implementation of an algorithm is given and the corresponding experiment shows that the output speed of the generated chaotic sequences can reach 571.4 Mbps indicating that the designed generator can be applied to the real-time video image encryption. (general)
Gaber, Rania; Watermann, Iris; Kugler, Christian; Vollmer, Ekkehard; Perner, Sven; Reck, Martin; Goldmann, Torsten
2017-01-01
Targeting epidermal growth factor receptor (EGFR) in patients with non-small-cell lung cancer (NSCLC) having EGFR mutations is associated with an improved overall survival. The aim of this study is to verify, if EGFR mutations detected by immunohistochemistry (IHC) is a convincing way to preselect patients for DNA-sequencing and to figure out, the statistical association between EGFR mutation, wild-type EGFR overexpression, gene copy number gain, which are the main factors inducing EGFR tumorigenic activity and the clinicopathological data. Two hundred sixteen tumor tissue samples of primarily chemotherapeutic naïve NSCLC patients were analyzed for EGFR mutations E746-A750del and L858R and correlated with DNA-sequencing. Two hundred six of which were assessed by IHC, using 6B6 and 43B2 specific antibodies followed by DNA-sequencing of positive cases and 10 already genotyped tumor tissues were also included to investigate debugging accuracy of IHC. In addition, EGFR wild-type overexpression was IHC evaluated and EGFR gene copy number determination was performed by fluorescence in situ hybridization (FISH). Forty-one÷206 (19.9%) cases were positive for mutated EGFR by IHC. Eight of them had EGFR mutations of exons 18-21 by DNA-sequencing. Hit rate of 10 already genotyped NSCLC mutated cases was 90% by IHC. Positive association was found between EGFR mutations determined by IHC and both EGFR overexpression and increased gene copy number (p=0.002 and p<0.001, respectively). Additionally, positive association was detected between EGFR mutations, high tumor grade and clinical stage (p<0.001). IHC staining with mutation specific antibodies was demonstrated as a possible useful screening test to preselect patients for DNA-sequencing.
International Nuclear Information System (INIS)
Bluszcz, Andrzej; Adamiec, Grzegorz; Heer, Aleksandra J.
2015-01-01
The current work focuses on the estimation of equivalent dose and its uncertainty using the single aliquot regenerative protocol in optically stimulated luminescence measurements. The authors show that the count numbers recorded with the use of photomultiplier tubes are well described by negative binomial distributions, different ones for background counts and photon induced counts. This fact is then exploited in pseudo-random count number generation and simulations of D e determination assuming a saturating exponential growth. A least squares fitting procedure is applied using different types of weights to determine whether the obtained D e 's and their error estimates are unbiased and accurate. A weighting procedure is suggested that leads to almost unbiased D e estimates. It is also shown that the assumption of Poisson distribution in D e estimation may lead to severe underestimation of the D e error. - Highlights: • Detailed analysis of statistics of count numbers in luminescence readers. • Generation of realistically scattered pseudo-random numbers of counts in luminescence measurements. • A practical guide for stringent analysis of D e values and errors assessment.
Pourcel, Christine; Visca, Paolo; Afshar, Baharak; D'Arezzo, Silvia; Vergnaud, Gilles; Fry, Norman K.
2007-01-01
The utility of a genotypic typing assay for Legionella pneumophila was investigated. A multiple-locus variable number of tandem repeats (VNTR) analysis (MLVA) scheme using PCR and agarose gel electrophoresis is proposed based on eight minisatellite markers. Panels of well-characterized strains were examined in a multicenter analysis to validate the assay and to compare its performance to that of other genotyping assays. Excellent typeability, reproducibility, stability, and epidemiological concordance were observed. The MLVA type or profile is composed of a string of allele numbers, corresponding to the number of repeats at each VNTR locus, separated by commas, in a predetermined order. A database containing information from 99 L. pneumophila serogroup 1 strains and four strains of other serogroups and their MLVA profiles, which can be queried online, is available from http://bacterial-genotyping.igmors.u-psud.fr/. PMID:17251393
A Fast, High Quality, and Reproducible Parallel Lagged-Fibonacci Pseudorandom Number Generator
Mascagni, Michael; Cuccaro, Steven A.; Pryor, Daniel V.; Robinson, M. L.
1995-07-01
We study the suitability of the additive lagged-Fibonacci pseudo-random number generator for parallel computation. This generator has relatively short period with respect to the size of its seed. However, the short period is more than made up for with the huge number of full-period cycles it contains. These different full period cycles are called equivalence classes. We show how to enumerate the equivalence classes and how to compute seeds to select a given equivalence class, In addition, we present some theoretical measures of quality for this generator when used in parallel. Next, we conjecture on the size of these measures of quality for this generator. Extensive empirical evidence supports this conjecture. In addition, a probabilistic interpretation of these measures leads to another conjecture similarly supported by empirical evidence. Finally we give an explicit parallelization suitable for a fully reproducible asynchronous MIMD implementation.
Jajou, Rana; de Neeling, Albert; Rasmussen, Erik Michael; Norman, Anders; Mulder, Arnout; van Hunen, Rianne; de Vries, Gerard; Haddad, Walid; Anthony, Richard; Lillebaek, Troels; van der Hoek, Wim; van Soolingen, Dick
In many countries,Mycobacterium tuberculosisisolates are routinely subjected to variable-number tandem-repeat (VNTR) typing to investigateM. tuberculosistransmission. Unexpectedly, cross-border clusters were identified among African refugees in the Netherlands and Denmark, although transmission in
Directory of Open Access Journals (Sweden)
Thomas W R Harrop
Full Text Available Widespread use of insecticides has led to insecticide resistance in many populations of insects. In some populations, resistance has evolved to multiple pesticides. In Drosophila melanogaster, resistance to multiple classes of insecticide is due to the overexpression of a single cytochrome P450 gene, Cyp6g1. Overexpression of Cyp6g1 appears to have evolved in parallel in Drosophila simulans, a sibling species of D. melanogaster, where it is also associated with insecticide resistance. However, it is not known whether the ability of the CYP6G1 enzyme to provide resistance to multiple insecticides evolved recently in D. melanogaster or if this function is present in all Drosophila species. Here we show that duplication of the Cyp6g1 gene occurred at least four times during the evolution of different Drosophila species, and the ability of CYP6G1 to confer resistance to multiple insecticides exists in D. melanogaster and D. simulans but not in Drosophila willistoni or Drosophila virilis. In D. virilis, which has multiple copies of Cyp6g1, one copy confers resistance to DDT and another to nitenpyram, suggesting that the divergence of protein sequence between copies subsequent to the duplication affected the activity of the enzyme. All orthologs tested conferred resistance to one or more insecticides, suggesting that CYP6G1 had the capacity to provide resistance to anthropogenic chemicals before they existed. Finally, we show that expression of Cyp6g1 in the Malpighian tubules, which contributes to DDT resistance in D. melanogaster, is specific to the D. melanogaster-D. simulans lineage. Our results suggest that a combination of gene duplication, regulatory changes and protein coding changes has taken place at the Cyp6g1 locus during evolution and this locus may play a role in providing resistance to different environmental toxins in different Drosophila species.
Hu, Yuan; Li, Bo Qing; Jin, Da Zhi; He, Li Hua; Tao, Xiao Xia; Zhang, Jian Zhong
2015-12-01
To develop a multiple-locus variable-number tandem-repeat (VNTR) analysis (MLVA) assay for Acinetobacter pittii typing. Polymorphic VNTRs were searched by Tandem Repeats Finder. The distribution and polymorphism of each VNTR locus were analyzed in all the A. pittii genomes deposited in the NCBI genome database by BLAST and were evaluated with a collection of 20 well-characterized clinical A. pittii strains and one reference strain. The MLVA assay was compared with pulsed-field gel electrophoresis (PFGE) for discriminating A. pittii isolates. Ten VNTR loci were identified upon bioinformatic screening of A. pittii genomes, but only five of them showed full amplifiability and good polymorphism. Therefore, an MLVA assay composed of five VNTR loci was developed. The typeability, reproducibility, stability, discriminatory power, and epidemiological concordance were excellent. Compared with PFGE, the new optimized MLVA typing scheme provided the same and even greater discrimination. Compared with PFGE, MLVA typing is a faster and more standardized alternative for studying the genetic relatedness of A. pittii isolates in disease surveillance and outbreak investigation. Copyright © 2015 The Editorial Board of Biomedical and Environmental Sciences. Published by China CDC. All rights reserved.
Directory of Open Access Journals (Sweden)
Ben S Cooper
Full Text Available An important determinant of a pathogen's success is the rate at which it is transmitted from infected to susceptible hosts. Although there are anecdotal reports that methicillin-resistant Staphylococcus aureus (MRSA clones vary in their transmissibility in hospital settings, attempts to quantify such variation are lacking for common subtypes, as are methods for addressing this question using routinely-collected MRSA screening data in endemic settings. Here we present a method to quantify the time-varying transmissibility of different subtypes of common bacterial nosocomial pathogens using routine surveillance data. The method adapts approaches for estimating reproduction numbers based on the probabilistic reconstruction of epidemic trees, but uses relative hazards rather than serial intervals to assign probabilities to different sources for observed transmission events. The method is applied to data collected as part of a retrospective observational study of a concurrent MRSA outbreak in the United Kingdom with dominant endemic MRSA clones (ST22 and ST36 and an Asian ST239 MRSA strain (ST239-TW in two linked adult intensive care units, and compared with an approach based on a fully parametric transmission model. The results provide support for the hypothesis that the clones responded differently to an infection control measure based on the use of topical antiseptics, which was more effective at reducing transmission of endemic clones. They also suggest that in one of the two ICUs patients colonized or infected with the ST239-TW MRSA clone had consistently higher risks of transmitting MRSA to patients free of MRSA. These findings represent some of the first quantitative evidence of enhanced transmissibility of a pandemic MRSA lineage, and highlight the potential value of tailoring hospital infection control measures to specific pathogen subtypes.
Tamayo, F; Casals-Coll, M; Sánchez-Benavides, G; Quintana, M; Manero, R M; Rognoni, T; Calvo, L; Palomo, R; Aranciva, F; Peña-Casanova, J
2012-01-01
Verbal and visuospatial span, Letter-Number Sequencing, Trail Making Test, and Symbol Digit Modalities Test are frequently used in clinical practice to assess attention, executive functions and memory. In the present study, as part of the Spanish normative studies of NEURONORMA young adults Project, normative data adjusted by age and education are provided for digits, Corsi Block-Tapping Task, Letter-Number Sequencing, Trail Making Test, and Symbol Digit Modalities Test. The sample consisted of 179 participants from 18 to 49 years old, who were cognitively normal. Tables to convert raw scores to scaled scores are provided. Age and education adjusted scores are provided by applying linear regressions. Education affected scores in most of the attention tests; age was found to be related to the visuospatial span and to speed of visuomotor tracking, and there was no relationship as regards sex. The data obtained will be useful in the clinical evaluation of young Spanish adults. Copyright © 2011 Sociedad Española de Neurología. Published by Elsevier Espana. All rights reserved.
Matsumoto, Mari; Ohba, Ryuji; Yasuda, Shin-ichi; Uchida, Ken; Tanamoto, Tetsufumi; Fujita, Shinobu
2008-08-01
The demand for random numbers for security applications is increasing. A conventional random number generator using thermal noise can generate unpredictable high-quality random numbers, but the circuit is extremely large because of large amplifier circuit for a small thermal signal. On the other hand, a pseudo-random number generator is small but the quality of randomness is bad. For a small circuit and a high quality of randomness, we purpose a non-stoichiometric SixN metal-oxide-semiconductor field-effect transistor (MOSFET) noise source device. This device generates a very large noise signal without an amplifier circuit. As a result, it is shown that, utilizing a SiN MOSFET, we can attain a compact random number generator with a high generation rate near 1 Mbit/s, which is suitable for almost all security applications.
Number words and number symbols a cultural history of numbers
Menninger, Karl
1992-01-01
Classic study discusses number sequence and language and explores written numerals and computations in many cultures. "The historian of mathematics will find much to interest him here both in the contents and viewpoint, while the casual reader is likely to be intrigued by the author's superior narrative ability.
Locating multiple optima using particle swarm optimization
CSIR Research Space (South Africa)
Brits, R
2007-01-01
Full Text Available in [37]). Faure-sequences are distributed with high uniformity within a n-dimensional unit cube. Other pseudo-random uniform number generators, such as Sobol-sequences [33], may also be used. Main swarm training: In the nbest algorithm, overlapping...
Grešak, Rozalija
2015-01-01
The field of real numbers is usually constructed using Dedekind cuts. In these thesis we focus on the construction of the field of real numbers using metric completion of rational numbers using Cauchy sequences. In a similar manner we construct the field of p-adic numbers, describe some of their basic and topological properties. We follow by a construction of complex p-adic numbers and we compare them with the ordinary complex numbers. We conclude the thesis by giving a motivation for the int...
A few Smarandache Integer Sequences
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.
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...
Directory of Open Access Journals (Sweden)
MADANI Mohammed
2017-10-01
Full Text Available In this paper, a new satellite image encryption algorithm based on the combination of multiple chaotic systems and a random cyclic rotation technique is proposed. Our contribution consists in implementing three different chaotic maps (logistic, sine, and standard combined to improve the security of satellite images. Besides enhancing the encryption, the proposed algorithm also focuses on advanced efficiency of the ciphered images. Compared with classical encryption schemes based on multiple chaotic maps and the Rubik's cube rotation, our approach has not only the same merits of chaos systems like high sensitivity to initial values, unpredictability, and pseudo-randomness, but also other advantages like a higher number of permutations, better performances in Peak Signal to Noise Ratio (PSNR and a Maximum Deviation (MD.
Recommendations and illustrations for the evaluation of photonic random number generators
Hart, Joseph D.; Terashima, Yuta; Uchida, Atsushi; Baumgartner, Gerald B.; Murphy, Thomas E.; Roy, Rajarshi
2017-09-01
The never-ending quest to improve the security of digital information combined with recent improvements in hardware technology has caused the field of random number generation to undergo a fundamental shift from relying solely on pseudo-random algorithms to employing optical entropy sources. Despite these significant advances on the hardware side, commonly used statistical measures and evaluation practices remain ill-suited to understand or quantify the optical entropy that underlies physical random number generation. We review the state of the art in the evaluation of optical random number generation and recommend a new paradigm: quantifying entropy generation and understanding the physical limits of the optical sources of randomness. In order to do this, we advocate for the separation of the physical entropy source from deterministic post-processing in the evaluation of random number generators and for the explicit consideration of the impact of the measurement and digitization process on the rate of entropy production. We present the Cohen-Procaccia estimate of the entropy rate h (𝜖 ,τ ) as one way to do this. In order to provide an illustration of our recommendations, we apply the Cohen-Procaccia estimate as well as the entropy estimates from the new NIST draft standards for physical random number generators to evaluate and compare three common optical entropy sources: single photon time-of-arrival detection, chaotic lasers, and amplified spontaneous emission.
Recommendations and illustrations for the evaluation of photonic random number generators
Directory of Open Access Journals (Sweden)
Joseph D. Hart
2017-09-01
Full Text Available The never-ending quest to improve the security of digital information combined with recent improvements in hardware technology has caused the field of random number generation to undergo a fundamental shift from relying solely on pseudo-random algorithms to employing optical entropy sources. Despite these significant advances on the hardware side, commonly used statistical measures and evaluation practices remain ill-suited to understand or quantify the optical entropy that underlies physical random number generation. We review the state of the art in the evaluation of optical random number generation and recommend a new paradigm: quantifying entropy generation and understanding the physical limits of the optical sources of randomness. In order to do this, we advocate for the separation of the physical entropy source from deterministic post-processing in the evaluation of random number generators and for the explicit consideration of the impact of the measurement and digitization process on the rate of entropy production. We present the Cohen-Procaccia estimate of the entropy rate h(,τ as one way to do this. In order to provide an illustration of our recommendations, we apply the Cohen-Procaccia estimate as well as the entropy estimates from the new NIST draft standards for physical random number generators to evaluate and compare three common optical entropy sources: single photon time-of-arrival detection, chaotic lasers, and amplified spontaneous emission.
Bennett, Ruth, Ed.; And Others
An introduction to the Hupa number system is provided in this workbook, one in a series of numerous materials developed to promote the use of the Hupa language. The book is written in English with Hupa terms used only for the names of numbers. The opening pages present the numbers from 1-10, giving the numeral, the Hupa word, the English word, and…
Indian Academy of Sciences (India)
Admin
Triangular number, figurate num- ber, rangoli, Brahmagupta–Pell equation, Jacobi triple product identity. Figure 1. The first four triangular numbers. Left: Anuradha S Garge completed her PhD from. Pune University in 2008 under the supervision of Prof. S A Katre. Her research interests include K-theory and number theory.
Directory of Open Access Journals (Sweden)
Schwarzweller Christoph
2015-02-01
Full Text Available In this article we introduce Proth numbers and prove two theorems on such numbers being prime [3]. We also give revised versions of Pocklington’s theorem and of the Legendre symbol. Finally, we prove Pepin’s theorem and that the fifth Fermat number is not prime.
Implementation of LT codes based on chaos
International Nuclear Information System (INIS)
Zhou Qian; Li Liang; Chen Zengqiang; Zhao Jiaxiang
2008-01-01
Fountain codes provide an efficient way to transfer information over erasure channels like the Internet. LT codes are the first codes fully realizing the digital fountain concept. They are asymptotically optimal rateless erasure codes with highly efficient encoding and decoding algorithms. In theory, for each encoding symbol of LT codes, its degree is randomly chosen according to a predetermined degree distribution, and its neighbours used to generate that encoding symbol are chosen uniformly at random. Practical implementation of LT codes usually realizes the randomness through pseudo-randomness number generator like linear congruential method. This paper applies the pseudo-randomness of chaotic sequence in the implementation of LT codes. Two Kent chaotic maps are used to determine the degree and neighbour(s) of each encoding symbol. It is shown that the implemented LT codes based on chaos perform better than the LT codes implemented by the traditional pseudo-randomness number generator. (general)
Mendonça, J. Ricardo G.
2012-01-01
We define a new class of numbers based on the first occurrence of certain patterns of zeros and ones in the expansion of irracional numbers in a given basis and call them Sagan numbers, since they were first mentioned, in a special case, by the North-american astronomer Carl E. Sagan in his science-fiction novel "Contact." Sagan numbers hold connections with a wealth of mathematical ideas. We describe some properties of the newly defined numbers and indicate directions for further amusement.
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.
Petersen, T Kyle
2015-01-01
This text presents the Eulerian numbers in the context of modern enumerative, algebraic, and geometric combinatorics. The book first studies Eulerian numbers from a purely combinatorial point of view, then embarks on a tour of how these numbers arise in the study of hyperplane arrangements, polytopes, and simplicial complexes. Some topics include a thorough discussion of gamma-nonnegativity and real-rootedness for Eulerian polynomials, as well as the weak order and the shard intersection order of the symmetric group. The book also includes a parallel story of Catalan combinatorics, wherein the Eulerian numbers are replaced with Narayana numbers. Again there is a progression from combinatorics to geometry, including discussion of the associahedron and the lattice of noncrossing partitions. The final chapters discuss how both the Eulerian and Narayana numbers have analogues in any finite Coxeter group, with many of the same enumerative and geometric properties. There are four supplemental chapters throughout, ...
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.
Indian Academy of Sciences (India)
Transfinite Numbers. What is Infinity? S M Srivastava. In a series of revolutionary articles written during the last quarter of the nineteenth century, the great Ger- man mathematician Georg Cantor removed the age-old mistrust of infinity and created an exceptionally beau- tiful and useful theory of transfinite numbers. This is.
A high speed digital noise generator
Obrien, J.; Gaffney, B.; Liu, B.
In testing of digital signal processing hardware, a high speed pseudo-random noise generator is often required to simulate an input noise source to the hardware. This allows the hardware to be exercised in a manner analogous to actual operating conditions. In certain radar and communication environments, a noise generator operating at speeds in excess of 60 MHz may be required. In this paper, a method of generating high speed pseudo-random numbers from an arbitrarily specified distribution (Gaussian, Log-Normal, etc.) using a transformation from a uniform noise source is described. A noise generator operating at 80 MHz has been constructed. Different distributions can be readily obtained by simply changing the ROM set. The hardware and test results will be described. Using this approach, the generation of pseudo-random sequences with arbitrary distributions at word rates in excess of 200 MHz can be readily achieved.
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...
Decidability of uniform recurrence of morphic sequences
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.
Andrews, George E
1994-01-01
Although mathematics majors are usually conversant with number theory by the time they have completed a course in abstract algebra, other undergraduates, especially those in education and the liberal arts, often need a more basic introduction to the topic.In this book the author solves the problem of maintaining the interest of students at both levels by offering a combinatorial approach to elementary number theory. In studying number theory from such a perspective, mathematics majors are spared repetition and provided with new insights, while other students benefit from the consequent simpl
Barnes, John
2016-01-01
In this intriguing book, John Barnes takes us on a journey through aspects of numbers much as he took us on a geometrical journey in Gems of Geometry. Similarly originating from a series of lectures for adult students at Reading and Oxford University, this book touches a variety of amusing and fascinating topics regarding numbers and their uses both ancient and modern. The author intrigues and challenges his audience with both fundamental number topics such as prime numbers and cryptography, and themes of daily needs and pleasures such as counting one's assets, keeping track of time, and enjoying music. Puzzles and exercises at the end of each lecture offer additional inspiration, and numerous illustrations accompany the reader. Furthermore, a number of appendices provides in-depth insights into diverse topics such as Pascal’s triangle, the Rubik cube, Mersenne’s curious keyboards, and many others. A theme running through is the thought of what is our favourite number. Written in an engaging and witty sty...
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}.
Number names and number understanding
DEFF Research Database (Denmark)
Ejersbo, Lisser Rye; Misfeldt, Morten
2014-01-01
This paper concerns the results from the first year of a three-year research project involving the relationship between Danish number names and their corresponding digits in the canonical base 10 system. The project aims to develop a system to help the students’ understanding of the base 10 syste...... the Danish number names are more complicated than in other languages. Keywords: A research project in grade 0 and 1th in a Danish school, Base-10 system, two-digit number names, semiotic, cognitive perspectives....
Directory of Open Access Journals (Sweden)
Theodore M. Porter
2012-12-01
Full Text Available The struggle over cure rate measures in nineteenth-century asylums provides an exemplary instance of how, when used for official assessments of institutions, these numbers become sites of contestation. The evasion of goals and corruption of measures tends to make these numbers “funny” in the sense of becoming dis-honest, while the mismatch between boring, technical appearances and cunning backstage manipulations supplies dark humor. The dangers are evident in recent efforts to decentralize the functions of governments and corporations using incen-tives based on quantified targets.
Murty, M Ram
2014-01-01
This book provides an introduction to the topic of transcendental numbers for upper-level undergraduate and graduate students. The text is constructed to support a full course on the subject, including descriptions of both relevant theorems and their applications. While the first part of the book focuses on introducing key concepts, the second part presents more complex material, including applications of Baker’s theorem, Schanuel’s conjecture, and Schneider’s theorem. These later chapters may be of interest to researchers interested in examining the relationship between transcendence and L-functions. Readers of this text should possess basic knowledge of complex analysis and elementary algebraic number theory.
Indian Academy of Sciences (India)
this is a characteristic difference between finite and infinite sets and created an immensely useful branch of mathematics based on this idea which had a great impact on the whole of mathe- matics. For example, the question of what is a number (finite or infinite) is almost a philosophical one. However Cantor's work turned it ...
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.
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.
A light weight secure image encryption scheme based on chaos & DNA computing
Directory of Open Access Journals (Sweden)
Bhaskar Mondal
2017-10-01
Full Text Available This paper proposed a new light weight secure cryptographic scheme for secure image communication. In this scheme the plain image is permuted first using a sequence of pseudo random number (PRN and encrypted by DeoxyriboNucleic Acid (DNA computation. Two PRN sequences are generated by a Pseudo Random Number Generator (PRNG based on cross coupled chaotic logistic map using two sets of keys. The first PRN sequence is used for permuting the plain image whereas the second PRN sequence is used for generating random DNA sequence. The number of rounds of permutation and encryption may be variable to increase security. The scheme is proposed for gray label images but the scheme may be extended for color images and text data. Simulation results exhibit that the proposed scheme can defy any kind of attack.
Decoding sequence learning from single-trial intracranial EEG in humans.
Directory of Open Access Journals (Sweden)
Marzia De Lucia
Full Text Available We propose and validate a multivariate classification algorithm for characterizing changes in human intracranial electroencephalographic data (iEEG after learning motor sequences. The algorithm is based on a Hidden Markov Model (HMM that captures spatio-temporal properties of the iEEG at the level of single trials. Continuous intracranial iEEG was acquired during two sessions (one before and one after a night of sleep in two patients with depth electrodes implanted in several brain areas. They performed a visuomotor sequence (serial reaction time task, SRTT using the fingers of their non-dominant hand. Our results show that the decoding algorithm correctly classified single iEEG trials from the trained sequence as belonging to either the initial training phase (day 1, before sleep or a later consolidated phase (day 2, after sleep, whereas it failed to do so for trials belonging to a control condition (pseudo-random sequence. Accurate single-trial classification was achieved by taking advantage of the distributed pattern of neural activity. However, across all the contacts the hippocampus contributed most significantly to the classification accuracy for both patients, and one fronto-striatal contact for one patient. Together, these human intracranial findings demonstrate that a multivariate decoding approach can detect learning-related changes at the level of single-trial iEEG. Because it allows an unbiased identification of brain sites contributing to a behavioral effect (or experimental condition at the level of single subject, this approach could be usefully applied to assess the neural correlates of other complex cognitive functions in patients implanted with multiple electrodes.
Experimental Method for Plotting S-N Curve with a Small Number of Specimens
Directory of Open Access Journals (Sweden)
Strzelecki Przemysław
2016-12-01
Full Text Available The study presents two approaches to plotting an S-N curve based on the experimental results. The first approach is commonly used by researchers and presented in detail in many studies and standard documents. The model uses a linear regression whose parameters are estimated by using the least squares method. A staircase method is used for an unlimited fatigue life criterion. The second model combines the S-N curve defined as a straight line and the record of random occurrence of the fatigue limit. A maximum likelihood method is used to estimate the S-N curve parameters. Fatigue data for C45+C steel obtained in the torsional bending test were used to compare the estimated S-N curves. For pseudo-random numbers generated by using the Mersenne Twister algorithm, the estimated S-N curve for 10 experimental results plotted by using the second model, estimates the fatigue life in the scatter band of the factor 3. The result gives good approximation, especially regarding the time required to plot the S-N curve.
Repdigits in k-Lucas sequences
Indian Academy of Sciences (India)
57(2) 2000 243-254) proved that 11 is the largest number with only one distinct digit (the so-called repdigit) in the sequence ( L n ( 2 ) ) n . In this paper, we address a similar problem in the family of -Lucas sequences. We also show that the -Lucas sequences have similar properties to those of -Fibonacci sequences ...
Pseudo-Random Modulation of a Laser Diode for Generating Ultrasonic Longitudinal Waves
Madaras, Eric I.; Anatasi, Robert F.
2004-01-01
Laser generated ultrasound systems have historically been more complicated and expensive than conventional piezoelectric based systems, and this fact has relegated the acceptance of laser based systems to niche applications for which piezoelectric based systems are less suitable. Lowering system costs, while improving throughput, increasing ultrasound signal levels, and improving signal-to-noise are goals which will help increase the general acceptance of laser based ultrasound. One current limitation with conventional laser generated ultrasound is a material s damage threshold limit. Increasing the optical power to generate more signal eventually damages the material being tested due to rapid, high heating. Generation limitations for laser based ultrasound suggests the use of pulse modulation techniques as an alternate generation method. Pulse modulation techniques can spread the laser energy over time or space, thus reducing laser power densities and minimizing damage. Previous experiments by various organizations using spatial or temporal pulse modulation have been shown to generate detectable surface, plate, and bulk ultrasonic waves with narrow frequency bandwidths . Using narrow frequency bandwidths improved signal detectability, but required the use of expensive and powerful lasers and opto-electronic systems. The use of a laser diode to generate ultrasound is attractive because of its low cost, small size, light weight, simple optics and modulation capability. The use of pulse compression techniques should allow certain types of laser diodes to produce usable ultrasonic signals. The method also does not need to be limited to narrow frequency bandwidths. The method demonstrated here uses a low power laser diode (approximately 150 mW) that is modulated by controlling the diode s drive current and the resulting signal is recovered by cross correlation. A potential application for this system which is briefly demonstrated is in detecting signals in thick composite materials where attenuation is high and signal amplitude and bandwidth are at a premium.
Neuhaus, Christine; Eisenberger, Tobias; Decker, Christian; Nagl, Sandra; Blank, Cornelia; Pfister, Markus; Kennerknecht, Ingo; Müller-Hofstede, Cornelie; Charbel Issa, Peter; Heller, Raoul; Beck, Bodo; Rüther, Klaus; Mitter, Diana; Rohrschneider, Klaus; Steinhauer, Ute; Korbmacher, Heike M; Huhle, Dagmar; Elsayed, Solaf M; Taha, Hesham M; Baig, Shahid M; Stöhr, Heidi; Preising, Markus; Markus, Susanne; Moeller, Fabian; Lorenz, Birgit; Nagel-Wolfrum, Kerstin; Khan, Arif O; Bolz, Hanno J
2017-09-01
Combined retinal degeneration and sensorineural hearing impairment is mostly due to autosomal recessive Usher syndrome (USH1: congenital deafness, early retinitis pigmentosa (RP); USH2: progressive hearing impairment, RP). Sanger sequencing and NGS of 112 genes (Usher syndrome, nonsyndromic deafness, overlapping conditions), MLPA, and array-CGH were conducted in 138 patients clinically diagnosed with Usher syndrome. A molecular diagnosis was achieved in 97% of both USH1 and USH2 patients, with biallelic mutations in 97% (USH1) and 90% (USH2), respectively. Quantitative readout reliably detected CNVs (confirmed by MLPA or array-CGH), qualifying targeted NGS as one tool for detecting point mutations and CNVs. CNVs accounted for 10% of identified USH2A alleles, often in trans to seemingly monoallelic point mutations. We demonstrate PTC124-induced read-through of the common p.Trp3955* nonsense mutation (13% of detected USH2A alleles), a potential therapy target. Usher gene mutations were found in most patients with atypical Usher syndrome, but the diagnosis was adjusted in case of double homozygosity for mutations in OTOA and NR2E3 , genes implicated in isolated deafness and RP. Two patients with additional enamel dysplasia had biallelic PEX26 mutations, for the first time linking this gene to Heimler syndrome. Targeted NGS not restricted to Usher genes proved beneficial in uncovering conditions mimicking Usher syndrome.
Energy Technology Data Exchange (ETDEWEB)
Nelson, R.N. (ed.)
1985-05-01
This publication lists all report number codes processed by the Office of Scientific and Technical Information. The report codes are substantially based on the American National Standards Institute, Standard Technical Report Number (STRN)-Format and Creation Z39.23-1983. The Standard Technical Report Number (STRN) provides one of the primary methods of identifying a specific technical report. The STRN consists of two parts: The report code and the sequential number. The report code identifies the issuing organization, a specific program, or a type of document. The sequential number, which is assigned in sequence by each report issuing entity, is not included in this publication. Part I of this compilation is alphabetized by report codes followed by issuing installations. Part II lists the issuing organization followed by the assigned report code(s). In both Parts I and II, the names of issuing organizations appear for the most part in the form used at the time the reports were issued. However, for some of the more prolific installations which have had name changes, all entries have been merged under the current name.
International Nuclear Information System (INIS)
Nelson, R.N.
1985-05-01
This publication lists all report number codes processed by the Office of Scientific and Technical Information. The report codes are substantially based on the American National Standards Institute, Standard Technical Report Number (STRN)-Format and Creation Z39.23-1983. The Standard Technical Report Number (STRN) provides one of the primary methods of identifying a specific technical report. The STRN consists of two parts: The report code and the sequential number. The report code identifies the issuing organization, a specific program, or a type of document. The sequential number, which is assigned in sequence by each report issuing entity, is not included in this publication. Part I of this compilation is alphabetized by report codes followed by issuing installations. Part II lists the issuing organization followed by the assigned report code(s). In both Parts I and II, the names of issuing organizations appear for the most part in the form used at the time the reports were issued. However, for some of the more prolific installations which have had name changes, all entries have been merged under the current name
International Nuclear Information System (INIS)
Falcon, Sergio; Plaza, Angel
2007-01-01
We introduce a general Fibonacci sequence that generalizes, between others, both the classic Fibonacci sequence and the Pell sequence. These general kth Fibonacci numbers {F k,n } n=0 ∼ were found by studying the recursive application of two geometrical transformations used in the well-known four-triangle longest-edge (4TLE) partition. Many properties of these numbers are deduce directly from elementary matrix algebra
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 ...
A quick and easy improvement of Monte Carlo codes for simulation
Lebrere, A.; Talhi, R.; Tripathy, M.; Pyée, M.
The simulation of trials of independent random variables of given distribution is a critical element of running Monte-Carlo codes. This is usually performed by using pseudo-random number generators (and in most cases linearcongruential ones). We present here an alternative way to generate sequences with given statistical properties. This sequences are purely deterministic and are given by closed formulae, and can give in some cases better results than classical generators.
Unsolved problems in number theory
Guy, Richard K
1994-01-01
Unsolved Problems in Number Theory contains discussions of hundreds of open questions, organized into 185 different topics. They represent numerous aspects of number theory and are organized into six categories: prime numbers, divisibility, additive number theory, Diophantine equations, sequences of integers, and miscellaneous. To prevent repetition of earlier efforts or duplication of previously known results, an extensive and up-to-date collection of references follows each problem. In the second edition, not only extensive new material has been added, but corrections and additions have been included throughout the book.
Random number generation and creativity.
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.
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.
Chameleon sequences in neurodegenerative diseases.
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.
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.
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.
Compact flow diagrams for state sequences
Buchin, K.A.; Buchin, M.E.; Gudmundsson, J.; Horton, M.J.; Sijben, S.
2016-01-01
We introduce the concept of compactly representing a large number of state sequences, e.g., sequences of activities, as a flow diagram. We argue that the flow diagram representation gives an intuitive summary that allows the user to detect patterns among large sets of state sequences. Simplified,
Yaroslavsky, Leonid P.
1996-11-01
We show that one can treat pseudo-random generators, evolutionary models of texture images, iterative local adaptive filters for image restoration and enhancement and growth models in biology and material sciences in a unified way as special cases of dynamic systems with a nonlinear feedback.
Computational analysis of sequence selection mechanisms.
Meyerguz, Leonid; Grasso, Catherine; Kleinberg, Jon; Elber, Ron
2004-04-01
Mechanisms leading to gene variations are responsible for the diversity of species and are important components of the theory of evolution. One constraint on gene evolution is that of protein foldability; the three-dimensional shapes of proteins must be thermodynamically stable. We explore the impact of this constraint and calculate properties of foldable sequences using 3660 structures from the Protein Data Bank. We seek a selection function that receives sequences as input, and outputs survival probability based on sequence fitness to structure. We compute the number of sequences that match a particular protein structure with energy lower than the native sequence, the density of the number of sequences, the entropy, and the "selection" temperature. The mechanism of structure selection for sequences longer than 200 amino acids is approximately universal. For shorter sequences, it is not. We speculate on concrete evolutionary mechanisms that show this behavior.
An upper bound on the number of errors corrected by a convolutional code
DEFF Research Database (Denmark)
Justesen, Jørn
2000-01-01
The number of errors that a convolutional codes can correct in a segment of the encoded sequence is upper bounded by the number of distinct syndrome sequences of the relevant length.......The number of errors that a convolutional codes can correct in a segment of the encoded sequence is upper bounded by the number of distinct syndrome sequences of the relevant length....
Static multiplicities in heterogeneous azeotropic distillation sequences
DEFF Research Database (Denmark)
Esbjerg, Klavs; Andersen, Torben Ravn; Jørgensen, Sten Bay
1998-01-01
In this paper the results of a bifurcation analysis on heterogeneous azeotropic distillation sequences are given. Two sequences suitable for ethanol dehydration are compared: The 'direct' and the 'indirect' sequence. It is shown, that the two sequences, despite their similarities, exhibit very...... different static behavior. The method of Petlyuk and Avet'yan (1971), Bekiaris et al. (1993), which assumes infinite reflux and infinite number of stages, is extended to and applied on heterogeneous azeotropic distillation sequences. The predictions are substantiated through simulations. The static sequence...
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
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
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)
Atashpendar, Arshia; Schilling, Tanja; Voigtmann, Thomas
2016-10-01
We analyze the structure of the state space of chess by means of transition path sampling Monte Carlo simulations. Based on the typical number of moves required to transpose a given configuration of chess pieces into another, we conclude that the state space consists of several pockets between which transitions are rare. Skilled players explore an even smaller subset of positions that populate some of these pockets only very sparsely. These results suggest that the usual measures to estimate both the size of the state space and the size of the tree of legal moves are not unique indicators of the complexity of the game, but that considerations regarding the connectedness of states are equally important.
Supplementary data: Table 1. Identification numbers of sequences ...
Indian Academy of Sciences (India)
Lenovo
. -. -. SP1. Stimulating protein 1, ubiquitous zinc finger transcription factor. +. +. GSH2. Homeodomain transcription factor Gsh-2. -. +. RUSH. SWI/SNF related nucleophosphoproteins with a RING finger DNA binding motif. +. +. TAL1. T-cell acute ...
The Fibonacci numbers of certain subgraphs of circulant graphs
Directory of Open Access Journals (Sweden)
Loiret Alejandría Dosal-Trujillo
2015-11-01
We prove that the total number of independent vertex sets of the family of graphs Cn[r] for all n≥r+1, and for several subgraphs of this family is completely determined by some sequences which are constructed recursively like the Fibonacci and Lucas sequences, even more, these new sequences generalize the Fibonacci and Lucas sequences.
Multineuronal Spike Sequences Repeat with Millisecond Precision
Directory of Open Access Journals (Sweden)
Koki eMatsumoto
2013-06-01
Full Text Available Cortical microcircuits are nonrandomly wired by neurons. As a natural consequence, spikes emitted by microcircuits are also nonrandomly patterned in time and space. One of the prominent spike organizations is a repetition of fixed patterns of spike series across multiple neurons. However, several questions remain unsolved, including how precisely spike sequences repeat, how the sequences are spatially organized, how many neurons participate in sequences, and how different sequences are functionally linked. To address these questions, we monitored spontaneous spikes of hippocampal CA3 neurons ex vivo using a high-speed functional multineuron calcium imaging technique that allowed us to monitor spikes with millisecond resolution and to record the location of spiking and nonspiking neurons. Multineuronal spike sequences were overrepresented in spontaneous activity compared to the statistical chance level. Approximately 75% of neurons participated in at least one sequence during our observation period. The participants were sparsely dispersed and did not show specific spatial organization. The number of sequences relative to the chance level decreased when larger time frames were used to detect sequences. Thus, sequences were precise at the millisecond level. Sequences often shared common spikes with other sequences; parts of sequences were subsequently relayed by following sequences, generating complex chains of multiple sequences.
A new pseudorandom number generator based on a complex number chaotic equation
International Nuclear Information System (INIS)
Liu Yang; Tong Xiao-Jun
2012-01-01
In recent years, various chaotic equation based pseudorandom number generators have been proposed. However, the chaotic equations are all defined in the real number field. In this paper, an equation is proposed and proved to be chaotic in the imaginary axis. And a pseudorandom number generator is constructed based on the chaotic equation. The alteration of the definitional domain of the chaotic equation from the real number field to the complex one provides a new approach to the construction of chaotic equations, and a new method to generate pseudorandom number sequences accordingly. Both theoretical analysis and experimental results show that the sequences generated by the proposed pseudorandom number generator possess many good properties
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.
Richardson, Thomas M.
2014-01-01
We introduce the super Patalan numbers, a generalization of the super Catalan numbers in the sense of Gessel, and prove a number of properties analagous to those of the super Catalan numbers. The super Patalan numbers generalize the super Catalan numbers similarly to how the Patalan numbers generalize the Catalan numbers.
Analysis of a Scenario for Chaotic Quantal Slowing Down of Inspiration
2013-01-01
On exposure to opiates, preparations from rat brain stems have been observed to continue to produce regular expiratory signals, but to fail to produce some inspiratory signals. The numbers of expirations between two successive inspirations form an apparently random sequence. Here, we propose an explanation based on the qualitative theory of dynamical systems. A relatively simple scenario for the dynamics of interaction between the generators of expiratory and inspiratory signals produces pseudo-random behaviour of the type observed. PMID:24040967
Graphical User Interface and Microprocessor Control Enhancement of a Pseudorandom Code Generator
National Research Council Canada - National Science Library
Kos, John
1999-01-01
.... This thesis addresses the issue of providing automated computer control to previously built, manually controlled hardware incorporating the Stanford Telecom STEL-1032 Pseudo-Random Number (PRN) Coder...
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.
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...
Some Remarks on Iterated Maps of Natural Numbers
Indian Academy of Sciences (India)
IAS Admin
happy numbers, Fibonacci Quart., Vol.41, 2003, No.4, pp.301–306,. 2003. [7]. H G Grundman and E A Teeple, Sequences of generalized happy numbers with small bases, J. Integer Seq., Vol.10, No.1, Article 07.1.8,. 6, 2007. [8]. H G Grundman and E A Teeple, Sequences of consecutive happy numbers, Rocky Mountain J.
Extended substitution-diffusion based image cipher using chaotic standard map
Kumar, Anil; Ghose, M. K.
2011-01-01
This paper proposes an extended substitution-diffusion based image cipher using chaotic standard map [1] and linear feedback shift register to overcome the weakness of previous technique by adding nonlinearity. The first stage consists of row and column rotation and permutation which is controlled by the pseudo-random sequences which is generated by standard chaotic map and linear feedback shift register, second stage further diffusion and confusion is obtained in the horizontal and vertical pixels by mixing the properties of the horizontally and vertically adjacent pixels, respectively, with the help of chaotic standard map. The number of rounds in both stage are controlled by combination of pseudo-random sequence and original image. The performance is evaluated from various types of analysis such as entropy analysis, difference analysis, statistical analysis, key sensitivity analysis, key space analysis and speed analysis. The experimental results illustrate that performance of this is highly secured and fast.
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.
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)
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
Occupational Sequences: Auto Engines 1. AT 121.
Korb, A. W.; And Others
In an attempt to individualize an automotive course, the Vocational-Technical Division of Northern Montana College has developed Occupational Sequences for an engine rebuilding course. Occupational Sequences, a learning or teaching aid, is an analysis of numbered operations involved in engine rebuilding. Job sheets, included in the book, provide a…
Sir Robert Sidney’s Poems Revisited: the alternative sequence
Relvas, Maria de Jesus C.
1997-01-01
The essay approaches the lyric sequence written by Sir Robert Sidney (1563-1626) in the Elizabethan age, by mainly exploring its unique formal structure, which encloses an alternative sequence formed by a re-numbering of several poems.
Nonparametric combinatorial sequence models.
Wauthier, Fabian L; Jordan, Michael I; Jojic, Nebojsa
2011-11-01
This work considers biological sequences that exhibit combinatorial structures in their composition: groups of positions of the aligned sequences are "linked" and covary as one unit across sequences. If multiple such groups exist, complex interactions can emerge between them. Sequences of this kind arise frequently in biology but methodologies for analyzing them are still being developed. This article presents a nonparametric prior on sequences which allows combinatorial structures to emerge and which induces a posterior distribution over factorized sequence representations. We carry out experiments on three biological sequence families which indicate that combinatorial structures are indeed present and that combinatorial sequence models can more succinctly describe them than simpler mixture models. We conclude with an application to MHC binding prediction which highlights the utility of the posterior distribution over sequence representations induced by the prior. By integrating out the posterior, our method compares favorably to leading binding predictors.
Random Generators and Normal Numbers
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...
Next Generation DNA Sequencing and the Future of Genomic Medicine
Anderson, Matthew W.; Schrijver, Iris
2010-01-01
In the years since the first complete human genome sequence was reported, there has been a rapid development of technologies to facilitate high-throughput sequence analysis of DNA (termed “next-generation” sequencing). These novel approaches to DNA sequencing offer the promise of complete genomic analysis at a cost feasible for routine clinical diagnostics. However, the ability to more thoroughly interrogate genomic sequence raises a number of important issues with regard to result interpreta...
Directory of Open Access Journals (Sweden)
T. Pathinathan
2015-01-01
Full Text Available In this paper we define diamond fuzzy number with the help of triangular fuzzy number. We include basic arithmetic operations like addition, subtraction of diamond fuzzy numbers with examples. We define diamond fuzzy matrix with some matrix properties. We have defined Nested diamond fuzzy number and Linked diamond fuzzy number. We have further classified Right Linked Diamond Fuzzy number and Left Linked Diamond Fuzzy number. Finally we have verified the arithmetic operations for the above mentioned types of Diamond Fuzzy Numbers.
Koninck, Jean-Marie De
2009-01-01
Who would have thought that listing the positive integers along with their most remarkable properties could end up being such an engaging and stimulating adventure? The author uses this approach to explore elementary and advanced topics in classical number theory. A large variety of numbers are contemplated: Fermat numbers, Mersenne primes, powerful numbers, sublime numbers, Wieferich primes, insolite numbers, Sastry numbers, voracious numbers, to name only a few. The author also presents short proofs of miscellaneous results and constantly challenges the reader with a variety of old and new n
Genome Sequences of Oryza Species
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.
Genome Sequences of Oryza Species
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.
Long sequence correlation coprocessor
Gage, Douglas W.
1994-09-01
A long sequence correlation coprocessor (LSCC) accelerates the bitwise correlation of arbitrarily long digital sequences by calculating in parallel the correlation score for 16, for example, adjacent bit alignments between two binary sequences. The LSCC integrated circuit is incorporated into a computer system with memory storage buffers and a separate general purpose computer processor which serves as its controller. Each of the LSCC's set of sequential counters simultaneously tallies a separate correlation coefficient. During each LSCC clock cycle, computer enable logic associated with each counter compares one bit of a first sequence with one bit of a second sequence to increment the counter if the bits are the same. A shift register assures that the same bit of the first sequence is simultaneously compared to different bits of the second sequence to simultaneously calculate the correlation coefficient by the different counters to represent different alignments of the two sequences.
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.
Anomaly Detection in Sequences
National Aeronautics and Space Administration — We present a set of novel algorithms which we call sequenceMiner, that detect and characterize anomalies in large sets of high-dimensional symbol sequences that...
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.
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....
Arbitrarily accurate twin composite π -pulse sequences
Torosov, Boyan T.; Vitanov, Nikolay V.
2018-04-01
We present three classes of symmetric broadband composite pulse sequences. The composite phases are given by analytic formulas (rational fractions of π ) valid for any number of constituent pulses. The transition probability is expressed by simple analytic formulas and the order of pulse area error compensation grows linearly with the number of pulses. Therefore, any desired compensation order can be produced by an appropriate composite sequence; in this sense, they are arbitrarily accurate. These composite pulses perform equally well as or better than previously published ones. Moreover, the current sequences are more flexible as they allow total pulse areas of arbitrary integer multiples of π .
Burkhart, Jerry
2009-01-01
Prime numbers are often described as the "building blocks" of natural numbers. This article shows how the author and his students took this idea literally by using prime factorizations to build numbers with blocks. In this activity, students explore many concepts of number theory, including the relationship between greatest common factors and…
Vazzana, Anthony; Garth, David
2007-01-01
One of the oldest branches of mathematics, number theory is a vast field devoted to studying the properties of whole numbers. Offering a flexible format for a one- or two-semester course, Introduction to Number Theory uses worked examples, numerous exercises, and two popular software packages to describe a diverse array of number theory topics.
Sequencing intractable DNA to close microbial genomes.
Directory of Open Access Journals (Sweden)
Richard A Hurt
Full Text Available Advancement in high throughput DNA sequencing technologies has supported a rapid proliferation of microbial genome sequencing projects, providing the genetic blueprint for in-depth studies. Oftentimes, difficult to sequence regions in microbial genomes are ruled "intractable" resulting in a growing number of genomes with sequence gaps deposited in databases. A procedure was developed to sequence such problematic regions in the "non-contiguous finished" Desulfovibrio desulfuricans ND132 genome (6 intractable gaps and the Desulfovibrio africanus genome (1 intractable gap. The polynucleotides surrounding each gap formed GC rich secondary structures making the regions refractory to amplification and sequencing. Strand-displacing DNA polymerases used in concert with a novel ramped PCR extension cycle supported amplification and closure of all gap regions in both genomes. The developed procedures support accurate gene annotation, and provide a step-wise method that reduces the effort required for genome finishing.
Sequencing Intractable DNA to Close Microbial Genomes
Energy Technology Data Exchange (ETDEWEB)
Hurt, Jr., Richard Ashley [ORNL; Brown, Steven D [ORNL; Podar, Mircea [ORNL; Palumbo, Anthony Vito [ORNL; Elias, Dwayne A [ORNL
2012-01-01
Advancement in high throughput DNA sequencing technologies has supported a rapid proliferation of microbial genome sequencing projects, providing the genetic blueprint for for in-depth studies. Oftentimes, difficult to sequence regions in microbial genomes are ruled intractable resulting in a growing number of genomes with sequence gaps deposited in databases. A procedure was developed to sequence such difficult regions in the non-contiguous finished Desulfovibrio desulfuricans ND132 genome (6 intractable gaps) and the Desulfovibrio africanus genome (1 intractable gap). The polynucleotides surrounding each gap formed GC rich secondary structures making the regions refractory to amplification and sequencing. Strand-displacing DNA polymerases used in concert with a novel ramped PCR extension cycle supported amplification and closure of all gap regions in both genomes. These developed procedures support accurate gene annotation, and provide a step-wise method that reduces the effort required for genome finishing.
On the number of special numbers
Indian Academy of Sciences (India)
without loss of any generality to be the first k primes), then the equation a + b = c has .... This is an elementary exercise in partial summation (see [12]). Thus ... This is easily done by inserting a stronger form of the prime number theorem into the.
Siegel, Z.; Siegel, Edward Carl-Ludwig
2011-03-01
RANDOMNESS of Numbers cognitive-semantics DEFINITION VIA Cognition QUERY: WHAT???, NOT HOW?) VS. computer-``science" mindLESS number-crunching (Harrel-Sipser-...) algorithmics Goldreich "PSEUDO-randomness"[Not.AMS(02)] mea-culpa is ONLY via MAXWELL-BOLTZMANN CLASSICAL-STATISTICS(NOT FDQS!!!) "hot-plasma" REPULSION VERSUS Newcomb(1881)-Weyl(1914;1916)-Benford(1938) "NeWBe" logarithmic-law digit-CLUMPING/ CLUSTERING NON-Randomness simple Siegel[AMS Joint.Mtg.(02)-Abs. # 973-60-124] algebraic-inversion to THE QUANTUM and ONLY BEQS preferentially SEQUENTIALLY lower-DIGITS CLUMPING/CLUSTERING with d = 0 BEC, is ONLY VIA Siegel-Baez FUZZYICS=CATEGORYICS (SON OF TRIZ)/"Category-Semantics"(C-S), latter intersection/union of Lawvere(1964)-Siegel(1964)] category-theory (matrix: MORPHISMS V FUNCTORS) "+" cognitive-semantics'' (matrix: ANTONYMS V SYNONYMS) yields Siegel-Baez FUZZYICS=CATEGORYICS/C-S tabular list-format matrix truth-table analytics: MBCS RANDOMNESS TRUTH/EMET!!!
IMPLEMENTATION OF NEURAL - CRYPTOGRAPHIC SYSTEM USING FPGA
Directory of Open Access Journals (Sweden)
KARAM M. Z. OTHMAN
2011-08-01
Full Text Available Modern cryptography techniques are virtually unbreakable. As the Internet and other forms of electronic communication become more prevalent, electronic security is becoming increasingly important. Cryptography is used to protect e-mail messages, credit card information, and corporate data. The design of the cryptography system is a conventional cryptography that uses one key for encryption and decryption process. The chosen cryptography algorithm is stream cipher algorithm that encrypt one bit at a time. The central problem in the stream-cipher cryptography is the difficulty of generating a long unpredictable sequence of binary signals from short and random key. Pseudo random number generators (PRNG have been widely used to construct this key sequence. The pseudo random number generator was designed using the Artificial Neural Networks (ANN. The Artificial Neural Networks (ANN providing the required nonlinearity properties that increases the randomness statistical properties of the pseudo random generator. The learning algorithm of this neural network is backpropagation learning algorithm. The learning process was done by software program in Matlab (software implementation to get the efficient weights. Then, the learned neural network was implemented using field programmable gate array (FPGA.
Directory of Open Access Journals (Sweden)
Roman Senkerik
2016-01-01
Full Text Available In this paper, evolutionary technique Differential Evolution (DE is used for the evolutionary tuning of controller parameters for the stabilization of selected discrete chaotic system, which is the two-dimensional Lozi map. The novelty of the approach is that the selected controlled discrete dissipative chaotic system is used within Chaos enhanced heuristic concept as the chaotic pseudo-random number generator to drive the mutation and crossover process in the DE. The idea was to utilize the hidden chaotic dynamics in pseudo-random sequences given by chaotic map to help Differential evolution algorithm in searching for the best controller settings for the same chaotic system. The optimizations were performed for three different required final behavior of the chaotic system, and two types of developed cost function. To confirm the robustness of presented approach, comparisons with canonical DE strategy and PSO algorithm have been performed.
A fast image encryption system based on chaotic maps with finite precision representation
International Nuclear Information System (INIS)
Kwok, H.S.; Tang, Wallace K.S.
2007-01-01
In this paper, a fast chaos-based image encryption system with stream cipher structure is proposed. In order to achieve a fast throughput and facilitate hardware realization, 32-bit precision representation with fixed point arithmetic is assumed. The major core of the encryption system is a pseudo-random keystream generator based on a cascade of chaotic maps, serving the purpose of sequence generation and random mixing. Unlike the other existing chaos-based pseudo-random number generators, the proposed keystream generator not only achieves a very fast throughput, but also passes the statistical tests of up-to-date test suite even under quantization. The overall design of the image encryption system is to be explained while detail cryptanalysis is given and compared with some existing schemes
International Nuclear Information System (INIS)
Duquesne, Henry; Schmitt, Andre; Poussot, Rene; Pelicier, Henri.
1976-05-01
The classical experiments of neutron time-of-flight spectrometry on bulk multiplying media are using recurrent neutron bursts from a linear accelerator. The adaptation of the ion beam issued from the Cadarache Van de Graaff accelerator is described with the test experiments which were effected. Both methods are compared with respect to the accuracy obtained, the energy resolution and the time consumed [fr
International Nuclear Information System (INIS)
Corran, E.R.; Cummins, J.D.; Hopkinson, A.
1964-02-01
An experiment was performed to assess the usefulness of the binary cross-correlation method in the context of the identification problem. An auxiliary burner was excited with a discrete interval binary code and the response to the perturbation of the input heat was observed by recording the variations of the primary inlet, primary outlet and secondary outlet temperatures. The observations were analysed to yield cross-correlation functions and frequency responses were subsequently determined between primary inlet and primary outlet temperatures and also between primary inlet and secondary outlet temperatures. The analysis verified (1) that these dynamic responses of this cross flow heat exchanger may be predicted theoretically, (2) in so far as this heat exchanger is representative of the generality of plant, that the binary cross-correlation method provides adequate identification of plant dynamics for control purposes in environments where small input variations and low signal to noise ratio are obligatory. (author)
Theory of analogous force on number sets
Energy Technology Data Exchange (ETDEWEB)
Canessa, Enrique [Abdus Salam International Centre for Theoretical Physics, Trieste (Italy)
2003-08-01
A general statistical thermodynamic theory that considers given sequences of x-integers to play the role of particles of known type in an isolated elastic system is proposed. By also considering some explicit discrete probability distributions p{sub x} for natural numbers, we claim that they lead to a better understanding of probabilistic laws associated with number theory. Sequences of numbers are treated as the size measure of finite sets. By considering p{sub x} to describe complex phenomena, the theory leads to derive a distinct analogous force f{sub x} on number sets proportional to ({partial_derivative}p{sub x}/{partial_derivative}x){sub T} at an analogous system temperature T. In particular, this yields to an understanding of the uneven distribution of integers of random sets in terms of analogous scale invariance and a screened inverse square force acting on the significant digits. The theory also allows to establish recursion relations to predict sequences of Fibonacci numbers and to give an answer to the interesting theoretical question of the appearance of the Benford's law in Fibonacci numbers. A possible relevance to prime numbers is also analyzed. (author)
On the number of special numbers
Indian Academy of Sciences (India)
We now apply the theory of the Thue equation to obtain an effective bound on m. Indeed, by Lemma 3.2, we can write m2 = ba3 and m2 − 4 = cd3 with b, c cubefree. By the above, both b, c are bounded since they are cubefree and all their prime factors are less than e63727. Now we have a finite number of. Thue equations:.
International Nuclear Information System (INIS)
Kaneko, K.
1987-01-01
A relationship between the number projection and the shell model methods is investigated in the case of a single-j shell. We can find a one-to-one correspondence between the number projected and the shell model states
Gallistel, C R
2017-12-01
The representation of discrete and continuous quantities appears to be ancient and pervasive in animal brains. Because numbers are the natural carriers of these representations, we may discover that in brains, it's numbers all the way down.
DEFF Research Database (Denmark)
Andersen, Torben
2014-01-01
had a marked singular and an unmarked plural. Synchronically, however, the singular is arguably the basic member of the number category as revealed by the use of the two numbers. In addition, some nouns have a collective form, which is grammatically singular. Number also plays a role...
DEFF Research Database (Denmark)
Elvik, Rune; Bjørnskau, Torkel
2017-01-01
Highlights •26 studies of the safety-in-numbers effect are reviewed. •The existence of a safety-in-numbers effect is confirmed. •Results are consistent. •Causes of the safety-in-numbers effect are incompletely known....
de Mestre, Neville
2008-01-01
Prime numbers are important as the building blocks for the set of all natural numbers, because prime factorisation is an important and useful property of all natural numbers. Students can discover them by using the method known as the Sieve of Eratosthenes, named after the Greek geographer and astronomer who lived from c. 276-194 BC. Eratosthenes…
DEFF Research Database (Denmark)
Karlskov-Mortensen, Peter; Hu, Z.L.; Gorodkin, Jan
2007-01-01
the human genome (BLAST cut-off threshold = 1 x 10-5). All microsatellite sequences placed on the comparative map are accessible at http://www.animalgenome.org/QTLdb/pig.html . These sequences increase the number of identified microsatellites in the porcine genome by several orders of magnitude...
All-optical fast random number generator.
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.
Sequence determinants of human microsatellite variability
Directory of Open Access Journals (Sweden)
Jakobsson Mattias
2009-12-01
Full Text Available Abstract Background Microsatellite loci are frequently used in genomic studies of DNA sequence repeats and in population studies of genetic variability. To investigate the effect of sequence properties of microsatellites on their level of variability we have analyzed genotypes at 627 microsatellite loci in 1,048 worldwide individuals from the HGDP-CEPH cell line panel together with the DNA sequences of these microsatellites in the human RefSeq database. Results Calibrating PCR fragment lengths in individual genotypes by using the RefSeq sequence enabled us to infer repeat number in the HGDP-CEPH dataset and to calculate the mean number of repeats (as opposed to the mean PCR fragment length, under the assumption that differences in PCR fragment length reflect differences in the numbers of repeats in the embedded repeat sequences. We find the mean and maximum numbers of repeats across individuals to be positively correlated with heterozygosity. The size and composition of the repeat unit of a microsatellite are also important factors in predicting heterozygosity, with tetra-nucleotide repeat units high in G/C content leading to higher heterozygosity. Finally, we find that microsatellites containing more separate sets of repeated motifs generally have higher heterozygosity. Conclusions These results suggest that sequence properties of microsatellites have a significant impact in determining the features of human microsatellite variability.
International Nuclear Information System (INIS)
Todorov, T.D.
1980-01-01
The set of asymptotic numbers A as a system of generalized numbers including the system of real numbers R, as well as infinitely small (infinitesimals) and infinitely large numbers, is introduced. The detailed algebraic properties of A, which are unusual as compared with the known algebraic structures, are studied. It is proved that the set of asymptotic numbers A cannot be isomorphically embedded as a subspace in any group, ring or field, but some particular subsets of asymptotic numbers are shown to be groups, rings, and fields. The algebraic operation, additive and multiplicative forms, and the algebraic properties are constructed in an appropriate way. It is shown that the asymptotic numbers give rise to a new type of generalized functions quite analogous to the distributions of Schwartz allowing, however, the operation multiplication. A possible application of these functions to quantum theory is discussed
Niederreiter, Harald
2015-01-01
This textbook effectively builds a bridge from basic number theory to recent advances in applied number theory. It presents the first unified account of the four major areas of application where number theory plays a fundamental role, namely cryptography, coding theory, quasi-Monte Carlo methods, and pseudorandom number generation, allowing the authors to delineate the manifold links and interrelations between these areas. Number theory, which Carl-Friedrich Gauss famously dubbed the queen of mathematics, has always been considered a very beautiful field of mathematics, producing lovely results and elegant proofs. While only very few real-life applications were known in the past, today number theory can be found in everyday life: in supermarket bar code scanners, in our cars’ GPS systems, in online banking, etc. Starting with a brief introductory course on number theory in Chapter 1, which makes the book more accessible for undergraduates, the authors describe the four main application areas in Chapters...
Characterization and sequence analysis of cysteine and glycine-rich ...
African Journals Online (AJOL)
Primers specific for CSRP3 were designed using known cDNA sequences of Bos taurus published in database with different accession numbers. Polymerase chain reaction (PCR) was performed and products were purified and sequenced. Sequence analysis and alignment were carried out using CLUSTAL W (1.83).
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
EGNAS: an exhaustive DNA sequence design algorithm
Directory of Open Access Journals (Sweden)
Kick Alfred
2012-06-01
Full Text Available Abstract Background The molecular recognition based on the complementary base pairing of deoxyribonucleic acid (DNA is the fundamental principle in the fields of genetics, DNA nanotechnology and DNA computing. We present an exhaustive DNA sequence design algorithm that allows to generate sets containing a maximum number of sequences with defined properties. EGNAS (Exhaustive Generation of Nucleic Acid Sequences offers the possibility of controlling both interstrand and intrastrand properties. The guanine-cytosine content can be adjusted. Sequences can be forced to start and end with guanine or cytosine. This option reduces the risk of “fraying” of DNA strands. It is possible to limit cross hybridizations of a defined length, and to adjust the uniqueness of sequences. Self-complementarity and hairpin structures of certain length can be avoided. Sequences and subsequences can optionally be forbidden. Furthermore, sequences can be designed to have minimum interactions with predefined strands and neighboring sequences. Results The algorithm is realized in a C++ program. TAG sequences can be generated and combined with primers for single-base extension reactions, which were described for multiplexed genotyping of single nucleotide polymorphisms. Thereby, possible foldback through intrastrand interaction of TAG-primer pairs can be limited. The design of sequences for specific attachment of molecular constructs to DNA origami is presented. Conclusions We developed a new software tool called EGNAS for the design of unique nucleic acid sequences. The presented exhaustive algorithm allows to generate greater sets of sequences than with previous software and equal constraints. EGNAS is freely available for noncommercial use at http://www.chm.tu-dresden.de/pc6/EGNAS.
DEFF Research Database (Denmark)
Jørgensen, Claus Bjørn; Suetens, Sigrid; Tyran, Jean-Robert
numbers based on recent drawings. While most players pick the same set of numbers week after week without regards of numbers drawn or anything else, we find that those who do change, act on average in the way predicted by the law of small numbers as formalized in recent behavioral theory. In particular......We investigate the “law of small numbers” using a unique panel data set on lotto gambling. Because we can track individual players over time, we can measure how they react to outcomes of recent lotto drawings. We can therefore test whether they behave as if they believe they can predict lotto......, on average they move away from numbers that have recently been drawn, as suggested by the “gambler’s fallacy”, and move toward numbers that are on streak, i.e. have been drawn several weeks in a row, consistent with the “hot hand fallacy”....
Ore, Oystein
2017-01-01
Number theory is the branch of mathematics concerned with the counting numbers, 1, 2, 3, … and their multiples and factors. Of particular importance are odd and even numbers, squares and cubes, and prime numbers. But in spite of their simplicity, you will meet a multitude of topics in this book: magic squares, cryptarithms, finding the day of the week for a given date, constructing regular polygons, pythagorean triples, and many more. In this revised edition, John Watkins and Robin Wilson have updated the text to bring it in line with contemporary developments. They have added new material on Fermat's Last Theorem, the role of computers in number theory, and the use of number theory in cryptography, and have made numerous minor changes in the presentation and layout of the text and the exercises.
Special Issue: Next Generation DNA Sequencing
Directory of Open Access Journals (Sweden)
Paul Richardson
2010-10-01
Full Text Available Next Generation Sequencing (NGS refers to technologies that do not rely on traditional dideoxy-nucleotide (Sanger sequencing where labeled DNA fragments are physically resolved by electrophoresis. These new technologies rely on different strategies, but essentially all of them make use of real-time data collection of a base level incorporation event across a massive number of reactions (on the order of millions versus 96 for capillary electrophoresis for instance. The major commercial NGS platforms available to researchers are the 454 Genome Sequencer (Roche, Illumina (formerly Solexa Genome analyzer, the SOLiD system (Applied Biosystems/Life Technologies and the Heliscope (Helicos Corporation. The techniques and different strategies utilized by these platforms are reviewed in a number of the papers in this special issue. These technologies are enabling new applications that take advantage of the massive data produced by this next generation of sequencing instruments. [...
Snake Genome Sequencing: Results and Future Prospects.
Kerkkamp, Harald M I; Kini, R Manjunatha; Pospelov, Alexey S; Vonk, Freek J; Henkel, Christiaan V; Richardson, Michael K
2016-12-01
Snake genome sequencing is in its infancy-very much behind the progress made in sequencing the genomes of humans, model organisms and pathogens relevant to biomedical research, and agricultural species. We provide here an overview of some of the snake genome projects in progress, and discuss the biological findings, with special emphasis on toxinology, from the small number of draft snake genomes already published. We discuss the future of snake genomics, pointing out that new sequencing technologies will help overcome the problem of repetitive sequences in assembling snake genomes. Genome sequences are also likely to be valuable in examining the clustering of toxin genes on the chromosomes, in designing recombinant antivenoms and in studying the epigenetic regulation of toxin gene expression.
Snake Genome Sequencing: Results and Future Prospects
Directory of Open Access Journals (Sweden)
Harald M. I. Kerkkamp
2016-12-01
Full Text Available Snake genome sequencing is in its infancy—very much behind the progress made in sequencing the genomes of humans, model organisms and pathogens relevant to biomedical research, and agricultural species. We provide here an overview of some of the snake genome projects in progress, and discuss the biological findings, with special emphasis on toxinology, from the small number of draft snake genomes already published. We discuss the future of snake genomics, pointing out that new sequencing technologies will help overcome the problem of repetitive sequences in assembling snake genomes. Genome sequences are also likely to be valuable in examining the clustering of toxin genes on the chromosomes, in designing recombinant antivenoms and in studying the epigenetic regulation of toxin gene expression.
Godefroy, Gilles
2004-01-01
Numbers are fascinating. The fascination begins in childhood, when we first learn to count. It continues as we learn arithmetic, algebra, geometry, and so on. Eventually, we learn that numbers not only help us to measure the world, but also to understand it and, to some extent, to control it. In The Adventure of Numbers, Gilles Godefroy follows the thread of our expanding understanding of numbers to lead us through the history of mathematics. His goal is to share the joy of discovering and understanding this great adventure of the mind. The development of mathematics has been punctuated by a n
DEFF Research Database (Denmark)
Suetens, Sigrid; Galbo-Jørgensen, Claus B.; Tyran, Jean-Robert Karl
2016-01-01
We investigate the ‘law of small numbers’ using a data set on lotto gambling that allows us to measure players’ reactions to draws. While most players pick the same set of numbers week after week, we find that those who do change react on average as predicted by the law of small numbers...... as formalized in recent behavioral theory. In particular, players tend to bet less on numbers that have been drawn in the preceding week, as suggested by the ‘gambler’s fallacy’, and bet more on a number if it was frequently drawn in the recent past, consistent with the ‘hot-hand fallacy’....
Diamond, Harold G; Cheung, Man Ping
2016-01-01
"Generalized numbers" is a multiplicative structure introduced by A. Beurling to study how independent prime number theory is from the additivity of the natural numbers. The results and techniques of this theory apply to other systems having the character of prime numbers and integers; for example, it is used in the study of the prime number theorem (PNT) for ideals of algebraic number fields. Using both analytic and elementary methods, this book presents many old and new theorems, including several of the authors' results, and many examples of extremal behavior of g-number systems. Also, the authors give detailed accounts of the L^2 PNT theorem of J. P. Kahane and of the example created with H. L. Montgomery, showing that additive structure is needed for proving the Riemann hypothesis. Other interesting topics discussed are propositions "equivalent" to the PNT, the role of multiplicative convolution and Chebyshev's prime number formula for g-numbers, and how Beurling theory provides an interpretation of the ...
Intuitive numbers guide decisions
Directory of Open Access Journals (Sweden)
Ellen Peters
2008-12-01
Full Text Available Measuring reaction times to number comparisons is thought to reveal a processing stage in elementary numerical cognition linked to internal, imprecise representations of number magnitudes. These intuitive representations of the mental number line have been demonstrated across species and human development but have been little explored in decision making. This paper develops and tests hypotheses about the influence of such evolutionarily ancient, intuitive numbers on human decisions. We demonstrate that individuals with more precise mental-number-line representations are higher in numeracy (number skills consistent with previous research with children. Individuals with more precise representations (compared to those with less precise representations also were more likely to choose larger, later amounts over smaller, immediate amounts, particularly with a larger proportional difference between the two monetary outcomes. In addition, they were more likely to choose an option with a larger proportional but smaller absolute difference compared to those with less precise representations. These results are consistent with intuitive number representations underlying: a perceived differences between numbers, b the extent to which proportional differences are weighed in decisions, and, ultimately, c the valuation of decision options. Human decision processes involving numbers important to health and financial matters may be rooted in elementary, biological processes shared with other species.
Sequences for Student Investigation
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…
Templates, Numbers & Watercolors.
Clemesha, David J.
1990-01-01
Describes how a second-grade class used large templates to draw and paint five-digit numbers. The lesson integrated artistic knowledge and vocabulary with their mathematics lesson in place value. Students learned how draftspeople use templates, and they studied number paintings by Charles Demuth and Jasper Johns. (KM)
A comparative evaluation of sequence classification programs
Directory of Open Access Journals (Sweden)
Bazinet Adam L
2012-05-01
Full Text Available Abstract Background A fundamental problem in modern genomics is to taxonomically or functionally classify DNA sequence fragments derived from environmental sampling (i.e., metagenomics. Several different methods have been proposed for doing this effectively and efficiently, and many have been implemented in software. In addition to varying their basic algorithmic approach to classification, some methods screen sequence reads for ’barcoding genes’ like 16S rRNA, or various types of protein-coding genes. Due to the sheer number and complexity of methods, it can be difficult for a researcher to choose one that is well-suited for a particular analysis. Results We divided the very large number of programs that have been released in recent years for solving the sequence classification problem into three main categories based on the general algorithm they use to compare a query sequence against a database of sequences. We also evaluated the performance of the leading programs in each category on data sets whose taxonomic and functional composition is known. Conclusions We found significant variability in classification accuracy, precision, and resource consumption of sequence classification programs when used to analyze various metagenomics data sets. However, we observe some general trends and patterns that will be useful to researchers who use sequence classification programs.
On Generalizations of the Stirling Number Triangles
Lang, Wolfdieter
2000-09-01
Sequences of generalized Stirling numbers of both kinds are introduced. These sequences of triangles (i.e. infinite-dimensional lower triangular matrices) of numbers will be denoted by S2(k;n,m) and S1(k;n,m) with k in Z. The original Stirling number triangles of the second and first kind arise when k = 1. S2(2;n,m) is identical with the unsigned S1(2;n,m) triangle, called S1p(2;n,m), which also represents the triangle of signless Lah numbers. Certain associated number triangles, denoted by s2(k;n,m) and s1(k;n,m), are also defined. Both s2(2;n,m) and s1(2;n + 1, m + 1) form Pascal's triangle, and s2(-1,n,m) turns out to be Catalan's triangle. Generating functions are given for the columns of these triangles. Each S2(k) and S1(k) matrix is an example of a Jabotinsky matrix. Therefore the generating functions for the rows of these triangular arrays constitute exponential convolution polynomials. The sequences of the row sums of these triangles are also considered. These triangles are related to the problem of obtaining finite transformations from infinitesimal ones generated by x^k d/dx, for k in Z.
Mixed Sequence Reader: A Program for Analyzing DNA Sequences with Heterozygous Base Calling
Chang, Chun-Tien; Tsai, Chi-Neu; Tang, Chuan Yi; Chen, Chun-Houh; Lian, Jang-Hau; Hu, Chi-Yu; Tsai, Chia-Lung; Chao, Angel; Lai, Chyong-Huey; Wang, Tzu-Hao; Lee, Yun-Shien
2012-01-01
The direct sequencing of PCR products generates heterozygous base-calling fluorescence chromatograms that are useful for identifying single-nucleotide polymorphisms (SNPs), insertion-deletions (indels), short tandem repeats (STRs), and paralogous genes. Indels and STRs can be easily detected using the currently available Indelligent or ShiftDetector programs, which do not search reference sequences. However, the detection of other genomic variants remains a challenge due to the lack of appropriate tools for heterozygous base-calling fluorescence chromatogram data analysis. In this study, we developed a free web-based program, Mixed Sequence Reader (MSR), which can directly analyze heterozygous base-calling fluorescence chromatogram data in .abi file format using comparisons with reference sequences. The heterozygous sequences are identified as two distinct sequences and aligned with reference sequences. Our results showed that MSR may be used to (i) physically locate indel and STR sequences and determine STR copy number by searching NCBI reference sequences; (ii) predict combinations of microsatellite patterns using the Federal Bureau of Investigation Combined DNA Index System (CODIS); (iii) determine human papilloma virus (HPV) genotypes by searching current viral databases in cases of double infections; (iv) estimate the copy number of paralogous genes, such as β-defensin 4 (DEFB4) and its paralog HSPDP3. PMID:22778697
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.
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.
Test Pattern Generator for Mixed Mode BIST
Energy Technology Data Exchange (ETDEWEB)
Kim, Hong Sik; Lee, Hang Kyu; Kang, Sung Ho [Yonsei University (Korea, Republic of)
1998-07-01
As the increasing integrity of VLSI, the BIST (Built-In Self Test) is used as an effective method to test chips. Generally the pseudo-random test pattern generation is used for BIST. But it requires lots of test patterns when there exist random resistant faults. Therefore deterministic testing is an interesting BIST technique due to the minimal number of test patterns and to its high fault coverage. However this is not applicable since the existing deterministic test pattern generators require too much area overhead despite their efficiency. Therefore we propose a mixed test scheme which applies to the circuit under test, a deterministic test sequence followed by a pseudo-random one. This scheme allows the maximum fault coverage detection to be achieved, furthermore the silicon area overhead of the mixed hardware generator can be reduced. The deterministic test generator is made with a finite state machine and a pseudo-random test generator is made with LFSR(linear feedback shift register). The results of ISCAS circuits show that the maximum fault coverage is guaranteed with small number of test set and little hardware overhead. (author). 15 refs., 10 figs., 4 tabs.
Zseq: An Approach for Preprocessing Next-Generation Sequencing Data.
Alkhateeb, Abedalrhman; Rueda, Luis
2017-08-01
Next-generation sequencing technology generates a huge number of reads (short sequences), which contain a vast amount of genomic data. The sequencing process, however, comes with artifacts. Preprocessing of sequences is mandatory for further downstream analysis. We present Zseq, a linear method that identifies the most informative genomic sequences and reduces the number of biased sequences, sequence duplications, and ambiguous nucleotides. Zseq finds the complexity of the sequences by counting the number of unique k-mers in each sequence as its corresponding score and also takes into the account other factors such as ambiguous nucleotides or high GC-content percentage in k-mers. Based on a z-score threshold, Zseq sweeps through the sequences again and filters those with a z-score less than the user-defined threshold. Zseq algorithm is able to provide a better mapping rate; it reduces the number of ambiguous bases significantly in comparison with other methods. Evaluation of the filtered reads has been conducted by aligning the reads and assembling the transcripts using the reference genome as well as de novo assembly. The assembled transcripts show a better discriminative ability to separate cancer and normal samples in comparison with another state-of-the-art method. Moreover, de novo assembled transcripts from the reads filtered by Zseq have longer genomic sequences than other tested methods. Estimating the threshold of the cutoff point is introduced using labeling rules with optimistic results.
Some Algebraic Aspects of MorseCode Sequences
Johann Cigler
2003-01-01
Morse code sequences are very useful to give combinatorial interpretations of various properties of Fibonacci numbers. In this note we study some algebraic and combinatorial aspects of Morse code sequences and obtain several q-analogues of Fibonacci numbers and Fibonacci polynomials and their generalizations.
Some Algebraic Aspects of MorseCode Sequences
Directory of Open Access Journals (Sweden)
Johann Cigler
2003-06-01
Full Text Available Morse code sequences are very useful to give combinatorial interpretations of various properties of Fibonacci numbers. In this note we study some algebraic and combinatorial aspects of Morse code sequences and obtain several q-analogues of Fibonacci numbers and Fibonacci polynomials and their generalizations.
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.)
Weiss, Edwin
1998-01-01
Careful organization and clear, detailed proofs characterize this methodical, self-contained exposition of basic results of classical algebraic number theory from a relatively modem point of view. This volume presents most of the number-theoretic prerequisites for a study of either class field theory (as formulated by Artin and Tate) or the contemporary treatment of analytical questions (as found, for example, in Tate's thesis).Although concerned exclusively with algebraic number fields, this treatment features axiomatic formulations with a considerable range of applications. Modem abstract te
Cohn, Harvey
1980-01-01
""A very stimulating book ... in a class by itself."" - American Mathematical MonthlyAdvanced students, mathematicians and number theorists will welcome this stimulating treatment of advanced number theory, which approaches the complex topic of algebraic number theory from a historical standpoint, taking pains to show the reader how concepts, definitions and theories have evolved during the last two centuries. Moreover, the book abounds with numerical examples and more concrete, specific theorems than are found in most contemporary treatments of the subject.The book is divided into three parts
Crossley, John N
1987-01-01
This book presents detailed studies of the development of three kinds of number. In the first part the development of the natural numbers from Stone-Age times right up to the present day is examined not only from the point of view of pure history but also taking into account archaeological, anthropological and linguistic evidence. The dramatic change caused by the introduction of logical theories of number in the 19th century is also treated and this part ends with a non-technical account of the very latest developments in the area of Gödel's theorem. The second part is concerned with the deve
Professor Stewart's incredible numbers
Stewart, Ian
2015-01-01
Ian Stewart explores the astonishing properties of numbers from 1 to10 to zero and infinity, including one figure that, if you wrote it out, would span the universe. He looks at every kind of number you can think of - real, imaginary, rational, irrational, positive and negative - along with several you might have thought you couldn't think of. He explains the insights of the ancient mathematicians, shows how numbers have evolved through the ages, and reveals the way numerical theory enables everyday life. Under Professor Stewart's guidance you will discover the mathematics of codes,
LeVeque, William J
1996-01-01
This excellent textbook introduces the basics of number theory, incorporating the language of abstract algebra. A knowledge of such algebraic concepts as group, ring, field, and domain is not assumed, however; all terms are defined and examples are given - making the book self-contained in this respect.The author begins with an introductory chapter on number theory and its early history. Subsequent chapters deal with unique factorization and the GCD, quadratic residues, number-theoretic functions and the distribution of primes, sums of squares, quadratic equations and quadratic fields, diopha
Kneusel, Ronald T
2015-01-01
This is a book about numbers and how those numbers are represented in and operated on by computers. It is crucial that developers understand this area because the numerical operations allowed by computers, and the limitations of those operations, especially in the area of floating point math, affect virtually everything people try to do with computers. This book aims to fill this gap by exploring, in sufficient but not overwhelming detail, just what it is that computers do with numbers. Divided into two parts, the first deals with standard representations of integers and floating point numb
Sierpinski, Waclaw
1988-01-01
Since the publication of the first edition of this work, considerable progress has been made in many of the questions examined. This edition has been updated and enlarged, and the bibliography has been revised.The variety of topics covered here includes divisibility, diophantine equations, prime numbers (especially Mersenne and Fermat primes), the basic arithmetic functions, congruences, the quadratic reciprocity law, expansion of real numbers into decimal fractions, decomposition of integers into sums of powers, some other problems of the additive theory of numbers and the theory of Gaussian
Directory of Open Access Journals (Sweden)
R. A. Mollin
1986-01-01
Full Text Available A powerful number is a positive integer n satisfying the property that p2 divides n whenever the prime p divides n; i.e., in the canonical prime decomposition of n, no prime appears with exponent 1. In [1], S.W. Golomb introduced and studied such numbers. In particular, he asked whether (25,27 is the only pair of consecutive odd powerful numbers. This question was settled in [2] by W.A. Sentance who gave necessary and sufficient conditions for the existence of such pairs. The first result of this paper is to provide a generalization of Sentance's result by giving necessary and sufficient conditions for the existence of pairs of powerful numbers spaced evenly apart. This result leads us naturally to consider integers which are representable as a proper difference of two powerful numbers, i.e. n=p1−p2 where p1 and p2 are powerful numbers with g.c.d. (p1,p2=1. Golomb (op.cit. conjectured that 6 is not a proper difference of two powerful numbers, and that there are infinitely many numbers which cannot be represented as a proper difference of two powerful numbers. The antithesis of this conjecture was proved by W.L. McDaniel [3] who verified that every non-zero integer is in fact a proper difference of two powerful numbers in infinitely many ways. McDaniel's proof is essentially an existence proof. The second result of this paper is a simpler proof of McDaniel's result as well as an effective algorithm (in the proof for explicitly determining infinitely many such representations. However, in both our proof and McDaniel's proof one of the powerful numbers is almost always a perfect square (namely one is always a perfect square when n≢2(mod4. We provide in §2 a proof that all even integers are representable in infinitely many ways as a proper nonsquare difference; i.e., proper difference of two powerful numbers neither of which is a perfect square. This, in conjunction with the odd case in [4], shows that every integer is representable in
Corry, Leo
2015-01-01
The world around us is saturated with numbers. They are a fundamental pillar of our modern society, and accepted and used with hardly a second thought. But how did this state of affairs come to be? In this book, Leo Corry tells the story behind the idea of number from the early days of the Pythagoreans, up until the turn of the twentieth century. He presents an overview of how numbers were handled and conceived in classical Greek mathematics, in the mathematics of Islam, in European mathematics of the middle ages and the Renaissance, during the scientific revolution, all the way through to the
Dudley, Underwood
2008-01-01
Ideal for a first course in number theory, this lively, engaging text requires only a familiarity with elementary algebra and the properties of real numbers. Author Underwood Dudley, who has written a series of popular mathematics books, maintains that the best way to learn mathematics is by solving problems. In keeping with this philosophy, the text includes nearly 1,000 exercises and problems-some computational and some classical, many original, and some with complete solutions. The opening chapters offer sound explanations of the basics of elementary number theory and develop the fundamenta
African Journals Online (AJOL)
OLUWOLE
Agro-Science Journal of Tropical Agriculture, Food, Environment and Extension. Volume 9 Number 1 ... of persistent dumping of cheap subsidized food imports from developed ... independence of the inefficiency effects in the two estimation ...
High Reynolds Number Turbulence
National Research Council Canada - National Science Library
Smits, Alexander J
2007-01-01
The objectives of the grant were to provide a systematic study to fill the gap between existing research on low Reynolds number turbulent flows to the kinds of turbulent flows encountered on full-scale vehicles...
International Development Research Centre (IDRC) Digital Library (Canada)
Operating a Demographic Surveillance System (DSS) like this one requires a blend of high-tech number-crunching ability and .... views follow a standardized format that takes several ... general levels of health and to the use of health services.
Quantum random number generator
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.
Solar Indices - Sunspot Numbers
National Oceanic and Atmospheric Administration, Department of Commerce — Collection includes a variety of indices related to solar activity contributed by a number of national and private solar observatories located worldwide. This...
Schwartz, Richard Evan
2014-01-01
In the American Mathematical Society's first-ever book for kids (and kids at heart), mathematician and author Richard Evan Schwartz leads math lovers of all ages on an innovative and strikingly illustrated journey through the infinite number system. By means of engaging, imaginative visuals and endearing narration, Schwartz manages the monumental task of presenting the complex concept of Big Numbers in fresh and relatable ways. The book begins with small, easily observable numbers before building up to truly gigantic ones, like a nonillion, a tredecillion, a googol, and even ones too huge for names! Any person, regardless of age, can benefit from reading this book. Readers will find themselves returning to its pages for a very long time, perpetually learning from and growing with the narrative as their knowledge deepens. Really Big Numbers is a wonderful enrichment for any math education program and is enthusiastically recommended to every teacher, parent and grandparent, student, child, or other individual i...
Indian Academy of Sciences (India)
One could endlessly churn out congruent numbers following the method in Box 1 without being certain when a given number n (or n x m 2, for some integer m) will ap- pear on the list. Continuing in this way ·would exhaust one's computing resources, not to mention one's patience! Also, this procedure is of no avail if n is not ...
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
Phylogenetic Trees From Sequences
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.
DEFF Research Database (Denmark)
Korsby, Trine Mygind
2017-01-01
Taking a point of departure in negotiations for access to a phone number for a brothel abroad, the article demonstrates how a group of pimps in Eastern Romania attempt to extend their local business into the rest of the EU. The article shows how the phone number works as a micro-infrastructure in......Taking a point of departure in negotiations for access to a phone number for a brothel abroad, the article demonstrates how a group of pimps in Eastern Romania attempt to extend their local business into the rest of the EU. The article shows how the phone number works as a micro...... in turn cultivate and maximize uncertainty about themselves in others. When making the move to go abroad into unknown terrains, accessing the infrastructure generated by the phone number can provide certainty and consolidate one’s position within criminal networks abroad. However, at the same time......, mishandling the phone number can be dangerous and in that sense produce new doubts and uncertainties....
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...
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...
The prime numbers and their distribution
Tenenbaum, Gerald
2000-01-01
One notable new direction this century in the study of primes has been the influx of ideas from probability. The goal of this book is to provide insights into the prime numbers and to describe how a sequence so tautly determined can incorporate such a striking amount of randomness. The book opens with some classic topics of number theory. It ends with a discussion of some of the outstanding conjectures in number theory. In between are an excellent chapter on the stochastic properties of primes and a walk through an elementary proof of the Prime Number Theorem. This book is suitable for anyone who has had a little number theory and some advanced calculus involving estimates. Its engaging style and invigorating point of view will make refreshing reading for advanced undergraduates through research mathematicians.
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
Sequence embedding for fast construction of guide trees for multiple sequence alignment
LENUS (Irish Health Repository)
Blackshields, Gordon
2010-05-14
Abstract Background The most widely used multiple sequence alignment methods require sequences to be clustered as an initial step. Most sequence clustering methods require a full distance matrix to be computed between all pairs of sequences. This requires memory and time proportional to N 2 for N sequences. When N grows larger than 10,000 or so, this becomes increasingly prohibitive and can form a significant barrier to carrying out very large multiple alignments. Results In this paper, we have tested variations on a class of embedding methods that have been designed for clustering large numbers of complex objects where the individual distance calculations are expensive. These methods involve embedding the sequences in a space where the similarities within a set of sequences can be closely approximated without having to compute all pair-wise distances. Conclusions We show how this approach greatly reduces computation time and memory requirements for clustering large numbers of sequences and demonstrate the quality of the clusterings by benchmarking them as guide trees for multiple alignment. Source code is available for download from http:\\/\\/www.clustal.org\\/mbed.tgz.
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.
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.
Lifescience Database Archive (English)
Full Text Available List Contact us Gclust Server Table of Cluster and Organism Species Number Data detail Data name Table of Cluster and Organism...resentative sequence ID of cluster, its length, the number of sequences contained in the cluster, organism s...pecies, the number of sequences belonging to the cluster for each of 95 organism ...t Us Table of Cluster and Organism Species Number - Gclust Server | LSDB Archive ...
Parametric Improper Integrals, Wallis Formula and Catalan Numbers
Dana-Picard, Thierry; Zeitoun, David G.
2012-01-01
We present a sequence of improper integrals, for which a closed formula can be computed using Wallis formula and a non-straightforward recurrence formula. This yields a new integral presentation for Catalan numbers.
DEFF Research Database (Denmark)
Levin, Bruce R; McCall, Ingrid C.; Perrot, Veronique
2017-01-01
We postulate that the inhibition of growth and low rates of mortality of bacteria exposed to ribosome-binding antibiotics deemed bacteriostatic can be attributed almost uniquely to these drugs reducing the number of ribosomes contributing to protein synthesis, i.e., the number of effective......-targeting bacteriostatic antibiotics, the time before these bacteria start to grow again when the drugs are removed, referred to as the post-antibiotic effect (PAE), is markedly greater for constructs with fewer rrn operons than for those with more rrn operons. We interpret the results of these other experiments reported...... here as support for the hypothesis that the reduction in the effective number of ribosomes due to binding to these structures provides a sufficient explanation for the action of bacteriostatic antibiotics that target these structures....
Alizée Dauvergne
2010-01-01
What makes the LHC the biggest particle accelerator in the world? Here are some of the numbers that characterise the LHC, and their equivalents in terms that are easier for us to imagine. Feature Number Equivalent Circumference ~ 27 km Distance covered by beam in 10 hours ~ 10 billion km a round trip to Neptune Number of times a single proton travels around the ring each second 11 245 Speed of protons first entering the LHC 299 732 500 m/s 99.9998 % of the speed of light Speed of protons when they collide 299 789 760 m/s 99.9999991 % of the speed of light Collision temperature ~ 1016 °C ove...
Divide and conquer: enriching environmental sequencing data.
Directory of Open Access Journals (Sweden)
Anne Bergeron
2007-09-01
Full Text Available In environmental sequencing projects, a mix of DNA from a whole microbial community is fragmented and sequenced, with one of the possible goals being to reconstruct partial or complete genomes of members of the community. In communities with high diversity of species, a significant proportion of the sequences do not overlap any other fragment in the sample. This problem will arise not only in situations with a relatively even distribution of many species, but also when the community in a particular environment is routinely dominated by the same few species. In the former case, no genomes may be assembled at all, while in the latter case a few dominant species in an environment will always be sequenced at high coverage to the detriment of coverage of the greater number of sparse species.Here we show that, with the same global sequencing effort, separating the species into two or more sub-communities prior to sequencing can yield a much higher proportion of sequences that can be assembled. We first use the Lander-Waterman model to show that, if the expected percentage of singleton sequences is higher than 25%, then, under the uniform distribution hypothesis, splitting the community is always a wise choice. We then construct simulated microbial communities to show that the results hold for highly non-uniform distributions. We also show that, for the distributions considered in the experiments, it is possible to estimate quite accurately the relative diversity of the two sub-communities.Given the fact that several methods exist to split microbial communities based on physical properties such as size, density, surface biochemistry, or optical properties, we strongly suggest that groups involved in environmental sequencing, and expecting high diversity, consider splitting their communities in order to maximize the information content of their sequencing effort.
Samuel, Pierre
2008-01-01
Algebraic number theory introduces students not only to new algebraic notions but also to related concepts: groups, rings, fields, ideals, quotient rings and quotient fields, homomorphisms and isomorphisms, modules, and vector spaces. Author Pierre Samuel notes that students benefit from their studies of algebraic number theory by encountering many concepts fundamental to other branches of mathematics - algebraic geometry, in particular.This book assumes a knowledge of basic algebra but supplements its teachings with brief, clear explanations of integrality, algebraic extensions of fields, Gal
Iwaniec, Henryk
2004-01-01
Analytic Number Theory distinguishes itself by the variety of tools it uses to establish results, many of which belong to the mainstream of arithmetic. One of the main attractions of analytic number theory is the vast diversity of concepts and methods it includes. The main goal of the book is to show the scope of the theory, both in classical and modern directions, and to exhibit its wealth and prospects, its beautiful theorems and powerful techniques. The book is written with graduate students in mind, and the authors tried to balance between clarity, completeness, and generality. The exercis
CONFUSION WITH TELEPHONE NUMBERS
Telecom Service
2002-01-01
he area code is now required for all telephone calls within Switzerland. Unfortunately this is causing some confusion. CERN has received complaints that incoming calls intended for CERN mobile phones are being directed to private subscribers. This is caused by mistakenly dialing the WRONG code (e.g. 022) in front of the mobile number. In order to avoid these problems, please inform your correspondents that the correct numbers are: 079 201 XXXX from Switzerland; 0041 79 201 XXXX from other countries. Telecom Service
CONFUSION WITH TELEPHONE NUMBERS
Telecom Service
2002-01-01
The area code is now required for all telephone calls within Switzerland. Unfortunately this is causing some confusion. CERN has received complaints that incoming calls intended for CERN mobile phones are being directed to private subscribers. This is caused by mistakenly dialing the WRONG code (e.g. 022) in front of the mobile number. In order to avoid these problems, please inform your correspondents that the correct numbers are: 079 201 XXXX from Switzerland; 0041 79 201 XXXX from other countries. Telecom Service
Earthquake number forecasts testing
Kagan, Yan Y.
2017-10-01
We study the distributions of earthquake numbers in two global earthquake catalogues: Global Centroid-Moment Tensor and Preliminary Determinations of Epicenters. The properties of these distributions are especially required to develop the number test for our forecasts of future seismic activity rate, tested by the Collaboratory for Study of Earthquake Predictability (CSEP). A common assumption, as used in the CSEP tests, is that the numbers are described by the Poisson distribution. It is clear, however, that the Poisson assumption for the earthquake number distribution is incorrect, especially for the catalogues with a lower magnitude threshold. In contrast to the one-parameter Poisson distribution so widely used to describe earthquake occurrences, the negative-binomial distribution (NBD) has two parameters. The second parameter can be used to characterize the clustering or overdispersion of a process. We also introduce and study a more complex three-parameter beta negative-binomial distribution. We investigate the dependence of parameters for both Poisson and NBD distributions on the catalogue magnitude threshold and on temporal subdivision of catalogue duration. First, we study whether the Poisson law can be statistically rejected for various catalogue subdivisions. We find that for most cases of interest, the Poisson distribution can be shown to be rejected statistically at a high significance level in favour of the NBD. Thereafter, we investigate whether these distributions fit the observed distributions of seismicity. For this purpose, we study upper statistical moments of earthquake numbers (skewness and kurtosis) and compare them to the theoretical values for both distributions. Empirical values for the skewness and the kurtosis increase for the smaller magnitude threshold and increase with even greater intensity for small temporal subdivision of catalogues. The Poisson distribution for large rate values approaches the Gaussian law, therefore its skewness
The quantum mechanical potential for the prime numbers
International Nuclear Information System (INIS)
Mussardo, G.
1997-12-01
A simple criterion is derived in order that a number sequence S n is a permitted spectrum of a quantized system. The sequence of the prime numbers fulfills the criterion and the corresponding one-dimensional quantum potential is explicitly computed in a semi-classical approximation. The existence of such a potential implies that the primality testing can in principle be resolved by the sole use of physical laws. (author)
Wetherell, Chris
2017-01-01
This is an edited extract from the keynote address given by Dr. Chris Wetherell at the 26th Biennial Conference of the Australian Association of Mathematics Teachers Inc. The author investigates the surprisingly rich structure that exists within a simple arrangement of numbers: the times tables.
Bell, Eric Temple
1991-01-01
From one of the foremost interpreters for lay readers of the history and meaning of mathematics: a stimulating account of the origins of mathematical thought and the development of numerical theory. It probes the work of Pythagoras, Galileo, Berkeley, Einstein, and others, exploring how ""number magic"" has influenced religion, philosophy, science, and mathematics
International Nuclear Information System (INIS)
Khan, T.A.; Baum, J.W.; Beckman, M.C.
1993-10-01
This document contains information dealing with the lessons learned from the experience of nuclear plants. In this issue the authors tried to avoid the 'tyranny' of numbers and concentrated on the main lessons learned. Topics include: filtration devices for air pollution abatement, crack repair and inspection, and remote handling equipment
Uniform random number generators
Farr, W. R.
1971-01-01
Methods are presented for the generation of random numbers with uniform and normal distributions. Subprogram listings of Fortran generators for the Univac 1108, SDS 930, and CDC 3200 digital computers are also included. The generators are of the mixed multiplicative type, and the mathematical method employed is that of Marsaglia and Bray.
International Nuclear Information System (INIS)
1994-01-01
The key numbers of energy give statistical data related to production, consumption, and to foreign trade of each energy in the World and in France. A chapter is dedicated to environment and brings quantitative elements on pollutant emissions connected to energy uses
Directory of Open Access Journals (Sweden)
Oli Brown
2008-10-01
Full Text Available Estimates of the potential number of ‘climate changemigrants’ vary hugely. In order to persuade policymakers ofthe need to act and to provide a sound basis for appropriateresponses, there is an urgent need for better analysis, betterdata and better predictions.
Trudgian, Timothy
2009-01-01
One of the difficulties in any teaching of mathematics is to bridge the divide between the abstract and the intuitive. Throughout school one encounters increasingly abstract notions, which are more and more difficult to relate to everyday experiences. This article examines a familiar approach to thinking about negative numbers, that is an…
Indian Academy of Sciences (India)
First page Back Continue Last page Overview Graphics. Typical Complexity Numbers. Say. 1000 tones,; 100 Users,; Transmission every 10 msec. Full Crosstalk cancellation would require. Full cancellation requires a matrix multiplication of order 100*100 for all the tones. 1000*100*100*100 operations every second for the ...
Indian Academy of Sciences (India)
IAS Admin
improved by Selberg [4] in 1941 who showed that a pos- ... be seen by entries of his first letter to G H Hardy in ... tary in the technical sense of the word, employed com- ..... III: On the expression of a number as a sum of primes, Acta Math.,.
Simulation techniques for determining reliability and availability of technical systems
International Nuclear Information System (INIS)
Lindauer, E.
1975-01-01
The system is described in the form of a fault tree with components representing part functions of the system and connections which reproduce the logical structure of the system. Both have the states intact or failed, they are defined here as in the programme FESIVAR of the IRS. For the simulation of components corresponding to the given probabilities, pseudo-random numbers are applied; these are numbers whose sequence is determined by the producing algorithm, but which for the given purpose sufficiently exhibit the behaviour of randomly successive numbers. This method of simulation is compared with deterministic methods. (HP/LH) [de
Genome sequencing and annotation of Serratia sp. strain TEL.
Lephoto, Tiisetso E; Gray, Vincent M
2015-12-01
We present the annotation of the draft genome sequence of Serratia sp. strain TEL (GenBank accession number KP711410). This organism was isolated from entomopathogenic nematode Oscheius sp. strain TEL (GenBank accession number KM492926) collected from grassland soil and has a genome size of 5,000,541 bp and 542 subsystems. The genome sequence can be accessed at DDBJ/EMBL/GenBank under the accession number LDEG00000000.
Genome sequencing and annotation of Serratia sp. strain TEL
Directory of Open Access Journals (Sweden)
Tiisetso E. Lephoto
2015-12-01
Full Text Available We present the annotation of the draft genome sequence of Serratia sp. strain TEL (GenBank accession number KP711410. This organism was isolated from entomopathogenic nematode Oscheius sp. strain TEL (GenBank accession number KM492926 collected from grassland soil and has a genome size of 5,000,541 bp and 542 subsystems. The genome sequence can be accessed at DDBJ/EMBL/GenBank under the accession number LDEG00000000.
Genome sequencing and annotation of Serratia sp. strain TEL
Lephoto, Tiisetso E.; Gray, Vincent M.
2015-01-01
We present the annotation of the draft genome sequence of Serratia sp. strain TEL (GenBank accession number KP711410). This organism was isolated from entomopathogenic nematode Oscheius sp. strain TEL (GenBank accession number KM492926) collected from grassland soil and has a genome size of 5,000,541 bp and 542 subsystems. The genome sequence can be accessed at DDBJ/EMBL/GenBank under the accession number LDEG00000000.
Adaptive Processing for Sequence Alignment
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.
Adaptive Processing for Sequence Alignment
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.
Computation and theory of Euler sums of generalized hyperharmonic numbers
Xu, Ce
2017-01-01
Recently, Dil and Boyadzhiev \\cite{AD2015} proved an explicit formula for the sum of multiple harmonic numbers whose indices are the sequence $\\left( {{{\\left\\{ 0 \\right\\}}_r},1} \\right)$. In this paper we show that the sums of multiple harmonic numbers whose indices are the sequence $\\left( {{{\\left\\{ 0 \\right\\}}_r,1};{{\\left\\{ 1 \\right\\}}_{k-1}}} \\right)$ can be expressed in terms of (multiple) zeta values, multiple harmonic numbers and Stirling numbers of the first kind, and give an explic...
PIMS sequencing extension: a laboratory information management system for DNA sequencing facilities
Directory of Open Access Journals (Sweden)
Baldwin Stephen A
2011-03-01
Full Text Available Abstract Background Facilities that provide a service for DNA sequencing typically support large numbers of users and experiment types. The cost of services is often reduced by the use of liquid handling robots but the efficiency of such facilities is hampered because the software for such robots does not usually integrate well with the systems that run the sequencing machines. Accordingly, there is a need for software systems capable of integrating different robotic systems and managing sample information for DNA sequencing services. In this paper, we describe an extension to the Protein Information Management System (PIMS that is designed for DNA sequencing facilities. The new version of PIMS has a user-friendly web interface and integrates all aspects of the sequencing process, including sample submission, handling and tracking, together with capture and management of the data. Results The PIMS sequencing extension has been in production since July 2009 at the University of Leeds DNA Sequencing Facility. It has completely replaced manual data handling and simplified the tasks of data management and user communication. Samples from 45 groups have been processed with an average throughput of 10000 samples per month. The current version of the PIMS sequencing extension works with Applied Biosystems 3130XL 96-well plate sequencer and MWG 4204 or Aviso Theonyx liquid handling robots, but is readily adaptable for use with other combinations of robots. Conclusions PIMS has been extended to provide a user-friendly and integrated data management solution for DNA sequencing facilities that is accessed through a normal web browser and allows simultaneous access by multiple users as well as facility managers. The system integrates sequencing and liquid handling robots, manages the data flow, and provides remote access to the sequencing results. The software is freely available, for academic users, from http://www.pims-lims.org/.
PIMS sequencing extension: a laboratory information management system for DNA sequencing facilities.
Troshin, Peter V; Postis, Vincent Lg; Ashworth, Denise; Baldwin, Stephen A; McPherson, Michael J; Barton, Geoffrey J
2011-03-07
Facilities that provide a service for DNA sequencing typically support large numbers of users and experiment types. The cost of services is often reduced by the use of liquid handling robots but the efficiency of such facilities is hampered because the software for such robots does not usually integrate well with the systems that run the sequencing machines. Accordingly, there is a need for software systems capable of integrating different robotic systems and managing sample information for DNA sequencing services. In this paper, we describe an extension to the Protein Information Management System (PIMS) that is designed for DNA sequencing facilities. The new version of PIMS has a user-friendly web interface and integrates all aspects of the sequencing process, including sample submission, handling and tracking, together with capture and management of the data. The PIMS sequencing extension has been in production since July 2009 at the University of Leeds DNA Sequencing Facility. It has completely replaced manual data handling and simplified the tasks of data management and user communication. Samples from 45 groups have been processed with an average throughput of 10000 samples per month. The current version of the PIMS sequencing extension works with Applied Biosystems 3130XL 96-well plate sequencer and MWG 4204 or Aviso Theonyx liquid handling robots, but is readily adaptable for use with other combinations of robots. PIMS has been extended to provide a user-friendly and integrated data management solution for DNA sequencing facilities that is accessed through a normal web browser and allows simultaneous access by multiple users as well as facility managers. The system integrates sequencing and liquid handling robots, manages the data flow, and provides remote access to the sequencing results. The software is freely available, for academic users, from http://www.pims-lims.org/.
Compact flow diagrams for state sequences
Buchin, Kevin; Buchin, Maike; Gudmundsson, Joachim; Horton, Michael; Sijben, Stef
2017-01-01
We introduce the concept of using a flow diagram to compactly represent the segmentation of a large number of state sequences according to a set of criteria. We argue that this flow diagram representation gives an intuitive summary that allows the user to detect patterns within the segmentations. In
1985-02-01
of the blade. The Darrieus VAWT has more complex aerodynamics. This type of wind turbine produces power as a result of the tangential thrust as...Horizontal Axis Propeller-Type b) Verticle Axis Darrieus -Type Figure 78. Wind Turbine Configurations 0 6 Q K [_ 2 -, C 4 UJ UJ...Sailplanes 23 5.2 Wind Turbines 23 6. CONCLUDING REMARKS 24 7. RECOMMENDATIONS FOR FUTURE RESEARCH 24 REFERENCES 25 FIGURES 32 yv/ LOW REYNOLDS NUMBER
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
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.
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...
New PN Even Balanced Sequences for Spread-Spectrum Systems
Directory of Open Access Journals (Sweden)
Inácio JAL
2005-01-01
Full Text Available A new class of pseudonoise even balanced (PN-EB binary spreading sequences is derived from existing classical odd-length families of maximum-length sequences, such as those proposed by Gold, by appending or inserting one extra-zero element (chip to the original sequences. The incentive to generate large families of PN-EB spreading sequences is motivated by analyzing the spreading effect of these sequences from a natural sampling point of view. From this analysis a new definition for PG is established, from which it becomes clear that very high processing gains (PGs can be achieved in band-limited direct-sequence spread-spectrum (DSSS applications by using spreading sequences with zero mean, given that certain conditions regarding spectral aliasing are met. To obtain large families of even balanced (i.e., equal number of ones and zeros sequences, two design criteria are proposed, namely the ranging criterion (RC and the generating ranging criterion (GRC. PN-EB sequences in the polynomial range are derived using these criteria, and it is shown that they exhibit secondary autocorrelation and cross-correlation peaks comparable to the sequences they are derived from. The methods proposed not only facilitate the generation of large numbers of new PN-EB spreading sequences required for CDMA applications, but simultaneously offer high processing gains and good despreading characteristics in multiuser SS scenarios with band-limited noise and interference spectra. Simulation results are presented to confirm the respective claims made.
LeVeque, William J
2002-01-01
Classic two-part work now available in a single volume assumes no prior theoretical knowledge on reader's part and develops the subject fully. Volume I is a suitable first course text for advanced undergraduate and beginning graduate students. Volume II requires a much higher level of mathematical maturity, including a working knowledge of the theory of analytic functions. Contents range from chapters on binary quadratic forms to the Thue-Siegel-Roth Theorem and the Prime Number Theorem. Includes numerous problems and hints for their solutions. 1956 edition. Supplementary Reading. List of Symb
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...
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
Twin anemia polycythemia sequence
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
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 ...
Targeted sequencing of plant genomes
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-...
Almost convergence of triple sequences
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.
A neurocomputational model of automatic sequence production.
Helie, Sebastien; Roeder, Jessica L; Vucovich, Lauren; Rünger, Dennis; Ashby, F Gregory
2015-07-01
Most behaviors unfold in time and include a sequence of submovements or cognitive activities. In addition, most behaviors are automatic and repeated daily throughout life. Yet, relatively little is known about the neurobiology of automatic sequence production. Past research suggests a gradual transfer from the associative striatum to the sensorimotor striatum, but a number of more recent studies challenge this role of the BG in automatic sequence production. In this article, we propose a new neurocomputational model of automatic sequence production in which the main role of the BG is to train cortical-cortical connections within the premotor areas that are responsible for automatic sequence production. The new model is used to simulate four different data sets from human and nonhuman animals, including (1) behavioral data (e.g., RTs), (2) electrophysiology data (e.g., single-neuron recordings), (3) macrostructure data (e.g., TMS), and (4) neurological circuit data (e.g., inactivation studies). We conclude with a comparison of the new model with existing models of automatic sequence production and discuss a possible new role for the BG in automaticity and its implication for Parkinson's disease.
The complete amino acid sequence of human erythrocyte diphosphoglycerate mutase.
Haggarty, N W; Dunbar, B; Fothergill, L A
1983-01-01
The complete amino acid sequence of human erythrocyte diphosphoglycerate mutase, comprising 239 residues, was determined. The sequence was deduced from the four cyanogen bromide fragments, and from the peptides derived from these fragments after digestion with a number of proteolytic enzymes. Comparison of this sequence with that of the yeast glycolytic enzyme, phosphoglycerate mutase, shows that these enzymes are 47% identical. Most, but not all, of the residues implicated as being important...
Sequence dependent aggregation of peptides and fibril formation
Hung, Nguyen Ba; Le, Duy-Manh; Hoang, Trinh X.
2017-09-01
Deciphering the links between amino acid sequence and amyloid fibril formation is key for understanding protein misfolding diseases. Here we use Monte Carlo simulations to study the aggregation of short peptides in a coarse-grained model with hydrophobic-polar (HP) amino acid sequences and correlated side chain orientations for hydrophobic contacts. A significant heterogeneity is observed in the aggregate structures and in the thermodynamics of aggregation for systems of different HP sequences and different numbers of peptides. Fibril-like ordered aggregates are found for several sequences that contain the common HPH pattern, while other sequences may form helix bundles or disordered aggregates. A wide variation of the aggregation transition temperatures among sequences, even among those of the same hydrophobic fraction, indicates that not all sequences undergo aggregation at a presumable physiological temperature. The transition is found to be the most cooperative for sequences forming fibril-like structures. For a fibril-prone sequence, it is shown that fibril formation follows the nucleation and growth mechanism. Interestingly, a binary mixture of peptides of an aggregation-prone and a non-aggregation-prone sequence shows the association and conversion of the latter to the fibrillar structure. Our study highlights the role of a sequence in selecting fibril-like aggregates and also the impact of a structural template on fibril formation by peptides of unrelated sequences.
Data selector group sequencer interface
International Nuclear Information System (INIS)
Zizka, G.; Turko, B.
1984-01-01
A CAMAC-based module for high rate data selection and transfer to Tracor Northern TN-1700 multichannel analysis system is described. The module can select any group of 4096 consecutive addresses of events, in the range of 24 bits. This module solves the problem of connecting a number of time digitizing systems to the memory of a multichannel analyzer. Continuous processing rate up to 200,000 events per second along with the live display make the testing of the above systems very efficient and relatively inexpensive. The module also can be programmed for storing the preset group of addresses into more than one section of the memory. The events are analyzed in each section of the memory during the preset time. Multiple spectra can thus be taken automatically in a sequence
Approaches for in silico finishing of microbial genome sequences
Directory of Open Access Journals (Sweden)
Frederico Schmitt Kremer
Full Text Available Abstract The introduction of next-generation sequencing (NGS had a significant effect on the availability of genomic information, leading to an increase in the number of sequenced genomes from a large spectrum of organisms. Unfortunately, due to the limitations implied by the short-read sequencing platforms, most of these newly sequenced genomes remained as “drafts”, incomplete representations of the whole genetic content. The previous genome sequencing studies indicated that finishing a genome sequenced by NGS, even bacteria, may require additional sequencing to fill the gaps, making the entire process very expensive. As such, several in silico approaches have been developed to optimize the genome assemblies and facilitate the finishing process. The present review aims to explore some free (open source, in many cases tools that are available to facilitate genome finishing.
Approaches for in silico finishing of microbial genome sequences.
Kremer, Frederico Schmitt; McBride, Alan John Alexander; Pinto, Luciano da Silva
The introduction of next-generation sequencing (NGS) had a significant effect on the availability of genomic information, leading to an increase in the number of sequenced genomes from a large spectrum of organisms. Unfortunately, due to the limitations implied by the short-read sequencing platforms, most of these newly sequenced genomes remained as "drafts", incomplete representations of the whole genetic content. The previous genome sequencing studies indicated that finishing a genome sequenced by NGS, even bacteria, may require additional sequencing to fill the gaps, making the entire process very expensive. As such, several in silico approaches have been developed to optimize the genome assemblies and facilitate the finishing process. The present review aims to explore some free (open source, in many cases) tools that are available to facilitate genome finishing.
Spent fuel bundle counter sequence error manual - BRUCE NGS
International Nuclear Information System (INIS)
Nicholson, L.E.
1992-01-01
The Spent Fuel Bundle Counter (SFBC) is used to count the number and type of spent fuel transfers that occur into or out of controlled areas at CANDU reactor sites. However if the transfers are executed in a non-standard manner or the SFBC is malfunctioning, the transfers are recorded as sequence errors. Each sequence error message typically contains adequate information to determine the cause of the message. This manual provides a guide to interpret the various sequence error messages that can occur and suggests probable cause or causes of the sequence errors. Each likely sequence error is presented on a 'card' in Appendix A. Note that it would be impractical to generate a sequence error card file with entries for all possible combinations of faults. Therefore the card file contains sequences with only one fault at a time. Some exceptions have been included however where experience has indicated that several faults can occur simultaneously
Spent fuel bundle counter sequence error manual - DARLINGTON NGS
International Nuclear Information System (INIS)
Nicholson, L.E.
1992-01-01
The Spent Fuel Bundle Counter (SFBC) is used to count the number and type of spent fuel transfers that occur into or out of controlled areas at CANDU reactor sites. However if the transfers are executed in a non-standard manner or the SFBC is malfunctioning, the transfers are recorded as sequence errors. Each sequence error message typically contains adequate information to determine the cause of the message. This manual provides a guide to interpret the various sequence error messages that can occur and suggests probable cause or causes of the sequence errors. Each likely sequence error is presented on a 'card' in Appendix A. Note that it would be impractical to generate a sequence error card file with entries for all possible combinations of faults. Therefore the card file contains sequences with only one fault at a time. Some exceptions have been included however where experience has indicated that several faults can occur simultaneously
Output-Sensitive Pattern Extraction in Sequences
DEFF Research Database (Denmark)
Grossi, Roberto; Menconi, Giulia; Pisanti, Nadia
2014-01-01
Genomic Analysis, Plagiarism Detection, Data Mining, Intrusion Detection, Spam Fighting and Time Series Analysis are just some examples of applications where extraction of recurring patterns in sequences of objects is one of the main computational challenges. Several notions of patterns exist...... or extend them causes a loss of significant information (where the number of occurrences changes). Output-sensitive algorithms have been proposed to enumerate and list these patterns, taking polynomial time O(nc) per pattern for constant c > 1, which is impractical for massive sequences of very large length...