Cryptographic pseudo-random sequences from the chaotic Hénon ...
Indian Academy of Sciences (India)
Pseudo-random number sequences are useful in many applications including Monte-Carlo simulation, spread spectrum ... a pseudo-random binary sequence from the two-dimensional chaotic Hénon map is explored. ... is the Hénon map, a two-dimensional discrete-time nonlinear dynamical system represented by the state ...
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.
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.
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.
Pseudo-random number generator based on asymptotic deterministic randomness
Energy Technology Data Exchange (ETDEWEB)
Wang Kai [Department of Radio Engineering, Southeast University, Nanjing (China)], E-mail: kaiwang@seu.edu.cn; Pei Wenjiang; Xia Haishan [Department of Radio Engineering, Southeast University, Nanjing (China); Cheung Yiuming [Department of Computer Science, Hong Kong Baptist University, Hong Kong (China)
2008-06-09
A novel approach to generate the pseudorandom-bit sequence from the asymptotic deterministic randomness system is proposed in this Letter. We study the characteristic of multi-value correspondence of the asymptotic deterministic randomness constructed by the piecewise linear map and the noninvertible nonlinearity transform, and then give the discretized systems in the finite digitized state space. The statistic characteristics of the asymptotic deterministic randomness are investigated numerically, such as stationary probability density function and random-like behavior. Furthermore, we analyze the dynamics of the symbolic sequence. Both theoretical and experimental results show that the symbolic sequence of the asymptotic deterministic randomness possesses very good cryptographic properties, which improve the security of chaos based PRBGs and increase the resistance against entropy attacks and symbolic dynamics attacks.
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 ...
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.
Concurrent Generation of Pseudo Random Numbers with LFSR of Fibonacci and Galois Type
Emina I. Milovanović; Stojčev, Mile K.; Igor Ž. Milovanović; Tatjana R. Nikolić; Zoran Stamenković
2016-01-01
We have considered implementation of parallel test pattern generator based on a linear feedback shift register (LFSR) with multiple outputs used as a building block in built-in-self-test (BIST) design within SoC. The proposed design can drive several circuits under test (CUT) simultaneously. The mathematical procedure for concurrent pseudo random number (PRN) generation is described. We have implemented LFSRs that generate two and three PRNs in FPGA and ASIC technology. The design was tested ...
Complexity and properties of a multidimensional Cat-Hadamard map for pseudo random number generation
Kim Hue, Ta Thi; Hoang, Thang Manh
2017-07-01
This paper presents a novel method to extend the Cat map from 2-dimension to higher dimension using the fast pseudo Hadamard Transform, and the resulted maps are called Cat-Hadamard maps. The complexity and properties of Cat-Hadamard maps are investigated under the point of view for cryptographic applications. In addition, we propose a method for constructing a pseudo random number generator using a novel design concept of the high dimensional Cat map. The simulation results show that the proposed generator fulfilled all the statistic tests of the NIST SP 800-90 A.
Koschate, J; Drescher, U; Thieschäfer, L; Heine, O; Baum, K; Hoffmann, U
2016-12-01
This study aims to compare cardiorespiratory kinetics as a response to a standardised work rate protocol with pseudo-random binary sequences between cycling and walking in young healthy subjects. Muscular and pulmonary oxygen uptake (V̇O2) kinetics as well as heart rate kinetics were expected to be similar for walking and cycling. Cardiac data and V̇O2 of 23 healthy young subjects were measured in response to pseudo-random binary sequences. Kinetics were assessed applying time series analysis. Higher maxima of cross-correlation functions between work rate and the respective parameter indicate faster kinetics responses. Muscular V̇O2 kinetics were estimated from heart rate and pulmonary V̇O2 using a circulatory model. Muscular (walking vs. cycling [mean±SD in arbitrary units]: 0.40±0.08 vs. 0.41±0.08) and pulmonary V̇O2 kinetics (0.35±0.06 vs. 0.35±0.06) were not different, although the time courses of the cross-correlation functions of pulmonary V̇O2 showed unexpected biphasic responses. Heart rate kinetics (0.50±0.14 vs. 0.40±0.14; P=0.017) was faster for walking. Regarding the biphasic cross-correlation functions of pulmonary V̇O2 during walking, the assessment of muscular V̇O2 kinetics via pseudo-random binary sequences requires a circulatory model to account for cardio-dynamic distortions. Faster heart rate kinetics for walking should be considered by comparing results from cycle and treadmill ergometry. © Georg Thieme Verlag KG Stuttgart · New York.
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.
Pseudo-random-bit-sequence phase modulation for reduced errors in a fiber optic gyroscope.
Chamoun, Jacob; Digonnet, Michel J F
2016-12-15
Low noise and drift in a laser-driven fiber optic gyroscope (FOG) are demonstrated by interrogating the sensor with a low-coherence laser. The laser coherence was reduced by broadening its optical spectrum using an external electro-optic phase modulator driven by either a sinusoidal or a pseudo-random bit sequence (PRBS) waveform. The noise reduction measured in a FOG driven by a modulated laser agrees with the calculations based on the broadened laser spectrum. Using PRBS modulation, the linewidth of a laser was broadened from 10 MHz to more than 10 GHz, leading to a measured FOG noise of only 0.00073 deg/√h and a drift of 0.023 deg/h. To the best of our knowledge, these are the lowest noise and drift reported in a laser-driven FOG, and this noise is below the requirement for the inertial navigation of aircraft.
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.
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.
New Design of Crypto-Based Pseudo random number generator (CBPRNG) using BLOW FISH cipher
T.Chalama Reddy; Dr.R.Seshadri
2013-01-01
Random Number Generators (RNGs) are an important building block for algorithms and protocols in cryptography. Random number generation is used in a wide variety of cryptographic operations, such as key generation and challenge/response protocols. A random number generator outputs a sequence of 0s and 1s such that at any position, the next bit cannot be expected on the previous bits. However, true random number produces non- deterministic output since if the same random generator is run twice,...
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)
Mersenne Twister: A 623-Dimensionally Equidistributed Uniform Pseudo-Random Number Generator
Matsumoto, Makoto; Nishimura, Takuji
1998-01-01
A new algorithm called Mersenne Twister (MT) is proposed for generating uniform pseudorandom numbers. For a particular choice of parameters, the algorithm provides a super astronomical period of 219937 - 1 and 623-dimensional equidistribution up to 32-bit accuracy, while using a working area of only 624 words. This is a new variant of the previously proposed generators, TGFSR, modified so as to admit a Mersenne-prime period. The characteristic polynomial has many terms. The distribution up to...
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 ...
Drescher, U; Koschate, J; Schiffer, T; Schneider, S; Hoffmann, U
2017-06-01
The aim of the study was to compare the kinetics responses of heart rate (HR), pulmonary (V˙O2pulm) and predicted muscular (V˙O2musc) oxygen uptake between two different pseudo-random binary sequence (PRBS) work rate (WR) amplitudes both below anaerobic threshold. Eight healthy individuals performed two PRBS WR protocols implying changes between 30W and 80W and between 30W and 110W. HR and V˙O2pulm were measured beat-to-beat and breath-by-breath, respectively. V˙O2musc was estimated applying the approach of Hoffmann et al. (Eur J Appl Physiol 113: 1745-1754, 2013) considering a circulatory model for venous return and cross-correlation functions (CCF) for the kinetics analysis. HR and V˙O2musc kinetics seem to be independent of WR intensity (p>0.05). V˙O2pulm kinetics show prominent differences in the lag of the CCF maximum (39±9s; 31±4s; pkinetics remain unchanged. Copyright © 2017 Elsevier B.V. All rights reserved.
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
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.
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%.
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.
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
Ren Jian
2004-01-01
Pseudo-random sequence with good correlation property and large linear span is widely used in code division multiple access (CDMA) communication systems and cryptology for reliable and secure information transmission. In this paper, sequences with long period, large complexity, balance statistics, and low cross-correlation property are constructed from the addition of m -sequences with pairwise-prime linear spans (AMPLS). Using m -sequences as building blocks, the proposed method proved to...
1.2 GBit/s Pseudo Random Pulse Generator Using Multiplexing with GaAs Mesfet Gates
DEFF Research Database (Denmark)
Hede, Carsten
1978-01-01
A l.2 Gbit/s RZ pseudo random bit generator using multiplexing of six 200 Mbit/s channels, and a GaAs-MESFET gate circuit which exhibits both high speed and simplicity are presented. As a new contribution to the treatment of pseudo random sequences it is shown how the autocorrelation function and...
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.
Calibration of correlation radiometers using pseudo-random noise signals.
Pérez, Isaac Ramos; Bosch-Lluis, Xavi; Camps, Adriano; Alvarez, Nereida Rodriguez; Hernandez, Juan Fernando Marchán; Domènech, Enric Valencia; Vernich, Carlos; de la Rosa, Sonia; Pantoja, Sebastián
2009-01-01
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.
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
Energy Technology Data Exchange (ETDEWEB)
V Yashchuk; R Conley; E Anderson; S Barber; N Bouet; W McKinney; P Takacs; D Voronov
2011-12-31
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] and [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 WiSi2/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
Energy Technology Data Exchange (ETDEWEB)
Yashchuk, Valeriy V., E-mail: VVYashchuk@lbl.gov [Advanced Light Source, Lawrence Berkeley National Laboratory, Berkeley, CA 94720 (United States); Conley, Raymond [NSLS-II, Brookhaven National Laboratory, Upton, NY 11973 (United States); Anderson, Erik H. [Center for X-ray Optics, Lawrence Berkeley National Laboratory, Berkeley, CA 94720 (United States); Barber, Samuel K. [Advanced Light Source, Lawrence Berkeley National Laboratory, Berkeley, CA 94720 (United States); Bouet, Nathalie [NSLS-II, Brookhaven National Laboratory, Upton, NY 11973 (United States); McKinney, Wayne R. [Advanced Light Source, Lawrence Berkeley National Laboratory, Berkeley, CA 94720 (United States); Takacs, Peter Z. [Brookhaven National Laboratory, Upton, NY 11973 (United States); Voronov, Dmitriy L. [Advanced Light Source, Lawrence Berkeley National Laboratory, Berkeley, CA 94720 (United States)
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 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{sub 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.
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.
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.
Algorithm for generation pseudo-random series with arbitrarily assigned distribution law
Directory of Open Access Journals (Sweden)
В.С. Єременко
2005-04-01
Full Text Available Method for generation pseudo-random series with arbitrarily assigned distribution law has been proposed. The praxis of using proposed method for generation pseudo-random series with anti-modal and approximate to Gaussian distribution law has been investigated.
Pseudo-random Spray Release to Measure World-wide Transfer Functions of Cloud Albedo Control.
Salter, Stephen
2010-05-01
Institute for Energy Systems, School of Engineering, University of Edinburgh. S.Salter@ed.ac.uk Previous climate models of Latham's proposal to reverse global warming by using sub-micron sea spray to increase cloud albedo have used a variety of spray patterns. Kettles forced CCN concentration to be 375/cm3 everywhere. Rasch et al used the 20% and 70% most susceptible regions. Bala and Caldeira used an even spread. Jones et al. concentrated spray in the 3.3% oceans with the highest susceptibility All used the same rate through the year. We want to choose a scheme for a climate-modelling experiment designed to identify simultaneously the effects of cloud albedo control at various seasons of the year from spray at all regions of the world on climates of all other regions the world. In particular we want to know seasons and spray places which might have an undesirable effect on precipitation. The spray systems in various regions of a numerical climate model will be modulated on an off with different but known pseudo-random sequences and a selection of seasons. The mean value of the resulting weather records of the parameters of interest, mainly temperature and water run-off, at each region will be subtracted from each value of the record so as to give just the alternating component with an average value of zero. This will be correlated with each of the chosen pseudo-random sequences to give the magnitude and polarity of the effect of a treatment at each input area and selected seasons of the year with the resulting effects on all regions. By doing a time-shifted correlation we can account for phase-shift and time delay. The signal-to-noise ratio should improve with the square root of the analysis time and so we may be able to measure the transfer function with quite a small stimulus. The results of a Mathcad simulation of the process with statistical distributions approximating to natural variations temperature and precipitation show that a single run of a climate
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.
Pseudo-random dynamic address configuration (PRDAC) algorithm for mobile ad hoc networks
Wu, Shaochuan; Tan, Xuezhi
2007-11-01
By analyzing all kinds of address configuration algorithms, this paper provides a new pseudo-random dynamic address configuration (PRDAC) algorithm for mobile ad hoc networks. Based on PRDAC, the first node that initials this network randomly chooses a nonlinear shift register that can generates an m-sequence. When another node joins this network, the initial node will act as an IP address configuration sever to compute an IP address according to this nonlinear shift register, and then allocates this address and tell the generator polynomial of this shift register to this new node. By this means, when other node joins this network, any node that has obtained an IP address can act as a server to allocate address to this new node. PRDAC can also efficiently avoid IP conflicts and deal with network partition and merge as same as prophet address (PA) allocation and dynamic configuration and distribution protocol (DCDP). Furthermore, PRDAC has less algorithm complexity, less computational complexity and more sufficient assumption than PA. In addition, PRDAC radically avoids address conflicts and maximizes the utilization rate of IP addresses. Analysis and simulation results show that PRDAC has rapid convergence, low overhead and immune from topological structures.
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.
Synchronizing microelectrode and electronic goniometer data using a pseudo-random binary signal.
Moore, Tyler Robert; Jacobs, Rennie Underwood; Yang, Alexander Cheung; Richter, Erich Oscar
2013-04-01
Intra-operative investigation of the subthalamic nucleus (STN) requires concurrent measurement of microelectrode voltage, electrode depth and joint movement during deep brain stimulation (DBS) surgery. Commercial solutions to this problem exist but are more expensive. Multiple instruments from different manufacturers can collect the same data, but data from incompatible instruments are collected on disparate clocks, precluding quantitative analysis. A pseudo-random binary signal recorded simultaneously by each set of instruments allows for chronological reconciliation. A custom program collects microelectrode data while simultaneously sending a pseudo-random binary signal to instruments measuring joint movement. The record of this signal is later used to express microelectrode voltage and joint position in a single chronological frame of reference. ClockSynch was used in 15 DBS procedures. After each surgery, records of microelectrode and joint movement were successfully chronologically reconciled. In conclusion, a pseudo-random binary signal integrates disparate systems of instrumentation at a significantly decreased cost.
Sequence Factorial of "g"-Gonal Numbers
Asiru, Muniru A.
2013-01-01
The gamma function, which has the property to interpolate the factorial whenever the argument is an integer, is a special case (the case "g"?=?2) of the general term of the sequence factorial of "g"-gonal numbers. In relation to this special case, a formula for calculating the general term of the sequence factorial of any…
Hurdles in Acquiring the Number Word Sequence
Gould, Peter
2016-01-01
Learning the sequence of number words in English up to 30 is not a simple process. In NSW government schools taking part in "Early Action for Success," over 800 students in each of the first 3 years of school were assessed every 5 weeks over the school year to determine the highest correct oral count they could produce. Rather than…
Energy Technology Data Exchange (ETDEWEB)
Yashchuk, Valeriy V.; McKinney, Wayne R.; Takacs, Peter Z.
2008-05-19
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.
Pseudo-Random Mating Populations. in Celebration of the 80th Anniversary of the Hardy-Weinberg Law
Li, C. C.
1988-01-01
That random mating leads to Hardy-Weinberg distribution of genotypes is well known. This report is to show that, if the deviations from random mating are of a certain pattern, the offspring generation will also be in Hardy-Weinberg proportions. This brings out the fact that random mating is a sufficient condition, not a necessary one, for the attainment of the Hardy-Weinberg proportions. Such nonrandom-mating populations are tentatively said to be pseudo-random mating. Pseudo-random-mating po...
Chromosome number9 specific repetitive DNA sequence
Energy Technology Data Exchange (ETDEWEB)
Joste, N.E.; Cram, L.S.; Hildebrand, C.E.; Jones, M.; Longmire, J.; Robinson, T.; Moyzis, R.K.
1986-05-01
Human repetitive DNA libraries have been constructed and various recombinant DNA clones isolated that are likely candidates for chromosome specific sequences. The first clone tested (pHuR 98; plasmid human repeat 98) was biotinylated and hybridized to human chromosomes in situ. The hybridized recombinant probe was detected with fluoresceinated avidin, and chromosomes were counter-stained with either propidium iodide or distamycin-DAPI. Specific hybridization to chromosome band 9q1 was obtained. The localization was confirmed by hybridizing radiolabeled pHuR 98 DNA to human chromosomes sorted by flow cytometry. Various methods, including orthogonal field pulsed gel electrophoresis analysis indicate that 75 kilobase blocks of this sequence are interspersed with other repetitive DNA sequences in this chromosome band. This study is the first to report a human repetitive DNA sequence uniquely localized to a specific chromosome. This clone provides an easily detected and highly specific chromosomal marker for molecular cytogenetic analyses in numerous basic research and clinical studies.
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.
Comparison theorems for summability methods of sequences of fuzzy numbers
Yavuz, Enes
2016-01-01
In this study we compare Ces\\`{a}ro and Euler weighted mean methods of summability of sequences of fuzzy numbers with Abel and Borel power series methods of summability of sequences of fuzzy numbers. Also some results dealing with series of fuzzy numbers are obtained.
de Manzano, Örjan; Ullén, Fredrik
2012-01-02
To what extent free response generation in different tasks uses common and task-specific neurocognitive processes has remained unclear. Here, we investigated overlap and differences in neural activity during musical improvisation and pseudo-random response generation. Brain activity was measured using fMRI in a group of professional classical pianists, who performed musical improvisation of melodies, pseudo-random key-presses and a baseline condition (sight-reading), on either two, six or twelve keys on a piano keyboard. The results revealed an extensive overlap in neural activity between the two generative conditions. Active regions included the dorsolateral and dorsomedial prefrontal cortices, inferior frontal gyrus, anterior cingulate cortex and pre-SMA. No regions showed higher activity in improvisation than in pseudo-random generation. These findings suggest that the activated regions fulfill generic functions that are utilized in different types of free generation tasks, independent of overall goal. In contrast, pseudo-random generation was accompanied by higher activity than improvisation in several regions. This presumably reflects the participants' musical expertise as well as the pseudo-random generation task's high load on attention, working memory, and executive control. The results highlight the significance of using naturalistic tasks to study human behavior and cognition. No brain activity was related to the size of the response set. We discuss that this may reflect that the musicians were able to use specific strategies for improvisation, by which there was no simple relationship between response set size and neural activity. Copyright © 2011 Elsevier Inc. All rights reserved.
Pseudo-random mating populations. In celebration of the 80th anniversary of the Hardy-Weinberg law.
Li, C C
1988-07-01
That random mating leads to Hardy-Weinberg distribution of genotypes is well known. This report is to show that, if the deviations from random mating are of a certain pattern, the offspring generation will also be in Hardy-Weinberg proportions. This brings out the fact that random mating is a sufficient condition, not a necessary one, for the attainment of the Hardy-Weinberg proportions. Such nonrandom-mating populations are tentatively said to be pseudo-random mating. Pseudo-random-mating populations exist for both autosomal and sex-linked systems with two or multiple alleles. This report covers the basic case of a two-allele autosomal locus in detail, but the possible extension to two loci and cytonuclear systems have also been mentioned in discussion.
Mapping copy number variation by population-scale genome sequencing
DEFF Research Database (Denmark)
Mills, Ryan E.; Walter, Klaudia; Stewart, Chip
2011-01-01
, 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...... differences in the size spectra of SVs originating from distinct formation mechanisms, and constructed a map of SV hotspots formed by common mechanisms. Our analytical framework and SV map serves as a resource for sequencing-based association studies....
Laugier, Alexandre; Saikia, Manjil P.
2012-01-01
In this paper we study the Fibonacci numbers and derive some interesting properties and recurrence relations. We prove some charecterizations for $F_p$, where $p$ is a prime of a certain type. We also define period of a Fibonacci sequence modulo an integer, $m$ and derive certain interesting properties related to them. Afterwards, we derive some new properties of a class of generalized Fibonacci numbers. In the last part of the paper we introduce some generalized Fibonacci polynomial sequence...
Understanding Number Sequences Leads to Understanding Mathematics Concepts
Pasnak, Robert; Schmerold, Katrina Lea; Robinson, Melissa Fetterer; Gadzichowski, K. Marinka; Bock, Allison M.; O'Brien, Sarah Eva; Kidd, Julie K.; Gallington, Deb A.
2016-01-01
Ninety-six first grade students in an urban school system were tested in October and May on reading, mathematics, and their understanding of sequences of letters and numbers. A time lag analysis was subsequently conducted. In such analyses, cross-correlations between the first measurement of one variable and the second measurement of another are…
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...
Comparative Copy Number Variation From Whole Genome Sequencing
Janevski, A.; Varadan, V.; Kamalakaran, S.; Banerjee, N.; Dimitrova, D.
2011-01-01
Whole genome sequencing enables a high resolution view of the humangenome and enables unique insights into copy number variations in anunprecedented scale. Numerous tools and studies have already been introduced that provide confirmatory and new genomic variability datain individuals and across
The resulting node number sequence may increase the bandwidth ...
Indian Academy of Sciences (India)
204 N Ramakrishnan, T_ Balakrishna Bhat and V S Arunachalam point of intersection and the nodal and elemental directories are appropriately altered. The resulting node number sequence may increase the bandwidth of the stiffness matrix. Therefore the region of interest is scanned and the nodal and the elemental.
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.
Mahmoudian, Massoud; Rezvani, Mohammad; Rohani, Mohammad; Benaissa, Foozya; Jalili, Mehdi; Ghourchian, Shadi
2015-01-05
Massive ischemic stroke causes significant mortality and morbidity in stroke patients. The main treatments for massive ischemic stroke are recombinant tissue plasminogen activator (rtPA), craniotomy, and endovascular interventions. Due to destructive effects of bradykinin on the nervous system in ischemic stroke, it seems reasonable that using Noscapine as a Bradykinin antagonist may improve patients' outcome after ischemic stroke. The effect of Noscapine on massive ischemic stroke was shown by the previous pilot study by our group. This pseudo-randomized clinical trial study was designed to assess the result of the pilot study. Patients who had clinical symptoms or computed tomography scan indicative of massive stroke (in full middle cerebral artery territory) were entered to the study. The cases received the drugs according to their turns in emergency ward (pseudo-randomized). The patient group received Noscapine, and the control group received common supportive treatments. The patients and data analyzer were blinded about the data. At the end of the study, to adjust confounding variables we used logistic regression. After 1-month follow-up, 16 patients in the control group and 11 patients in the case group expired (P = 0.193). Analyzing the data extracted from Rankin scale and Barthel index check lists, revealed no significant differences in the two groups. Despite the absence of significant statistical results in our study, the reduction rate of 16% for mortality rate in Noscapine recipients is clinically remarkable and motivates future studies with larger sample sizes.
Estimation of copy number alterations from exome sequencing data.
Directory of Open Access Journals (Sweden)
Rafael Valdés-Mas
Full Text Available Exome sequencing constitutes an important technology for the study of human hereditary diseases and cancer. However, the ability of this approach to identify copy number alterations in primary tumor samples has not been fully addressed. Here we show that somatic copy number alterations can be reliably estimated using exome sequencing data through a strategy that we have termed exome2cnv. Using data from 86 paired normal and primary tumor samples, we identified losses and gains of complete chromosomes or large genomic regions, as well as smaller regions affecting a minimum of one gene. Comparison with high-resolution comparative genomic hybridization (CGH arrays revealed a high sensitivity and a low number of false positives in the copy number estimation between both approaches. We explore the main factors affecting sensitivity and false positives with real data, and provide a side by side comparison with CGH arrays. Together, these results underscore the utility of exome sequencing to study cancer samples by allowing not only the identification of substitutions and indels, but also the accurate estimation of copy number alterations.
Humans cannot consciously generate random numbers sequences: Polemic study.
Figurska, Małgorzata; Stańczyk, Maciej; Kulesza, Kamil
2008-01-01
It is widely believed, that randomness exists in Nature. In fact such an assumption underlies many scientific theories and is embedded in the foundations of quantum mechanics. Assuming that this hypothesis is valid one can use natural phenomena, like radioactive decay, to generate random numbers. Today, computers are capable of generating the so-called pseudorandom numbers. Such series of numbers are only seemingly random (bias in the randomness quality can be observed). Question whether people can produce random numbers, has been investigated by many scientists in the recent years. The paper "Humans can consciously generate random numbers sequences..." published recently in Medical Hypotheses made claims that were in many ways contrary to state of art; it also stated far-reaching hypotheses. So, we decided to repeat the experiments reported, with special care being taken of proper laboratory procedures. Here, we present the results and discuss possible implications in computer and other sciences.
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.
Energy Technology Data Exchange (ETDEWEB)
Yashchuk, Valeriy V.; McKinney, Wayne R.; Takacs, Peter Z.
2007-07-25
The task of designing high performance X-ray optical systemsrequires the development of sophisticated X-ray scattering calculationsbased on rigorous information about the optics. One of the mostinsightful approaches to these calculations is based on the powerspectral density (PSD) distribution of the surface height. The majorproblem of measurement of a PSD distribution with an interferometricand/or atomic force microscope arises due to the unknown ModulationTransfer Function (MTF) of the instruments. The MTF characterizes theperturbation of the PSD distribution at higher spatial frequencies. Here,we describe a new method and dedicated test surfaces for calibration ofthe MTF of a microscope. The method is based on use of a speciallydesigned Binary Pseudo-random (BPR) grating. Comparison of atheoretically calculated PSD spectrum of a BPR grating with a spectrummeasured with the grating provides the desired calibration of theinstrumental MTF. The theoretical background of the method, as well asresults of experimental investigations are presented.
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.
Cooperative multi-user detection and ranging based on pseudo-random codes
Morhart, C.; Biebl, E. M.
2009-05-01
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.
p-Absolutely summable sequences of fuzzy real numbers
Directory of Open Access Journals (Sweden)
Ayhan Esi
2013-03-01
Full Text Available In this paper the fuzzy sequence space is introduced and some algebraic properties such as solidness, symmetricalness, convergence free and sequence algebra are studied, and some inclusion relations for the space are provided.
Energy Technology Data Exchange (ETDEWEB)
YASHCHUK,V.V.; MCKINNEY, W.R.; TAKACS, P.Z.
2007-08-01
The task of designing high performance X-ray optical systems requires the development of sophisticated X-ray scattering calculations based on rigorous information about the optics. One of the most insightful approaches to these calculations is based on the power spectral density (PSD) distribution of the surface height. The major problem of measurement of a PSD distribution with an interferometric and/or atomic force microscope arises due to the unknown Modulation Transfer Function (MTF) of the instruments. The MTF characterizes the perturbation of the PSD distribution at higher spatial frequencies. Here, we describe a new method and dedicated test surfaces for calibration of the MTF of a microscope. The method is based on use of a specially designed Binary Pseudo-random (BPR) grating. Comparison of a theoretically calculated PSD spectrum of a BPR grating with a spectrum measured with the grating provides the desired calibration of the instrumental MTF. The theoretical background of the method, as well as results of experimental investigations are presented.
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…
Energy Technology Data Exchange (ETDEWEB)
Barber, Samuel K.; Anderson, Erik H.; Cambie, Rossana; Marchesini, Stefano; McKinney, Wayne R.; Takacs, Peter Z.; Voronov, Dmitry L.; Yashchuk, Valeriy V.
2010-03-31
The major problem of measurement of a power spectral density (PSD) distribution of surface heights with surface profilometers arises due to the unknown Modulation Transfer Function (MTF) of the instruments, which tends to distort the PSD at higher spatial frequencies. The special mathematical properties of binary pseudo-random patterns make them an ideal basis for developing MTF calibration test surfaces. Two-dimensional binary pseudo-random arrays (BPRAs) have been fabricated and used for the MTF calibration of the MicroMap{trademark}-570 interferometric microscope with all available objectives. An investigation into the effects of fabrication imperfections on the quality of the MTF calibration and a procedure for accounting for such imperfections are presented.
Vu, Trang; Harris, Anthony; Duncan, Gregg; Sussman, Geoff
2007-09-01
To evaluate the cost-effectiveness of a multidisciplinary wound care team in the nursing home setting from a health system perspective. Pseudo-randomized pragmatic cluster trial with 20-week follow-up involving 342 uncomplicated leg and pressure ulcers in 176 residents located in 44 high-care nursing homes in Melbourne, Australia in 1999-2000. Twenty-one nursing homes (180 wounds in 94 residents) were assigned to the intervention arm and 23 to the control arm (162 wounds in 82 residents). Residents in the intervention arm received standardized treatment from a wound care team comprising of trained community pharmacists and nurses. Residents in the control arm received usual care. More wounds healed during the trial in the intervention arm than in the control arm (61.7% versus 52.5%, P = 0.07). A Cox regression with shared frailty predicted that the chances of healing increased 73% for intervention wounds [95% confidence interval (CI) 20-150%, P = 0.003]. The mean treatment cost was $A616.4 for intervention and $A977.9 for control patients (P = 0.006). Most cost reduction was obtained from decreases in nursing time and waste disposal. The mean cost saving per wound, adjusted for baseline wound severity and random censoring, was $A277.9 (95% CI $A21.6-$A534.1). Standardized treatment provided by a multidisciplinary wound care team saved costs and improved chronic wound healing in nursing homes. The main source of saving was in the cost of nursing time in applying traditional dressings and in the cost of their disposal.
Lockwood, M.; Owens, M. J.; Barnard, L.
2016-11-01
We use five test data series to search for, and quantify, putative discontinuities around 1946 in five different annual-mean sunspot-number or sunspot-group-number data sequences. The data series tested are the original and new versions of the Wolf/Zürich/International sunspot number composite [R_{{ISNv1}} and R_{{ISNv2}}] (respectively Clette et al. in Adv. Space Res. 40, 919, 2007 and Clette et al. in The Solar Activity Cycle 35, Springer, New York, 2015); the corrected version of R ISNv1 proposed by Lockwood, Owens, and Barnard ( J. Geophys. Res. 119, 5193, 2014a) [R C]; the new "backbone" group-number composite proposed by Svalgaard and Schatten ( Solar Phys. 291, 2016) [R_{{BB}}]; and the new group-number composite derived by Usoskin et al. ( Solar Phys. 291, 2016) [R_{{UEA}}]. The test data series used are the group-number [NG] and total sunspot area [A G] from the Royal Observatory, Greenwich/Royal Greenwich Observatory (RGO) photoheliographic data; the Ca K index from the recent re-analysis of Mount Wilson Observatory (MWO) spectroheliograms in the Calcium ii K ion line; the sunspot-group-number from the MWO sunspot drawings [N_{{MWO}}]; and the dayside ionospheric F2-region critical frequencies measured by the Slough ionosonde [foF2]. These test data all vary in close association with sunspot numbers, in some cases non-linearly. The tests are carried out using both the before-and-after fit-residual comparison method and the correlation method of Lockwood, Owens, and Barnard, applied to annual mean data for intervals iterated to minimise errors and to eliminate uncertainties associated with the precise date of the putative discontinuity. It is not assumed that the correction required is by a constant factor, nor even linear in sunspot number. It is shown that a non-linear correction is required by RC, R_{BB}, and R_{{ISNv1}}, but not by R_{{ISNv2}} or R_{{UEA}}. The five test datasets give very similar results in all cases. By multiplying the probability
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.
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 Classes of Difference Sequence Spaces of Fuzzy Real Numbers Defined by Orlicz Function
Directory of Open Access Journals (Sweden)
Binod Chandra Tripathy
2011-01-01
Full Text Available We introduce the classes of generalized difference bounded, convergent, and null sequences of fuzzy real numbers defined by an Orlicz function. Some properties of these sequence spaces like solidness, symmetricity, and convergence-free are studied. We obtain some inclusion relations involving these sequence spaces.
$\\mathcal{I}$ and $\\mathcal{I}^{\\ast}$ convergence of multiple sequences of fuzzy numbers
Directory of Open Access Journals (Sweden)
Pankaj Kumar
2015-07-01
Full Text Available Recently, the concept of statistical convergence for multiple sequences of fuzzy numbers has been studied by Kumar et al. This motivate us to extend the idea of $\\mathcal{I}$-convergence to sequences of fuzzy numbers of multiplicity greater than two.
RefCNV: Identification of Gene-Based Copy Number Variants Using Whole Exome Sequencing
Lun-Ching Chang; Biswajit Das; Chih-Jian Lih; Han Si; Camalier, Corinne E.; Paul M. McGregor III; Eric Polley
2016-01-01
With rapid advances in DNA sequencing technologies, whole exome sequencing (WES) has become a popular approach for detecting somatic mutations in oncology studies. The initial intent of WES was to characterize single nucleotide variants, but it was observed that the number of sequencing reads that mapped to a genomic region correlated with the DNA copy number variants (CNVs). We propose a method RefCNV that uses a reference set to estimate the distribution of the coverage for each exon. The c...
On some generalised I-convergent sequence spaces of double interval numbers
Directory of Open Access Journals (Sweden)
Esi Esi
2016-04-01
Full Text Available In this article we introduce and study some spaces of I-convergent sequences of double interval numbers with the help of a double sequence F=(f_{i,j} of modulii and double bounded sequence p=(p_{i,j} of positive real numbers. We study some topological and algebraic properties, prove the decomposition theorem and study some inclusion relations on these spaces.
EPCGen2 pseudorandom number generators: analysis of J3Gen.
Peinado, Alberto; Munilla, Jorge; Fúster-Sabater, Amparo
2014-04-09
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.
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.
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
EXCAVATOR: detecting copy number variants from whole-exome sequencing data
National Research Council Canada - National Science Library
Magi, Alberto; Tattini, Lorenzo; Cifola, Ingrid; D'Aurizio, Romina; Benelli, Matteo; Mangano, Eleonora; Battaglia, Cristina; Bonora, Elena; Kurg, Ants; Seri, Marco; Magini, Pamela; Giusti, Betti; Romeo, Giovanni; Pippucci, Tommaso; De Bellis, Gianluca; Abbate, Rosanna; Gensini, Gian Franco
2013-01-01
...) from whole-exome sequencing data. EXCAVATOR combines a three-step normalization procedure with a novel heterogeneous hidden Markov model algorithm and a calling method that classifies genomic regions into five copy number states...
Investigating Triangular Numbers with greatest integer function, Sequences and Double Factorial
Directory of Open Access Journals (Sweden)
Tilahun A Muche
2016-11-01
Full Text Available The Triangular number denoted by is defined as the sum of the first consecutive positive integers. A positive integer is a Triangular Number if and only if [1]. We stated and proved a sequence of positive integers is consecutive triangular numbers if and only if √ − √ =1 and √ . We consider a ceiling function ⌈ ⌉ to state and prove a necessary and sufficient condition for a number ⌈ ⌉ ⌈ ⌉ to be a triangular number for each . A formula to find and of any two consecutive triangular numbers and a double factorial is introduced to find products of triangular numbers.
Individualized cattle copy number and segmental duplication maps using next generation sequencing
Copy Number Variations (CNVs) affect a wide range of phenotypic traits; however, CNVs in or near segmental duplication regions are often intractable. Using a read depth approach based on next generation sequencing, we examined genome-wide copy number differences among five taurine (three Angus, one ...
Copy number variation of individual cattle genomes using next-generation sequencing
Copy number variations (CNVs) affect a wide range of phenotypic traits; however, CNVs in or near segmental duplication regions are often intractable. Using a read depth approach based on next-generation sequencing, we examined genome-wide copy number differences among five taurine (three Angus, one ...
Sequenza: allele-specific copy number and mutation profiles from tumor sequencing data
DEFF Research Database (Denmark)
Favero, Francesco; Joshi, Tejal; Marquard, Andrea Marion
2015-01-01
specimen, by intratumor heterogeneity, and by the sheer size of the raw data. In particular, determination of copy number variations from exome sequencing data alone has proven difficult; thus SNP arrays have often been used for this task. Recently, algorithms to estimate absolute, but not allele...... data simulating normal-tumor admixtures, Sequenza detected the correct ploidy in samples with tumor content as low as 30%. Conclusions : The agreement between Sequenza and SNP array-based copy number profiles suggests that exome sequencing alone is sufficient not only for identifying small scale......Background : Exome or whole genome deep sequencing of tumor DNA along with paired normal DNA can potentially provide a detailed picture of the somatic mutations that characterize the tumor. However, analysis of such sequence data can be complicated by the presence of normal cells in the tumor...
CNVkit: Genome-Wide Copy Number Detection and Visualization from Targeted DNA Sequencing.
Directory of Open Access Journals (Sweden)
Eric Talevich
2016-04-01
Full Text Available Germline copy number variants (CNVs and somatic copy number alterations (SCNAs are of significant importance in syndromic conditions and cancer. Massively parallel sequencing is increasingly used to infer copy number information from variations in the read depth in sequencing data. However, this approach has limitations in the case of targeted re-sequencing, which leaves gaps in coverage between the regions chosen for enrichment and introduces biases related to the efficiency of target capture and library preparation. We present a method for copy number detection, implemented in the software package CNVkit, that uses both the targeted reads and the nonspecifically captured off-target reads to infer copy number evenly across the genome. This combination achieves both exon-level resolution in targeted regions and sufficient resolution in the larger intronic and intergenic regions to identify copy number changes. In particular, we successfully inferred copy number at equivalent to 100-kilobase resolution genome-wide from a platform targeting as few as 293 genes. After normalizing read counts to a pooled reference, we evaluated and corrected for three sources of bias that explain most of the extraneous variability in the sequencing read depth: GC content, target footprint size and spacing, and repetitive sequences. We compared the performance of CNVkit to copy number changes identified by array comparative genomic hybridization. We packaged the components of CNVkit so that it is straightforward to use and provides visualizations, detailed reporting of significant features, and export options for integration into existing analysis pipelines. CNVkit is freely available from https://github.com/etal/cnvkit.
Mapping the acquisition of the number word sequence in the first year of school
Gould, Peter
2017-03-01
Learning to count and to produce the correct sequence of number words in English is not a simple process. In NSW government schools taking part in Early Action for Success, over 800 students in each of the first 3 years of school were assessed every 5 weeks over the school year to determine the highest correct oral count they could produce. Rather than displaying a steady increase in the accurate sequence of the number words produced, the kindergarten data reported here identified clear, substantial hurdles in the acquisition of the counting sequence. The large-scale, longitudinal data also provided evidence of learning to count through the teens being facilitated by the semi-regular structure of the number words in English. Instead of occurring as hurdles to starting the next counting sequence, number words corresponding to some multiples of ten (10, 20 and 100) acted as if they were rest points. These rest points appear to be artefacts of how the counting sequence is acquired.
Energy Technology Data Exchange (ETDEWEB)
Ethridge, C.D.; Worth, G.M.
1977-01-01
A scientific calculating system for large distributed-task processing systems and for small isolated intelligent data acquisition and instrumentation systems is established with a number-oriented microprocessor sequenced by a single-component microcomputer. A MOS/LSI number-oriented microprocessor provides the scientific calculating capability with Reverse Polish Notation data entry. Input data sequencing, computation processing, intermediate result comparison, answer display and/or answer feed-back to master processors is controlled by a single-component microcomputer. 3 figures, 1 table.
ReadDepth: a parallel R package for detecting copy number alterations from short sequencing reads.
Directory of Open Access Journals (Sweden)
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/.
Some Additions to the Fuzzy Convergent and Fuzzy Bounded Sequence Spaces of Fuzzy Numbers
M. Şengönül; Zararsız, Z.
2011-01-01
Some properties of the fuzzy convergence and fuzzy boundedness of a sequence of fuzzy numbers were studied in Choi (1996). In this paper, we have consider, some important problems on these spaces and shown that these spaces are fuzzy complete module spaces. Also, the fuzzy α-, fuzzy β-, and fuzzy γ-duals of the fuzzy module spaces of fuzzy numbers have been computeded, and some matrix transformations are given.
Detection of clinically relevant copy number variants with whole-exome sequencing
Ligt, J. de; Boone, P.M.; Pfundt, R.; Vissers, L.E.L.M.; Richmond, T.; Geoghegan, J.; O'Moore, K.; Leeuw, N. de; Shaw, C.; Brunner, H.G.; Lupski, J.R.; Veltman, J.A.; Hehir-Kwa, J.Y.
2013-01-01
Copy number variation (CNV) is a common source of genetic variation that has been implicated in many genomic disorders. This has resulted in the widespread application of genomic microarrays as a first-tier diagnostic tool for CNV detection. More recently, whole-exome sequencing (WES) has been
MSRV pol sequence copy number as a potential marker of multiple sclerosis.
Zawada, Mariola; Liwień, Izabela; Pernak, Monika; Januszkiewicz-Lewandowska, Danuta; Nowicka-Kujawska, Karina; Rembowska, Jolanta; Lewandowski, Krzysztof; Hertmanowska, Hanna; Wender, Mieczysław; Nowak, Jerzy
2003-01-01
Multiple sclerosis (MS) is a neurological disease in which demyelination in the brain and spinal cord is observed. The causal influence of bacterial/viral infections and genetic/immune factors in the etiology of multiple sclerosis is suggested. Multiple sclerosis-related retrovirus (MSRV) is one of the potential agents, which can lead to development of the disease. The aim of cytogenetic studies was assessment of MSRV pol sequence copy number in patients with MS compared to normal individuals. Cytogenetic slides with interphase nuclei and extended chromatin fibers were prepared from peripheral blood of 16 patients with MS and 10 healthy individuals. Fluorescence in situ hybridization (FISH) with biotinylated product of polymerase chain reaction was used in order to analyze MSRV pol sequence copy number in the examined material. Detection of MSRV pol probe was carried out by immunological reaction with avidin-fluorescein and biotinylated anti-avidin. MSRV pol sequence copy number was significantly greater in MS patients than in normal individuals. Using FISH technique to extended chromatin fibers, it was observed that MSRV pol exists as tandem repeats on various chromosomes. The increased number of MSRV pol sequence has been found on chromatin fibers of MS patients as compared to healthy controls.
Long insert whole genome sequencing for copy number variant and translocation detection.
Liang, Winnie S; Aldrich, Jessica; Tembe, Waibhav; Kurdoglu, Ahmet; Cherni, Irene; Phillips, Lori; Reiman, Rebecca; Baker, Angela; Weiss, Glen J; Carpten, John D; Craig, David W
2014-01-01
As next-generation sequencing continues to have an expanding presence in the clinic, the identification of the most cost-effective and robust strategy for identifying copy number changes and translocations in tumor genomes is needed. We hypothesized that performing shallow whole genome sequencing (WGS) of 900-1000-bp inserts (long insert WGS, LI-WGS) improves our ability to detect these events, compared with shallow WGS of 300-400-bp inserts. A priori analyses show that LI-WGS requires less sequencing compared with short insert WGS to achieve a target physical coverage, and that LI-WGS requires less sequence coverage to detect a heterozygous event with a power of 0.99. We thus developed an LI-WGS library preparation protocol based off of Illumina's WGS library preparation protocol and illustrate the feasibility of performing LI-WGS. We additionally applied LI-WGS to three separate tumor/normal DNA pairs collected from patients diagnosed with different cancers to demonstrate our application of LI-WGS on actual patient samples for identification of somatic copy number alterations and translocations. With the evolution of sequencing technologies and bioinformatics analyses, we show that modifications to current approaches may improve our ability to interrogate cancer genomes.
The sequence to hydrogenate coronene cations: A journey guided by magic numbers
Cazaux, Stéphanie; Rougeau, Nathalie; Reitsma, Geert; Hoekstra, Ronnie; Teillet-Billy, Dominique; Morisset, Sabine; Spaans, Marco; Schlathölter, Thomas
2016-01-01
The understanding of hydrogen attachment to carbonaceous surfaces is essential to a wide variety of research fields and technologies such as hydrogen storage for transportation, precise localization of hydrogen in electronic devices and the formation of cosmic H2. For coronene cations as prototypical Polycyclic Aromatic Hydrocarbon (PAH) molecules, the existence of magic numbers upon hydrogenation was uncovered experimentally. Quantum chemistry calculations show that hydrogenation follows a site-specific sequence leading to the appearance of cations having 5, 11, or 17 hydrogen atoms attached, exactly the magic numbers found in the experiments. For these closed-shell cations, further hydrogenation requires appreciable structural changes associated with a high transition barrier. Controlling specific hydrogenation pathways would provide the possibility to tune the location of hydrogen attachment and the stability of the system. The sequence to hydrogenate PAHs, leading to PAHs with magic numbers of H atoms att...
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.
Long insert whole genome sequencing for copy number variant and translocation detection
Liang, Winnie S.; Aldrich, Jessica; Tembe, Waibhav; Kurdoglu, Ahmet; Cherni, Irene; Phillips, Lori; Reiman, Rebecca; Baker, Angela; Weiss, Glen J.; Carpten, John D.; Craig, David W.
2013-01-01
As next-generation sequencing continues to have an expanding presence in the clinic, the identification of the most cost-effective and robust strategy for identifying copy number changes and translocations in tumor genomes is needed. We hypothesized that performing shallow whole genome sequencing (WGS) of 900–1000-bp inserts (long insert WGS, LI-WGS) improves our ability to detect these events, compared with shallow WGS of 300–400-bp inserts. A priori analyses show that LI-WGS requires less s...
RefCNV: Identification of Gene-Based Copy Number Variants Using Whole Exome Sequencing.
Chang, Lun-Ching; Das, Biswajit; Lih, Chih-Jian; Si, Han; Camalier, Corinne E; McGregor, Paul M; Polley, Eric
2016-01-01
With rapid advances in DNA sequencing technologies, whole exome sequencing (WES) has become a popular approach for detecting somatic mutations in oncology studies. The initial intent of WES was to characterize single nucleotide variants, but it was observed that the number of sequencing reads that mapped to a genomic region correlated with the DNA copy number variants (CNVs). We propose a method RefCNV that uses a reference set to estimate the distribution of the coverage for each exon. The construction of the reference set includes an evaluation of the sources of variability in the coverage distribution. We observed that the processing steps had an impact on the coverage distribution. For each exon, we compared the observed coverage with the expected normal coverage. Thresholds for determining CNVs were selected to control the false-positive error rate. RefCNV prediction correlated significantly (r = 0.96-0.86) with CNV measured by digital polymerase chain reaction for MET (7q31), EGFR (7p12), or ERBB2 (17q12) in 13 tumor cell lines. The genome-wide CNV analysis showed a good overall correlation (Spearman's coefficient = 0.82) between RefCNV estimation and publicly available CNV data in Cancer Cell Line Encyclopedia. RefCNV also showed better performance than three other CNV estimation methods in genome-wide CNV analysis.
Effective normalization for copy number variation detection from whole genome sequencing.
Janevski, Angel; Varadan, Vinay; Kamalakaran, Sitharthan; Banerjee, Nilanjana; Dimitrova, Nevenka
2012-01-01
Whole genome sequencing enables a high resolution view of the human genome and provides unique insights into genome structure at an unprecedented scale. There have been a number of tools to infer copy number variation in the genome. These tools, while validated, also include a number of parameters that are configurable to genome data being analyzed. These algorithms allow for normalization to account for individual and population-specific effects on individual genome CNV estimates but the impact of these changes on the estimated CNVs is not well characterized. We evaluate in detail the effect of normalization methodologies in two CNV algorithms FREEC and CNV-seq using whole genome sequencing data from 8 individuals spanning four populations. We apply FREEC and CNV-seq to a sequencing data set consisting of 8 genomes. We use multiple configurations corresponding to different read-count normalization methodologies in FREEC, and statistically characterize the concordance of the CNV calls between FREEC configurations and the analogous output from CNV-seq. The normalization methodologies evaluated in FREEC are: GC content, mappability and control genome. We further stratify the concordance analysis within genic, non-genic, and a collection of validated variant regions. The GC content normalization methodology generates the highest number of altered copy number regions. Both mappability and control genome normalization reduce the total number and length of copy number regions. Mappability normalization yields Jaccard indices in the 0.07 - 0.3 range, whereas using a control genome normalization yields Jaccard index values around 0.4 with normalization based on GC content. The most critical impact of using mappability as a normalization factor is substantial reduction of deletion CNV calls. The output of another method based on control genome normalization, CNV-seq, resulted in comparable CNV call profiles, and substantial agreement in variable gene and CNV region calls
Tests of Sunspot Number Sequences: 2. Using Geomagnetic and Auroral Data
Lockwood, M.; Owens, M. J.; Barnard, L.; Scott, C. J.; Usoskin, I. G.; Nevanlinna, H.
2016-11-01
We compare four sunspot-number data sequences against geomagnetic and terrestrial auroral observations. The comparisons are made for the original Solar Influences Data Center (SIDC) composite of Wolf/Zürich/International sunspot number [R_{{ISNv}1}], the group sunspot number [RG] by Hoyt and Schatten ( Solar Phys. 181, 491, 1998), the new "backbone" group sunspot number [R_{BB}] by Svalgaard and Schatten ( Solar Phys., DOI: 10.1007/s11207-015-0815-8, 2016), and the "corrected" sunspot number [RC] by Lockwood, Owens, and Barnard ( J. Geophys. Res. 119, 5172, 2014a). Each sunspot number is fitted with terrestrial observations, or parameters derived from terrestrial observations to be linearly proportional to sunspot number, over a 30-year calibration interval of 1982 - 2012. The fits are then used to compute test sequences, which extend further back in time and which are compared to R_{{ISNv}1}, RG, R_{{BB}}, and RC. To study the long-term trends, comparisons are made using averages over whole solar cycles (minimum-to-minimum). The test variations are generated in four ways: i) using the IDV(1d) and IDV geomagnetic indices (for 1845 - 2013) fitted over the calibration interval using the various sunspot numbers and the phase of the solar cycle; ii) from the open solar flux (OSF) generated for 1845 - 2013 from four pairings of geomagnetic indices by Lockwood et al. ( Ann. Geophys. 32, 383, 2014a) and analysed using the OSF continuity model of Solanki, Schüssler, and Fligge ( Nature, 408, 445, 2000), which employs a constant fractional OSF loss rate; iii) the same OSF data analysed using the OSF continuity model of Owens and Lockwood ( J. Geophys. Res. 117, A04102, 2012), in which the fractional loss rate varies with the tilt of the heliospheric current sheet and hence with the phase of the solar cycle; iv) the occurrence frequency of low-latitude aurora for 1780 - 1980 from the survey of Legrand and Simon ( Ann. Geophys. 5, 161, 1987). For all cases, R_{BB} exceeds
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.
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
Directory of Open Access Journals (Sweden)
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.
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.
Sequences of ground states and classification of frustration in odd-numbered antiferromagnetic rings
Florek, Wojciech; Antkowiak, Michał; Kamieniarz, Grzegorz
2016-12-01
The sequences of ground states in frustrated antiferromagnetic rings with odd number of local spins characterized by a single bond defect or by arbitrary uniform couplings to an additional spin located at the center are determined. The sequences provide firm constraints on the total ground-state quantum numbers, which are more stringent than those arising from the Lieb-Mattis theorem for bipartite quantum spin systems. Apart from their theoretical importance, they suggest the possibility of tailoring a given class of the molecular nanomagnets with desired ground-state properties by tuning the relevant couplings. In particular, they predict the spin S =1 /2 ground state for the centered rings composed of the half-integer spins with approximately uniform interactions. They confirm the applicability of the recent classification of spin frustration in both types of molecular nanomagnets. The classification is also discussed in the classical limit for the first class of the rings, providing a direct picture of frustration types. The Lieb-Mattis energy-level ordering and an analog of the Landé band, i.e., the energy spectra properties simplifying the characterization of the rings using the bulk magnetic or NMR measurements, are briefly discussed.
Directory of Open Access Journals (Sweden)
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.
Nishino, Jo; Mano, Shuhei
2013-01-01
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
2017-10-23
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.
Rampášek, Ladislav; Arbabi, Aryan; Brudno, Michael
2014-06-15
The past several years have seen the development of methodologies to identify genomic variation within a fetus through the non-invasive sequencing of maternal blood plasma. These methods are based on the observation that maternal plasma contains a fraction of DNA (typically 5-15%) originating from the fetus, and such methodologies have already been used for the detection of whole-chromosome events (aneuploidies), and to a more limited extent for smaller (typically several megabases long) copy number variants (CNVs). Here we present a probabilistic method for non-invasive analysis of de novo CNVs in fetal genome based on maternal plasma sequencing. Our novel method combines three types of information within a unified Hidden Markov Model: the imbalance of allelic ratios at SNP positions, the use of parental genotypes to phase nearby SNPs and depth of coverage to better differentiate between various types of CNVs and improve precision. Our simulation results, based on in silico introduction of novel CNVs into plasma samples with 13% fetal DNA concentration, demonstrate a sensitivity of 90% for CNVs >400 kb (with 13 calls in an unaffected genome), and 40% for 50-400 kb CNVs (with 108 calls in an unaffected genome). Implementation of our model and data simulation method is available at http://github.com/compbio-UofT/fCNV. © The Author 2014. Published by Oxford University Press.
LPEseq: Local-Pooled-Error Test for RNA Sequencing Experiments with a Small Number of Replicates.
Gim, Jungsoo; Won, Sungho; Park, Taesung
2016-01-01
RNA-Sequencing (RNA-Seq) provides valuable information for characterizing the molecular nature of the cells, in particular, identification of differentially expressed transcripts on a genome-wide scale. Unfortunately, cost and limited specimen availability often lead to studies with small sample sizes, and hypothesis testing on differential expression between classes with a small number of samples is generally limited. The problem is especially challenging when only one sample per each class exists. In this case, only a few methods among many that have been developed are applicable for identifying differentially expressed transcripts. Thus, the aim of this study was to develop a method able to accurately test differential expression with a limited number of samples, in particular non-replicated samples. We propose a local-pooled-error method for RNA-Seq data (LPEseq) to account for non-replicated samples in the analysis of differential expression. Our LPEseq method extends the existing LPE method, which was proposed for microarray data, to allow examination of non-replicated RNA-Seq experiments. We demonstrated the validity of the LPEseq method using both real and simulated datasets. By comparing the results obtained using the LPEseq method with those obtained from other methods, we found that the LPEseq method outperformed the others for non-replicated datasets, and showed a similar performance with replicated samples; LPEseq consistently showed high true discovery rate while not increasing the rate of false positives regardless of the number of samples. Our proposed LPEseq method can be effectively used to conduct differential expression analysis as a preliminary design step or for investigation of a rare specimen, for which a limited number of samples is available.
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…
Human PTCHD3 nulls: rare copy number and sequence variants suggest a non-essential gene
Directory of Open Access Journals (Sweden)
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
PartTree: an algorithm to build an approximate tree from a large number of unaligned sequences.
Katoh, Kazutaka; Toh, Hiroyuki
2007-02-01
To construct a multiple sequence alignment (MSA) of a large number (> approximately 10,000) of sequences, the calculation of a guide tree with a complexity of O(N2) to O(N3), where N is the number of sequences, is the most time-consuming process. To overcome this limitation, we have developed an approximate algorithm, PartTree, to construct a guide tree with an average time complexity of O(N log N). The new MSA method with the PartTree algorithm can align approximately 60,000 sequences in several minutes on a standard desktop computer. The loss of accuracy in MSA caused by this approximation was estimated to be several percent in benchmark tests using Pfam. The present algorithm has been implemented in the MAFFT sequence alignment package (http://align.bmr.kyushu-u.ac.jp/mafft/software/). Supplementary information is available at Bioinformatics online.
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.
A note on the strong law of large numbers for associated sequences
Directory of Open Access Journals (Sweden)
A. Nezakati
2005-01-01
Full Text Available We prove that the sequence {bn−1∑i=1n(Xi−EXi}n≥1 converges a.e. to zero if {Xn,n≥1} is anassociated sequence of random variables with ∑n=1∞bkn−2Var(∑i=kn−1+1knXi<∞ where {bn,n≥1} is a positive nondecreasing sequence and {kn,n≥1} is a strictly increasing sequence, both tending to infinity as n tends to infinity and 0
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.
On generalized difference sequence spaces of fuzzy numbers - doi: 10.4025/actascitechnol.v35i1.15566
Directory of Open Access Journals (Sweden)
Binod Chandra Tripathy
2013-01-01
Full Text Available The idea of difference sequence space was introduced by Kizmaz (1981 and this concept was generalized by Tripathy and Esi (2006. In this article we introduced the paranormed sequence spaces cF(f,Λ,Δm,p, (f,Λ,Δm,p and (f,Λ,Δm,p of fuzzy numbers associated with the multiplier sequence Λ= (λk defined by a modulus function f. We study some of their properties like solidity, symmetricity, completeness etc. and prove some inclusion results.
Energy Technology Data Exchange (ETDEWEB)
Calvayrac, Florent [Laboratoire de Physique de l' Etat Condense, UMR CNRS 6087 and FR 2575, Universite du Maine, 72085 Le Mans Cedex 9 (France)
2005-09-01
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.
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.
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.
Chikayama, Eisuke; Kurotani, Atsushi; Kuroda, Yutaka; Yokoyama, Shigeyuki
2004-11-01
ProteoMix is a suite of JAVA programs for identifying, annotating and predicting regions of interest in large sets of amino acid sequences, according to systematic and consistent criteria. It is based on two concepts (1) the integration of results from different sequence analysis tools increases the prediction reliability; and (2) the integration protocol is critical and needs to be easily adaptable in a case-by-case manner. ProteoMix was designed to analyze simultaneously multiple protein sequences using several bioinformatics tools, merge the results of the analyses using logical functions and display them on an integrated viewer. In addition, new sequences can be added seamlessly to an analysis performed on an initial set of sequences. ProteoMix has a modular design, and bioinformatics tools are run on remote servers accessed using the Internet Simple Object Access Protocol (SOAP), ensuring the swift implementation of additional tools. ProteoMix has a user-friendly interactive graphical user interface environment and runs on PCs with Microsoft OS. ProteoMix is freely available for academic users at http://bio.gsc.riken.jp/ProteoMix/
Directory of Open Access Journals (Sweden)
Yuki Kuniyoshi
Full Text Available Identification of immunoglobulin genes in hybridomas is essential for producing antibodies for research and clinical applications. A couple of methods such as RACE and degenerative PCR have been developed for determination of the Igh and Igl/Igk coding sequences (CDSs but it has been difficult to process a number of hybridomas both with accuracy and rapidness. Here, we propose a new strategy for antibody sequence determination by mRNA-seq of hybridomas. We demonstrated that hybridomas highly expressed the Igh and Igl/Igk genes and that de novo transcriptome assembly using mRNA-seq data enabled identification of the CDS of both Igh and Igl/Igk accurately. Furthermore, we estimated that only 30,000 sequenced reads are required to identify immunoglobulin sequences from four different hybridoma clones. Thus, our approach would facilitate determining variable CDSs drastically.
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
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)
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.
Native Chromatin Immunoprecipitation-Sequencing (ChIP-Seq) from Low Cell Numbers.
Ribarska, Teodora; Gilfillan, Gregor D
2018-01-01
ChIP-seq is the current method of choice for genome-wide protein location analysis. Here, we present a native (non-cross-linked) ChIP procedure suitable for histone proteins, coupled with an efficient library preparation technique for subsequent next-generation sequencing. The method enables ChIP-seq starting with 50,000 or more cells.
Andrew J., Wood; R.Joel, Duff; Melvin J., Oliver; Department of Plant Biology, Southern Illinois University-Carbondale; Plant Stress and Water Conservation Unit, Cropping Systems Research Laboratory
1999-01-01
The desiccation-tolerant moss Tortula ruralis [Hedw.] Gaerten., Meyer & Scherb.has both a constitutive protection system and an active rehydration induced recovery mechanism apparently unique to bryophytes. Immediately following rehydration, desiccated T.ruralis gametophytes produce a set of polypeptides whose synthesis is unique to the rehydrated state. We report the construction of a cDNA expression library from the polysomal mRNA of desiccated gametophytes and the single-pass sequencing of...
Energy Technology Data Exchange (ETDEWEB)
Zietkiewicz, E.; Labuda, D. [Universite de Montreal, Que (Canada); Jurka, J. [Linus Pauling Institute, Palo Alto, CA (United States)
1994-09-01
Paleogenomics is the research activity aiming to reconstruct ancient genetic events and/or structures from the {open_quotes}fossil{close_quotes} genomic record. With about 120,000 copies, mammalian interspersed repeats, MIRs, represent the second most abundant family of short interspersed repeats in human DNA, only outnumbered by Alu elements. MIR consensus sequence of 100 nucleotides was reconstructed from 455 mutated copies preserved in contemporary genome (GenBank release 69). As no division into subfamilies was observed, we assume that this consensus represents an ancestral MIR sequence. To find out how far MIRs can be traced down the phylogenetic tree, we examined their distribution in a variety of mammalian and non-mammalian DNAs. Oligonucleotide primers based on the MIR consensus were used, one at a time, for PCR amplification of the genomic fragments flanked by MIR repeats (inter-MIR-PCR). Significant amplification in DNA samples from a variety of placental orders as well as marsupials and monotremes indicates that MIRs originated in early mammals. Sequence analysis is consistent with their proliferation during the Mesozoic era. Electrophoretic profiles of inter-MIR-PCR products are distinct among different species. Intra-species comparison of multiple human samples reveals polymorphic bands segregating as Mendelian traits which can be used as genetic markers in both mapping and fingerprinting.
Directory of Open Access Journals (Sweden)
Jack A Gilbert
2008-08-01
Full Text Available 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.
Kim, Hyung-Yong; Choi, Jin-Woo; Lee, Jeong-Yeon; Kong, Gu
2017-04-18
Accurate detection of copy number alterations (CNAs) using next-generation sequencing technology is essential for the development and application of more precise medical treatments for human cancer. Here, we evaluated seven CNA estimation tools (ExomeCNV, CoNIFER, VarScan2, CODEX, ngCGH, saasCNV, and falcon) using whole-exome sequencing data from 419 breast cancer tumor-normal sample pairs from The Cancer Genome Atlas. Estimations generated using each tool were converted into gene-based copy numbers; concordance for gains and losses and the sensitivity and specificity of each tool were compared to validated copy numbers from a single nucleotide polymorphism reference array. The concordance and sensitivity of the tumor-normal pair methods for estimating CNAs (saasCNV, ExomeCNV, and VarScan2) were better than those of the tumor batch methods (CoNIFER and CODEX). SaasCNV had the highest gain and loss concordances (65.0%), sensitivity (69.4%), and specificity (89.1%) for estimating copy number gains or losses. These findings indicate that improved CNA detection algorithms are needed to more accurately interpret whole-exome sequencing results in human cancer.
Waszak, Sebastian M; Hasin, Yehudit; Zichner, Thomas; Olender, Tsviya; Keydar, Ifat; Khen, Miriam; Stütz, Adrian M; Schlattl, Andreas; Lancet, Doron; Korbel, Jan O
2010-11-11
Copy-number variations (CNVs) are widespread in the human genome, but comprehensive assignments of integer locus copy-numbers (i.e., copy-number genotypes) that, for example, enable discrimination of homozygous from heterozygous CNVs, have remained challenging. Here we present CopySeq, a novel computational approach with an underlying statistical framework that analyzes the depth-of-coverage of high-throughput DNA sequencing reads, and can incorporate paired-end and breakpoint junction analysis based CNV-analysis approaches, to infer locus copy-number genotypes. We benchmarked CopySeq by genotyping 500 chromosome 1 CNV regions in 150 personal genomes sequenced at low-coverage. The assessed copy-number genotypes were highly concordant with our performed qPCR experiments (Pearson correlation coefficient 0.94), and with the published results of two microarray platforms (95-99% concordance). We further demonstrated the utility of CopySeq for analyzing gene regions enriched for segmental duplications by comprehensively inferring copy-number genotypes in the CNV-enriched >800 olfactory receptor (OR) human gene and pseudogene loci. CopySeq revealed that OR loci display an extensive range of locus copy-numbers across individuals, with zero to two copies in some OR loci, and two to nine copies in others. Among genetic variants affecting OR loci we identified deleterious variants including CNVs and SNPs affecting ~15% and ~20% of the human OR gene repertoire, respectively, implying that genetic variants with a possible impact on smell perception are widespread. Finally, we found that for several OR loci the reference genome appears to represent a minor-frequency variant, implying a necessary revision of the OR repertoire for future functional studies. CopySeq can ascertain genomic structural variation in specific gene families as well as at a genome-wide scale, where it may enable the quantitative evaluation of CNVs in genome-wide association studies involving high
Qi, Qingwei; Lu, Sijia; Zhou, Xiya; Yao, Fengxia; Hao, Na; Yin, Guangjun; Li, Wenhui; Bai, Junjie; Li, Ning; Cram, David S
2016-06-01
The study aimed to determine whether cell-free fetal DNA (cffDNA) present in amniotic fluid supernatant can be used as a surrogate for amniocyte-based diagnosis of fetal chromosomal abnormalities. Amniocentesis was performed on 28 high-risk pregnancies. Amniocytes and the cffDNA fraction were prepared from the amniotic fluid samples. Chromosomal analysis of amniocytes was performed by either karyotyping or single nucleotide polymorphism (SNP) arrays. The corresponding cffDNA samples were blindly analyzed by copy number variation (CNV) sequencing in an independent laboratory. In the 28 matching amniocyte and cffDNA samples, there was a high diagnostic concordance for detection of euploidy, aneuploidy and CNVs. From ten samples referred for karyotyping, two aneuploidies (20%) were identified. From 18 samples referred for SNP array analysis, three pathogenic CNVs (16.7%) were identified. CNV sequencing of the 28 cffDNA samples also detected the two aneuploidies and the three pathogenic CNVs, giving an overall concordance rate of 100% for detection of pathogenic chromosome abnormalities. Compared with SNP array analysis, CNV sequencing returned a higher yield of benign or variants of unknown significance. Copy number variation sequencing of cffDNA represents an alternative approach to conventional prenatal diagnostic methods for reliable and accurate detection of clinically significant chromosomal abnormalities. © 2016 John Wiley & Sons, Ltd. © 2016 John Wiley & Sons, Ltd.
Retterer, Kyle; Scuffins, Julie; Schmidt, Daniel; Lewis, Rachel; Pineda-Alvarez, Daniel; Stafford, Amanda; Schmidt, Lindsay; Warren, Stephanie; Gibellini, Federica; Kondakova, Anastasia; Blair, Amanda; Bale, Sherri; Matyakhina, Ludmila; Meck, Jeanne; Aradhya, Swaroop; Haverfield, Eden
2015-08-01
Detection of copy-number variation (CNV) is important for investigating many genetic disorders. Testing a large clinical cohort by array comparative genomic hybridization provides a deep perspective on the spectrum of pathogenic CNV. In this context, we describe a bioinformatics approach to extract CNV information from whole-exome sequencing and demonstrate its utility in clinical testing. Exon-focused arrays and whole-genome chromosomal microarray analysis were used to test 14,228 and 14,000 individuals, respectively. Based on these results, we developed an algorithm to detect deletions/duplications in whole-exome sequencing data and a novel whole-exome array. In the exon array cohort, we observed a positive detection rate of 2.4% (25 duplications, 318 deletions), of which 39% involved one or two exons. Chromosomal microarray analysis identified 3,345 CNVs affecting single genes (18%). We demonstrate that our whole-exome sequencing algorithm resolves CNVs of three or more exons. These results demonstrate the clinical utility of single-exon resolution in CNV assays. Our whole-exome sequencing algorithm approaches this resolution but is complemented by a whole-exome array to unambiguously identify intragenic CNVs and single-exon changes. These data illustrate the next advancements in CNV analysis through whole-exome sequencing and whole-exome array.Genet Med 17 8, 623-629.
The Hardy-Littlewood Problem for Regular and Uniformly Distributed Number Sequences
Oskolkov, V. A.
1995-04-01
Let H be the set of functions f(x) defined in (0,1), f(0+0)=f(1-0)=+\\infty, monotone in neighborhoods of singular points and such that the improper Riemann integral \\int_0^1 f(x)\\,dx converges. Let Q be an arbitrary set of sequences (\\{x_i\\})_{i=1}^\\infty uniformly distributed in the interval \\lbrack 0,1\\rbrack. We find the set of those pairs in H\\times Q for which the following equality is valid: \\displaystyle \\lim_{n\\to\\infty} \\frac{1}{n} \\sum_{i=1}^n f(\\{x_i\\})=\\int_0^1 f(x)\\,dx.
Some new sets of sequences of fuzzy numbers with respect to the partial metric.
Kadak, Uğur; Ozluk, Muharrem
2015-01-01
In this paper, we essentially deal with Köthe-Toeplitz duals of fuzzy level sets defined using a partial metric. Since the utilization of Zadeh's extension principle is quite difficult in practice, we prefer the idea of level sets in order to construct some classical notions. In this paper, we present the sets of bounded, convergent, and null series and the set of sequences of bounded variation of fuzzy level sets, based on the partial metric. We examine the relationships between these sets and their classical forms and give some properties including definitions, propositions, and various kinds of partial metric spaces of fuzzy level sets. Furthermore, we study some of their properties like completeness and duality. Finally, we obtain the Köthe-Toeplitz duals of fuzzy level sets with respect to the partial metric based on a partial ordering.
Ji, Haiting; Lu, Jingqiao; Wang, Jianjun; Li, Huawei; Lin, Xi
2014-01-01
Background Copy number variations (CNVs) are the major type of structural variation in the human genome, and are more common than DNA sequence variations in populations. CNVs are important factors for human genetic and phenotypic diversity. Many CNVs have been associated with either resistance to diseases or identified as the cause of diseases. Currently little is known about the role of CNVs in causing deafness. CNVs are currently not analyzed by conventional genetic analysis methods to stud...
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.
Implementing and Testing Self-Timed Rings on a FPGA as Entropy Sources
Einar, Marcus
2015-01-01
Random number generators are basic building blocks of modern cryptographic systems. Usually pseudo random number generators, carefully constructed deter- ministic algorithms that generate seemingly random numbers, are used. These are built upon foundations of thorough mathematical analysis and have been subjected to stringent testing to make sure that they can produce pseudo random sequences at a high bit-rate with good statistical properties. A pseudo random number generator must be initiate...
Directory of Open Access Journals (Sweden)
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.
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
identified by MLPA in 48 Danish breast and/or ovarian cancer families were analyzed. Moreover, 120 patient samples previously determined as negative for BRCA1/BRCA2 CNVs by MLPA were included in the analysis. Comparison of the NGS data with the data from MLPA revealed that the sensitivity was 100%, whereas......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...... the specificity was 95%. Taken together, this study validates a one-step bioinformatics work-flow to call germline BRCA1/2 CNVs using data obtained by NGS of a breast cancer gene panel. The work-flow represents a robust and easy-to-use method for full BRCA1/2 screening, which can be easily implemented in routine...
Directory of Open Access Journals (Sweden)
Xuchao Li
Full Text Available BACKGROUND: Copy number variations (CNVs represent an important type of genetic variation that deeply impact phenotypic polymorphisms and human diseases. The advent of high-throughput sequencing technologies provides an opportunity to revolutionize the discovery of CNVs and to explore their relationship with diseases. However, most of the existing methods depend on sequencing depth and show instability with low sequence coverage. In this study, using low coverage whole-genome sequencing (LCS we have developed an effective population-scale CNV calling (PSCC method. METHODOLOGY/PRINCIPAL FINDINGS: In our novel method, two-step correction was used to remove biases caused by local GC content and complex genomic characteristics. We chose a binary segmentation method to locate CNV segments and designed combined statistics tests to ensure the stable performance of the false positive control. The simulation data showed that our PSCC method could achieve 99.7%/100% and 98.6%/100% sensitivity and specificity for over 300 kb CNV calling in the condition of LCS (∼2× and ultra LCS (∼0.2×, respectively. Finally, we applied this novel method to analyze 34 clinical samples with an average of 2× LCS. In the final results, all the 31 pathogenic CNVs identified by aCGH were successfully detected. In addition, the performance comparison revealed that our method had significant advantages over existing methods using ultra LCS. CONCLUSIONS/SIGNIFICANCE: Our study showed that PSCC can sensitively and reliably detect CNVs using low coverage or even ultra-low coverage data through population-scale sequencing.
Ji, Haiting; Lu, Jingqiao; Wang, Jianjun; Li, Huawei; Lin, Xi
2014-01-01
Copy number variations (CNVs) are the major type of structural variation in the human genome, and are more common than DNA sequence variations in populations. CNVs are important factors for human genetic and phenotypic diversity. Many CNVs have been associated with either resistance to diseases or identified as the cause of diseases. Currently little is known about the role of CNVs in causing deafness. CNVs are currently not analyzed by conventional genetic analysis methods to study deafness. Here we detected both DNA sequence variations and CNVs affecting 80 genes known to be required for normal hearing. Coding regions of the deafness genes were captured by a hybridization-based method and processed through the standard next-generation sequencing (NGS) protocol using the Illumina platform. Samples hybridized together in the same reaction were analyzed to obtain CNVs. A read depth based method was used to measure CNVs at the resolution of a single exon. Results were validated by the quantitative PCR (qPCR) based method. Among 79 sporadic cases clinically diagnosed with sensorineural hearing loss, we identified previously-reported disease-causing sequence mutations in 16 cases. In addition, we identified a total of 97 CNVs (72 CNV gains and 25 CNV losses) in 27 deafness genes. The CNVs included homozygous deletions which may directly give rise to deleterious effects on protein functions known to be essential for hearing, as well as heterozygous deletions and CNV gains compounded with sequence mutations in deafness genes that could potentially harm gene functions. We studied how CNVs in known deafness genes may result in deafness. Data provided here served as a basis to explain how CNVs disrupt normal functions of deafness genes. These results may significantly expand our understanding about how various types of genetic mutations cause deafness in humans.
Directory of Open Access Journals (Sweden)
van Cuyck Hélène
2012-10-01
Full Text Available Abstract Background Streptococcus pneumoniae infections remain a major cause of morbidity and mortality worldwide. The diversity of pneumococci was first evidenced by serotyping of their capsular polysaccharides, responsible of virulence, resolving into more than 93 serotypes. Molecular tools have been developed to track the emergence and the spread of resistant, hyper virulent or non-vaccine type clones, particularly DNA-based methods using genetic polymorphism. Pulsed-Field Gel Electrophoresis analysis (PFGE and Multiple Loci Sequence Typing (MLST are the most frequently used genotyping techniques for S. pneumoniae. MLST is based on sequence comparison of housekeeping genes clustering isolates within sequence types. The availability of genome sequence data from different S. pneumoniae strains facilitated the search for other class of genetic markers as polymorphic DNA sequences for a Multiple-Locus Variable-Number Tandem-Repeat Analysis (MLVA. This study aims at confirming the relevance of MLVA of S. pneumoniae, comparing MLST and MLVA performances when discriminating subgroups of strains belonging to the same Sequence Type (ST, and defining a restricted but universal set of MLVA markers that has at least the same discriminatory power as MLST for S. pneumoniae by applying marker sets used by different authors on 331 isolates selected in UK. Results A minimum spanning tree was built including the serotypes distribution and comparing MLVA and MLST results. 220 MLVA types were determined grouped in 10 Sequence Types (ST. MLVA differentiated ST162 in two clonal complexes. A minimal set was defined: ms 25 and ms37, ms17, ms19, ms33, ms39, and ms40 including two universal markers. The selection was based on MLVA markers with a Diversity Index >0.8 and a selection of others depending of the population tested and the aim of the study. This set of 7 MLVA markers yields strain clusters similar to those obtained by MLST. Conclusions MLVA can discriminate
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.
Gasparrini, S; Alborali, G L; Pitozzi, A; Guarneri, F; Giacomini, E; Baldo, V; Scali, F; Lazzaro, M; Boniotti, M B
2017-08-01
To evaluate and compare the capabilities of multilocus sequence typing (MLST) and multiple locus variable number tandem repeat analysis (MLVA) techniques to characterize Brachyspira hyodysenteriae isolates and to investigate the relationship between pleuromutilin resistance and genetic variability. MLST genotyping was performed on 180 B. hyodysenteriae isolates, and the results were evaluated considering profiles from 108 other strains previously reported in the database. In total, 37 sequence types were obtained. The MLVA approach completely characterized 172 strains and grouped the isolates into 22 different profiles. The combination of MLST and MLVA showed a slight increase in the discriminatory power, identifying 33 joint profiles. An antibiotic resistance analysis showed a reduction in the susceptibility to pleuromutilins over time, and a weak association between susceptibility to valnemulin and inclusion in clonal complex 4. MLST and MLVA are reliable methods for characterizing B. hyodysenteriae strains and they have comparable discriminatory power. The genotyping of B. hyodysenteriae isolates and a database of all the genetic profiles collected during the diagnostic activities could support traditional epidemiological investigations in identifying infection sources and routes of transmission among herds, and in developing more effective control measures. © 2017 The Society for Applied Microbiology.
Peng, Chien-Hua; Liao, Chun-Ta; Ng, Ka-Pou; Tai, An-Shun; Peng, Shih-Chi; Yeh, Jen-Pao; Chen, Shu-Jen; Tsao, Kuo-Chien; Yen, Tzu-Chen; Hsieh, Wen-Ping
2015-08-14
Ultra-deep targeted sequencing (UDT-Seq) has advanced our knowledge on the incidence and functional significance of somatic mutations. However, the utility of UDT-Seq in detecting copy number alterations (CNAs) remains unclear. With the goal of improving molecular prognostication and identifying new therapeutic targets, we designed this study to assess whether UDT-Seq may be useful for detecting CNA in oral cavity squamous cell carcinoma (OSCC). We sequenced a panel of clinically actionable cancer mutations in 310 formalin-fixed paraffin-embedded OSCC specimens. A linear model was developed to overcome uneven coverage across target regions and multiple samples. The 5-year rates of secondary primary tumors, local recurrence, neck recurrence, distant metastases, and survival served as the outcome measures. We confirmed the prognostic significance of the CNA signatures in an independent sample of 105 primary OSCC specimens. The CNA burden across 10 targeted genes was found to predict prognosis in two independent cohorts. FGFR1 and PIK3CAamplifications were associated with prognosis independent of clinical risk factors. Genes exhibiting CNA were clustered in the proteoglycan metabolism, the FOXO signaling, and the PI3K-AKT signaling pathways, for which targeted drugs are already available or currently under development. UDT-Seq is clinically useful to identify CNA, which significantly improve the prognostic information provided by traditional clinicopathological risk factors in OSCC patients.
Liu, Biao; Morrison, Carl D.; Johnson, Candace S.; Trump, Donald L.; Qin, Maochun; Conroy, Jeffrey C.; Wang, Jianmin; Liu, Song
2013-01-01
Accurate detection of somatic copy number variations (CNVs) is an essential part of cancer genome analysis, and plays an important role in oncotarget identifications. Next generation sequencing (NGS) holds the promise to revolutionize somatic CNV detection. In this review, we provide an overview of current analytic tools used for CNV detection in NGS-based cancer studies. We summarize the NGS data types used for CNV detection, decipher the principles for data preprocessing, segmentation, and interpretation, and discuss the challenges in somatic CNV detection. This review aims to provide a guide to the analytic tools used in NGS-based cancer CNV studies, and to discuss the important factors that researchers need to consider when analyzing NGS data for somatic CNV detections. PMID:24240121
Directory of Open Access Journals (Sweden)
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.
Directory of Open Access Journals (Sweden)
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.
Palmeri, P.; Quinet, P.; Mendoza, C.; Bautista, M. A.; Witthoeft, M. C.; Kallman, T. R.
2016-01-01
Context. With the recent launching of the Hitomi X-ray space observatory, K lines and edges of chemical elements with low cosmic abundances, namely F, Na, P, Cl, K, Sc, Ti, V, Cr, Mn, Co, Cu and Zn, can be resolved and used to determine important properties of supernova remnants, galaxy clusters and accreting black holes and neutron stars.Aims. The second stage of the present ongoing project involves the computation of the accurate photoabsorption and photoionisation cross sections required to interpret the X-ray spectra of such trace elements.Methods. Depending on target complexity and computer tractability, ground-state cross sections are computed either with the close-coupling Breit-Pauli R-matrix method or with the autostructure atomic structure code in the isolated-resonance approximation. The intermediate-coupling scheme is used whenever possible. In order to determine a realistic K-edge behaviour for each species, both radiative and Auger dampings are taken into account, the latter being included in the R-matrix formalism by means of an optical potential.Results. Photoabsorption and total and partial photoionisation cross sections are reported for isoelectronic sequences with electron numbers 3 11 as they contribute significantly to the monotonic background of the cross section between the L and K edges. Configurations with 3d orbitals are important in rendering an accurate L edge, but they can be practically neglected in the K-edge region.
Lieber, Daniel S; Hershman, Steven G; Slate, Nancy G; Calvo, Sarah E; Sims, Katherine B; Schmahmann, Jeremy D; Mootha, Vamsi K
2014-03-06
D-bifunctional protein deficiency, caused by recessive mutations in HSD17B4, is a severe, infantile-onset disorder of peroxisomal fatty acid oxidation. Few affected patients survive past two years of age. Compound heterozygous mutations in HSD17B4 have also been reported in two sisters diagnosed with Perrault syndrome (MIM # 233400), who presented in adolescence with ovarian dysgenesis, hearing loss, and ataxia. An adult male presented with cerebellar ataxia, peripheral neuropathy, hearing loss, and azoospermia. The clinical presentation, in combination with biochemical findings in serum, urine, and muscle biopsy, suggested a mitochondrial disorder. Commercial genetic testing of 18 ataxia and mitochondrial disease genes was negative. Targeted exome sequencing followed by analysis of single nucleotide variants and small insertions/deletions failed to reveal a genetic basis of disease. Application of a computational algorithm to infer copy number variants (CNVs) from exome data revealed a heterozygous 12 kb deletion of exons 10-13 of HSD17B4 that was compounded with a rare missense variant (p.A196V) at a highly conserved residue. Retrospective review of patient records revealed mildly elevated ratios of pristanic:phytanic acid and arachidonic:docosahexaenoic acid, consistent with dysfunctional peroxisomal fatty acid oxidation. Our case expands the phenotypic spectrum of HSD17B4-deficiency, representing the first male case reported with infertility. Furthermore, it points to crosstalk between mitochondria and peroxisomes in HSD17B4-deficiency and Perrault syndrome.
Energy Technology Data Exchange (ETDEWEB)
Cornejo Diaz, N.; Vergara Gil, A. [Centre for Radiological Protection and Higiene, P.O. Box 6195, Habana (Cuba); Jurado Vargas, M. [Physics Department, University of Extremadura, 06071 Badajoz (Spain)], E-mail: mjv@unex.es
2010-03-15
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.
Directory of Open Access Journals (Sweden)
Clara Serra-Juhé
2017-05-01
Full Text Available Obesity is a multifactorial disorder with high heritability (50-75%, which is probably higher in early-onset and severe cases. Although rare monogenic forms and several genes and regions of susceptibility, including copy number variants (CNVs, have been described, the genetic causes underlying the disease still remain largely unknown. We searched for rare CNVs (>100kb in size, altering genes and present in 3 standard deviations above the mean at <3 years of age using SNP array molecular karyotypes. We then performed case control studies (480 EOO cases/480 non-obese controls with the validated CNVs and rare sequence variants (RSVs detected by targeted resequencing of selected CNV genes (n = 14, and also studied the inheritance patterns in available first-degree relatives. A higher burden of gain-type CNVs was detected in EOO cases versus controls (OR = 1.71, p-value = 0.0358. In addition to a gain of the NPY gene in a familial case with EOO and attention deficit hyperactivity disorder, likely pathogenic CNVs included gains of glutamate receptors (GRIK1, GRM7 and the X-linked gastrin-peptide receptor (GRPR, all inherited from obese parents. Putatively functional RSVs absent in controls were also identified in EOO cases at NPY, GRIK1 and GRPR. A patient with a heterozygous deletion disrupting two contiguous and related genes, SLCO4C1 and SLCO6A1, also had a missense RSV at SLCO4C1 on the other allele, suggestive of a recessive model. The genes identified showed a clear enrichment of shared co-expression partners with known genes strongly related to obesity, reinforcing their role in the pathophysiology of the disease. Our data reveal a higher burden of rare CNVs and RSVs in several related genes in patients with EOO compared to controls, and implicate NPY, GRPR, two glutamate receptors and SLCO4C1 in highly penetrant forms of familial obesity.
Serra-Juhé, Clara; Martos-Moreno, Gabriel Á; Bou de Pieri, Francesc; Flores, Raquel; González, Juan R; Rodríguez-Santiago, Benjamín; Argente, Jesús; Pérez-Jurado, Luis A
2017-05-01
Obesity is a multifactorial disorder with high heritability (50-75%), which is probably higher in early-onset and severe cases. Although rare monogenic forms and several genes and regions of susceptibility, including copy number variants (CNVs), have been described, the genetic causes underlying the disease still remain largely unknown. We searched for rare CNVs (>100kb in size, altering genes and present in obesity (EOO: body mass index >3 standard deviations above the mean at obese controls) with the validated CNVs and rare sequence variants (RSVs) detected by targeted resequencing of selected CNV genes (n = 14), and also studied the inheritance patterns in available first-degree relatives. A higher burden of gain-type CNVs was detected in EOO cases versus controls (OR = 1.71, p-value = 0.0358). In addition to a gain of the NPY gene in a familial case with EOO and attention deficit hyperactivity disorder, likely pathogenic CNVs included gains of glutamate receptors (GRIK1, GRM7) and the X-linked gastrin-peptide receptor (GRPR), all inherited from obese parents. Putatively functional RSVs absent in controls were also identified in EOO cases at NPY, GRIK1 and GRPR. A patient with a heterozygous deletion disrupting two contiguous and related genes, SLCO4C1 and SLCO6A1, also had a missense RSV at SLCO4C1 on the other allele, suggestive of a recessive model. The genes identified showed a clear enrichment of shared co-expression partners with known genes strongly related to obesity, reinforcing their role in the pathophysiology of the disease. Our data reveal a higher burden of rare CNVs and RSVs in several related genes in patients with EOO compared to controls, and implicate NPY, GRPR, two glutamate receptors and SLCO4C1 in highly penetrant forms of familial obesity.
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
Liu, Hongtai; Gao, Ya; Hu, Zhiyang; Lin, Linhua; Yin, Xuyang; Wang, Jun; Chen, Dayang; Chen, Fang; Jiang, Hui; Ren, Jinghui; Wang, Wei
2016-01-01
The aim of this study was to assess the performance of noninvasively prenatal testing (NIPT) for fetal copy number variants (CNVs) in clinical samples, using a whole-genome sequencing method. A total of 919 archived maternal plasma samples with karyotyping/microarray results, 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 through Maternal Plasma Sequencing (FCAPS) to compare to the karyotyping/microarray results. Sensitivity, specificity and were evaluated. 33 samples with deletions/duplications ranging from 1 to 129 Mb were detected with the consistent CNV size and location to karyotyping/microarray results in the study. Ten false positive results and two false negative results were obtained. The sensitivity and specificity of detection deletions/duplications were 84.21% and 98.42%, respectively. Whole-genome sequencing-based NIPT has high performance in detecting genome-wide CNVs, in particular >10Mb CNVs using the current FCAPS algorithm. It is possible to implement the current method in NIPT to prenatally screening for fetal CNVs.
Directory of Open Access Journals (Sweden)
Hongtai Liu
Full Text Available The aim of this study was to assess the performance of noninvasively prenatal testing (NIPT for fetal copy number variants (CNVs in clinical samples, using a whole-genome sequencing method.A total of 919 archived maternal plasma samples with karyotyping/microarray results, 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 through Maternal Plasma Sequencing (FCAPS to compare to the karyotyping/microarray results. Sensitivity, specificity and were evaluated.33 samples with deletions/duplications ranging from 1 to 129 Mb were detected with the consistent CNV size and location to karyotyping/microarray results in the study. Ten false positive results and two false negative results were obtained. The sensitivity and specificity of detection deletions/duplications were 84.21% and 98.42%, respectively.Whole-genome sequencing-based NIPT has high performance in detecting genome-wide CNVs, in particular >10Mb CNVs using the current FCAPS algorithm. It is possible to implement the current method in NIPT to prenatally screening for fetal CNVs.
Jenke, Christian; Lindstedt, Björn Arne; Harmsen, Dag; Karch, Helge; Brandal, Lin Thorstensen; Mellmann, Alexander
2011-01-01
Multilocus variable-number tandem-repeat analysis (MLVA) was compared to multilocus sequence typing (MLST) to differentiate hemolytic uremic syndrome-associated enterohemorrhagic Escherichia coli strains. Although MLVA—like MLST—was highly discriminatory (index of diversity, 0.988 versus 0.984), a low level of concordance demonstrated the limited ability of MLVA to reflect long-term evolutionary events. PMID:21832012
Lockwood, M.; Owens, M. J.; Barnard, L.; Usoskin, I. G.
2016-11-01
We use sunspot-group observations from the Royal Greenwich Observatory (RGO) to investigate the effects of intercalibrating data from observers with different visual acuities. The tests are made by counting the number of groups [RB] above a variable cut-off threshold of observed total whole spot area (uncorrected for foreshortening) to simulate what a lower-acuity observer would have seen. The synthesised annual means of RB are then re-scaled to the full observed RGO group number [RA] using a variety of regression techniques. It is found that a very high correlation between RA and RB (r_{AB} > 0.98) does not prevent large errors in the intercalibration (for example sunspot-maximum values can be over 30 % too large even for such levels of r_{AB}). In generating the backbone sunspot number [R_{BB}], Svalgaard and Schatten ( Solar Phys., 2016) force regression fits to pass through the scatter-plot origin, which generates unreliable fits (the residuals do not form a normal distribution) and causes sunspot-cycle amplitudes to be exaggerated in the intercalibrated data. It is demonstrated that the use of Quantile-Quantile ("Q-Q") plots to test for a normal distribution is a useful indicator of erroneous and misleading regression fits. Ordinary least-squares linear fits, not forced to pass through the origin, are sometimes reliable (although the optimum method used is shown to be different when matching peak and average sunspot-group numbers). However, other fits are only reliable if non-linear regression is used. From these results it is entirely possible that the inflation of solar-cycle amplitudes in the backbone group sunspot number as one goes back in time, relative to related solar-terrestrial parameters, is entirely caused by the use of inappropriate and non-robust regression techniques to calibrate the sunspot data.
He, Xinjie; Tong, Shelley Xiuli
2017-08-10
The present study investigated the onset of statistical learning and examined whether the number of exposures to a repeated sequence influences the learning performance of children with dyslexia on a serial reaction time task. Three groups of children (29 with dyslexia, 29 age-matched controls, and 30 reading level-matched controls) were administered a serial reaction time task, and their statistical learning performances after a small and a large number of exposures (40 vs. 180 exposures) were recorded and compared. Children with dyslexia showed impaired statistical learning after a small number of exposures to a sequence, but intact statistical learning after a large number of exposures. In contrast, the age-matched and reading level-matched control groups showed intact statistical learning after both small and large numbers of exposures. Children with dyslexia also exhibited a slower learning rate than either control group. These results suggest that the amount of exposure to statistical patterns influences statistical learning performance in children with dyslexia.
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.
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)
Zhongyang Zhang
2015-11-01
Full Text Available 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)
Rosenstiel Philip
2010-04-01
Full Text Available Abstract Background The beta-defensin gene cluster (DEFB at chromosome 8p23.1 is one of the most copy number (CN variable regions of the human genome. Whereas individual DEFB CNs have been suggested as independent genetic risk factors for several diseases (e.g. psoriasis and Crohn's disease, the role of multisite sequence variations (MSV is less well understood and to date has only been reported for prostate cancer. Simultaneous assessment of MSVs and CNs can be achieved by PCR, cloning and Sanger sequencing, however, these methods are labour and cost intensive as well as prone to methodological bias introduced by bacterial cloning. Here, we demonstrate that amplicon sequencing of pooled individual PCR products by the 454 technology allows in-depth determination of MSV haplotypes and estimation of DEFB CNs in parallel. Results Six PCR products spread over ~87 kb of DEFB and harbouring 24 known MSVs were amplified from 11 DNA samples, pooled and sequenced on a Roche 454 GS FLX sequencer. From ~142,000 reads, ~120,000 haplotype calls (HC were inferred that identified 22 haplotypes ranging from 2 to 7 per amplicon. In addition to the 24 known MSVs, two additional sequence variations were detected. Minimal CNs were estimated from the ratio of HCs and compared to absolute CNs determined by alternative methods. Concordance in CNs was found for 7 samples, the CNs differed by one in 2 samples and the estimated minimal CN was half of the absolute in one sample. For 7 samples and 2 amplicons, the 454 haplotyping results were compared to those by cloning/Sanger sequencing. Intrinsic problems related to chimera formation during PCR and differences between haplotyping by 454 and cloning/Sanger sequencing are discussed. Conclusion Deep amplicon sequencing using the 454 technology yield thousands of HCs per amplicon for an affordable price and may represent an effective method for parallel haplotyping and CN estimation in small to medium-sized cohorts. The
Krishnan, Neeraja M.; Gaur, Prakhar; Chaudhary, Rakshit; Rao, Arjun A.; Panda, Binay
2012-01-01
Copy Number Alterations (CNAs) such as deletions and duplications; compose a larger percentage of genetic variations than single nucleotide polymorphisms or other structural variations in cancer genomes that undergo major chromosomal re-arrangements. It is, therefore, imperative to identify cancer-specific somatic copy number alterations (SCNAs), with respect to matched normal tissue, in order to understand their association with the disease. We have devised an accurate, sensitive, and easy-to-use tool, COPS, COpy number using Paired Samples, for detecting SCNAs. We rigorously tested the performance of COPS using short sequence simulated reads at various sizes and coverage of SCNAs, read depths, read lengths and also with real tumor:normal paired samples. We found COPS to perform better in comparison to other known SCNA detection tools for all evaluated parameters, namely, sensitivity (detection of true positives), specificity (detection of false positives) and size accuracy. COPS performed well for sequencing reads of all lengths when used with most upstream read alignment tools. Additionally, by incorporating a downstream boundary segmentation detection tool, the accuracy of SCNA boundaries was further improved. Here, we report an accurate, sensitive and easy to use tool in detecting cancer-specific SCNAs using short-read sequence data. In addition to cancer, COPS can be used for any disease as long as sequence reads from both disease and normal samples from the same individual are available. An added boundary segmentation detection module makes COPS detected SCNA boundaries more specific for the samples studied. COPS is available at ftp://115.119.160.213 with username “cops” and password “cops”. PMID:23110103
Directory of Open Access Journals (Sweden)
Neeraja M Krishnan
Full Text Available Copy Number Alterations (CNAs such as deletions and duplications; compose a larger percentage of genetic variations than single nucleotide polymorphisms or other structural variations in cancer genomes that undergo major chromosomal re-arrangements. It is, therefore, imperative to identify cancer-specific somatic copy number alterations (SCNAs, with respect to matched normal tissue, in order to understand their association with the disease. We have devised an accurate, sensitive, and easy-to-use tool, COPS, COpy number using Paired Samples, for detecting SCNAs. We rigorously tested the performance of COPS using short sequence simulated reads at various sizes and coverage of SCNAs, read depths, read lengths and also with real tumor:normal paired samples. We found COPS to perform better in comparison to other known SCNA detection tools for all evaluated parameters, namely, sensitivity (detection of true positives, specificity (detection of false positives and size accuracy. COPS performed well for sequencing reads of all lengths when used with most upstream read alignment tools. Additionally, by incorporating a downstream boundary segmentation detection tool, the accuracy of SCNA boundaries was further improved. Here, we report an accurate, sensitive and easy to use tool in detecting cancer-specific SCNAs using short-read sequence data. In addition to cancer, COPS can be used for any disease as long as sequence reads from both disease and normal samples from the same individual are available. An added boundary segmentation detection module makes COPS detected SCNA boundaries more specific for the samples studied. COPS is available at ftp://115.119.160.213 with username "cops" and password "cops".
Directory of Open Access Journals (Sweden)
Andrew P. Morgan
2016-12-01
Full Text Available Wild-derived mouse inbred strains are becoming increasingly popular for complex traits analysis, evolutionary studies, and systems genetics. Here, we report the whole-genome sequencing of two wild-derived mouse inbred strains, LEWES/EiJ and ZALENDE/EiJ, of Mus musculus domesticus origin. These two inbred strains were selected based on their geographic origin, karyotype, and use in ongoing research. We generated 14× and 18× coverage sequence, respectively, and discovered over 1.1 million novel variants, most of which are private to one of these strains. This report expands the number of wild-derived inbred genomes in the Mus genus from six to eight. The sequence variation can be accessed via an online query tool; variant calls (VCF format and alignments (BAM format are available for download from a dedicated ftp site. Finally, the sequencing data have also been stored in a lossless, compressed, and indexed format using the multi-string Burrows-Wheeler transform. All data can be used without restriction.
Morgan, Andrew P; Didion, John P; Doran, Anthony G; Holt, James M; McMillan, Leonard; Keane, Thomas M; de Villena, Fernando Pardo-Manuel
2016-12-07
Wild-derived mouse inbred strains are becoming increasingly popular for complex traits analysis, evolutionary studies, and systems genetics. Here, we report the whole-genome sequencing of two wild-derived mouse inbred strains, LEWES/EiJ and ZALENDE/EiJ, of Mus musculus domesticus origin. These two inbred strains were selected based on their geographic origin, karyotype, and use in ongoing research. We generated 14× and 18× coverage sequence, respectively, and discovered over 1.1 million novel variants, most of which are private to one of these strains. This report expands the number of wild-derived inbred genomes in the Mus genus from six to eight. The sequence variation can be accessed via an online query tool; variant calls (VCF format) and alignments (BAM format) are available for download from a dedicated ftp site. Finally, the sequencing data have also been stored in a lossless, compressed, and indexed format using the multi-string Burrows-Wheeler transform. All data can be used without restriction. Copyright © 2016 Morgan et al.
Directory of Open Access Journals (Sweden)
Zou Fei
2010-10-01
Full Text Available Abstract Background The primer and amplicon length have been found to affect PCR based estimates of microbial diversity by pyrosequencing, while other PCR conditions have not been addressed using any deep sequencing method. The present study determined the effects of polymerase, template dilution and PCR cycle number using the Solexa platform. Results The PfuUltra II Fusion HS DNA Polymerase (Stratagene with higher fidelity showed lower amount of PCR artifacts and determined lower taxa richness than the Ex Taq (Takara. More importantly, the two polymerases showed different efficiencies for amplifying some of very abundant sequences, and determined significantly different community structures. As expected, the dilution of the DNA template resulted in a reduced estimation of taxa richness, particularly at the 200 fold dilution level, but the community structures were similar for all dilution levels. The 30 cycle group increased the PCR artifacts while comparing to the 25 cycle group, but the determined taxa richness was lower than that of the 25 cycle group. The PCR cycle number did not changed the microbial community structure significantly. Conclusions These results highlight the PCR conditions, particularly the polymerase, have significant effect on the analysis of microbial diversity with next generation sequencing methods.
Yu, Zhenhua; Liu, Yuanning; Shen, Yi; Wang, Minghui; Li, Ao
2014-09-15
Whole-genome sequencing of tumor samples has been demonstrated as an efficient approach for comprehensive analysis of genomic aberrations in cancer genome. Critical issues such as tumor impurity and aneuploidy, GC-content and mappability bias have been reported to complicate identification of copy number alteration and loss of heterozygosity in complex tumor samples. Therefore, efficient computational methods are required to address these issues. We introduce CLImAT (CNA and LOH Assessment in Impure and Aneuploid Tumors), a bioinformatics tool for identification of genomic aberrations from tumor samples using whole-genome sequencing data. Without requiring a matched normal sample, CLImAT takes integrated analysis of read depth and allelic frequency and provides extensive data processing procedures including GC-content and mappability correction of read depth and quantile normalization of B-allele frequency. CLImAT accurately identifies copy number alteration and loss of heterozygosity even for highly impure tumor samples with aneuploidy. We evaluate CLImAT on both simulated and real DNA sequencing data to demonstrate its ability to infer tumor impurity and ploidy and identify genomic aberrations in complex tumor samples. The CLImAT software package can be freely downloaded at http://bioinformatics.ustc.edu.cn/CLImAT/. © The Author 2014. Published by Oxford University Press.
AlSagob, Maysoon; Colak, Dilek; Kaya, Namik
2015-05-01
Autism spectrum disorder (ASD) is a large group of neurodevelopmental conditions that share common characteristics such as social and language impairment and repetitive and stereotypic behaviors. It is reported that ASD is on increase in recent years reaching ratios up to 1 in 68 children. The disease is seen four times more frequently in males than females. ASD is heritable with complex inheritance and genetic heterogeneity, and frequently coexists with other diseases such as intellectual disability, seizure disorders, and fragile-x. Recent advances in genomic technologies have led to a greater understanding of genetic mechanisms in ASD, discovery of novel genetic loci and risk factors, as well as submicroscopic chromosomal changes also known as copy number variations (CNVs). Here we review recent developments in the genetics field and hereditary and sporadic CNVs leading to ASD.
DEFF Research Database (Denmark)
Liu, Hongtai; Gao, Ya; Hu, Zhiyang
2016-01-01
Objectives The aim of this study was to assess the performance of noninvasively prenatal testing (NIPT) for fetal copy number variants (CNVs) in clinical samples, using a whole-genome sequencing method. Method A total of 919 archived maternal plasma samples with karyotyping/microarray results...... in the study. Ten false positive results and two false negative results were obtained. The sensitivity and specificity of detection deletions/duplications were 84.21% and 98.42%, respectively. Conclusion Whole-genome sequencing-based NIPT has high performance in detecting genome-wide CNVs, in particular > 10Mb...... CNVs using the current FCAPS algorithm. It is possible to implement the current method in NIPT to prenatally screening for fetal CNVs. Keywords...
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
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 Pediococcusclaussenii 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
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.
Liu, Yu; Gong, Li-Ping; Dong, Xiao-Li; Liu, Hong-Gang
2013-06-01
The aim of this study was to determine the translocation and copy number change of the C-MYC gene in patients with laryngeal dysplasia and laryngeal squamous cell carcinoma (LSCC), and to evaluate the prevalence of such expression in relation to the normal-dysplasia-carcinoma sequence. Fluorescent in situ hybridization (FISH) was applied on formalin-fixed paraffin-embedded blocks of 93 laryngeal lesion specimens (14 normal epithelium, 15 mild dysplasia, 18 moderate dysplasia, 16 severe dysplasia, 9 carcinoma in situ, and 21 invasive carcinoma). C-MYC translocation was not observed in all laryngeal tissue. The high frequency for C-MYC copy-number increased (100%) in invasive carcinoma: 57.14% amplifications and 42.86% gains, and the positive rate of C-MYC amplification and copy-number change increased with the increasing severity of laryngeal lesions (P < 0.0001). The results suggest that C-MYC may be activated by gain/amplification in LSCC and precancerous lesions. Thus, C-MYC may play an important role in promoting LSCC progression, and early FISH detection of C-MYC may be exploited to set a screening test for laryngeal dysplasia. Copyright © 2012 Wiley Periodicals, Inc.
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.
Lou, Haiyi; Lu, Yan; Lu, Dongsheng; Fu, Ruiqing; Wang, Xiaoji; Feng, Qidi; Wu, Sijie; Yang, Yajun; Li, Shilin; Kang, Longli; Guan, Yaqun; Hoh, Boon-Peng; Chung, Yeun-Jun; Jin, Li; Su, Bing; Xu, Shuhua
2015-07-02
Tibetan high-altitude adaptation (HAA) has been studied extensively, and many candidate genes have been reported. Subsequent efforts targeting HAA functional variants, however, have not been that successful (e.g., no functional variant has been suggested for the top candidate HAA gene, EPAS1). With WinXPCNVer, a method developed in this study, we detected in microarray data a Tibetan-enriched deletion (TED) carried by 90% of Tibetans; 50% were homozygous for the deletion, whereas only 3% carried the TED and 0% carried the homozygous deletion in 2,792 worldwide samples (p hemoglobin. It was also in complete LD with the 5-SNP motif, which was suspected to be introgressed from Denisovans, but the deletion itself was absent from the Denisovan sequence. Correspondingly, we detected that footprints of positive selection for the TED occurred 12,803 (95% confidence interval = 12,075-14,725) years ago. We further whole-genome deep sequenced (>60×) seven Tibetans and verified the TED but failed to identify any other copy-number variations with comparable patterns, giving this TED top priority for further study. We speculate that the specific patterns of the TED resulted from its own functionality in HAA of Tibetans or LD with a functional variant of EPAS1. Copyright © 2015 The American Society of Human Genetics. Published by Elsevier Inc. All rights reserved.
Zhang, Y; Song, Y; Cao, H; Mo, X; Yang, H; Wang, J; Lu, Z; Zhang, T
2017-03-01
HLA-DRB3, DRB4 and DRB5 (DRB3/4/5) are paralogues of HLA-DRB1. They have important roles in transplantation and have been reported to be related to many diseases. HLA typing methods for DRB3/4/5 based on NGS data have many limitations now, such as need of polymerase chain reaction (PCR) or low accuracy. We present a HLA typing method for DRB3/4/5 based on read mapping and haplotype assembly from NGS data. Also, copy number of DRB3/4/5 is determined by a k-means clustering method according to ratio of sequencing depth between DRB3/4/5 and DRB1. We achieved 100%, 100%, 100% accuracy on simulated data and 95.88%, 98.89%, 99.34% accuracy on MHC capture Illumina sequencing data at 4-digit resolution with 30-fold coverage for DRB3/4/5 separately. We also explored the DRB3/4/5 profiles in five continental populations through low coverage WGS data generated by the 1000 Genome Project. We found that frequency of DRB4 in African were significantly lower than that in all other populations. Our method for DRB3/4/5 typing has high accuracy. It is a good supplement to regular HLA typing and could help in disease studies, medical applications and human population diversity studies. © 2017 John Wiley & Sons A/S. Published by John Wiley & Sons Ltd.
Kader, Tanjina; Goode, David L; Wong, Stephen Q; Connaughton, Jacquie; Rowley, Simone M; Devereux, Lisa; Byrne, David; Fox, Stephen B; Mir Arnau, Gisela; Tothill, Richard W; Campbell, Ian G; Gorringe, Kylie L
2016-11-15
Unlocking clinically translatable genomic information, including copy number alterations (CNA), from formalin-fixed paraffin-embedded (FFPE) tissue is challenging due to low yields and degraded DNA. We describe a robust, cost-effective low-coverage whole genome sequencing (LC WGS) method for CNA detection using 5 ng of FFPE-derived DNA. CN profiles using 100 ng or 5 ng input DNA were highly concordant and comparable with molecular inversion probe (MIP) array profiles. LC WGS improved CN profiles of samples that performed poorly using MIP arrays. Our technique enables identification of driver and prognostic CNAs in archival patient samples previously deemed unsuitable for genomic analysis due to DNA limitations.
Mendoza, C.; Bautista, M. A.; Palmeri, P.; Quinet, P.; Witthoeft, M. C.; Kallman, T. R.
2017-08-01
Context. We are concerned with improving the diagnostic potential of the K lines and edges of elements with low cosmic abundances, namely F, Na, P, Cl, K, Sc, Ti, V, Cr, Mn, Co, Cu, and Zn, that are observed in the X-ray spectra of supernova remnants, galaxy clusters, and accreting black holes and neutron stars. Aims: Since accurate photoabsorption and photoionization cross sections are needed in their spectral models, they have been computed for isoelectronic sequences with electron number 12 ≤ N ≤ 18 using a multi-channel method. Methods: Target representations are obtained with the atomic structure code autostructure, and ground-state cross sections are computed with the Breit-Pauli R-matrix method (bprm) in intermediate coupling, including damping (radiative and Auger) effects. Results: Following the findings in our earlier work on sequences with 2 ≤ N ≤ 11, the contributions from channels associated with the 2s-hole [2s] μ target configurations and those containing 3d orbitals are studied in the Mg (N = 12) and Ar (N = 18) isoelectronic sequences. Cross sections for the latter ions are also calculated in the isolated-resonance approximation as implemented in autostructure and compared with bprm to test their accuracy. Conclusions: It is confirmed that the collisional channels associated with the [2s] μ target configurations must be taken into account owing to significant increases in the monotonic background cross section between the L and K edges. Target configurations with 3d orbitals give rise to fairly conspicuous unresolved transition arrays in the L-edge region, but to a much lesser extent in the K-edge that is our main concern; therefore, they have been neglected throughout owing to their computationally intractable channel inventory, thus allowing the computation of cross sections for all the ions with 12 ≤ N ≤ 18 in intermediate coupling with bprm. We find that the isolated-resonance approximations performs satisfactorily and will be our
Haeseler, Friedrich
2003-01-01
Automatic sequences are sequences which are produced by a finite automaton. Although they are not random they may look as being random. They are complicated, in the sense of not being not ultimately periodic, they may look rather complicated, in the sense that it may not be easy to name the rule by which the sequence is generated, however there exists a rule which generates the sequence. The concept automatic sequences has special applications in algebra, number theory, finite automata and formal languages, combinatorics on words. The text deals with different aspects of automatic sequences, in particular:· a general introduction to automatic sequences· the basic (combinatorial) properties of automatic sequences· the algebraic approach to automatic sequences· geometric objects related to automatic sequences.
Gamble, Tony; Coryell, Jessi; Ezaz, Tariq; Lynch, Joshua; Scantlebury, Daniel P; Zarkower, David
2015-05-01
Sex chromosomes have evolved many times in animals and studying these replicate evolutionary "experiments" can help broaden our understanding of the general forces driving the origin and evolution of sex chromosomes. However this plan of study has been hindered by the inability to identify the sex chromosome systems in the large number of species with cryptic, homomorphic sex chromosomes. Restriction site-associated DNA sequencing (RAD-seq) is a critical enabling technology that can identify the sex chromosome systems in many species where traditional cytogenetic methods have failed. Using newly generated RAD-seq data from 12 gecko species, along with data from the literature, we reinterpret the evolution of sex-determining systems in lizards and snakes and test the hypothesis that sex chromosomes can routinely act as evolutionary traps. We uncovered between 17 and 25 transitions among gecko sex-determining systems. This is approximately one-half to two-thirds of the total number of transitions observed among all lizards and snakes. We find support for the hypothesis that sex chromosome systems can readily become trap-like and show that adding even a small number of species from understudied clades can greatly enhance hypothesis testing in a model-based phylogenetic framework. RAD-seq will undoubtedly prove useful in evaluating other species for male or female heterogamety, particularly the majority of fish, amphibian, and reptile species that lack visibly heteromorphic sex chromosomes, and will significantly accelerate the pace of biological discovery. © The Author 2015. Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.
Zhang, Xianghong; Müller, Sebastian; Möller, Michael; Huse, Klaus; Taudien, Stefan; Book, Malte; Stuber, Frank; Platzer, Matthias; Groth, Marco
2014-01-24
The copy number variation (CNV) in beta-defensin genes (DEFB) on human chromosome 8p23 has been proposed to contribute to the phenotypic differences in inflammatory diseases. However, determination of exact DEFB CN is a major challenge in association studies. Quantitative real-time PCR (qPCR), paralog ratio tests (PRT) and multiplex ligation-dependent probe amplification (MLPA) have been extensively used to determine DEFB CN in different laboratories, but inter-method inconsistencies were observed frequently. In this study we asked which one is superior among the three methods for DEFB CN determination. We developed a clustering approach for MLPA and PRT to statistically correlate data from a single experiment. Then we compared qPCR, a newly designed PRT and MLPA for DEFB CN determination in 285 DNA samples. We found MLPA had the best convergence and clustering results of the raw data and the highest call rate. In addition, the concordance rates between MLPA or PRT and qPCR (32.12% and 37.99%, respectively) were unacceptably low with underestimated CN by qPCR. Concordance rate between MLPA and PRT (90.52%) was high but PRT systematically underestimated CN by one in a subset of samples. In these samples a sequence variant which caused complete PCR dropout of the respective DEFB cluster copies was found in one primer binding site of one of the targeted paralogous pseudogenes. MLPA is superior to PRT and even more to qPCR for DEFB CN determination. Although the applied PRT provides in most cases reliable results, such a test is particularly sensitive to low-frequency sequence variations preferably accumulating in loci like pseudogenes which are most likely not under selective pressure. In the light of the superior performance of multiplex assays, the drawbacks of such single PRTs could be overcome by combining more test markers.
Yamamoto, Toshiyuki; Shimojima, Keiko; Ondo, Yumiko; Imai, Katsumi; Chong, Pin Fee; Kira, Ryutaro; Amemiya, Mitsuhiro; Saito, Akira; Okamoto, Nobuhiko
2016-01-01
Next-generation sequencing (NGS) is widely used for the detection of disease-causing nucleotide variants. The challenges associated with detecting copy number variants (CNVs) using NGS analysis have been reported previously. Disease-related exome panels such as Illumina TruSight One are more cost-effective than whole-exome sequencing (WES) because of their selective target regions (~21% of the WES). In this study, CNVs were analyzed using data extracted through a disease-related exome panel analysis and the eXome Hidden Markov Model (XHMM). Samples from 61 patients with undiagnosed developmental delays and 52 healthy parents were included in this study. In the preliminary study to validate the constructed XHMM system (microarray-first approach), 34 patients who had previously been analyzed by chromosomal microarray testing were used. Among the five CNVs larger than 200 kb that were considered as non-pathogenic CNVs and were used as positive controls, four CNVs was successfully detected. The system was subsequently used to analyze different samples from 27 patients (NGS-first approach); 2 of these patients were successfully diagnosed as having pathogenic CNVs (an unbalanced translocation der(5)t(5;14) and a 16p11.2 duplication). These diagnoses were re-confirmed by chromosomal microarray testing and/or fluorescence in situ hybridization. The NGS-first approach generated no false-negative or false-positive results for pathogenic CNVs, indicating its high sensitivity and specificity in detecting pathogenic CNVs. The results of this study show the possible clinical utility of pathogenic CNV screening using disease-related exome panel analysis and XHMM.
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...
Giorgio, Elisa; Ciolfi, Andrea; Biamino, Elisa; Caputo, Viviana; Di Gregorio, Eleonora; Belligni, Elga Fabia; Calcia, Alessandro; Gaidolfi, Elena; Bruselles, Alessandro; Mancini, Cecilia; Cavalieri, Simona; Molinatto, Cristina; Cirillo Silengo, Margherita; Ferrero, Giovanni Battista; Tartaglia, Marco; Brusco, Alfredo
2016-07-01
Whole exome sequencing (WES) is a powerful tool to identify clinically undefined forms of intellectual disability/developmental delay (ID/DD), especially in consanguineous families. Here we report the genetic definition of two sporadic cases, with syndromic ID/DD for whom array-Comparative Genomic Hybridization (aCGH) identified a de novo copy number variant (CNV) of uncertain significance. The phenotypes included microcephaly with brachycephaly and a distinctive facies in one proband, and hypotonia in the legs and mild ataxia in the other. WES allowed identification of a functionally relevant homozygous variant affecting a known disease gene for rare syndromic ID/DD in each proband, that is, c.1423C>T (p.Arg377*) in the Trafficking Protein Particle Complex 9 (TRAPPC9), and c.154T>C (p.Cys52Arg) in the Very Low Density Lipoprotein Receptor (VLDLR). Four mutations affecting TRAPPC9 have been previously reported, and the present finding further depicts this syndromic form of ID, which includes microcephaly with brachycephaly, corpus callosum hypoplasia, facial dysmorphism, and overweight. VLDLR-associated cerebellar hypoplasia (VLDLR-CH) is characterized by non-progressive congenital ataxia and moderate-to-profound intellectual disability. The c.154T>C (p.Cys52Arg) mutation was associated with a very mild form of ataxia, mild intellectual disability, and cerebellar hypoplasia without cortical gyri simplification. In conclusion, we report two novel cases with rare causes of autosomal recessive ID, which document how interpreting de novo array-CGH variants represents a challenge in consanguineous families; as such, clinical WES should be considered in diagnostic testing. © 2016 Wiley Periodicals, Inc. © 2016 Wiley Periodicals, Inc.
Pritchard, Colin C; Salipante, Stephen J; Koehler, Karen; Smith, Christina; Scroggins, Sheena; Wood, Brent; Wu, David; Lee, Ming K; Dintzis, Suzanne; Adey, Andrew; Liu, Yajuan; Eaton, Keith D; Martins, Renato; Stricker, Kari; Margolin, Kim A; Hoffman, Noah; Churpek, Jane E; Tait, Jonathan F; King, Mary-Claire; Walsh, Tom
2014-01-01
Recent years have seen development and implementation of anticancer therapies targeted to particular gene mutations, but methods to assay clinical cancer specimens in a comprehensive way for the critical mutations remain underdeveloped. We have developed UW-OncoPlex, a clinical molecular diagnostic assay to provide simultaneous deep-sequencing information, based on >500× average coverage, for all classes of mutations in 194 clinically relevant genes. To validate UW-OncoPlex, we tested 98 previously characterized clinical tumor specimens from 10 different cancer types, including 41 formalin-fixed paraffin-embedded tissue samples. Mixing studies indicated reliable mutation detection in samples with ≥ 10% tumor cells. In clinical samples with ≥ 10% tumor cells, UW-OncoPlex correctly identified 129 of 130 known mutations [sensitivity 99.2%, (95% CI, 95.8%-99.9%)], including single nucleotide variants, small insertions and deletions, internal tandem duplications, gene copy number gains and amplifications, gene copy losses, chromosomal gains and losses, and actionable genomic rearrangements, including ALK-EML4, ROS1, PML-RARA, and BCR-ABL. In the same samples, the assay also identified actionable point mutations in genes not previously analyzed and novel gene rearrangements of MLL and GRIK4 in melanoma, and of ASXL1, PIK3R1, and SGCZ in acute myeloid leukemia. To best guide existing and emerging treatment regimens and facilitate integration of genomic testing with patient care, we developed a framework for data analysis, decision support, and reporting clinically actionable results. Copyright © 2014 American Society for Investigative Pathology and the Association for Molecular Pathology. Published by Elsevier Inc. All rights reserved.
Information Encoding on a Pseudo Random Noise Radar Waveform
2013-03-01
antenna under test AWG arbitrary waveform generator AWGN additive white Gaussian noise BPSK binary phase shift keying CDMA code division multiple...focused on the orthogonal frequency-division multiplexing (OFDM) and code division multiple access ( CDMA ) waveforms. The Ohio State University has...components into a single unit allows for a more mobile compact platform. The plan is diagrammed in Figure 3.5. Figure 3.5: Planned modifications to
National Research Council Canada - National Science Library
Do, Hongdo; Dobrovic, Alexander
2009-01-01
.... 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...
Yu, Zhenhua; Li, Ao; Wang, Minghui
2017-03-15
Copy number alterations (CNA) and loss of heterozygosity (LOH) represent a large proportion of genetic structural variations of cancer genomes. These aberrations are continuously accumulated during the procedure of clonal evolution and patterned by phylogenetic branching. This invariably results in the emergence of multiple cell populations with distinct complement of mutational landscapes in tumor sample. With the advent of next-generation sequencing technology, inference of subclonal populations has become one of the focused interests in cancer-associated studies, and is usually based on the assessment of combinations of somatic single-nucleotide variations (SNV), CNA and LOH. However, cancer samples often have several inherent issues, such as contamination of normal stroma, tumor aneuploidy and intra-tumor heterogeneity. Addressing these critical issues is imperative for accurate profiling of clonal architecture. We present CLImAT-HET, a computational method designed for capturing clonal diversity in the CNA/LOH dimensions by taking into account the intra-tumor heterogeneity issue, in the case where a reference or matched normal sample is absent. The algorithm quantitatively represents the clonal identification problem using a factorial hidden Markov model, and takes an integrated analysis of read counts and allele frequency data. It is able to infer subclonal CNA and LOH events as well as the fraction of cells harboring each event. The results on simulated datasets indicate that CLImAT-HET has high power to identify CNA/LOH segments, it achieves an average accuracy of 0.87. It can also accurately infer proportion of each clonal population with an overall Pearson correlation coefficient of 0.99 and a mean absolute error of 0.02. CLImAT-HET shows significant advantages when compared with other existing methods. Application of CLImAT-HET to 5 primary triple negative breast cancer samples demonstrates its ability to capture clonal diversity in the CAN
Random Number Generation for Petascale Quantum Monte Carlo
Energy Technology Data Exchange (ETDEWEB)
Ashok Srinivasan
2010-03-16
The quality of random number generators can affect the results of Monte Carlo computations, especially when a large number of random numbers are consumed. Furthermore, correlations present between different random number streams in a parallel computation can further affect the results. The SPRNG software, which the author had developed earlier, has pseudo-random number generators (PRNGs) capable of producing large numbers of streams with large periods. However, they had been empirically tested on only thousand streams earlier. In the work summarized here, we tested the SPRNG generators with over a hundred thousand streams, involving over 10^14 random numbers per test, on some tests. We also tested the popular Mersenne Twister. We believe that these are the largest tests of PRNGs, both in terms of the numbers of streams tested and the number of random numbers tested. We observed defects in some of these generators, including the Mersenne Twister, while a few generators appeared to perform well. We also corrected an error in the implementation of one of the SPRNG generators.
Gupta, Prabal; Singh, Balpreet; Arora, Krishan
2017-07-01
The very high peak to average power ratio (PAPR) is the biggest problem faced by OFDM system which ultimately causes distortion in the transmitted data. In the literatures various techniques have been proposed for the reduction of PAPR. One of the important technique which is known as Selected Mapping (SLM) or distortion-less technique proposed by several literature for the reduction of PAPR. But SLM technique generally uses several number of randomly designed phase sequence in frequency domain so that after inverse fast Fourier transform (IFFT) when data is converted into corresponding time domain sequence it can be optimized accordingly. Henceforth, in this paper we are proposing a higher number of novel phase sequence based SLM with 32-Quadrature amplitude modulation (QAM) under various sub carriers like 32, 64, 128, 256 and 512. Probabilistic analysis with the help of complementary cumulative distribution function (CCDF) clearly depicts the remarkable performance of our proposed algorithm in comparison with conventional OFDM system.
DEFF Research Database (Denmark)
Scheibye-Alsing, Karsten; Hoffmann, S.; Frankel, Annett Maria
2009-01-01
Despite the rapidly increasing number of sequenced and re-sequenced genomes, many issues regarding the computational assembly of large-scale sequencing data have remain unresolved. Computational assembly is crucial in large genome projects as well for the evolving high-throughput technologies...... and plays an important role in processing the information generated by these methods. Here, we provide a comprehensive overview of the current publicly available sequence assembly programs. We describe the basic principles of computational assembly along with the main concerns, such as repetitive sequences...... in genomic DNA, highly expressed genes and alternative transcripts in EST sequences. We summarize existing comparisons of different assemblers and provide a detailed descriptions and directions for download of assembly programs at: http://genome.ku.dk/resources/assembly/methods.html....
Pritchard, Colin C.; Salipante, Stephen J.; Koehler, Karen; Smith, Christina; Scroggins, Sheena; Wood, Brent; Wu, David; Lee, Ming K.; Dintzis, Suzanne; Adey, Andrew; Liu, Yajuan; Keith D Eaton; Martins, Renato; Stricker, Kari; Margolin, Kim A
2014-01-01
Recent years have seen development and implementation of anticancer therapies targeted to particular gene mutations, but methods to assay clinical cancer specimens in a comprehensive way for the critical mutations remain underdeveloped. We have developed UW-OncoPlex, a clinical molecular diagnostic assay to provide simultaneous deep-sequencing information, based on >500× average coverage, for all classes of mutations in 194 clinically relevant genes. To validate UW-OncoPlex, we tested 98 prev...
Exact Ramsey Theory: Green-Tao numbers and SAT
Kullmann, Oliver
2010-01-01
We consider the links between Ramsey theory in the integers, based on van der Waerden's theorem, and (boolean, CNF) SAT solving. We aim at using the problems from exact Ramsey theory, concerned with computing Ramsey-type numbers, as a rich source of test problems, where especially methods for solving hard problems can be developed. In order to control the growth of the problem instances, we introduce "transversal extensions" as a natural way of constructing mixed parameter tuples (k_1, ..., k_m) for van-der-Waerden-like numbers N(k_1, ..., k_m), such that the growth of these numbers is guaranteed to be linear. Based on Green-Tao's theorem we introduce the "Green-Tao numbers" grt(k_1, ..., k_m), which in a sense combine the strict structure of van der Waerden problems with the (pseudo-)randomness of the distribution of prime numbers. Using standard SAT solvers (look-ahead, conflict-driven, and local search) we determine the basic values. It turns out that already for this single form of Ramsey-type problems, w...
Harrop, Thomas W R; Sztal, Tamar; Lumb, Christopher; Good, Robert T; Daborn, Phillip J; Batterham, Philip; Chung, Henry
2014-01-01
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.
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.
Kłodowska, Izabella; Rodziewicz, Joanna; Janczukowicz, Wojciech; Gotkowska-Płachta, Anna; Cydzik-Kwiatkowska, Agnieszka
2016-01-01
This work reports on the effect of electric current density and anode material (platinum, carbon) on the concentration of oxidized and mineral forms of nitrogen, on physical parameters (pH, redox potential, electrical conductivity) and the number of denitrifying bacteria in the biofilm (MPN). Experiments were conducted under anaerobic conditions without and with the flow of electric current (with density of 79 mA · m(-2) and 132 mA · m(-2)). Results obtained in the study enabled concluding that increasing density of electric current caused a decreasing concentration of nitrate in the reactor with platinum anode (R1) and carbon anode (R2). Its concentration depended on anode material. The highest hydrogenotrophic denitrification efficiency was achieved in R2 in which the process was aided by inorganic carbon (CO2) that originated from carbon anode oxidation and the electrical conductivity of wastewater increased as a result of the presence of HCO3(-) and CO3(2-) ions. Strong oxidizing properties of the platinum anode (R1) prevented the accumulation of adverse forms of nitrogen, including nitrite and ammonia. The increase in electric current density affected also a lower number of denitrifying bacteria (MPN) in the biofilm in both reactors (R1 and R2). Metal oxides accumulated on the surface of the cathode had a toxic effect upon microorganisms and impaired the production of a hydrogen donor.
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.
Ono, Kentaro; Matsuhashi, Masao; Mima, Tatsuya; Fukuyama, Hidenao; Altmann, Christian F
2013-09-01
Numerous studies have reported that perceptual grouping affects the pre-attentive processing of sound omission in a sequence of tones. However, it remains unclear whether or not the perceptual grouping and musical experience affect the attentive processing of sound omission. To this end, we created a sequence of loud (L) and soft (S) tones grouped as 'LLSLLS…' and a random sequence of the L and S tones. The omission of the L tones was inserted pseudo-randomly in the random sequence, and there were two positions at which it was inserted. For within-group omission, the omission was after the first L tone within the 'LLS' pattern. For between-group omission, the omission was inserted between the patterns. The brain response to the omission in musicians and non-musicians was measured using magnetoencephalography. During the magnetoencephalography measurement, the subjects' performance in a task to detect the omission was faster in the random sequence than in the group sequence. Source analysis showed that the omission in the random sequence caused greater activity than that in the group sequence. The increase was found in the right inferior parietal lobe in musicians, whereas it was found in the left superior temporal gyrus in non-musicians. These results suggest that the attentive processing of perceptual grouping might implicate the left superior temporal gyrus or right inferior parietal lobe, depending on musical experience. © 2013 Federation of European Neuroscience Societies and John Wiley & Sons Ltd.
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...
The sequence of sequencers: The history of sequencing DNA
Heather, James M.; Chain, Benjamin
2016-01-01
Determining the order of nucleic acid residues in biological samples is an integral component of a wide variety of research applications. Over the last fifty years large numbers of researchers have applied themselves to the production of techniques and technologies to facilitate this feat, sequencing DNA and RNA molecules. This time-scale has witnessed tremendous changes, moving from sequencing short oligonucleotides to millions of bases, from struggling towards the deduction of the coding sequence of a single gene to rapid and widely available whole genome sequencing. This article traverses those years, iterating through the different generations of sequencing technology, highlighting some of the key discoveries, researchers, and sequences along the way. PMID:26554401
Gironde, S.
2012-01-01
Pseudomonas syringae pv. maculicola causes bacterial spot on Brassicaceae worldwide, and for the last 10 years severe outbreaks have been reported in the Loire Valley, France. P. syringae pv. maculicola resembles P. syringae pv. tomato in that it is also pathogenic for tomato and causes the same types of symptoms. We used a collection of 106 strains of P. syringae to characterize the relationships between P. syringae pv. maculicola and related pathovars, paying special attention to P. syringae pv. tomato. Phylogenetic analysis of gyrB and rpoD gene sequences showed that P. syringae pv. maculicola, which causes diseases in Brassicaceae, forms six genetic lineages within genomospecies 3 of P. syringae strains as defined by L. Gardan et al. (Int. J. Syst. Bacteriol. 49[Pt 2]:469–478, 1999), whereas P. syringae pv. tomato forms two distinct genetic lineages. A multilocus variable-number tandem-repeat (VNTR) analysis (MLVA) conducted with eight minisatellite loci confirmed the genetic structure obtained with rpoD and gyrB sequence analyses. These results provide promising tools for fine-scale epidemiological studies on diseases caused by P. syringae pv. maculicola and P. syringae pv. tomato. The two pathovars had distinct host ranges; only P. syringae pv. maculicola strains were pathogenic for Brassicaceae. A subpopulation of P. syringae pv. maculicola strains that are pathogenic for Pto-expressing tomato plants were shown to lack avrPto1 and avrPtoB or to contain a disrupted avrPtoB homolog. Taking phylogenetic and pathological features into account, our data suggest that the DC3000 strain belongs to P. syringae pv. maculicola. This study shows that P. syringae pv. maculicola and P. syringae pv. tomato appear multiclonal, as they did not diverge from a single common ancestral group within the ancestral P. syringae genomospecies 3, and suggests that pathovar specificity within P. syringae may be due to independent genetic events. PMID:22389364
Number names and number understanding
DEFF Research Database (Denmark)
Ejersbo, Lisser Rye; Misfeldt, Morten
2014-01-01
through using mathematical names for the numbers such as one-ten-one for 11 and five-ten-six for 56. The project combines the renaming of numbers with supporting the teaching with the new number names. Our hypothesis is that Danish children have more difficulties learning and working with numbers, because...
An Empirical Analysis of the Cascade Secret Key Reconciliation Protocol for Quantum Key Distribution
2011-09-01
sifted key generation, the simulation utilizes the pseudo-random number generator Mersenne Twister developed by Matsumoto and Nishimura (Matsumoto...Mersenne Twister pseudo-random number generator. A cryptographically secure pseudo-random number generator may be a better choice for future... twister : a 623-dimensionally equidistributed uniform pseudo-random number generator. ACM Trans. Model. Comput. Simul. , 8 (1), 3-30. Maurer, U. M
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.
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.
Vorob'ev, Nikolai Nikolaevich
2011-01-01
Fibonacci numbers date back to an 800-year-old problem concerning the number of offspring born in a single year to a pair of rabbits. This book offers the solution and explores the occurrence of Fibonacci numbers in number theory, continued fractions, and geometry. A discussion of the ""golden section"" rectangle, in which the lengths of the sides can be expressed as a ration of two successive Fibonacci numbers, draws upon attempts by ancient and medieval thinkers to base aesthetic and philosophical principles on the beauty of these figures. Recreational readers as well as students and teacher
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.
Directory of Open Access Journals (Sweden)
Watase Yasushige
2016-12-01
Full Text Available This article provides definitions and examples upon an integral element of unital commutative rings. An algebraic number is also treated as consequence of a concept of “integral”. Definitions for an integral closure, an algebraic integer and a transcendental numbers [14], [1], [10] and [7] are included as well. As an application of an algebraic number, this article includes a formal proof of a ring extension of rational number field ℚ induced by substitution of an algebraic number to the polynomial ring of ℚ[x] turns to be a field.
Cordial Languages and Cordial Numbers
Directory of Open Access Journals (Sweden)
J. Baskar BABUJEE
2012-01-01
Full Text Available The concept of cordial labeling in graphs motivated us to introduce cordial words, cordial languages and cordial numbers. We interpret the notion of cordial labeling in Automata and thereby study the corresponding languages. In this paper we develop a new sequence of numbers called the cordial numbers in number theory using the labeling techniques in graph theory on automata theory.
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, ...
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
Helleloid, Geir; Khalid, Madeeha; Moulton, David Petrie; Wood, Philip Matchett
2008-01-01
In graph pegging, we view each vertex of a graph as a hole into which a peg can be placed, with checker-like ``pegging moves'' allowed. Motivated by well-studied questions in graph pebbling, we introduce two pegging quantities. The pegging number (respectively, the optimal pegging number) of a graph is the minimum number of pegs such that for every (respectively, some) distribution of that many pegs on the graph, any vertex can be reached by a sequence of pegging moves. We prove several basic...
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...
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.
Indian Academy of Sciences (India)
How many points are there on a line? Which is more in number- points on a line or lines in a plane? These are some natural questions that have occurred to us sometime or the other. It is interesting to note the difference between the two questions. Do we have to know how many points and lines there are to answer.
Indian Academy of Sciences (India)
Admin
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. Besides mathematics, she is interested in (singing) indian classical music and yoga. Right: Shailesh Shirali is. Director of Sahyadri School.
Psychoacoustic Properties of Fibonacci Sequences
Directory of Open Access Journals (Sweden)
J. Sokoll
2008-01-01
Full Text Available 1202, Fibonacci set up one of the most interesting sequences in number theory. This sequence can be represented by so-called Fibonacci Numbers, and by a binary sequence of zeros and ones. If such a binary Fibonacci Sequence is played back as an audio file, a very dissonant sound results. This is caused by the “almost-periodic”, “self-similar” property of the binary sequence. The ratio of zeros and ones converges to the golden ratio, as do the primary and secondary spectral components intheir frequencies and amplitudes. These Fibonacci Sequences will be characterized using listening tests and psychoacoustic analyses.
Curling Numbers of Certain Graph Powers
C, Susanth; Kalayathankal, Sunny Joseph; Sudev, N. K.; Chithra, K. P.; Kok, Johan
2015-01-01
Given a finite nonempty sequence $S$ of integers, write it as $XY^k$, where $Y^k$ is a power of greatest exponent that is a suffix of $S$: this $k$ is the curling number of $S$. The concept of curling number of sequences has already been extended to the degree sequences of graphs to define the curling number of a graph. In this paper we study the curling number of graph powers, graph products and certain other graph operations.
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...
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.
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.
Sequence Factorial and Its Applications
Asiru, Muniru A.
2012-01-01
In this note, we introduce sequence factorial and use this to study generalized M-bonomial coefficients. For the sequence of natural numbers, the twin concepts of sequence factorial and generalized M-bonomial coefficients, respectively, extend the corresponding concepts of factorial of an integer and binomial coefficients. Some latent properties…
DEFF Research Database (Denmark)
Sato, Shusei; Andersen, Stig Uggerhøj
2014-01-01
The current Lotus japonicus reference genome sequence is based on a hybrid assembly of Sanger TAC/BAC, Sanger shotgun and Illumina shotgun sequencing data generated from the Miyakojima-MG20 accession. It covers nearly all expressed L. japonicus genes and has been annotated mainly based...... on transcriptional evidence. Analysis of repetitive sequences suggests that they are underrepresented in the reference assembly, reflecting an enrichment of gene-rich regions in the current assembly. Characterization of Lotus natural variation by resequencing of L. japonicus accessions and diploid Lotus species...... is currently ongoing, facilitated by the MG20 reference sequence...
Jamieson, F B; Teatero, S; Guthrie, J L; Neemuchwala, A; Fittipaldi, N; Mehaffy, C
2014-10-01
Mycobacterium tuberculosis isolates of the Manila sublineage are genetically homogeneous. In this study, we used whole-genome sequencing (WGS) to type a collection of 36 M. tuberculosis isolates of the Manila family. WGS enabled the subtyping of these 36 isolates into at least 10 distinct clusters. Our results indicate that WGS is a powerful approach to determining the relatedness of Manila family M. tuberculosis isolates. Copyright © 2014, American Society for Microbiology. All Rights Reserved.
Information Theory of DNA Sequencing
Motahari, Abolfazl; Tse, David
2012-01-01
DNA sequencing is the basic workhorse of modern day biology and medicine. Shotgun sequencing is the dominant technique used: many randomly located short fragments called reads are extracted from the DNA sequence, and these reads are assembled to reconstruct the original sequence. By drawing an analogy between the DNA sequencing problem and the classic communication problem, we define an information theoretic notion of sequencing capacity. This is the maximum number of DNA base pairs that can be resolved reliably per read, and provides a fundamental limit to the performance that can be achieved by any assembly algorithm. We compute the sequencing capacity explicitly for a simple statistical model of the DNA sequence and the read process. Using this framework, we also study the impact of noise in the read process on the sequencing capacity.
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.
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.
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.
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.
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.
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.
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 ...
Graded sets, points and numbers
Herencia González, José Antonio
1998-01-01
The basic tool considered in this paper is the so-called "graded set", defined on the analogy of the family of α-cuts of a fuzzy set. It is also considered the corresponding extensions of the concepts of a point and of a real number (again on the analogy of the fuzzy case). These new "graded concepts" avoid the disadvantages pointed out by Gerla (for the fuzzy points) and by Kaleva and Seikkala (for the convergence of sequences of fuzzy numbers).
Lifescience Database Archive (English)
Full Text Available Sequences Nucleotide Sequence Nucleotide sequence of full length cDNA (trimmed sequence) kome_ine_full_se...quence_db.fasta.zip kome_ine_full_sequence_db.zip kome_ine_full_sequence_db ...
On Paranorm Zweier -Convergent Sequence Spaces
Directory of Open Access Journals (Sweden)
Vakeel A. Khan
2013-01-01
Full Text Available In this paper, we introduce the paranorm Zweier -convergent sequence spaces , , and , a sequence of positive real numbers. We study some topological properties, prove the decomposition theorem, and study some inclusion relations on these spaces.
Optimal sequence for Parrondo games
Dinis, Luis
2008-02-01
An algorithm based on backward induction is devised in order to compute the optimal sequence of games to be played in Parrondo games. The algorithm can be used to find the optimal sequence for any finite number of turns or in the steady state, showing that ABABB… is the sequence with the highest steady state average gain. The algorithm can also be generalized to find the optimal adaptive strategy in a multiplayer version of the games, where a finite number of players may choose, at every turn, the game the whole ensemble should play.
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....
Large-Scale Sequence Comparison.
Lal, Devi; Verma, Mansi
2017-01-01
There are millions of sequences deposited in genomic databases, and it is an important task to categorize them according to their structural and functional roles. Sequence comparison is a prerequisite for proper categorization of both DNA and protein sequences, and helps in assigning a putative or hypothetical structure and function to a given sequence. There are various methods available for comparing sequences, alignment being first and foremost for sequences with a small number of base pairs as well as for large-scale genome comparison. Various tools are available for performing pairwise large sequence comparison. The best known tools either perform global alignment or generate local alignments between the two sequences. In this chapter we first provide basic information regarding sequence comparison. This is followed by the description of the PAM and BLOSUM matrices that form the basis of sequence comparison. We also give a practical overview of currently available methods such as BLAST and FASTA, followed by a description and overview of tools available for genome comparison including LAGAN, MumMER, BLASTZ, and AVID.
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.
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, ...
Magic Numbers in Protein Structures
DEFF Research Database (Denmark)
Lindgård, Per-Anker; Bohr, Henrik
1996-01-01
A homology measure for protein fold classes has been constructed by locally projecting consecutive secondary structures onto a lattice. Taking into account hydrophobic forces we have found a mechanism for formation of domains containing magic numbers of secondary structures and multipla...... of these domains. We have performed a statistical analysis of available protein structures and found agreement with the predicted preferred abundances. Furthermore, a connection between sequence information and fold classes is established in terms of hinge forces between the structural elements....
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.
On the Curling Number of Certain Graphs
Kok, Johan; Sudev, Naduvath; Sudev, Chithra
2015-01-01
In this paper, we introduce the concept of curling subsequence of simple, finite and connected graphs. A curling subsequence is a maximal subsequence $C$ of the degree sequence of a simple connected graph $G$ for which the curling number $cn(G)$ corresponds to the curling number of the degree sequence per se and hence we call it the curling number of the graph $G$. A maximal degree subsequence with equal entries is called an identity subsequence. The number of identity curling subsequences in...
Repdigits in k-Lucas sequences
Indian Academy of Sciences (India)
(2) n )n. In this paper, we address a similar problem in the family of k-Lucas sequences. We also show that the k-Lucas sequences have similar properties to those of k-Fibonacci sequences and occur in formulae simultaneously with the latter. Keywords. Generalized Fibonacci and Lucas numbers; lower bounds for nonzero.
Generalized Vector-Valued Sequence Spaces Defined by Modulus Functions
Directory of Open Access Journals (Sweden)
Işik Mahmut
2010-01-01
Full Text Available We introduce the vector-valued sequence spaces , , and , and , using a sequence of modulus functions and the multiplier sequence of nonzero complex numbers. We give some relations related to these sequence spaces. It is also shown that if a sequence is strongly -Cesàro summable with respect to the modulus function then it is -statistically convergent.
DEFF Research Database (Denmark)
Piskur, Jure; Langkjær, Rikke Breinhold
2004-01-01
they are short and degenerate and occupy different positions. Comparative genomics helps to understand the origin of yeasts and points out crucial molecular events in yeast evolutionary history, such as whole-genome duplication and horizontal gene transfer(s). In addition, the accumulating sequence data provide...... that the minimum number of genes from each species that need to be compared to produce a reliable phylogeny is about 20. Yeast has also become an attractive model to study speciation in eukaryotes, especially to understand molecular mechanisms behind the establishment of reproductive isolation. Comparison...... of closely related species helps in gene annotation and to answer how many genes there really are within the genomes. Analysis of non-coding regions among closely related species has provided an example of how to determine novel gene regulatory sequences, which were previously difficult to analyse because...
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...
Children, everyday numbers and school numbers
Directory of Open Access Journals (Sweden)
Clélia Maria Ignatius Nogueira
2008-08-01
Full Text Available Relationship made by school children between “daily” numbers, or rather, numbers deployed outside the school, and numbers worked out in school under various circumstances, or rather, orally and in writing, is investigated. Analysis has been undertaken with ten six-year-old children by means of a clinical and critical method. Research results show that children interact with the environment and recognized the figures, name them, conjecture on their written mode and give coherent meaning to the figures. Analysis also demonstrates that children use numbers outside the school. They understand and exemplify the number’s different meanings in an out-class context. Since the children do not give a weighty meaning to “school” numbers, pedagogical activity with numbers fails to put into practice the recommendations of the official policy.
Sadhana | Indian Academy of Sciences
Indian Academy of Sciences (India)
Home; Journals; Sadhana; Volume 34; Issue 5. Issue front cover thumbnail. Volume 34, Issue 5. October 2009, pages 689-864. pp 689-701. Cryptographic pseudo-random sequences from the chaotic Hénon map · Madhekar Suneel · More Details Abstract Fulltext PDF. A scheme for pseudo-random binary sequence ...
Mappings of Type Special Space of Sequences
Directory of Open Access Journals (Sweden)
Awad A. Bakery
2016-01-01
Full Text Available We give sufficient conditions on a special space of sequences defined by Mohamed and Bakery (2013 such that the finite rank operators are dense in the complete space of operators whose approximation numbers belong to this sequence space. Hence, under a few conditions, every compact operator would be approximated by finite rank operators. We apply it on the sequence space defined by Tripathy and Mahanta (2003. Our results match those known for p-absolutely summable sequences of reals.
A generalized sense of number.
Arrighi, Roberto; Togoli, Irene; Burr, David C
2014-12-22
Much evidence has accumulated to suggest that many animals, including young human infants, possess an abstract sense of approximate quantity, a number sense. Most research has concentrated on apparent numerosity of spatial arrays of dots or other objects, but a truly abstract sense of number should be capable of encoding the numerosity of any set of discrete elements, however displayed and in whatever sensory modality. Here, we use the psychophysical technique of adaptation to study the sense of number for serially presented items. We show that numerosity of both auditory and visual sequences is greatly affected by prior adaptation to slow or rapid sequences of events. The adaptation to visual stimuli was spatially selective (in external, not retinal coordinates), pointing to a sensory rather than cognitive process. However, adaptation generalized across modalities, from auditory to visual and vice versa. Adaptation also generalized across formats: adapting to sequential streams of flashes affected the perceived numerosity of spatial arrays. All these results point to a perceptual system that transcends vision and audition to encode an abstract sense of number in space and in time.
Magic Numbers and Pascal's Triangle
López-Cruz, Elías
2002-03-01
Papers concerning the so called "magic numbers"^1-3 span different areas of Solid State Physics. Treatment of the growth of metal clusters and its stability conditions from the theoretical point of view in Ref. 1 leads to the conclusion that the clusters can take place in two or three dimensions. The clusters are triangular or tetrahedral and are obtained only for certain "magic numbers". Experimental work concerning the growth of metal clusters in two dimensions^2 have confirmed the growth only for certain magic numbers and these are the same as the calculated ones in Ref. 1. The present work shows that these "magic numbers" can be deduced from the numeric arrangement called Pascal's Triangle as two of the many numeric sequences contained in the triangle. Some other sequences will be discussed. 1. S.M. Reimann, M. Kuskinen, H. Häkkinen, P.E. Lindelof, and M. Manninen, Phys. Rev. B 56, 12147 (1997-I) 2. M.Y. Lai and Y.L. Wang, Phys. Rev. Lett. 81, 164 (1998) 3. T.E.M. Staab, M. Haugk, Th. Frauenheim, and H.S. Leipner, Phys. REv. Lett. 83, 5519 (1999)
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
Numbers Defy the Law of Large Numbers
Falk, Ruma; Lann, Avital Lavie
2015-01-01
As the number of independent tosses of a fair coin grows, the rates of heads and tails tend to equality. This is misinterpreted by many students as being true also for the absolute numbers of the two outcomes, which, conversely, depart unboundedly from each other in the process. Eradicating that misconception, as by coin-tossing experiments,…
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.
Operator Ideal of Cesaro Type Sequence Spaces Involving Lacunary Sequence
Directory of Open Access Journals (Sweden)
Awad A. Bakery
2014-01-01
Full Text Available The aim of this paper is to give the sufficient conditions on the sequence space Cesθ,p defined in Lim (1977 such that the class of all bounded linear operators between any arbitrary Banach spaces with nth approximation numbers of the bounded linear operators in Cesθ,p form an operator ideal.
Lifescience Database Archive (English)
Full Text Available Sequences Amino Acid Sequence Amino Acid sequence of full length cDNA (Longest ORF) kome_ine_full_se...quence_amino_db.fasta.zip kome_ine_full_sequence_amino_db.zip kome_ine_full_sequence_amino_db ...
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.
Markwig, Hannah; Rau, Johannes
2014-01-01
In this paper, we define tropical analogues of real Hurwitz numbers, i.e. numbers of covers of surfaces with compatible involutions satisfying prescribed ramification properties. We prove a correspondence theorem stating the equality of the tropical numbers with their real counterparts. We apply this theorem to the case of double Hurwitz numbers (which generalizes our result from arXiv:1409.8095).
A note on bifix-free sequences
DEFF Research Database (Denmark)
Nielsen, Peter Tolstrup
1973-01-01
A bifix of anL-aryn-tuple is a sequence which is both a prefix and a suffix of thatn-tuple. The practical importance of bifix-free patterns is emphasized, and we devise a systematic way of generating all such sequences and determine their number.......A bifix of anL-aryn-tuple is a sequence which is both a prefix and a suffix of thatn-tuple. The practical importance of bifix-free patterns is emphasized, and we devise a systematic way of generating all such sequences and determine their number....
... you want to learn. Search form Search Whole Genome Sequencing You are here Home Testing & Services Testing ... the full story, click here . What is whole genome sequencing? Whole genome sequencing is the mapping out ...
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...
Jarvis, Frazer
2014-01-01
The technical difficulties of algebraic number theory often make this subject appear difficult to beginners. This undergraduate textbook provides a welcome solution to these problems as it provides an approachable and thorough introduction to the topic. Algebraic Number Theory takes the reader from unique factorisation in the integers through to the modern-day number field sieve. The first few chapters consider the importance of arithmetic in fields larger than the rational numbers. Whilst some results generalise well, the unique factorisation of the integers in these more general number fields often fail. Algebraic number theory aims to overcome this problem. Most examples are taken from quadratic fields, for which calculations are easy to perform. The middle section considers more general theory and results for number fields, and the book concludes with some topics which are more likely to be suitable for advanced students, namely, the analytic class number formula and the number field sieve. This is the fi...
Coordinate cytokine regulatory sequences
Frazer, Kelly A.; Rubin, Edward M.; Loots, Gabriela G.
2005-05-10
The present invention provides CNS sequences that regulate the cytokine gene expression, expression cassettes and vectors comprising or lacking the CNS sequences, host cells and non-human transgenic animals comprising the CNS sequences or lacking the CNS sequences. The present invention also provides methods for identifying compounds that modulate the functions of CNS sequences as well as methods for diagnosing defects in the CNS sequences of patients.
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.......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....
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 Cl...uster and Organism Species Number DOI 10.18908/lsdba.nbdc00464-010 Description of data contents Cluster, rep...- Data acquisition method - Data analysis method - Number of data entries - Data item Description Number... Cluster ID ID Sequence ID Length Sequence length seqs Number of sequences belonging to cluster homologs Numbe...r of sequences belonging to cluster ATH Number of sequences belonging to cluster in
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!!!
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:.
On Period of the Sequence of Fibonacci Polynomials Modulo
Directory of Open Access Journals (Sweden)
İnci Gültekin
2013-01-01
Full Text Available It is shown that the sequence obtained by reducing modulo coefficient and exponent of each Fibonacci polynomials term is periodic. Also if is prime, then sequences of Fibonacci polynomial are compared with Wall numbers of Fibonacci sequences according to modulo . It is found that order of cyclic group generated with matrix is equal to the period of these sequences.
Numerical Investigation of the Primety of Real numbers
DEFF Research Database (Denmark)
Jensen, Kristoffer
2011-01-01
The Farey sequences can be used [1] to create the Eulers totient function φ(n), by identifying the fractions for number n that did not occur in all Farey sequences up to n-1. This function creates, when divided by n-1, what is here called the Primety measure, which is a measure of how close to be......(n) is from n, the less n is a prime. φ(n) and P(n) is generalized to real numbers through the use of real numbered Farey sequences. The corresponding numerical sequences are shown to have interesting mathematical and artistic properties....
Energy Technology Data Exchange (ETDEWEB)
Somers, E.
1987-03-01
Regulatory agencies require numbers to provide health protection. The manner in which these numbers are derived from animal experiments and human epidemiology is considered together with the limitations and inadequacies of these numbers. Some recent examples of risk assessment in Canada are given including asbestos, drinking water, and indoor air quality. The value of these numbers in providing a measure of the hazard in a wider perspective is stressed, although they can never be the sole determinant of public policy.
Xu, Junyan
2012-01-01
We point out that the recursive formula that appears in Erickson's presentation "Fusible Numbers" is incorrect, and pose an alternate conjecture about the structure of fusible numbers. Although we are unable to solve the conjecture, we succeed in establishing some basic properties of fusible numbers. We suggest some possible approaches to the conjecture, and list further problems in the final chapter.
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…
Matsumoto, Kohji
2002-01-01
The book includes several survey articles on prime numbers, divisor problems, and Diophantine equations, as well as research papers on various aspects of analytic number theory such as additive problems, Diophantine approximations and the theory of zeta and L-function Audience Researchers and graduate students interested in recent development of number theory
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.
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.
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...
A fast image encryption system based on chaotic maps with finite precision representation
Energy Technology Data Exchange (ETDEWEB)
Kwok, H.S. [Department of Electronic Engineering, City University of Hong Kong, Hong Kong (China)]. E-mail: hskwok@ee.cityu.edu.hk; Tang, Wallace K.S. [Department of Electronic Engineering, City University of Hong Kong, Hong Kong (China)]. E-mail: kstang@ee.cityu.edu.hk
2007-05-15
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.
RNAome sequencing delineates the complete RNA landscape.
Derks, Kasper W J; Pothof, Joris
2015-09-01
Standard RNA expression profiling methods rely on enrichment steps for specific RNA classes, thereby not detecting all RNA species. For example, small and large RNAs from the same sample cannot be sequenced in a single sequence run. We designed RNAome sequencing, which is a strand-specific method to determine the expression of small and large RNAs from ribosomal RNA-depleted total RNA in a single sequence run. RNAome sequencing quantitatively preserves all RNA classes. This characteristic allows comparisons between RNA classes, thereby facilitating relationships between different RNA classes. Here, we describe in detail the experimental procedure associated with RNAome sequencing published by Derks and colleagues in RNA Biology (2015) [1]. We also provide the R code for the developed Total Rna Analysis Pipeline (TRAP), an algorithm to analyze RNAome sequencing datasets (deposited at the Gene Expression Omnibus data repository, accession number GSE48084).
RNAome sequencing delineates the complete RNA landscape
Directory of Open Access Journals (Sweden)
Kasper W.J. Derks
2015-09-01
Full Text Available Standard RNA expression profiling methods rely on enrichment steps for specific RNA classes, thereby not detecting all RNA species. For example, small and large RNAs from the same sample cannot be sequenced in a single sequence run. We designed RNAome sequencing, which is a strand-specific method to determine the expression of small and large RNAs from ribosomal RNA-depleted total RNA in a single sequence run. RNAome sequencing quantitatively preserves all RNA classes. This characteristic allows comparisons between RNA classes, thereby facilitating relationships between different RNA classes. Here, we describe in detail the experimental procedure associated with RNAome sequencing published by Derks and colleagues in RNA Biology (2015 [1]. We also provide the R code for the developed Total Rna Analysis Pipeline (TRAP, an algorithm to analyze RNAome sequencing datasets (deposited at the Gene Expression Omnibus data repository, accession number GSE48084.
Counting sequences, Gray codes and lexicodes
Suparta, I.N.
2006-01-01
A counting sequence of length n is a list of all 2^n binary n-tuples (binary codewords of length n). The number of bit positions where two codewords differ is called the Hamming distance of these two codewords. The average Hamming distance of a counting sequence of length n is defined as the average
Directory of Open Access Journals (Sweden)
Hafnani Hafnani
2015-04-01
Full Text Available Study of the set properties is simple and rarely investigated at the Department of Mathematics. This paper examines some set properties on the irrational numbers. The study is about the properties applying to the real numbers which are a complete ordered field. However, the results of this study show that those properties do not imply to the irrational numbers, but the ordered property. The prove of the irrational numberby some examples is demonstrated in this study.
Zalesny, Jaroslaw
2008-01-01
A new simple geometrical interpretation of complex numbers is presented. It differs from their usual interpretation as points in the complex plane. From the new point of view the complex numbers are rather operations on vectors than points. Moreover, in this approach the real, imaginary and complex numbers have similar interpretation. They are simply some operations on vectors. The presented interpretation is simpler, more natural, and better adjusted to possible applications in geometry and ...
Polynomially Bounded Sequences and Polynomial Sequences
Directory of Open Access Journals (Sweden)
Okazaki Hiroyuki
2015-09-01
Full Text Available In this article, we formalize polynomially bounded sequences that plays an important role in computational complexity theory. Class P is a fundamental computational complexity class that contains all polynomial-time decision problems [11], [12]. It takes polynomially bounded amount of computation time to solve polynomial-time decision problems by the deterministic Turing machine. Moreover we formalize polynomial sequences [5].
Jorgensen, C.B.; Suetens, S.; Tyran, J.R.
2011-01-01
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 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 th...
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)
Jørgensen, Claus Bjørn; Suetens, Sigrid; Tyran, Jean-Robert
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...... 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...
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.
Topological properties of some sequences defined over 2-normed spaces.
Dutta, Hemen; Kilicman, Adem; Altun, Omer
2016-01-01
The paper investigates some classes of real number sequences over 2-normed spaces defined by means of Orlicz functions, a bounded sequence of strictly positive real numbers, a multiplier and a normal paranormed sequence space. Relevant properties of such classes have been investigated. Moreover, relationships among different such classes of sequences have also been studied under various parameters and conditions. Finally, the spaces are investigated for some other useful properties. The conclusion section provides many interesting facts for further research.
Sequencing and comparative analysis of the gorilla MHC genomic sequence
Wilming, Laurens G.; Hart, Elizabeth A.; Coggill, Penny C.; Horton, Roger; Gilbert, James G. R.; Clee, Chris; Jones, Matt; Lloyd, Christine; Palmer, Sophie; Sims, Sarah; Whitehead, Siobhan; Wiley, David; Beck, Stephan; Harrow, Jennifer L.
2013-01-01
Major histocompatibility complex (MHC) genes play a critical role in vertebrate immune response and because the MHC is linked to a significant number of auto-immune and other diseases it is of great medical interest. Here we describe the clone-based sequencing and subsequent annotation of the MHC region of the gorilla genome. Because the MHC is subject to extensive variation, both structural and sequence-wise, it is not readily amenable to study in whole genome shotgun sequence such as the recently published gorilla genome. The variation of the MHC also makes it of evolutionary interest and therefore we analyse the sequence in the context of human and chimpanzee. In our comparisons with human and re-annotated chimpanzee MHC sequence we find that gorilla has a trimodular RCCX cluster, versus the reference human bimodular cluster, and additional copies of Class I (pseudo)genes between Gogo-K and Gogo-A (the orthologues of HLA-K and -A). We also find that Gogo-H (and Patr-H) is coding versus the HLA-H pseudogene and, conversely, there is a Gogo-DQB2 pseudogene versus the HLA-DQB2 coding gene. Our analysis, which is freely available through the VEGA genome browser, provides the research community with a comprehensive dataset for comparative and evolutionary research of the MHC. PMID:23589541
Indian Academy of Sciences (India)
IAS Admin
doctoral thesis, R Balasubramanian [8] improved this further and showed that one can take θ = 1/3. 4. Littlewood's Problem on Diophantine Ap- proximation. For any real number x, let ||x|| denote the distance of x to the nearest integer. For any pair of real numbers α, β, Littlewood conjectured that lim inf n→∞ n||nα||||nβ|| = 0.
Indian Academy of Sciences (India)
Home; Journals; Resonance – Journal of Science Education; Volume 3; Issue 7. The Class Number Problem - An Introduction to Algebraic Number Theory. Rajat Tandon. General Article Volume 3 Issue 7 July 1998 pp 28-37. Fulltext. Click here to view fulltext PDF. Permanent link:
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...
Indian Academy of Sciences (India)
In Mathematics, especially number theory, one of- .... 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 a congruent number. ..... If p and q are odd primes, then the Legendre symbol (p/q) is 1 if P is a quadratic residue.
Avogadro's Number Ferromagnetically
Houari, Ahmed
2010-01-01
Avogadro's number, usually denoted by N[subscript A], plays a fundamental role in both physics and chemistry. It defines the extremely useful concept of the mole, which is the base unit of the amount of matter in the international system of units. The fundamental character of this number can also be illustrated by its appearance in the definitions…
Efficient computational methods for sequence analysis of small RNAs
Cozen, Gozde
2007-01-01
With the discovery of small regulatory RNAs, there has been a tremendous increase in the number of RNA sequencing projects. Meanwhile, novel high-throughput sequencing technologies, which can sequence as much as 500000 small RNA sequences in one run, have emerged. The challenge of processing this rapidly growing data can be addressed by optimizing current analysis approaches for small RNA sequences. We present fast register-level methods for small RNA pairwise alignment and small RNA to genom...
Ossification sequence heterochrony among amphibians.
Harrington, Sean M; Harrison, Luke B; Sheil, Christopher A
2013-01-01
Heterochrony is an important mechanism in the evolution of amphibians. Although studies have centered on the relationship between size and shape and the rates of development, ossification sequence heterochrony also may have been important. Rigorous, phylogenetic methods for assessing sequence heterochrony are relatively new, and a comprehensive study of the relative timing of ossification of skeletal elements has not been used to identify instances of sequence heterochrony across Amphibia. In this study, a new version of the program Parsimov-based genetic inference (PGi) was used to identify shifts in ossification sequences across all extant orders of amphibians, for all major structural units of the skeleton. PGi identified a number of heterochronic sequence shifts in all analyses, the most interesting of which seem to be tied to differences in metamorphic patterns among major clades. Early ossification of the vomer, premaxilla, and dentary is retained by Apateon caducus and members of Gymnophiona and Urodela, which lack the strongly biphasic development seen in anurans. In contrast, bones associated with the jaws and face were identified as shifting late in the ancestor of Anura. The bones that do not shift late, and thereby occupy the earliest positions in the anuran cranial sequence, are those in regions of the skull that undergo the least restructuring throughout anuran metamorphosis. Additionally, within Anura, bones of the hind limb and pelvic girdle were also identified as shifting early in the sequence of ossification, which may be a result of functional constraints imposed by the drastic metamorphosis of most anurans. © 2013 Wiley Periodicals, Inc.
Sequencing Needs for Viral Diagnostics
Energy Technology Data Exchange (ETDEWEB)
Gardner, S N; Lam, M; Mulakken, N J; Torres, C L; Smith, J R; Slezak, T
2004-01-26
We built a system to guide decisions regarding the amount of genomic sequencing required to develop diagnostic DNA signatures, which are short sequences that are sufficient to uniquely identify a viral species. We used our existing DNA diagnostic signature prediction pipeline, which selects regions of a target species genome that are conserved among strains of the target (for reliability, to prevent false negatives) and unique relative to other species (for specificity, to avoid false positives). We performed simulations, based on existing sequence data, to assess the number of genome sequences of a target species and of close phylogenetic relatives (''near neighbors'') that are required to predict diagnostic signature regions that are conserved among strains of the target species and unique relative to other bacterial and viral species. For DNA viruses such as variola (smallpox), three target genomes provide sufficient guidance for selecting species-wide signatures. Three near neighbor genomes are critical for species specificity. In contrast, most RNA viruses require four target genomes and no near neighbor genomes, since lack of conservation among strains is more limiting than uniqueness. SARS and Ebola Zaire are exceptional, as additional target genomes currently do not improve predictions, but near neighbor sequences are urgently needed. Our results also indicate that double stranded DNA viruses are more conserved among strains than are RNA viruses, since in most cases there was at least one conserved signature candidate for the DNA viruses and zero conserved signature candidates for the RNA viruses.
Automated DNA Sequencing System
Energy Technology Data Exchange (ETDEWEB)
Armstrong, G.A.; Ekkebus, C.P.; Hauser, L.J.; Kress, R.L.; Mural, R.J.
1999-04-25
Oak Ridge National Laboratory (ORNL) is developing a core DNA sequencing facility to support biological research endeavors at ORNL and to conduct basic sequencing automation research. This facility is novel because its development is based on existing standard biology laboratory equipment; thus, the development process is of interest to the many small laboratories trying to use automation to control costs and increase throughput. Before automation, biology Laboratory personnel purified DNA, completed cycle sequencing, and prepared 96-well sample plates with commercially available hardware designed specifically for each step in the process. Following purification and thermal cycling, an automated sequencing machine was used for the sequencing. A technician handled all movement of the 96-well sample plates between machines. To automate the process, ORNL is adding a CRS Robotics A- 465 arm, ABI 377 sequencing machine, automated centrifuge, automated refrigerator, and possibly an automated SpeedVac. The entire system will be integrated with one central controller that will direct each machine and the robot. The goal of this system is to completely automate the sequencing procedure from bacterial cell samples through ready-to-be-sequenced DNA and ultimately to completed sequence. The system will be flexible and will accommodate different chemistries than existing automated sequencing lines. The system will be expanded in the future to include colony picking and/or actual sequencing. This discrete event, DNA sequencing system will demonstrate that smaller sequencing labs can achieve cost-effective the laboratory grow.
Multiple alignment of sequences on parallel computers.
Date, S; Kulkarni, R; Kulkarni, B; Kulkarni-Kale, U; Kolaskar, A S
1993-08-01
A software package that allows one to carry out multiple alignment of protein and nucleic acid sequences of almost unlimited length and number of sequences is developed on C-DAC parallel computer--a transputer-based machine. The farming approach is used for data parallelization. The speed gains are almost linear when the number of transputers is increased from 4 to 64. The software is used to carry out multiple alignment of 100 sequences each of alpha-chain and beta-chain of hemoglobin and 83 cytochrome c sequences. The signature sequence of cytochrome c was found to be PGTKMXF. The single parameter, multiple alignment score, S, has been used to categorize proteins in different subfamilies and groups.
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
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
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
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
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
Supersymmetric Displaced Number States
Directory of Open Access Journals (Sweden)
Fredy R. Zypman
2015-06-01
Full Text Available We introduce, generate and study a family of supersymmetric displaced number states (SDNS that can be considered generalized coherent states of the supersymmetric harmonic oscillator. The family is created from the seminal supersymmetric boson-fermion entangling annihilation operator introduced by Aragone and Zypman and later expanded by Kornbluth and Zypman. Using the momentum representation, the states are obtained analytically in compact form as displaced supersymmetric number states. We study their position-momentum uncertainties, and their bunchiness by classifying them according to their Mandel Q-parameter in phase space. We were also able to find closed form analytical representations in the space and number basis.
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
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
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
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,
Alemany-Fernandez, Reyes; Gorbonosov, Roman; Khasbulatov, Denis; Lamont, Mike; Le Roux, Pascal; Roderick, Chris
2011-01-01
The Large Hadron Collider (LHC) at CERN is a highly complex system made of many different sub-systems whose operation implies the execution of many tasks with stringent constraints on the order and duration of the execution. To be able to operate such a system in the most efficient and reliable way, the operators in the CERN control room use a high level control system: the LHC Sequencer. The LHC Sequencer system is composed of several components, including an Oracle database where operational sequences are configured, a core server that orchestrates the execution of the sequences, and two graphical user interfaces: one for sequence edition, and another for sequence execution. This paper describes the architecture of the LHC Sequencer system, and how the sequences are prepared and used for LHC operation.
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)
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.
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....
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.
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.
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...
Quantum random number generators
Herrero-Collantes, Miguel; Garcia-Escartin, Juan Carlos
2017-01-01
Random numbers are a fundamental resource in science and engineering with important applications in simulation and cryptography. The inherent randomness at the core of quantum mechanics makes quantum systems a perfect source of entropy. Quantum random number generation is one of the most mature quantum technologies with many alternative generation methods. This review discusses the different technologies in quantum random number generation from the early devices based on radioactive decay to the multiple ways to use the quantum states of light to gather entropy from a quantum origin. Randomness extraction and amplification and the notable possibility of generating trusted random numbers even with untrusted hardware using device-independent generation protocols are also discussed.
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...
DEFF Research Database (Denmark)
Wanscher, Jørgen Bundgaard; Sørensen, Majken Vildrik
2006-01-01
highly uniform multidimensional draws, which are highly relevant for todays traffic models. This paper shows among others combined shuffling and scrambling seems needless, that scrambling gives the lowest correlation and that there are detectable differences between random numbers, dependent...
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.
Lifescience Database Archive (English)
Full Text Available Data acquisition method - Data analysis method - Number of data entries - Data item Description Field 1 ID o...f amino acid sequence (Sequence ID) Field 2 Length of amino acid sequence Field 3
Mitogenome sequence accuracy using different elucidation methods.
Velozo Timbó, Renata; Coiti Togawa, Roberto; M C Costa, Marcos; A Andow, David; Paula, Débora P
2017-01-01
Mitogenome sequences are highly desired because they are used in several biological disciplines. Their elucidation has been facilitated through the development of massive parallel sequencing, accelerating their deposition in public databases. However, sequencing, assembly and annotation methods might induce variability in their quality, raising concerns about the accuracy of the sequences that have been deposited in public databases. In this work we show that different sequencing methods (number of species pooled in a library, insert size and platform) and assembly and annotation methods generated variable completeness and similarity of the resulting mitogenome sequences, using three species of predaceous ladybird beetles as models. The identity of the sequences varied considerably depending on the method used and ranged from 38.19 to 90.1% for Cycloneda sanguinea, 72.85 to 91.06% for Harmonia axyridis and 41.15 to 93.60% for Hippodamia convergens. Dissimilarities were frequently found in the non-coding A+T rich region, but were also common in coding regions, and were not associated with low coverage. Mitogenome completeness and sequence identity were affected by the sequencing and assembly/annotation methods, and high within-species variation was also found for other mitogenome depositions in GenBank. This indicates a need for methods to confirm sequence accuracy, and guidelines for verifying mitogenomes should be discussed and developed by the scientific community.
Mitogenome sequence accuracy using different elucidation methods.
Directory of Open Access Journals (Sweden)
Renata Velozo Timbó
Full Text Available Mitogenome sequences are highly desired because they are used in several biological disciplines. Their elucidation has been facilitated through the development of massive parallel sequencing, accelerating their deposition in public databases. However, sequencing, assembly and annotation methods might induce variability in their quality, raising concerns about the accuracy of the sequences that have been deposited in public databases. In this work we show that different sequencing methods (number of species pooled in a library, insert size and platform and assembly and annotation methods generated variable completeness and similarity of the resulting mitogenome sequences, using three species of predaceous ladybird beetles as models. The identity of the sequences varied considerably depending on the method used and ranged from 38.19 to 90.1% for Cycloneda sanguinea, 72.85 to 91.06% for Harmonia axyridis and 41.15 to 93.60% for Hippodamia convergens. Dissimilarities were frequently found in the non-coding A+T rich region, but were also common in coding regions, and were not associated with low coverage. Mitogenome completeness and sequence identity were affected by the sequencing and assembly/annotation methods, and high within-species variation was also found for other mitogenome depositions in GenBank. This indicates a need for methods to confirm sequence accuracy, and guidelines for verifying mitogenomes should be discussed and developed by the scientific community.
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...
Kruecken, R
2010-01-01
The nuclear shell model is a benchmark for the description of the structure of atomic nuclei. The magic numbers associated with closed shells have long been assumed to be valid across the whole nuclear chart. Investigations in recent years of nuclei far away from nuclear stability at facilities for radioactive ion beams have revealed that the magic numbers may change locally in those exotic nuclei leading to the disappearance of classic shell gaps and the appearance of new magic numbers. These changes in shell structure also have important implications for the synthesis of heavy elements in stars and stellar explosions. In this review a brief overview of the basics of the nuclear shell model will be given together with a summary of recent theoretical and experimental activities investigating these changes in the nuclear shell structure.
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
Gruber, Peter M
1987-01-01
This volume contains a fairly complete picture of the geometry of numbers, including relations to other branches of mathematics such as analytic number theory, diophantine approximation, coding and numerical analysis. It deals with convex or non-convex bodies and lattices in euclidean space, etc.This second edition was prepared jointly by P.M. Gruber and the author of the first edition. The authors have retained the existing text (with minor corrections) while adding to each chapter supplementary sections on the more recent developments. While this method may have drawbacks, it has the definit
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
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
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
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
Schreuder, M.F.
2012-01-01
A low nephron number is, according to Brenner's hyperfiltration hypothesis, associated with hypertension, glomerular damage and proteinuria, and starts a vicious cycle that ends in renal failure over the long term. Nephron endowment is set during foetal life, and there is no formation of nephrons
Jorgensen, C.B.; Suetens, S.; Tyran, J.R.
2011-01-01
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
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
Hahn, Nic
2012-01-01
Remember paint by numbers? This revived trend was a perfect solution to teaching geometric shapes to the author's first-grade students. Geometric shapes are identified and used in early elementary art classrooms, but this lesson gives students a deeper understanding of shape, encourages problem-solving, and makes a strong correlation between math…
Dirac's Large Numbers Hypothesis
Indian Academy of Sciences (India)
Home; Journals; Resonance – Journal of Science Education; Volume 8; Issue 8. Dirac's Large Numbers Hypothesis. Biman Nath. Article-in-a-Box Volume 8 Issue 8 August 2003 pp 7-7. Fulltext. Click here to view fulltext PDF. Permanent link: http://www.ias.ac.in/article/fulltext/reso/008/08/0007-0007. Author Affiliations.
Indian Academy of Sciences (India)
Home; Journals; Resonance – Journal of Science Education; Volume 18; Issue 9. Littlewood and Number Theory. M Ram Murty. General Article Volume 18 Issue 9 September 2013 pp 789-798. Fulltext. Click here to view fulltext PDF. Permanent link: http://www.ias.ac.in/article/fulltext/reso/018/09/0789-0798. Keywords.
Context and Number Conservation.
Silverman, Irwin W.
1979-01-01
A replication study was conducted to determine whether conservation-of-number performance would be improved by questioning the subject only after the transformation is performed, rather than before and after the transformation, as is done in the standard conservation test. Subjects were preschoolers, aged 0-4 to 5-7. (Author/MP)
Alladi, Krishnaswami
2008-01-01
Contains chapters on number theory and related topics. This title covers topics that focus on multipartitions, congruences and identities, the formulas of Koshliakov and Guinand in Ramanujan's "Lost Notebook", alternating sign matrices and the Weyl character formulas, theta functions in complex analysis, and elliptic functions
African Journals Online (AJOL)
OLUWOLE
Volume 9 Number 2 May 2010 PP. 131 – 136 ... The study assessed the effectiveness of Songhai-Delta fish culture training programme. A structured ..... The high adoption of these technologies might be due to the fact that these farmers are fish farmers and would like to adopt improved technologies that would meet their ...
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)
JX) over Q, and Q is a subfield of Q( .JX). This process can easily be generalised. For in- stance, let p be a prime and ( = e27ri/p. Let Q(() be the set of complex numbers of the form XO+Xl( +X2(2+ .. '+Xp_2(p-2 with Xi rational. Note that 1 + ( + (2 ...
African Journals Online (AJOL)
OLUWOLE
for egg-laying industry in Akwa Ibom State, Nigeria utilizing Cobb-Douglas production function based on .... machinery, equipment, implements, cost of machine hire, transportation, interest, charges on loan. X2 = Farm size measured by total number of birds housed. л1*, л2* ... using the computer software frontier version.
Physical Constraints of Numbers
Mueckenheim, W.
2005-01-01
All sciences need and many arts apply mathematics whereas mathematics seems to be independent of all of them, but only based upon logic. This conservative concept, however, needs to be revised because, contrary to Platonic idealism (frequently called "realism" by mathematicians), mathematical ideas, notions, and, in particular, numbers are not at all independent of physical laws and prerequisites.
Numerical Investigation of the Primety of Real numbers
DEFF Research Database (Denmark)
Jensen, Kristoffer
2011-01-01
The Farey sequences can be used [1] to create the Eulers totient function φ(n), by identifying the fractions for number n that did not occur in all Farey sequences up to n-1. This function creates, when divided by n-1, what is here called the Primety measure, which is a measure of how close to be......(n) is from n, the less n is a prime. φ(n) and P(n) is generalized to real numbers through the use of real numbered Farey sequences. The corresponding numerical sequences are shown to have interesting mathematical and artistic properties.......The Farey sequences can be used [1] to create the Eulers totient function φ(n), by identifying the fractions for number n that did not occur in all Farey sequences up to n-1. This function creates, when divided by n-1, what is here called the Primety measure, which is a measure of how close...... to being a prime number n is. P(n)=φ(n)/(n-1) has maximum 1 for all prime numbers and minimum that decreases non-uniformly with n. Thus P(n) is the Primety function, which permits to designate a value of Primety of a number n. If P(n)==1, then n is a prime. If P(n)
Simulations Using Random-Generated DNA and RNA Sequences
Bryce, C. F. A.
1977-01-01
Using a very simple computer program written in BASIC, a very large number of random-generated DNA or RNA sequences are obtained. Students use these sequences to predict complementary sequences and translational products, evaluate base compositions, determine frequencies of particular triplet codons, and suggest possible secondary structures.…
Analysis of expressed sequence tags derived from inflorescence ...
African Journals Online (AJOL)
From all the sequences analysed, only 186 (32.8%) sequences were given the GO numbers and grouped into the three GO main categories namely biological process, cellular component and molecular function. Several important ESTs were highlighted based on their functional categories. There were five sequences ...
Directory of Open Access Journals (Sweden)
Marco Ruffino
2001-12-01
Full Text Available In this paper I discuss the intuition behind Frege's and Russell's definitions of numbers as sets, as well as Benacerraf's criticism of it. I argue that Benacerraf's argument is not as strong as some philosophers tend to think. Moreover, I examine an alternative to the Fregean-Russellian definition of numbers proposed by Maddy, and point out some problems faced by it.Neste artigo discuto a intuição subjacente à definição de n∨meros como conjuntos proposta por Frege e Russell, assim como a crítica de Benacerraf a esta definição. Eu tento mostrar que o argumento de Benacerraf não é tão forte como alguns filósofos o tomaram. Adicionalmente, examino uma alternativa à definição de Frege e Russell proposta por Maddy, e indico algumas dificuldades encontrada pela mesma.
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
From Natural Numbers to Numbers and Curves in Nature - I
Indian Academy of Sciences (India)
According to Kronecker, a famous European mathematician, only natural numbers, i.e., positive integers like 1, 2, 3, ... are given by God or belong to the nature. All other numbers like negative numbers, fractional numbers, irrational numbers, tran- scendental numbers, complex numbers, etc., are a creation of the.
Fast, scalable generation of high‐quality protein multiple sequence alignments using Clustal Omega
National Research Council Canada - National Science Library
Sievers, Fabian; Wilm, Andreas; Dineen, David; Gibson, Toby J; Karplus, Kevin; Li, Weizhong; Lopez, Rodrigo; McWilliam, Hamish; Remmert, Michael; Söding, Johannes; Thompson, Julie D; Higgins, Desmond G
...‐quality alignments, but scale badly with the number of sequences. In this paper, we describe a new program called Clustal Omega, which can align virtually any number of protein sequences quickly and that delivers accurate alignments...
TASSEL-GBS: a high capacity genotyping by sequencing analysis pipeline
National Research Council Canada - National Science Library
Glaubitz, Jeffrey C; Casstevens, Terry M; Lu, Fei; Harriman, James; Elshire, Robert J; Sun, Qi; Buckler, Edward S
2014-01-01
Genotyping by sequencing (GBS) is a next generation sequencing based method that takes advantage of reduced representation to enable high throughput genotyping of large numbers of individuals at a large number of SNP markers...
Haydn, N; Lunedei, E; Vaienti, S
2007-09-01
We introduce a new indicator for dynamical systems, namely the averaged number of visits, to estimate the frequency of visits in small regions when a map is iterated up to the inverse of the measure of this region. We compute this quantity analytically and numerically for various systems and we show that it depends on the ergodic properties of the systems and on their topological properties, such as the presence of periodic points.
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... Wind turbine blades also require high aerodynamic efficiency and all-weather capabilities. The need for efficient low Reynolds number airfoils which...application. The design of this type of propeller is similar to the design of low solidity wind turbine blades and will be discussed in the next
A Numbering System for MFS Transporter Proteins.
Lee, Joanna; Sands, Zara A; Biggin, Philip C
2016-01-01
The Major Facilitator Superfamily (MFS) is one of the largest classes of secondary active transporters and is widely expressed in many domains of life. It is characterized by a common 12-transmembrane helix motif that allows the selective transport of a vast range of diverse substrates across the membrane. MFS transporters play a central role in many physiological processes and are increasingly recognized as potential drug targets. Despite intensive efforts, there are still only a handful of crystal structures and therefore homology modeling is likely to be a necessary process for providing models to interpret experiments for many years to come. However, the diversity of sequences and the multiple conformational states these proteins can exist in makes the process significantly more complicated, especially for sequences for which there is very little sequence identity to known templates. Inspired by the approach adopted many years ago for GPCRs, we have analyzed the large number of MFS sequences now available alongside the current structural information to propose a series of conserved contact points that can provide additional guidance for the homology modeling process. To enable cross-comparison across MFS models we also present a numbering scheme that can be used to provide a point of reference within each of the 12 transmembrane regions.
Rocker, Graeme M; Verma, Jennifer Y; Demmons, Jillian; Mittmann, Nicole
2015-02-06
The 'Number Needed to Treat' (NNT) is a useful measure for estimating the number of patients that would need to receive a therapeutic intervention to avoid one of the adverse events that the treatment is designed to prevent. We explored the possibility of an adaption of NNT to estimate the 'Number Needed to $ave' (NN$) as a new, conceptual systems metric to estimate potential cost-savings to the health system from implementation of a treatment, or in this case, a program. We used the outcomes of the INSPIRED COPD Outreach ProgramTM to calculate that 26 patients would need to complete the program to avoid healthcare expenditures of $100,000, based on hospital bed days avoided. The NN$ does not translate into 'cost savings' per se, but redirection of resource expenditures for other purposes. We propose that the NN$ metric, if further developed, could help to inform system-level resource allocation decisions in a manner similar to the way that the NNT metric helps to inform individual-level treatment decisions.
Directory of Open Access Journals (Sweden)
Richard F. Patterson
1999-01-01
Full Text Available In 1900, Pringsheim gave a definition of the convergence of double sequences. In this paper, that notion is extended by presenting definitions for the limit inferior and limit superior of double sequences. Also the core of a double sequence is defined. By using these definitions and the notion of regularity for 4-dimensional matrices, extensions, and variations of the Knopp Core theorem are proved.
Efficient probability sequence
Regnier, Eva
2014-01-01
A probability sequence is an ordered set of probability forecasts for the same event. Although single-period probabilistic forecasts and methods for evaluating them have been extensively analyzed, we are not aware of any prior work on evaluating probability sequences. This paper proposes an efficiency condition for probability sequences and shows properties of efficient forecasting systems, including memorylessness and increasing discrimination. These results suggest tests for efficiency and ...
Efficient probability sequences
Regnier, Eva
2014-01-01
DRMI working paper A probability sequence is an ordered set of probability forecasts for the same event. Although single-period probabilistic forecasts and methods for evaluating them have been extensively analyzed, we are not aware of any prior work on evaluating probability sequences. This paper proposes an efficiency condition for probability sequences and shows properties of efficiency forecasting systems, including memorylessness and increasing discrimination. These res...
DEFF Research Database (Denmark)
Ferreira, Elisa N; Pires, Lilian C; Parmigiani, Raphael B
2004-01-01
the human genome sequence. We generated 47 complete human transcript sequences, comprising 27 unannotated and 20 annotated sequences. Eight of these transcripts are variants of previously known genes. These transcripts were characterized according to size, number of exons, and chromosomal localization...
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. [...
Relating the annihilation number and the 2-domination number of a tree
DEFF Research Database (Denmark)
Desormeaux, Wyatt J.; Henning, Michael A.; Rall, Douglas F.
2014-01-01
terms of the nondecreasing degree sequence of G is at most the number of edges in G. The conjecture-generating computer program, Graffiti.pc, conjectured that γ2(G)≤a(G)+1 holds for every connected graph G. It is known that this conjecture is true when the minimum degree is at least 3. The conjecture...
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.
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.
Metagenomics using next-generation sequencing.
Bragg, Lauren; Tyson, Gene W
2014-01-01
Traditionally, microbial genome sequencing has been restricted to the small number of species that can be grown in pure culture. The progressive development of culture-independent methods over the last 15 years now allows researchers to sequence microbial communities directly from environmental samples. This approach is commonly referred to as "metagenomics" or "community genomics". However, the term metagenomics is applied liberally in the literature to describe any culture-independent analysis of microbial communities. Here, we define metagenomics as shotgun ("random") sequencing of the genomic DNA of a sample taken directly from the environment. The metagenome can be thought of as a sampling of the collective genome of the microbial community. We outline the considerations and analyses that should be undertaken to ensure the success of a metagenomic sequencing project, including the choice of sequencing platform and methods for assembly, binning, annotation, and comparative analysis.
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.
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.
2016-01-01
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. PMID:27916957
Whole Genome Sequencing and Newborn Screening.
Botkin, Jeffrey R; Rothwell, Erin
2016-03-01
Clinical applications of next generation sequencing are growing at a tremendous pace. Currently the largest application of genetic testing in medicine occurs with newborn screening through state-mandated public health programs, and there are suggestions that sequencing could become a standard component of newborn care within the next decade. As such, newborn screening may appear to be a logical starting point to explore whole genome and whole exome sequencing on a population level. Yet, there are a number of ethical, social and legal implications about the use of a mandatory public health screening program that create challenges for the use of sequencing technologies in this context. Additionally, at this time we still have limited understanding and strategies for managing genomic data, supporting our conclusion that genome sequencing is not justified within population based public health programs for newborn screening.
Universal codes of the natural numbers
Filmus, Yuval
2013-01-01
A code of the natural numbers is a uniquely-decodable binary code of the natural numbers with non-decreasing codeword lengths, which satisfies Kraft's inequality tightly. We define a natural partial order on the set of codes, and show how to construct effectively a code better than a given sequence of codes, in a certain precise sense. As an application, we prove that the existence of a scale of codes (a well-ordered set of codes which contains a code better than any given code) is independen...
Sequencing and Analysis of Neanderthal Genomic DNA
Noonan, James P.; Coop, Graham; Kudaravalli, Sridhar; Smith, Doug; Krause, Johannes; Alessi, Joe; Chen, Feng; Platt, Darren; Paabo, Svante; Pritchard, Jonathan K.; Rubin, Edward M.
2006-01-01
Our knowledge of Neanderthals is based on a limited number of remains and artifacts from which we must make inferences about their biology, behavior, and relationship to ourselves. Here, we describe the characterization of these extinct hominids from a new perspective, based on the development of a Neanderthal metagenomic library and its high-throughput sequencing and analysis. Several lines of evidence indicate that the 65,250 base pairs of hominid sequence so far identified in the library a...
Thurston, H A
2007-01-01
The teaching of mathematics has undergone extensive changes in approach, with a shift in emphasis from rote memorization to acquiring an understanding of the logical foundations and methodology of problem solving. This book offers guidance in that direction, exploring arithmetic's underlying concepts and their logical development.This volume's great merit lies in its wealth of explanatory material, designed to promote an informal and intuitive understanding of the rigorous logical approach to the number system. The first part explains and comments on axioms and definitions, making their subseq
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)
Korsby, Trine Mygind
2017-01-01
-infrastructure in its own right, providing an entry point into the wider infrastructure of transnational pimping. The pimps’ embodied certainty of how to operate successfully in their neighbourhood in Romania is produced in resonance with the local, urban materiality. This interplay generates body techniques, which...... 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...
Copy Number Variation across European Populations
Chen, Wanting; Hayward, Caroline; Wright, Alan F.; Hicks, Andrew A.; Vitart, Veronique; Knott, Sara; Wild, Sarah H.; Pramstaller, Peter P.; Wilson, James F.; Rudan, Igor; Porteous, David J.
2011-01-01
Genome analysis provides a powerful approach to test for evidence of genetic variation within and between geographical regions and local populations. Copy number variants which comprise insertions, deletions and duplications of genomic sequence provide one such convenient and informative source. Here, we investigate copy number variants from genome wide scans of single nucleotide polymorphisms in three European population isolates, the island of Vis in Croatia, the islands of Orkney in Scotland and the South Tyrol in Italy. We show that whereas the overall copy number variant frequencies are similar between populations, their distribution is highly specific to the population of origin, a finding which is supported by evidence for increased kinship correlation for specific copy number variants within populations. PMID:21829696
Copy number variation across European populations.
Directory of Open Access Journals (Sweden)
Wanting Chen
Full Text Available Genome analysis provides a powerful approach to test for evidence of genetic variation within and between geographical regions and local populations. Copy number variants which comprise insertions, deletions and duplications of genomic sequence provide one such convenient and informative source. Here, we investigate copy number variants from genome wide scans of single nucleotide polymorphisms in three European population isolates, the island of Vis in Croatia, the islands of Orkney in Scotland and the South Tyrol in Italy. We show that whereas the overall copy number variant frequencies are similar between populations, their distribution is highly specific to the population of origin, a finding which is supported by evidence for increased kinship correlation for specific copy number variants within populations.
Sequences with M-Bonacci Property and Their Finite Sums
Asiru, Muniru A.
2008-01-01
The note introduces sequences having M-bonacci property. Two summation formulas for sequences with M-bonacci property are derived. The formulas are generalizations of corresponding summation formulas for both M-bonacci numbers and Fibonacci numbers that have appeared previously in the literature. Applications to the Arithmetic series, "m"th "g -…
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.
Directory of Open Access Journals (Sweden)
Mikkel Meyn Liljegren
Full Text Available Microsatellites are DNA sequences consisting of repeated, short (1-6 bp sequence motifs that are highly mutable by enzymatic slippage during replication. Due to their high intrinsic variability, microsatellites have important applications in population genetics, forensics, genome mapping, as well as cancer diagnostics and prognosis. The current analytical standard for microsatellites is based on length scoring by high precision electrophoresis, but due to increasing efficiency next-generation sequencing techniques may provide a viable alternative. Here, we evaluated single molecule real time (SMRT sequencing, implemented in the PacBio series of sequencing apparatuses, as a means of microsatellite length scoring. To this end we carried out multiplexed SMRT sequencing of plasmid-carried artificial microsatellites of varying structure under different pre-sequencing PCR regimes. For each repeat structure, reads corresponding to the target length dominated. We found that pre-sequencing amplification had large effects on scoring accuracy and error distribution relative to controls, but that the effects of the number of amplification cycles were generally weak. In line with expectations enzymatic slippage decreased proportionally with microsatellite repeat unit length and increased with repetition number. Finally, we determined directional mutation trends, showing that PCR and SMRT sequencing introduced consistent but opposing error patterns in contraction and expansion of the microsatellites on the repeat motif and single nucleotide level.
Mixed Sequence Reader: A Program for Analyzing DNA Sequences with Heterozygous Base Calling
Directory of Open Access Journals (Sweden)
Chun-Tien Chang
2012-01-01
Full Text Available 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.
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.
Pierre Robin sequence (or syndrome) is a condition in which an infant has a smaller than normal lower jaw, a tongue ... The exact causes of Pierre Robin sequence are unknown. It may be ... jaw develops slowly before birth, but may grow faster during ...
Cosmetology: Scope and Sequence.
Nashville - Davidson County Metropolitan Public Schools, TN.
This scope and sequence guide, developed for a cosmetology vocational education program, represents an initial step in the development of a systemwide articulated curriculum sequence for all vocational programs within the Metropolitan Nashville Public School System. It was developed as a result of needs expressed by teachers, parents, and the…
African Journals Online (AJOL)
Milena
Author(s) retain the copyright of this article http://www.academicjournals.org/AJB. African Journal of Biotechnology. Full Length Research Paper. Evaluation of genetic divergence and phylogenetic relationship using sequence-tagged microsatellite. (STMS) sequences in Chickpea (Cicer arietinum L.) genotypes. Himanshu ...
Sequences, Series, and Mathematica.
Mathews, John H.
1992-01-01
Describes how the computer algebra system Mathematica can be used to enhance the teaching of the topics of sequences and series. Examines its capabilities to find exact, approximate, and graphically generated approximate solutions to problems from these topics and to understand proofs about sequences. (MDH)
Exact correspondence between walk in nucleotide and protein sequence spaces.
Directory of Open Access Journals (Sweden)
Dmitry N Ivankov
Full Text Available In the course of evolution, genes traverse the nucleotide sequence space, which translates to a trajectory of changes in the protein sequence in protein sequence space. The correspondence between regions of the nucleotide and protein sequence spaces is understood in general but not in detail. One of the unexplored questions is how many sequences a protein can reach with a certain number of nucleotide substitutions in its gene sequence. Here I propose an algorithm to calculate the volume of protein sequence space accessible to a given protein sequence as a function of the number of nucleotide substitutions made in the protein-coding sequence. The algorithm utilizes the power of the dynamic programming approach, and makes all calculations within a couple of seconds on a desktop computer. I apply the algorithm to green fluorescence protein, and get the number of sequences four times higher than estimated before. However, taking into account the astronomically huge size of the protein sequence space, the previous estimate can be considered as acceptable as an order of magnitude estimation. The proposed algorithm has practical applications in the study of evolutionary trajectories in sequence space.
Nanotechnology and Nanopore Sequencing.
Abedini-Nassab, Roozbeh
2017-01-01
DNA sequencing is one of the crucially important tasks in the fields of genetics and cellular biology, which is benefiting from nanotechnology. DNA carries genetic information and sequencing it in a quick way helps researchers in achieving essential goals, including personalized medicine. Solid state nanopores potentially can offer more durability, in sequencing biomolecules, over the proteinbased nanopores. In recent years, various ideas are introduced towards the goal of fast and low cost sequencing. In this review article recent advances presented in journal articles as well as patents in this field, including sequencing methods, membrane materials and their fabrication techniques, drilling methods, and biomolecule translocation speed control ideas are investigated. Copyright© Bentham Science Publishers; For any queries, please email at epub@benthamscience.org.
DEFF Research Database (Denmark)
Kristoffersen, Jette Hedegaard; Lackner, Andrea
2017-01-01
Singularis is the marking of the noun if it refers to an entity only. Often languages distinguish between singularis and non-singularis. The term used for these two forms are singular and plural. While singular is generally the unmarked form, plural is usually marked. Depending on the morphosynta......Singularis is the marking of the noun if it refers to an entity only. Often languages distinguish between singularis and non-singularis. The term used for these two forms are singular and plural. While singular is generally the unmarked form, plural is usually marked. Depending...... on the morphosyntactic properties of the language under investigation, plural can be expressed on various lexical items such as nouns [Lexicon – Section 3.1], verbs [Lexicon – Section 3.2], adjectives [Lexicon – Section 3.4], number words [Lexicon – Section 3.10.1], quantifiers [Lexicon – Section 3.10.2] or classifier...
Komatsu, Takao; Zhu, Huilin
2016-01-01
For a nonnegative integer $N$, define hypergeometric Euler numbers $E_{N,n}$ by $$ \\frac{1}{{}_1 F_2(1;N+1,(2 N+1)/2;t^2/4)}=\\sum_{n=0}^\\infty E_{N,n}\\frac{t^n}{n!}\\,, $$ where ${}_1 F_2(a;b,c;z)$ is the hypergeometric function defined by $$ {}_1 F_2(a;b,c;z)=\\sum_{n=0}^\\infty\\frac{(a)^{(n)}}{(b)^{(n)}(c)^{(n)}}\\frac{z^n}{n!}\\,. $$ Here, $(x)^{(n)}$ is the rising factorial, defined by $(x)^{(n)}=x(x+1)\\cdots(x+n-1)$ ($n\\ge 1$) with $(x)^{(0)}=1$. When $N=0$, then $E_n=E_{0,n}$ are classical E...
Clustering metagenomic sequences with interpolated Markov models
2010-01-01
Background Sequencing of environmental DNA (often called metagenomics) has shown tremendous potential to uncover the vast number of unknown microbes that cannot be cultured and sequenced by traditional methods. Because the output from metagenomic sequencing is a large set of reads of unknown origin, clustering reads together that were sequenced from the same species is a crucial analysis step. Many effective approaches to this task rely on sequenced genomes in public databases, but these genomes are a highly biased sample that is not necessarily representative of environments interesting to many metagenomics projects. Results We present SCIMM (Sequence Clustering with Interpolated Markov Models), an unsupervised sequence clustering method. SCIMM achieves greater clustering accuracy than previous unsupervised approaches. We examine the limitations of unsupervised learning on complex datasets, and suggest a hybrid of SCIMM and supervised learning method Phymm called PHYSCIMM that performs better when evolutionarily close training genomes are available. Conclusions SCIMM and PHYSCIMM are highly accurate methods to cluster metagenomic sequences. SCIMM operates entirely unsupervised, making it ideal for environments containing mostly novel microbes. PHYSCIMM uses supervised learning to improve clustering in environments containing microbial strains from well-characterized genera. SCIMM and PHYSCIMM are available open source from http://www.cbcb.umd.edu/software/scimm. PMID:21044341
Bonobos extract meaning from call sequences.
Directory of Open Access Journals (Sweden)
Zanna Clay
Full Text Available Studies on language-trained bonobos have revealed their remarkable abilities in representational and communication tasks. Surprisingly, however, corresponding research into their natural communication has largely been neglected. We address this issue with a first playback study on the natural vocal behaviour of bonobos. Bonobos produce five acoustically distinct call types when finding food, which they regularly mix together into longer call sequences. We found that individual call types were relatively poor indicators of food quality, while context specificity was much greater at the call sequence level. We therefore investigated whether receivers could extract meaning about the quality of food encountered by the caller by integrating across different call sequences. We first trained four captive individuals to find two types of foods, kiwi (preferred and apples (less preferred at two different locations. We then conducted naturalistic playback experiments during which we broadcasted sequences of four calls, originally produced by a familiar individual responding to either kiwi or apples. All sequences contained the same number of calls but varied in the composition of call types. Following playbacks, we found that subjects devoted significantly more search effort to the field indicated by the call sequence. Rather than attending to individual calls, bonobos attended to the entire sequences to make inferences about the food encountered by a caller. These results provide the first empirical evidence that bonobos are able to extract information about external events by attending to vocal sequences of other individuals and highlight the importance of call combinations in their natural communication system.
Clustering metagenomic sequences with interpolated Markov models.
Kelley, David R; Salzberg, Steven L
2010-11-02
Sequencing of environmental DNA (often called metagenomics) has shown tremendous potential to uncover the vast number of unknown microbes that cannot be cultured and sequenced by traditional methods. Because the output from metagenomic sequencing is a large set of reads of unknown origin, clustering reads together that were sequenced from the same species is a crucial analysis step. Many effective approaches to this task rely on sequenced genomes in public databases, but these genomes are a highly biased sample that is not necessarily representative of environments interesting to many metagenomics projects. We present SCIMM (Sequence Clustering with Interpolated Markov Models), an unsupervised sequence clustering method. SCIMM achieves greater clustering accuracy than previous unsupervised approaches. We examine the limitations of unsupervised learning on complex datasets, and suggest a hybrid of SCIMM and supervised learning method Phymm called PHYSCIMM that performs better when evolutionarily close training genomes are available. SCIMM and PHYSCIMM are highly accurate methods to cluster metagenomic sequences. SCIMM operates entirely unsupervised, making it ideal for environments containing mostly novel microbes. PHYSCIMM uses supervised learning to improve clustering in environments containing microbial strains from well-characterized genera. SCIMM and PHYSCIMM are available open source from http://www.cbcb.umd.edu/software/scimm.
Clustering metagenomic sequences with interpolated Markov models
Directory of Open Access Journals (Sweden)
Kelley David R
2010-11-01
Full Text Available Abstract Background Sequencing of environmental DNA (often called metagenomics has shown tremendous potential to uncover the vast number of unknown microbes that cannot be cultured and sequenced by traditional methods. Because the output from metagenomic sequencing is a large set of reads of unknown origin, clustering reads together that were sequenced from the same species is a crucial analysis step. Many effective approaches to this task rely on sequenced genomes in public databases, but these genomes are a highly biased sample that is not necessarily representative of environments interesting to many metagenomics projects. Results We present SCIMM (Sequence Clustering with Interpolated Markov Models, an unsupervised sequence clustering method. SCIMM achieves greater clustering accuracy than previous unsupervised approaches. We examine the limitations of unsupervised learning on complex datasets, and suggest a hybrid of SCIMM and supervised learning method Phymm called PHYSCIMM that performs better when evolutionarily close training genomes are available. Conclusions SCIMM and PHYSCIMM are highly accurate methods to cluster metagenomic sequences. SCIMM operates entirely unsupervised, making it ideal for environments containing mostly novel microbes. PHYSCIMM uses supervised learning to improve clustering in environments containing microbial strains from well-characterized genera. SCIMM and PHYSCIMM are available open source from http://www.cbcb.umd.edu/software/scimm.
The autocorrelation structure of Tausworthe pseudorandom number generators
Neuman, F.; Martin, C. F.
1976-01-01
An algorithm for determining the autocorrelation structure of a new sequence generated from an original sequence by proper decimation (a shift with each q-th term of the original sequence used) is presented, once autocorrelations for any repeating number sequence are known. The autocorrelation structure of the Tausworthe random number generator (RNG), based on proper decimation by q, is accepted as a RNG structure in which a proper decimation generates a long interval over which autocorrelations are small for all shifts. It is shown that if L bits of an N-bit Tausworthe RNG are L-bit binary numbers, L + 1 levels of correlation will exist, and L levels of correlation will each occur twice per RNG cycle length.
Tipu, Hamid Nawaz; Shabbir, Ambreen
2015-03-01
Sanger and coworkers introduced DNA sequencing in 1970s for the first time. It principally relied on termination of growing nucleotide chain when a dideoxythymidine triphosphate (ddTTP) was inserted in it. Detection of terminated sequences was done radiographically on Polyacrylamide Gel Electrophoresis (PAGE). Improvements that have evolved over time in original Sanger sequencing include replacement of radiography with fluorescence, use of separate fluorescent markers for each nucleotide, use of capillary electrophoresis instead of polyacrylamide gel electrophoresis and then introduction of capillary array electrophoresis. However, this technique suffered from few inherent limitations like decreased sensitivity for low level mutant alleles, complexities in analyzing highly polymorphic regions like Major Histocompatibility Complex (MHC) and high DNA concentrations required. Several Next Generation Sequencing (NGS) technologies have been introduced by Roche, Illumina and other commercial manufacturers that tend to overcome Sanger sequencing limitations and have been reviewed. Introduction of NGS in clinical research and medical diagnostics is expected to change entire diagnostic approach. These include study of cancer variants, detection of minimal residual disease, exome sequencing, detection of Single Nucleotide Polymorphisms (SNPs) and their disease association, epigenetic regulation of gene expression and sequencing of microorganisms genome.
Lepton family number violation
Energy Technology Data Exchange (ETDEWEB)
Herczeg, P.
1999-03-01
At present there is evidence from neutrino oscillation searches that the neutrinos are in fact massive particles and that they mix. If confirmed, this would imply that the conservation of LFN is not exact. Lepton family number violation (LFNV) has been searched for with impressive sensitivities in many processes involving charged leptons. The present experimental limits on some of them (those which the author shall consider here) are shown in Table 1. These stringent limits are not inconsistent with the neutrino oscillation results since, given the experimental bounds on the masses of the known neutrinos and the neutrino mass squared differences required by the oscillation results, the effects of LFNV from neutrino mixing would be too small to be seen elsewhere (see Section 2). The purpose of experiments searching for LFNV involving the charged leptons is to probe the existence of other sources of LFNV. Such sources are present in many extensions of the SM. In this lecture the author shall discuss some of the possibilities, focusing on processes that require muon beams. Other LFNV processes, such as the decays of the kaons and of the {tau}, provide complementary information. In the next Section he shall consider some sources of LFNV that do not require an extension of the gauge group of the SM (the added leptons or Higgs bosons may of course originate from models with extended gauge groups). In Section 3 he discusses LFNV in left-right symmetric models. In Section 4 he considers LFNV in supersymmetric models, first in R-parity conserving supersymmetric grand unified models, and then in the minimal supersymmetric standard model with R-parity violation. The last section is a brief summary of the author`s conclusions.
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.
DEFF Research Database (Denmark)
Weingart, Scott D; Trueger, N Seth; Wong, Nelson
2015-01-01
, patients were paralyzed and intubated. The primary outcome of this study was the difference in oxygen saturations after maximal attempts at preoxygenation before delayed sequence intubation compared with saturations just before intubation. Predetermined secondary outcomes and complications were also...... assessed. RESULTS: A total of 62 patients were enrolled: 19 patients required delayed sequence intubation to allow nonrebreather mask, 39 patients required it to allow NIPPV, and 4 patients required it for nasogastric tube placement. Saturations increased from a mean of 89.9% before delayed sequence...... intubation to 98.8% afterward, with an increase of 8.9% (95% confidence interval 6.4% to 10.9%). Thirty-two patients were in a predetermined group with high potential for critical desaturation (pre-delayed sequence intubation saturations ≤93%). All of these patients increased their saturations post...
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...
Autocorrelation peaks in congruential pseudorandom number generators
Neuman, F.; Merrick, R. B.
1976-01-01
The complete correlation structure of several congruential pseudorandom number generators (PRNG) of the same type and small cycle length was studied to deal with the problem of congruential PRNG almost repeating themselves at intervals smaller than their cycle lengths, during simulation of bandpass filtered normal random noise. Maximum period multiplicative and mixed congruential generators were studied, with inferences drawn from examination of several tractable members of a class of random number generators, and moduli from 2 to the 5th power to 2 to the 9th power. High correlation is shown to exist in mixed and multiplicative congruential random number generators and prime moduli Lehmer generators for shifts a fraction of their cycle length. The random noise sequences in question are required when simulating electrical noise, air turbulence, or time variation of wind parameters.
What's Decidable About Sequences?
Furia, Carlo A.
2010-01-01
We present a first-order theory of sequences with integer elements, Presburger arithmetic, and regular constraints, which can model significant properties of data structures such as arrays and lists. We give a decision procedure for the quantifier-free fragment, based on an encoding into the first-order theory of concatenation; the procedure has PSPACE complexity. The quantifier-free fragment of the theory of sequences can express properties such as sortedness and injectivity, as well as Bool...
Random numbers spring from alpha decay
Energy Technology Data Exchange (ETDEWEB)
Frigerio, N.A.; Sanathanan, L.P.; Morley, M.; Clark, N.A.; Tyler, S.A.
1980-05-01
Congruential random number generators, which are widely used in Monte Carlo simulations, are deficient in that the number they generate are concentrated in a relatively small number of hyperplanes. While this deficiency may not be a limitation in small Monte Carlo studies involving a few variables, it introduces a significant bias in large simulations requiring high resolution. This bias was recognized and assessed during preparations for an accident analysis study of nuclear power plants. This report describes a random number device based on the radioactive decay of alpha particles from a /sup 235/U source in a high-resolution gas proportional counter. The signals were fed to a 4096-channel analyzer and for each channel the frequency of signals registered in a 20,000-microsecond interval was recorded. The parity bits of these frequency counts (0 for an even count and 1 for an odd count) were then assembled in sequence to form 31-bit binary random numbers and transcribed to a magnetic tape. This cycle was repeated as many times as were necessary to create 3 million random numbers. The frequency distribution of counts from the present device conforms to the Brockwell-Moyal distribution, which takes into account the dead time of the counter (both the dead time and decay constant of the underlying Poisson process were estimated). Analysis of the count data and tests of randomness on a sample set of the 31-bit binary numbers indicate that this random number device is a highly reliable source of truly random numbers. Its use is, therefore, recommended in Monte Carlo simulations for which the congruential pseudorandom number generators are found to be inadequate. 6 figures, 5 tables.
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.
Fungal genome sequencing: basic biology to biotechnology.
Sharma, Krishna Kant
2016-08-01
The genome sequences provide a first glimpse into the genomic basis of the biological diversity of filamentous fungi and yeast. The genome sequence of the budding yeast, Saccharomyces cerevisiae, with a small genome size, unicellular growth, and rich history of genetic and molecular analyses was a milestone of early genomics in the 1990s. The subsequent completion of fission yeast, Schizosaccharomyces pombe and genetic model, Neurospora crassa initiated a revolution in the genomics of the fungal kingdom. In due course of time, a substantial number of fungal genomes have been sequenced and publicly released, representing the widest sampling of genomes from any eukaryotic kingdom. An ambitious genome-sequencing program provides a wealth of data on metabolic diversity within the fungal kingdom, thereby enhancing research into medical science, agriculture science, ecology, bioremediation, bioenergy, and the biotechnology industry. Fungal genomics have higher potential to positively affect human health, environmental health, and the planet's stored energy. With a significant increase in sequenced fungal genomes, the known diversity of genes encoding organic acids, antibiotics, enzymes, and their pathways has increased exponentially. Currently, over a hundred fungal genome sequences are publicly available; however, no inclusive review has been published. This review is an initiative to address the significance of the fungal genome-sequencing program and provides the road map for basic and applied research.
Vander Lugt correlation of DNA sequence data
Christens-Barry, William A.; Hawk, James F.; Martin, James C.
1990-12-01
DNA, the molecule containing the genetic code of an organism, is a linear chain of subunits. It is the sequence of subunits, of which there are four kinds, that constitutes the unique blueprint of an individual. This sequence is the focus of a large number of analyses performed by an army of geneticists, biologists, and computer scientists. Most of these analyses entail searches for specific subsequences within the larger set of sequence data. Thus, most analyses are essentially pattern recognition or correlation tasks. Yet, there are special features to such analysis that influence the strategy and methods of an optical pattern recognition approach. While the serial processing employed in digital electronic computers remains the main engine of sequence analyses, there is no fundamental reason that more efficient parallel methods cannot be used. We describe an approach using optical pattern recognition (OPR) techniques based on matched spatial filtering. This allows parallel comparison of large blocks of sequence data. In this study we have simulated a Vander Lugt1 architecture implementing our approach. Searches for specific target sequence strings within a block of DNA sequence from the Co/El plasmid2 are performed.
Sherman, Westley Arthur; Kuchibhatla, Durga Bhavani; Limviphuvadh, Vachiranee; Maurer-Stroh, Sebastian; Eisenhaber, Birgit; Eisenhaber, Frank
2015-10-01
Next-generation sequencing advances are rapidly expanding the number of human mutations to be analyzed for causative roles in genetic disorders. Our Human Protein Mutation Viewer (HPMV) is intended to explore the biomolecular mechanistic significance of non-synonymous human mutations in protein-coding genomic regions. The tool helps to assess whether protein mutations affect the occurrence of sequence-architectural features (globular domains, targeting signals, post-translational modification sites, etc.). As input, HPMV accepts protein mutations - as UniProt accessions with mutations (e.g. HGVS nomenclature), genome coordinates, or FASTA sequences. As output, HPMV provides an interactive cartoon showing the mutations in relation to elements of the sequence architecture. A large variety of protein sequence architectural features were selected for their particular relevance to mutation interpretation. Clicking a sequence feature in the cartoon expands a tree view of additional information including multiple sequence alignments of conserved domains and a simple 3D viewer mapping the mutation to known PDB structures, if available. The cartoon is also correlated with a multiple sequence alignment of similar sequences from other organisms. In cases where a mutation is likely to have a straightforward interpretation (e.g. a point mutation disrupting a well-understood targeting signal), this interpretation is suggested. The interactive cartoon can be downloaded as standalone viewer in Java jar format to be saved and viewed later with only a standard Java runtime environment. The HPMV website is: http://hpmv.bii.a-star.edu.sg/ .
Directory of Open Access Journals (Sweden)
McWilliam Sean
2010-08-01
Full Text Available Abstract Background The advent of cheap high through-put sequencing methods has facilitated low coverage skims of a large number of organisms. To maximise the utility of the sequences, assembly into contigs and then ordering of those contigs is required. Whilst sequences can be assembled into contigs de novo, using assembled genomes of closely related organisms as a framework can considerably aid the process. However, the preferred search programs and parameters that will optimise the sensitivity and specificity of the alignments between the sequence reads and the framework genome(s are not necessarily obvious. Here we demonstrate a process that uses paired-end sequence reads to choose an optimal program and alignment parameters. Results Unlike two single fragment reads, in paired-end sequence reads, such as BAC-end sequences, the two sequences in the pair have a known positional relationship in the original genome. This provides an additional level of confidence over match scores and e-values in the accuracy of the positional assignment of the reads in the comparative genome. Three commonly used sequence alignment programs: MegaBLAST, Blastz and PatternHunter were used to align a set of ovine BAC-end sequences against the equine genome assembly. A range of different search parameters, with a particular focus on contiguous and discontiguous seeds, were used for each program. The number of reads with a hit and the number of read pairs with hits for the two end sequences in the tail-to-tail paired-end configuration were plotted relative to the theoretical maximum expected curve. Of the programs tested, MegaBLAST with short contiguous seed lengths (word size 8-11 performed best in this particular task. In addition the data also provides estimates of the false positive and false negative rates, which can be used to determine the appropriate values of additional parameters, such as score cut-off, to balance sensitivity and specificity. To determine
Generalized Lacunary Statistical Difference Sequence Spaces of Fractional Order
Directory of Open Access Journals (Sweden)
Ugur Kadak
2015-01-01
Full Text Available We generalize the lacunary statistical convergence by introducing the generalized difference operator Δνα of fractional order, where α is a proper fraction and ν=(νk is any fixed sequence of nonzero real or complex numbers. We study some properties of this operator and investigate the topological structures of related sequence spaces. Furthermore, we introduce some properties of the strongly Cesaro difference sequence spaces of fractional order involving lacunary sequences and examine various inclusion relations of these spaces. We also determine the relationship between lacunary statistical and strong Cesaro difference sequence spaces of fractional order.
The genome sequence of Schizosaccharomyces pombe
Wood, [No Value; Gwilliam, R; Rajandream, MA; Lyne, M; Lyne, R; Stewart, A; Sgouros, J; Peat, N; Hayles, J; Baker, S; Basham, D; Bowman, S; Brooks, K; Brown, D; Brown, S; Chillingworth, T; Churcher, C; Collins, M; Connor, R; Cronin, A; Davis, P; Feltwell, T; Fraser, A; Gentles, S; Goble, A; Hamlin, N; Harris, D; Hidalgo, J; Hodgson, G; Holroyd, S; Hornsby, T; Howarth, S; Huckle, EJ; Hunt, S; Jagels, K; James, K; Jones, L; Jones, M; Leather, S; McDonald, S; McLean, J; Mooney, P; Moule, S; Mungall, K; Murphy, L; Niblett, D; Odell, C; Oliver, K; O'Neil, S; Pearson, D; Quail, MA; Rabbinowitsch, E; Rutherford, K; Rutter, S; Saunders, D; Seeger, K; Sharp, S; Skelton, J; Simmonds, M; Squares, R; Squares, S; Stevens, K; Taylor, K; Taylor, RG; Tivey, A; Walsh, S; Warren, T; Whitehead, S; Woodward, J; Volckaert, G; Aert, R; Robben, J; Grymonprez, B; Weltjens, [No Value; Vanstreels, E; Rieger, M; Schafer, M; Muller-Auer, S; Gabel, C; Fuchs, M; Fritzc, C; Holzer, E; Moestl, D; Hilbert, H; Borzym, K; Langer, [No Value; Beck, A; Lehrach, H; Reinhardt, R; Pohl, TM; Eger, P; Zimmermann, W; Wedler, H; Wambutt, R; Purnelle, B; Goffeau, A; Cadieu, E; Dreano, S; Gloux, S; Lelaure, [No Value; Mottier, S; Galibert, F; Aves, SJ; Xiang, Z; Hunt, C; Moore, K; Hurst, SM; Lucas, M; Rochet, M; Gaillardin, C; Tallada, VA; Garzon, A; Thode, G; Daga, RR; Cruzado, L; Jimenez, J; Sanchez, M; del Rey, F; Benito, J; Dominguez, A; Revuelta, JL; Moreno, S; Armstrong, J; Forsburg, SL; Cerrutti, L; Lowe, T; McCombie, WR; Paulsen, [No Value; Potashkin, J; Shpakovski, GV; Ussery, D; Barrell, BG; Nurse, P
2002-01-01
We have sequenced and annotated the genome of fission yeast (Schizosaccharomyces pombe), which contains the smallest number of protein-coding genes yet recorded for a eukaryote: 4,824. The centromeres are between 35 and 110 kilobases (kb) and contain related repeats including a highly conserved
Statistical Convergence of Double Sequences of Order
Directory of Open Access Journals (Sweden)
R. Çolak
2013-01-01
Full Text Available We intend to make a new approach and introduce the concepts of statistical convergence of order and strongly -Cesàro summability of order for double sequences of complex or real numbers. Also, some relations between the statistical convergence of order and strong -Cesàro summability of order are given.
Sequencing Errors Rife in Genome Databases.
2017-04-01
Low-frequency genetic variants in cancer genome datasets are often simply artifacts of DNA damage introduced by routine sample preparation, not tumor-driving mutations. A new algorithm found that around three quarters of all the samples in The Cancer Genome Atlas contain large numbers of these sequencing errors. ©2017 American Association for Cancer Research.
A Δ0 definition for finite sequences
Jumelet, M.D.
Throughout the following we will be interested in the solution of the problem whether finite sequences of natural numbers can be coded by means of Ao-formulae in such a way that the theory IAo proves some basic facts about this way of coding.
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/.
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.
Program Synthesizes UML Sequence Diagrams
Barry, Matthew R.; Osborne, Richard N.
2006-01-01
A computer program called "Rational Sequence" generates Universal Modeling Language (UML) sequence diagrams of a target Java program running on a Java virtual machine (JVM). Rational Sequence thereby performs a reverse engineering function that aids in the design documentation of the target Java program. Whereas previously, the construction of sequence diagrams was a tedious manual process, Rational Sequence generates UML sequence diagrams automatically from the running Java code.
[Progress on whole genome sequencing in woody plants].
Shi, Ji-Sen; Wang, Zhan-Jun; Chen, Jin-Hui
2012-02-01
In recent years, the number of sequencing data of plant whole genome have been increasing rapidly and the whole genome sequencing has been also performed widely in woody plants. However, there are a set of obstacles in investigating the whole genome sequencing in woody plants, which include larger genome, complex genome structure, limitations of assembly, annotation, functional analysis, and restriction of the funds for scientific research. Therefore, to promote the efficiency of the whole genome sequencing in woody plants, the development and defect of this field should be analyzed. The three-generation sequencing technologies (i.e., Sanger sequencing, synthesis sequencing, and single molecule sequencing) were compared in our studies. The progress mainly focused on the whole genome sequencing in four woody plants (Populus, Grapevine, Papaya, and Apple), and the application of sequencing results also was analyzed. The future of whole genome sequencing research in woody plants, consisting of material selection, establishment of genetic map and physical map, selection of sequencing technology, bioinformatic analysis, and application of sequencing results, was discussed.
Miszczak, Jarosław Adam
2013-01-01
numbers generated by quantum real number generator. Reasons for new version: Added support for the high-speed on-line quantum random number generator and improved methods for retrieving lists of random numbers. Summary of revisions: The presented version provides two signicant improvements. The first one is the ability to use the on-line Quantum Random Number Generation service developed by PicoQuant GmbH and the Nano-Optics groups at the Department of Physics of Humboldt University. The on-line service supported in the version 2.0 of the TRQS package provides faster access to true randomness sources constructed using the laws of quantum physics. The service is freely available at https://qrng.physik.hu-berlin.de/. The use of this service allows using the presented package with the need of a physical quantum random number generator. The second improvement introduced in this version is the ability to retrieve arrays of random data directly for the used source. This increases the speed of the random number generation, especially in the case of an on-line service, where it reduces the time necessary to establish the connection. Thanks to the speed improvement of the presented version, the package can now be used in simulations requiring larger amounts of random data. Moreover, the functions for generating random numbers provided by the current version of the package more closely follow the pattern of functions for generating pseudo- random numbers provided in Mathematica. Additional comments: Speed comparison: The implementation of the support for the QRNG on-line service provides a noticeable improvement in the speed of random number generation. For the samples of real numbers of size 101; 102,…,107 the times required to generate these samples using Quantis USB device and QRNG service are compared in Fig. 1. The presented results show that the use of the on-line service provides faster access to random numbers. One should note, however, that the speed gain can increase or
DEFF Research Database (Denmark)
Rieneck, Klaus; Bak, Mads; Jønson, Lars
2013-01-01
information obtained allows well for statistical analysis of the data. This general approach can be integrated into current laboratory practice and has numerous applications. Besides DNA-based predictions of blood group phenotypes, platelet phenotypes, or sickle cell anemia, and the determination of zygosity......, Illumina); several millions of PCR sequences were analyzed. RESULTS: The results demonstrated the feasibility of diagnosing the fetal KEL1 or KEL2 blood group from cell-free DNA purified from maternal plasma. CONCLUSION: This method requires only one primer pair, and the large amount of sequence...
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.
Pascal's triangle and other number triangles in Clifford analysis
Tomaz, G.; Falcão, M. I.; Malonek, H. R.
2012-09-01
The recent introduction of generalized Appell sequences in the framework of Clifford Analysis solved an open question about a suitable construction of power-like monogenic polynomials as generalizations of the integer powers of a complex variable. The deep connection between Appell sequences and Pascal's triangle called also attention to other number triangles and, at the same time, to the construction of generalized Pascal matrices. Both aspects are considered in this communication.
THE RELATIONSHIP BETWEEN NUMBER NAMES AND NUMBER CONCEPTS
DEFF Research Database (Denmark)
Ejersbo, Lisser Rye; Misfeldt, Morten
2016-01-01
the regularity or irregularity of number naming affects children’s formation of number concepts and arithmetic performance. We investigate this issue by reviewing relevant literature and undertaking a design research project addressing the specific irregularities of the Danish number names. In this project......, a second, regular set of number names is introduced in primary school. The study’s findings suggest that the regularity of number names influences the development of number concepts and creates a positive impact on the understanding of the base-10 system....
Cosmic numbers the numbers that define our universe
Stein, James D
2011-01-01
Our fascination with numbers begins when we are children and continues throughout our lives. We start counting our fingers and toes and end up balancing checkbooks and calculating risk. So powerful is the appeal of numbers that many people ascribe to them a mystical significance. Other numbers go beyond the supernatural, working to explain our universe and how it behaves. In Cosmic Numbers , mathematics professor James D. Stein traces the discovery, evolution, and interrelationships of the numbers that define our world. Everyone knows about the speed of light and absolute zero, but numbers lik
Refined Pichia pastoris reference genome sequence
Sturmberger, Lukas; Chappell, Thomas; Geier, Martina; Krainer, Florian; Day, Kasey J.; Vide, Ursa; Trstenjak, Sara; Schiefer, Anja; Richardson, Toby; Soriaga, Leah; Darnhofer, Barbara; Birner-Gruenberger, Ruth; Glick, Benjamin S.; Tolstorukov, Ilya; Cregg, James; Madden, Knut; Glieder, Anton
2016-01-01
Strains of the species Komagataella phaffii are the most frequently used “Pichia pastoris” strains employed for recombinant protein production as well as studies on peroxisome biogenesis, autophagy and secretory pathway analyses. Genome sequencing of several different P. pastoris strains has provided the foundation for understanding these cellular functions in recent genomics, transcriptomics and proteomics experiments. This experimentation has identified mistakes, gaps and incorrectly annotated open reading frames in the previously published draft genome sequences. Here, a refined reference genome is presented, generated with genome and transcriptome sequencing data from multiple P. pastoris strains. Twelve major sequence gaps from 20 to 6000 base pairs were closed and 5111 out of 5256 putative open reading frames were manually curated and confirmed by RNA-seq and published LC-MS/MS data, including the addition of new open reading frames (ORFs) and a reduction in the number of spliced genes from 797 to 571. One chromosomal fragment of 76 kbp between two previous gaps on chromosome 1 and another 134 kbp fragment at the end of chromosome 4, as well as several shorter fragments needed re-orientation. In total more than 500 positions in the genome have been corrected. This reference genome is presented with new chromosomal numbering, positioning ribosomal repeats at the distal ends of the four chromosomes, and includes predicted chromosomal centromeres as well as the sequence of two linear cytoplasmic plasmids of 13.1 and 9.5 kbp found in some strains of P. pastoris. PMID:27084056
Phase-defined complete sequencing of the HLA genes by next-generation sequencing.
Hosomichi, Kazuyoshi; Jinam, Timothy A; Mitsunaga, Shigeki; Nakaoka, Hirofumi; Inoue, Ituro
2013-05-28
The human leukocyte antigen (HLA) region, the 3.8-Mb segment of the human genome at 6p21, has been associated with more than 100 different diseases, mostly autoimmune diseases. Due to the complex nature of HLA genes, there are difficulties in elucidating complete HLA gene sequences especially HLA gene haplotype structures by the conventional sequencing method. We propose a novel, accurate, and cost-effective method for generating phase-defined complete sequencing of HLA genes by using indexed multiplex next generation sequencing. A total of 33 HLA homozygous samples, 11 HLA heterozygous samples, and 3 parents-child families were subjected to phase-defined HLA gene sequencing. We applied long-range PCR to amplify six HLA genes (HLA-A, -C, -B, DRB1, -DQB1, and -DPB1) followed by transposase-based library construction and multiplex sequencing with the MiSeq sequencer. Paired-end reads (2 × 250 bp) derived from the sequencer were aligned to the six HLA gene segments of UCSC hg19 allowing at most 80 bases mismatch. For HLA homozygous samples, the six amplicons of an individual were pooled and simultaneously sequenced and mapped as an individual-tagging method. The paired-end reads were aligned to corresponding genes of UCSC hg19 and unambiguous, continuous sequences were obtained. For HLA heterozygous samples, each amplicon was separately sequenced and mapped as a gene-tagging method. After alignments, we detected informative paired-end reads harboring SNVs on both forward and reverse reads that are used to separate two chromosomes and to generate two phase-defined sequences in an individual. Consequently, we were able to determine the phase-defined HLA gene sequences from promoter to 3'-UTR and assign up to 8-digit HLA allele numbers, regardless of whether the alleles are rare or novel. Parent-child trio-based sequencing validated our sequencing and phasing methods. Our protocol generated phased-defined sequences of the entire HLA genes, resulting in high
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
Sequence Classification: 893720 [
Lifescience Database Archive (English)
Full Text Available ial ribosomal protein of the large subunit; MRP51 exhibits genetic interactions with mutations in the COX2 and COX3 mRNA 5'-untransla...ted leader sequences; Mrp51p || http://www.ncbi.nlm.nih.gov/protein/6325139 ...
Goldbach Partitions and Sequences
Indian Academy of Sciences (India)
Home; Journals; Resonance – Journal of Science Education; Volume 19; Issue 11. Goldbach Partitions and Sequences. Subhash Kak. General Article Volume 19 Issue 11 November 2014 pp 1028-1037. Fulltext. Click here to view fulltext PDF. Permanent link: http://www.ias.ac.in/article/fulltext/reso/019/11/1028-1037 ...
Sims, Anntarie L.
1989-01-01
Describes and examines 150 tape-recorded compliment sequences. Reports that the course and outcome of compliments and compliment responses are affected by: (1) the way a compliment is worded; (2) the type of statement that precedes or follows the compliment; and (3) the status and sex of the compliment participants. (RAE)
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...
absolutely regular random sequences
Directory of Open Access Journals (Sweden)
Michel Harel
1996-01-01
Full Text Available In this paper, the central limit theorems for the density estimator and for the integrated square error are proved for the case when the underlying sequence of random variables is nonstationary. Applications to Markov processes and ARMA processes are provided.
Base-calling for next-generation sequencing platforms
Ledergerber, Christian; Dessimoz, Christophe
2011-01-01
Next-generation sequencing platforms are dramatically reducing the cost of DNA sequencing. With these technologies, bases are inferred from light intensity signals, a process commonly referred to as base-calling. Thus, understanding and improving the quality of sequence data generated using these approaches are of high interest. Recently, a number of papers have characterized the biases associated with base-calling and proposed methodological improvements. In this review, we summarize recent ...
How Spencer Made Number: First Uses of the Number Words
Mix, Kelly S.
2009-01-01
This article describes the development of number concepts between infancy and early childhood. It is based on a diary study that tracked number word use in a child from 12 to 38 months of age. Number words appeared early in the child's vocabulary, but accurate reference to specific numerosities evolved gradually over the entire 27-month period.…
The Mental Number Line in Dyscalculia: Impaired Number Sense or Access from Symbolic Numbers?
Lafay, Anne; St-Pierre, Marie-Catherine; Macoir, Joël
2017-01-01
Numbers may be manipulated and represented mentally over a compressible number line oriented from left to right. According to numerous studies, one of the primary reasons for dyscalculia is related to improper understanding of the mental number line. Children with dyscalculia usually show difficulty when they have to place Arabic numbers on a…
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-...
Spent fuel bundle counter sequence error manual - BRUCE NGS
Energy Technology Data Exchange (ETDEWEB)
Nicholson, L.E
1992-03-20
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
Energy Technology Data Exchange (ETDEWEB)
Nicholson, L.E
1992-03-25
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.
Next generation sequencing of disseminated tumor cells
Directory of Open Access Journals (Sweden)
Elen Kristine Møller
2013-12-01
Full Text Available Disseminated tumor cells (DTCs detected in the bone marrow have been shown as an independent prognostic factor for women with breast cancer. However, the mechanisms behind the tumor cell dissemination are still unclear and more detailed knowledge is needed to fully understand why some cells remain dormant and others metastasize. Sequencing of single cells has opened for the possibility to dissect the genetic content of subclones of a primary tumor, as well as DTCs. Previous studies of genetic changes in DTCs have employed single-cell array comparative genomic hybridization which provides information about larger aberrations. To date, next generation sequencing provides the possibility to discover new, smaller and copy neutral genetic changes. In this study, we performed whole genome amplification and subsequently next generation sequencing to analyze DTCs from two breast cancer patients. We compared copy number profiles of the DTCs and the corresponding primary tumor generated from sequencing and SNP-CGH data, respectively. While one tumor revealed mostly whole arm gains and losses, the other had more complex alterations, as well as subclonal amplification and deletions. Whole arm gains or losses in the primary tumor were in general also observed in the corresponding DTC. Both primary tumors showed amplification of chromosome 1q and deletion of parts of chromosome 16q, which was recaptured in the corresponding DTCs. Interestingly, clear differences were also observed, indicating that the DTC underwent further evolution at the copy number level. This study provides a proof-of-principle for sequencing of DTCs and correlation with primary copy number profiles. The analyses allow insight into tumor cell dissemination and show ongoing copy number evolution in DTCs compared to the primary tumors.
Directory of Open Access Journals (Sweden)
Balajee Maram K.
2016-02-01
Full Text Available Data security is a major issue because of rapid evolution of data communication over unsecured internetwork. Here the proposed system is concerned with the problem of randomly generated S-box. The generation of S-box depends on Pseudo-Random-Number-Generators and shared-secret-key. The process of Pseudo-Random-Number-Generator depends on large prime numbers. All Pseudo-Random-Numbers are scrambled according to shared-secret-key. After scrambling, the S-box is generated. In this research, large prime numbers are the inputs to the Pseudo-Random-Number-Generator. The proposed S-box will reduce the complexity of S-box generation. Based on S-box parameters, it experimentally investigates the quality and robustness of the proposed algorithm which was tested. It yields better results with the S-box parameters like Hamming Distance, Balanced Output and Avalanche Effect and can be embedded to popular cryptography algorithms
Metaheuristic approaches to order sequencing on a unidirectional ...
African Journals Online (AJOL)
In this paper the sequencing of orders on a unidirectional picking line is considered. The aim of the order sequencing is to minimise the number of cycles travelled by a picker within the picking line to complete all orders. A tabu search, simulated annealing, genetic algorithm, generalised extremal optimisation and a random ...
Complete Genome Sequence of the Human Gut Symbiont Roseburia hominis
DEFF Research Database (Denmark)
Travis, Anthony J.; Kelly, Denise; Flint, Harry J
2015-01-01
We report here the complete genome sequence of the human gut symbiont Roseburia hominis A2-183(T) (= DSM 16839(T) = NCIMB 14029(T)), isolated from human feces. The genome is represented by a 3,592,125-bp chromosome with 3,405 coding sequences. A number of potential functions contributing to host-...
Aligning protein sequence and analysing substitution pattern using ...
Indian Academy of Sciences (India)
Prakash
Alpha test set extracted from reference 1 of. BAliBASE 2.0. BAliBASE subgroupa. Reference name. Protein class. Sequence number. Average sequence pair identityb. Short. 1fjlA_ref1 ...... amino acid substitution behaviours of different matrices are compared based on the entry values of the matrices. The entry values of the ...
Inferring phylogenies from RAD sequence data.
Directory of Open Access Journals (Sweden)
Benjamin E R Rubin
Full Text Available Reduced-representation genome sequencing represents a new source of data for systematics, and its potential utility in interspecific phylogeny reconstruction has not yet been explored. One approach that seems especially promising is the use of inexpensive short-read technologies (e.g., Illumina, SOLiD to sequence restriction-site associated DNA (RAD--the regions of the genome that flank the recognition sites of restriction enzymes. In this study, we simulated the collection of RAD sequences from sequenced genomes of different taxa (Drosophila, mammals, and yeasts and developed a proof-of-concept workflow to test whether informative data could be extracted and used to accurately reconstruct "known" phylogenies of species within each group. The workflow consists of three basic steps: first, sequences are clustered by similarity to estimate orthology; second, clusters are filtered by taxonomic coverage; and third, they are aligned and concatenated for "total evidence" phylogenetic analysis. We evaluated the performance of clustering and filtering parameters by comparing the resulting topologies with well-supported reference trees and we were able to identify conditions under which the reference tree was inferred with high support. For Drosophila, whole genome alignments allowed us to directly evaluate which parameters most consistently recovered orthologous sequences. For the parameter ranges explored, we recovered the best results at the low ends of sequence similarity and taxonomic representation of loci; these generated the largest supermatrices with the highest proportion of missing data. Applications of the method to mammals and yeasts were less successful, which we suggest may be due partly to their much deeper evolutionary divergence times compared to Drosophila (crown ages of approximately 100 and 300 versus 60 Mya, respectively. RAD sequences thus appear to hold promise for reconstructing phylogenetic relationships in younger clades in
On the Sum of Corresponding Factorials and Triangular Numbers: Some Preliminary Results
Directory of Open Access Journals (Sweden)
Romer C. Castillo
2015-11-01
Full Text Available A new sequence of natural numbers can be formed by adding corresponding factorials and triangular numbers. In this paper, such numbers were named factoriangular numbers. Mathematical experimentations on these numbers resulted to the establishment of some of its characteristics. These include the parity, compositeness, the number and sum of its positive divisors, abundancy and deficiency, Zeckendorf’s decomposition, end digits, and digital roots of factoriangular numbers. Several theorems and corollaries were proven and some conjectures were also presented.
Fliess, Amit; Motro, Benny; Unger, Ron
2002-08-01
An important question in protein evolution is to what extent proteins may have undergone swaps (switches of domain or fragment order) during evolution. Such events might have occurred in several forms: Swaps of short fragments, swaps of structural and functional motifs, or recombination of domains in multidomain proteins. This question is important for the theoretical understanding of the evolution of proteins, and has practical implications for using swaps as a design tool in protein engineering. In order to analyze the question systematically, we conducted a large scale survey of possible swaps and permutations among all pairs of protein from the Swissport database. A swap is defined as a specific kind of sequence mutation between two proteins in which two fragments that appear in both sequences have different relative order in the two sequences. For example, aXbYc and dYeXf are defined as a swap, where X and Y represent sequence fragments that switched their order. Identifying such swaps is difficult using standard sequence comparison packages. One of the main problems in the analysis stems from the fact that many sequences contain repeats, which may be identified as false-positive swaps. We have used two different approaches to detect pairs of proteins with swaps. The first approach is based on the predefined list of domains in Pfam. We identified all the proteins that share at least two domains and analyzed their relative order, looking for pairs in which the order of these domains was switched. We designed an algorithm to distinguish between real swaps and duplications. In the second approach, we used Blast to detect pairs of proteins that share several fragments. Then, we used an automatic procedure to select pairs that are likely to contain swaps. Those pairs were analyzed visually, using a graphical tool, to eliminate duplications. Combining these approaches, about 140 different cases of swaps in the Swissprot database were found (after eliminating
The entire sequence over Musielak p-metric space
Directory of Open Access Journals (Sweden)
C. Murugesan
2016-04-01
Full Text Available In this paper, we introduce fibonacci numbers of Γ2(F sequence space over p-metric spaces defined by Musielak function and examine some topological properties of the resulting these spaces.
Origin of introns by 'intronization' of exonic sequences
DEFF Research Database (Denmark)
Irimia, Manuel; Rukov, Jakob Lewin; Penny, David
2008-01-01
The mechanisms of spliceosomal intron creation have proved elusive. Here we describe a new mechanism: the recruitment of internal exonic sequences ('intronization') in Caenorhabditis species. The numbers of intronization events and introns gained by other mechanisms are similar, suggesting...
Distribution theory of algebraic numbers
Yang, Chung-Chun
2008-01-01
The book timely surveys new research results and related developments in Diophantine approximation, a division of number theory which deals with the approximation of real numbers by rational numbers. The book is appended with a list of challenging open problems and a comprehensive list of references. From the contents: Field extensions Algebraic numbers Algebraic geometry Height functions The abc-conjecture Roth''s theorem Subspace theorems Vojta''s conjectures L-functions.
The theory of algebraic numbers
Pollard, Harry
1998-01-01
An excellent introduction to the basics of algebraic number theory, this concise, well-written volume examines Gaussian primes; polynomials over a field; algebraic number fields; and algebraic integers and integral bases. After establishing a firm introductory foundation, the text explores the uses of arithmetic in algebraic number fields; the fundamental theorem of ideal theory and its consequences; ideal classes and class numbers; and the Fermat conjecture. 1975 edition. References. List of Symbols. Index.
The theory of algebraic numbers
Pollard, Harry
1975-01-01
An excellent introduction to the basics of algebraic number theory, this concise, well-written volume examines Gaussian primes; polynomials over a field; algebraic number fields; and algebraic integers and integral bases. After establishing a firm introductory foundation, the text explores the uses of arithmetic in algebraic number fields; the fundamental theorem of ideal theory and its consequences; ideal classes and class numbers; and the Fermat conjecture. 1975 edition. References. List of Symbols. Index.
Elementary number theory with programming
Lewinter, Marty
2015-01-01
A successful presentation of the fundamental concepts of number theory and computer programming Bridging an existing gap between mathematics and programming, Elementary Number Theory with Programming provides a unique introduction to elementary number theory with fundamental coverage of computer programming. Written by highly-qualified experts in the fields of computer science and mathematics, the book features accessible coverage for readers with various levels of experience and explores number theory in the context of programming without relying on advanced prerequisite knowledge and con
Some sums related to the terms of generalized Fibonacci autocorrelation sequences
Directory of Open Access Journals (Sweden)
Neşe Ömür
2017-06-01
Full Text Available In this paper, we give the terms of the generalized Fibonacci autocorrelation sequences defined as and some interesting sums involving terms of these sequences for an odd integer number and nonnegative integers.
On Some Relationships Among Pell, Pell-Lucas and Modified Pell Sequences
Directory of Open Access Journals (Sweden)
Serpil Halıcı
2010-12-01
Full Text Available In this study, Pell, Pell-Lucas and Modified Pell numbers are investigated. Using Binet formulas for these sequences, some relations among these sequences are obtained. Also, some sum formulas are given by these properties.
Mr-factors and Qr-factors for near quasinorm on certain sequence spaces
Directory of Open Access Journals (Sweden)
Piyapong Niamsup
2005-01-01
Full Text Available We study the multiplicativity factor and quadraticity factor for near quasinorm on certain sequence spaces of Maddox, namely, l(p and l∞(p, where p=(pk is a bounded sequence of positive real numbers.
The Mental Number Line in Dyscalculia: Impaired Number Sense or Access From Symbolic Numbers?
Lafay, Anne; St-Pierre, Marie-Catherine; Macoir, Joël
Numbers may be manipulated and represented mentally over a compressible number line oriented from left to right. According to numerous studies, one of the primary reasons for dyscalculia is related to improper understanding of the mental number line. Children with dyscalculia usually show difficulty when they have to place Arabic numbers on a physical number line. However, it remains unclear whether they have a deficit with the mental number line per se or a deficit with accessing it from nonsymbolic and/or symbolic numbers. Quebec French-speaking 8- to 9-year-old children with (24) and without (37) dyscalculia were assessed with transcoding tasks ( number-to-position and position-to-number) designed to assess the acuity of the mental number line with Arabic and spoken numbers as well as with analogic numerosities. Results showed that children with dyscalculia produced a larger percentage absolute error than children without mathematics difficulties in every task except the number-to-position transcoding task with analogic numerosities. Hence, these results suggested that children with dyscalculia do not have a general deficit of the mental number line but rather a deficit with accessing it from symbolic numbers.
Numbers and Math. Beginnings Workshop.
Gross, Fred E.; Elkind, CavidEpstein, Ann S.; Copley, Juanita V.; Haugen, Ginny; Haugen, Kirsten
2003-01-01
Presents five articles addressing numbers and math instruction for young children: "Math Talk with Young Children: One Parent's Experience" (Fred E. Gross); "How Children Build Their Understanding of Numbers" (David Elkind); "Early Math: It's More than Numbers" (Ann S. Epstein); "Assessing Mathematical Learning: Observing and Listening to…
Indian Academy of Sciences (India)
Abstract. In this paper, we consider a two-parameter polynomial generalization, denoted by Ga,b(n, k; r), of the r-Lah numbers which reduces to these recently intro- duced numbers when a = b = 1. We present several identities for Ga,b(n, k; r) that generalize earlier identities given for the r-Lah and r-Stirling numbers.
New Ramanujan-Type Formulas and Quasi-Fibonacci Numbers of Order 7
Wituła, Roman; Słota, Damian
2007-06-01
We give applications of the quasi-Fibonacci numbers of order 7, the so-called sine-Fibonacci numbers of order 7, and many other new kinds of recurrent sequences to the decompositions of some polynomials. We also present the characteristic equations, generating functions and some properties of all these sequences. Finally, some new Ramanujan-type formulas are generated.
Transposon facilitated DNA sequencing
Energy Technology Data Exchange (ETDEWEB)
Berg, D.E.; Berg, C.M.; Huang, H.V.
1990-01-01
The purpose of this research is to investigate and develop methods that exploit the power of bacterial transposable elements for large scale DNA sequencing: Our premise is that the use of transposons to put primer binding sites randomly in target DNAs should provide access to all portions of large DNA fragments, without the inefficiencies of methods involving random subcloning and attendant repetitive sequencing, or of sequential synthesis of many oligonucleotide primers that are used to match systematically along a DNA molecule. Two unrelated bacterial transposons, Tn5 and {gamma}{delta}, are being used because they have both proven useful for molecular analyses, and because they differ sufficiently in mechanism and specificity of transposition to merit parallel development.
Moebius syndrome (moebius sequence)
A.A. Desai; Bansal, Sandeep
1999-01-01
Moebius Syndrome is one of the rare disorder amongst the oromandibular limb hypogenesis. It is of a unknown atiology with sporadic occurrence in which there is congenital bilateral facial palsy,-bilateral involvement of abducent nerve along with other cranial nerves like III, V, IX, X, Xllth and the patient having masklike expressionless face. We are reporting a case of Moebius Sequence who presented to us in the department of ENT and Head and Neck Surgery, Baroda.
Moebius syndrome (moebius sequence).
Desai, A A; Bansal, S
1999-10-01
Moebius Syndrome is one of the rare disorder amongst the oromandibular limb hypogenesis. It is of a unknown atiology with sporadic occurrence in which there is congenital bilateral facial palsy,-bilateral involvement of abducent nerve along with other cranial nerves like III, V, IX, X, Xllth and the patient having masklike expressionless face. We are reporting a case of Moebius Sequence who presented to us in the department of ENT and Head and Neck Surgery, Baroda.
Goldbach Partitions and Sequences
Indian Academy of Sciences (India)
IAS Admin
There is another version of the conjecture that states that every odd number greater than 7 is a sum of three odd primes. This is called the 'weak' Goldbach con- jecture. Computer experiments have shown that the conjectures are true for n ≤ 4 × 10. 18 . A representation of a number as a sum of primes is a prime partition.
Energy Technology Data Exchange (ETDEWEB)
Gukov, Sergei [Walter Burke Institute for Theoretical Physics, California Institute of Technology,1200 E California Blvd, Pasadena, CA 91125 (United States); Max-Planck-Institut für Mathematik,Vivatsgasse 7, D-53111 Bonn (Germany); Nawata, Satoshi [Walter Burke Institute for Theoretical Physics, California Institute of Technology,1200 E California Blvd, Pasadena, CA 91125 (United States); Centre for Quantum Geometry of Moduli Spaces, University of Aarhus,Nordre Ringgade 1, DK-8000 (Denmark); Saberi, Ingmar [Walter Burke Institute for Theoretical Physics, California Institute of Technology,1200 E California Blvd, Pasadena, CA 91125 (United States); Stošić, Marko [CAMGSD, Departamento de Matemática, Instituto Superior Técnico,Av. Rovisco Pais, 1049-001 Lisbon (Portugal); Mathematical Institute SANU,Knez Mihajlova 36, 11000 Belgrade (Serbia); Sułkowski, Piotr [Walter Burke Institute for Theoretical Physics, California Institute of Technology,1200 E California Blvd, Pasadena, CA 91125 (United States); Faculty of Physics, University of Warsaw,ul. Pasteura 5, 02-093 Warsaw (Poland)
2016-03-02
This paper provides both a detailed study of color-dependence of link homologies, as realized in physics as certain spaces of BPS states, and a broad study of the behavior of BPS states in general. We consider how the spectrum of BPS states varies as continuous parameters of a theory are perturbed. This question can be posed in a wide variety of physical contexts, and we answer it by proposing that the relationship between unperturbed and perturbed BPS spectra is described by a spectral sequence. These general considerations unify previous applications of spectral sequence techniques to physics, and explain from a physical standpoint the appearance of many spectral sequences relating various link homology theories to one another. We also study structural properties of colored HOMFLY homology for links and evaluate Poincaré polynomials in numerous examples. Among these structural properties is a novel “sliding” property, which can be explained by using (refined) modular S-matrix. This leads to the identification of modular transformations in Chern-Simons theory and 3d N=2 theory via the 3d/3d correspondence. Lastly, we introduce the notion of associated varieties as classical limits of recursion relations of colored superpolynomials of links, and study their properties.
1981-01-01
The processing of image sequences has a broad spectrum of important applica tions including target tracking, robot navigation, bandwidth compression of TV conferencing video signals, studying the motion of biological cells using microcinematography, cloud tracking, and highway traffic monitoring. Image sequence processing involves a large amount of data. However, because of the progress in computer, LSI, and VLSI technologies, we have now reached a stage when many useful processing tasks can be done in a reasonable amount of time. As a result, research and development activities in image sequence analysis have recently been growing at a rapid pace. An IEEE Computer Society Workshop on Computer Analysis of Time-Varying Imagery was held in Philadelphia, April 5-6, 1979. A related special issue of the IEEE Transactions on Pattern Anal ysis and Machine Intelligence was published in November 1980. The IEEE Com puter magazine has also published a special issue on the subject in 1981. The purpose of this book ...
Motif discovery in ranked lists of sequences
DEFF Research Database (Denmark)
Nielsen, Morten Muhlig; Tataru, Paula; Madsen, Tobias
2016-01-01
. These features make Regmex well suited for a range of biological sequence analysis problems related to motif discovery, exemplified by microRNA seed enrichment, but also including enrichment problems involving complex motifs and combinations of motifs. We demonstrate a number of usage scenarios that take......Motif analysis has long been an important method to characterize biological functionality and the current growth of sequencing-based genomics experiments further extends its potential. These diverse experiments often generate sequence lists ranked by some functional property. There is therefore...... a growing need for motif analysis methods that can exploit this coupled data structure and be tailored for specific biological questions. Here, we present an exploratory motif analysis tool, Regmex (REGular expression Motif EXplorer), which offers several methods to evaluate the correlation of motifs...
2016 Gainesville Number Theory Conference
Garvan, Frank
2017-01-01
Gathered from the 2016 Gainesville Number Theory Conference honoring Krishna Alladi on his 60th birthday, these proceedings present recent research in number theory. Extensive and detailed, this volume features 40 articles by leading researchers on topics in analytic number theory, probabilistic number theory, irrationality and transcendence, Diophantine analysis, partitions, basic hypergeometric series, and modular forms. Readers will also find detailed discussions of several aspects of the path-breaking work of Srinivasa Ramanujan and its influence on current research. Many of the papers were motivated by Alladi's own research on partitions and q-series as well as his earlier work in number theory. Alladi is well known for his contributions in number theory and mathematics. His research interests include combinatorics, discrete mathematics, sieve methods, probabilistic and analytic number theory, Diophantine approximations, partitions and q-series identities. Graduate students and researchers will find th...
Quantum algorithms for number fields
Energy Technology Data Exchange (ETDEWEB)
Haase, D.; Maier, H. [Universitaet Ulm, Fakultaet fuer Mathematik und Wirtschaftswissenschaften, Helmholtzstrasse 18, 89069 Ulm (Germany)
2006-08-23
This is a survey of recent results on quantum algorithms for the computation of invariants of number fields, namely the class number and the regulator. Most known classical algorithms for the computation of these values are of subexponential complexity and depend on the truth of a still unproven hypothesis of analytic number theory. We use an important number theoretic concept, Minkowski's Geometry of Numbers, to visualize these invariants, and describe the quantum algorithms developed by Hallgren, Schmidt and Vollmer which compute these invariants using a polynomial number of steps. Computational techniques in number fields, which are necessary to justify the classical part of these quantum algorithms, are the focus of the research of our project group, and are explained in detail. (Abstract Copyright [2006], Wiley Periodicals, Inc.)
On Fibonacci Numbers Which Are Elliptic Korselt Numbers
2014-11-17
On Fibonacci numbers which are elliptic Korselt numbers Florian Luca School of Mathematics University of the Witwatersrand P. O. Box Wits 2050, South...is a CM elliptic curve with CM field Q( √ −d), then the set of n for which the nth Fibonacci number Fn satisfies an elliptic Korselt criterion for Q...Directorate for Information Operations and Reports, 1215 Jefferson Davis Highway, Suite 1204, Arlington VA 22202-4302. Respondents should be aware that
Bernoulli numbers and zeta functions
Arakawa, Tsuneo; Kaneko, Masanobu
2014-01-01
Two major subjects are treated in this book. The main one is the theory of Bernoulli numbers and the other is the theory of zeta functions. Historically, Bernoulli numbers were introduced to give formulas for the sums of powers of consecutive integers. The real reason that they are indispensable for number theory, however, lies in the fact that special values of the Riemann zeta function can be written by using Bernoulli numbers. This leads to more advanced topics, a number of which are treated in this book: Historical remarks on Bernoulli numbers and the formula for the sum of powers of consecutive integers; a formula for Bernoulli numbers by Stirling numbers; the Clausen–von Staudt theorem on the denominators of Bernoulli numbers; Kummer's congruence between Bernoulli numbers and a related theory of p-adic measures; the Euler–Maclaurin summation formula; the functional equation of the Riemann zeta function and the Dirichlet L functions, and their special values at suitable integers; various formulas of ...
Plant DNA sequencing for phylogenetic analyses: from plants to sequences.
Neves, Susana S; Forrest, Laura L
2011-01-01
DNA sequences are important sources of data for phylogenetic analysis. Nowadays, DNA sequencing is a routine technique in molecular biology laboratories. However, there are specific questions associated with project design and sequencing of plant samples for phylogenetic analysis, which may not be familiar to researchers starting in the field. This chapter gives an overview of methods and protocols involved in the sequencing of plant samples, including general recommendations on the selection of species/taxa and DNA regions to be sequenced, and field collection of plant samples. Protocols of plant sample preparation, DNA extraction, PCR and cloning, which are critical to the success of molecular phylogenetic projects, are described in detail. Common problems of sequencing (using the Sanger method) are also addressed. Possible applications of second-generation sequencing techniques in plant phylogenetics are briefly discussed. Finally, orientation on the preparation of sequence data for phylogenetic analyses and submission to public databases is also given.
Compendium of Experimental Cetane Numbers
Energy Technology Data Exchange (ETDEWEB)
Yanowitz, Janet [Ecoengineering, Sharonville, OH (United States); Ratcliff, Matthew A. [National Renewable Energy Lab. (NREL), Golden, CO (United States); McCormick, Robert L. [National Renewable Energy Lab. (NREL), Golden, CO (United States); Taylor, J. D. [National Renewable Energy Lab. (NREL), Golden, CO (United States); Murphy, M. J. [Battelle, Columbus, OH (United States)
2017-02-22
This report is an updated version of the 2014 Compendium of Experimental Cetane Number Data and presents a compilation of measured cetane numbers for pure chemical compounds. It includes all available single-compound cetane number data found in the scientific literature up until December 2016 as well as a number of previously unpublished values, most measured over the past decade at the National Renewable Energy Laboratory. This version of the compendium contains cetane values for 496 pure compounds, including 204 hydrocarbons and 292 oxygenates. 176 individual measurements are new to this version of the compendium, all of them collected using ASTM Method D6890, which utilizes an Ignition Quality Tester (IQT) a type of constant-volume combustion chamber. For many compounds, numerous measurements are included, often collected by different researchers using different methods. The text of this document is unchanged from the 2014 version, except for the numbers of compounds in Section 3.1, the Appendices, Table 1. Primary Cetane Number Data Sources and Table 2. Number of Measurements Included in Compendium. Cetane number is a relative ranking of a fuel's autoignition characteristics for use in compression ignition engines. It is based on the amount of time between fuel injection and ignition, also known as ignition delay. The cetane number is typically measured either in a single-cylinder engine or a constant-volume combustion chamber. Values in the previous compendium derived from octane numbers have been removed and replaced with a brief analysis of the correlation between cetane numbers and octane numbers. The discussion on the accuracy and precision of the most commonly used methods for measuring cetane number has been expanded, and the data have been annotated extensively to provide additional information that will help the reader judge the relative reliability of individual results.
Continuous Online Sequence Learning with an Unsupervised Neural Network Model.
Cui, Yuwei; Ahmad, Subutar; Hawkins, Jeff
2016-09-14
The ability to recognize and predict temporal sequences of sensory inputs is vital for survival in natural environments. Based on many known properties of cortical neurons, hierarchical temporal memory (HTM) sequence memory recently has been proposed as a theoretical framework for sequence learning in the cortex. In this letter, we analyze properties of HTM sequence memory and apply it to sequence learning and prediction problems with streaming data. We show the model is able to continuously learn a large number of variableorder temporal sequences using an unsupervised Hebbian-like learning rule. The sparse temporal codes formed by the model can robustly handle branching temporal sequences by maintaining multiple predictions until there is sufficient disambiguating evidence. We compare the HTM sequence memory with other sequence learning algorithms, including statistical methods: autoregressive integrated moving average; feedforward neural networks-time delay neural network and online sequential extreme learning machine; and recurrent neural networks-long short-term memory and echo-state networks on sequence prediction problems with both artificial and real-world data. The HTM model achieves comparable accuracy to other state-of-the-art algorithms. The model also exhibits properties that are critical for sequence learning, including continuous online learning, the ability to handle multiple predictions and branching sequences with high-order statistics, robustness to sensor noise and fault tolerance, and good performance without task-specific hyperparameter tuning. Therefore, the HTM sequence memory not only advances our understanding of how the brain may solve the sequence learning problem but is also applicable to real-world sequence learning problems from continuous data streams.
The adjacency-Jacobsthal-circulant sequence in groups
Deveci, Ömür; Adıgüzel, Zafer
2017-04-01
In this work, we study the adjacency-Jacobsthal-circulant sequence modulo α and we obtain the cyclic groups from the generating matrix of the adjacency-Jacobsthal-circulant numbers when read modulo α. Then, we derive the relationship among the periods of the adjacency-Jacobsthal-circulant sequence modulo α and the orders of the cyclic groups obtained. Furthermore, we extend the adjacency-Jacobsthal-circulant sequence to groups. Finally, we obtain the length of the period of the adjacency-Jacobsthal-circulant sequence in the quaternion group Q8 as applications of the results obtained.
SMRT sequencing data for Garcinia mangostana L. variety Mesta
Directory of Open Access Journals (Sweden)
Mohd Razik Midin
2017-06-01
Full Text Available The “Queen of Fruits” mangosteen (Garcinia mangostana L. produces commercially important fruits with desirable taste of flesh and pericarp rich in xanthones with medicinal properties. To date, only limited knowledge is available on the cytogenetics and genome sequences of a common variety of mangosteen (Abu Bakar et al., 2016 [1]. Here, we report the first single-molecule real-time (SMRT sequencing data from whole genome sequencing of mangosteen of Mesta variety. Raw reads of the SMRT sequencing project can be obtained from SRA database with the accession numbers SRX2718652 until SRX2718659.
The genome of the horn fly, Haematobia irritans, was sequenced using Illumina- and Pac Bio-based protocols. Following quality filtering, the raw reads have been deposited at NCBI under the BioProject and BioSample accession numbers PRJNA30967 and SAMN07830356, respectively. The Illumina reads are un...
454 sequencing put to the test using the complex genome of barley
Directory of Open Access Journals (Sweden)
Keller Beat
2006-10-01
Full Text Available Abstract Background During the past decade, Sanger sequencing has been used to completely sequence hundreds of microbial and a few higher eukaryote genomes. In recent years, a number of alternative technologies became available, among them adaptations of the pyrosequencing procedure (i.e. "454 sequencing", promising a ~100-fold increase in throughput over Sanger technology – an advancement which is needed to make large and complex genomes more amenable to full genome sequencing at affordable costs. Although several studies have demonstrated its potential usefulness for sequencing small and compact microbial genomes, it was unclear how the new technology would perform in large and highly repetitive genomes such as those of wheat or barley. Results To study its performance in complex genomes, we used 454 technology to sequence four barley Bacterial Artificial Chromosome (BAC clones and compared the results to those from ABI-Sanger sequencing. All gene containing regions were covered efficiently and at high quality with 454 sequencing whereas repetitive sequences were more problematic with 454 sequencing than with ABI-Sanger sequencing. 454 sequencing provided a much more even coverage of the BAC clones than ABI-Sanger sequencing, resulting in almost complete assembly of all genic sequences even at only 9 to 10-fold coverage. To obtain highly advanced working draft sequences for the BACs, we developed a strategy to assemble large parts of the BAC sequences by combining comparative genomics, detailed repeat analysis and use of low-quality reads from 454 sequencing. Additionally, we describe an approach of including small numbers of ABI-Sanger sequences to produce hybrid assemblies to partly compensate the short read length of 454 sequences. Conclusion Our data indicate that 454 pyrosequencing allows rapid and cost-effective sequencing of the gene-containing portions of large and complex genomes and that its combination with ABI-Sanger sequencing
Spot Accession Protein Protein Unique Secuence Number number ...
Indian Academy of Sciences (India)
Classification of the proteins identified as altered in the cardiac left ventricles from TPCN1 KO vs. WT mice by 2-DE-MADI-MS. The spot number, SwissProt accession number, protein name, relative fold-change and P-value. (given by the software SameSpots), experimental and theoretical pI and Mw values, Mascot score, ...
An optical CDMA system based on chaotic sequences
Liu, Xiao-lei; En, De; Wang, Li-guo
2014-03-01
In this paper, a coherent asynchronous optical code division multiple access (OCDMA) system is proposed, whose encoder/decoder is an all-optical generator. This all-optical generator can generate analog and bipolar chaotic sequences satisfying the logistic maps. The formula of bit error rate (BER) is derived, and the relationship of BER and the number of simultaneous transmissions is analyzed. Due to the good property of correlation, this coherent OCDMA system based on these bipolar chaotic sequences can support a large number of simultaneous users, which shows that these chaotic sequences are suitable for asynchronous OCDMA system.
Dynamic Virtual Credit Card Numbers
Molloy, Ian; Li, Jiangtao; Li, Ninghui
Theft of stored credit card information is an increasing threat to e-commerce. We propose a dynamic virtual credit card number scheme that reduces the damage caused by stolen credit card numbers. A user can use an existing credit card account to generate multiple virtual credit card numbers that are either usable for a single transaction or are tied with a particular merchant. We call the scheme dynamic because the virtual credit card numbers can be generated without online contact with the credit card issuers. These numbers can be processed without changing any of the infrastructure currently in place; the only changes will be at the end points, namely, the card users and the card issuers. We analyze the security requirements for dynamic virtual credit card numbers, discuss the design space, propose a scheme using HMAC, and prove its security under the assumption the underlying function is a PRF.
Number-unconstrained quantum sensing
Mitchell, Morgan W.
2017-12-01
Quantum sensing is commonly described as a constrained optimization problem: maximize the information gained about an unknown quantity using a limited number of particles. Important sensors including gravitational wave interferometers and some atomic sensors do not appear to fit this description, because there is no external constraint on particle number. Here, we develop the theory of particle-number-unconstrained quantum sensing, and describe how optimal particle numbers emerge from the competition of particle-environment and particle-particle interactions. We apply the theory to optical probing of an atomic medium modeled as a resonant, saturable absorber, and observe the emergence of well-defined finite optima without external constraints. The results contradict some expectations from number-constrained quantum sensing and show that probing with squeezed beams can give a large sensitivity advantage over classical strategies when each is optimized for particle number.
The characterization of twenty sequenced human genomes.
Directory of Open Access Journals (Sweden)
Kimberly Pelak
2010-09-01
Full Text Available We present the analysis of twenty human genomes to evaluate the prospects for identifying rare functional variants that contribute to a phenotype of interest. We sequenced at high coverage ten "case" genomes from individuals with severe hemophilia A and ten "control" genomes. We summarize the number of genetic variants emerging from a study of this magnitude, and provide a proof of concept for the identification of rare and highly-penetrant functional variants by confirming that the cause of hemophilia A is easily recognizable in this data set. We also show that the number of novel single nucleotide variants (SNVs discovered per genome seems to stabilize at about 144,000 new variants per genome, after the first 15 individuals have been sequenced. Finally, we find that, on average, each genome carries 165 homozygous protein-truncating or stop loss variants in genes representing a diverse set of pathways.
Visualizing Dynamic Hierarchies in Graph Sequences.
Vehlow, Corinna; Beck, Fabian; Weiskopf, Daniel
2016-10-01
Graphs are used to model relations between objects, where these objects can be grouped hierarchically based on their connectivity. In many applications, the relations change over time and so does the hierarchical group structure. We developed a visualization technique that supports the analysis of the topology and the hierarchical group structure of a dynamic graph and the tracking of changes over time. Each graph of a sequence is visualized by an adjacency matrix, where the hierarchical group structure is encoded within the matrix using indentation and nested contours, complemented by icicle plots attached to the matrices. The density within and between subgroups of the hierarchy is represented within the matrices using a gray scale. To visualize changes, transitions and dissimilarities between the hierarchically structured graphs are shown using a flow metaphor and color coding. The design of our visualization technique allows us to show more than one hierarchical group structure of the same graph by stacking the sequences, where hierarchy comparison is supported not only within but also between sequences. To improve the readability, we minimize the number of crossing curves within and between sequences based on a sorting algorithm that sweeps through the sequences of hierarchies.
BLEACHING EUCALYPTUS PULPS WITH SHORT SEQUENCES
Directory of Open Access Journals (Sweden)
Flaviana Reis Milagres
2011-03-01
Full Text Available Eucalyptus spp kraft pulp, due to its high content of hexenuronic acids, is quite easy to bleach. Therefore, investigations have been made attempting to decrease the number of stages in the bleaching process in order to minimize capital costs. This study focused on the evaluation of short ECF (Elemental Chlorine Free and TCF (Totally Chlorine Free sequences for bleaching oxygen delignified Eucalyptus spp kraft pulp to 90% ISO brightness: PMoDP (Molybdenum catalyzed acid peroxide, chlorine dioxide and hydrogen peroxide, PMoD/P (Molybdenum catalyzed acid peroxide, chlorine dioxide and hydrogen peroxide, without washing PMoD(PO (Molybdenum catalyzed acid peroxide, chlorine dioxide and pressurized peroxide, D(EPODP (chlorine dioxide, extraction oxidative with oxygen and peroxide, chlorine dioxide and hydrogen peroxide, PMoQ(PO (Molybdenum catalyzed acid peroxide, DTPA and pressurized peroxide, and XPMoQ(PO (Enzyme, molybdenum catalyzed acid peroxide, DTPA and pressurized peroxide. Uncommon pulp treatments, such as molybdenum catalyzed acid peroxide (PMo and xylanase (X bleaching stages, were used. Among the ECF alternatives, the two-stage PMoD/P sequence proved highly cost-effective without affecting pulp quality in relation to the traditional D(EPODP sequence and produced better quality effluent in relation to the reference. However, a four stage sequence, XPMoQ(PO, was required to achieve full brightness using the TCF technology. This sequence was highly cost-effective although it only produced pulp of acceptable quality.
Detecting false positive signals in exome sequencing
Fajardo, Karin V Fuentes; Adams, David; Mason, Christopher E; Sincan, Murat; Tifft, Cynthia; Toro, Camilo; Boerkoel, Cornelius F; Gahl, William; Markello, Thomas
2012-01-01
Disease gene discovery has been transformed by affordable sequencing of exomes and genomes. Identification of disease-causing mutations requires sifting through a large number of sequence variants. A subset of the variants are unlikely to be good candidates for disease causation based on one or more of the following criteria: (1) being located in genomic regions known to be highly polymorphic, (2) having characteristics suggesting assembly misalignment, and/or (3) being labeled as variants based on misleading reference genome information. We analyzed exome sequence data from 118 individuals in 29 families seen in the NIH Undiagnosed Diseases Program (UDP) to create lists of variants and genes with these characteristics. Specifically, we identified several groups of genes that are candidates for provisional exclusion during exome analysis; 23,389 positions with excess heterozygosity suggestive of alignment errors; and 1,009 positions in which the hg18 human genome reference sequence appeared to contain a minor allele. Exclusion of such variants, which we provide in supplemental lists, will likely enhance identification of disease-causing mutations using exome sequence data. PMID:22294350
Novel expressed sequence tag- simple sequence repeats (EST-SSR)
African Journals Online (AJOL)
Using different bioinformatic criteria, the SUCEST database was used to mine for simple sequence repeat (SSR) markers. Among 42,189 clusters, 1,425 expressed sequence tag- simple sequence repeats (EST-SSRs) were identified in silico. Trinucleotide repeats were the most abundant SSRs detected. Of 212 primer pairs ...
Covering Numbers for Semicontinuous Functions
2016-04-29
Considering the metric space of extended real-valued lower semicontinuous functions under the epi-distance, the paper gives an upper bound on the...the latter class of functions as well, but now under the hypo-distance metric . Keywords: covering numbers, metric entropy numbers, semicontinuous...functions, epi-distance, Attouch-Wets topology , epi-convergence, epi-spline, approximation theory. Date: April 29, 2016 1 Introduction Covering numbers of
Delannoy numbers and Legendre polytopes
Hetyei, Gábor
2008-01-01
International audience; We construct an $n$-dimensional polytope whose boundary complex is compressed and whose face numbers for any pulling triangulation are the coefficients of the powers of $(x-1)/2$ in the $n$-th Legendre polynomial. We show that the non-central Delannoy numbers count all faces in the lexicographic pulling triangulation that contain a point in a given open quadrant. We thus provide a geometric interpretation of a relation between the central Delannoy numbers and Legendre ...
Simulating the Spread of an Outbreak of Foot and Mouth Disease in California
2012-06-01
capability. Seed: Randomly chosen using a Mersenne Twister generator (Matsumoto & Nishimura, 1998). 31 Random Generator Name...Mersenne twister : A 623-dimensionally equidistributed uniform pseudo-random number generator. ACM Transactions on Modeling and Computer Simulation
Compendium of Experimental Cetane Numbers
Energy Technology Data Exchange (ETDEWEB)
Yanowitz, J.; Ratcliff, M. A.; McCormick, R. L.; Taylor, J. D.; Murphy, M. J.
2014-08-01
This report is an updated version of the 2004 Compendium of Experimental Cetane Number Data and presents a compilation of measured cetane numbers for pure chemical compounds. It includes all available single compound cetane number data found in the scientific literature up until March 2014 as well as a number of unpublished values, most measured over the past decade at the National Renewable Energy Laboratory. This Compendium contains cetane values for 389 pure compounds, including 189 hydrocarbons and 201 oxygenates. More than 250 individual measurements are new to this version of the Compendium. For many compounds, numerous measurements are included, often collected by different researchers using different methods. Cetane number is a relative ranking of a fuel's autoignition characteristics for use in compression ignition engines; it is based on the amount of time between fuel injection and ignition, also known as ignition delay. The cetane number is typically measured either in a single-cylinder engine or a constant volume combustion chamber. Values in the previous Compendium derived from octane numbers have been removed, and replaced with a brief analysis of the correlation between cetane numbers and octane numbers. The discussion on the accuracy and precision of the most commonly used methods for measuring cetane has been expanded and the data has been annotated extensively to provide additional information that will help the reader judge the relative reliability of individual results.
Synaptotagmin gene content of the sequenced genomes
Directory of Open Access Journals (Sweden)
Craxton Molly
2004-07-01
Full Text Available Abstract Background Synaptotagmins exist as a large gene family in mammals. There is much interest in the function of certain family members which act crucially in the regulated synaptic vesicle exocytosis required for efficient neurotransmission. Knowledge of the functions of other family members is relatively poor and the presence of Synaptotagmin genes in plants indicates a role for the family as a whole which is wider than neurotransmission. Identification of the Synaptotagmin genes within completely sequenced genomes can provide the entire Synaptotagmin gene complement of each sequenced organism. Defining the detailed structures of all the Synaptotagmin genes and their encoded products can provide a useful resource for functional studies and a deeper understanding of the evolution of the gene family. The current rapid increase in the number of sequenced genomes from different branches of the tree of life, together with the public deposition of evolutionarily diverse transcript sequences make such studies worthwhile. Results I have compiled a detailed list of the Synaptotagmin genes of Caenorhabditis, Anopheles, Drosophila, Ciona, Danio, Fugu, Mus, Homo, Arabidopsis and Oryza by examining genomic and transcript sequences from public sequence databases together with some transcript sequences obtained by cDNA library screening and RT-PCR. I have compared all of the genes and investigated the relationship between plant Synaptotagmins and their non-Synaptotagmin counterparts. Conclusions I have identified and compared 98 Synaptotagmin genes from 10 sequenced genomes. Detailed comparison of transcript sequences reveals abundant and complex variation in Synaptotagmin gene expression and indicates the presence of Synaptotagmin genes in all animals and land plants. Amino acid sequence comparisons indicate patterns of conservation and diversity in function. Phylogenetic analysis shows the origin of Synaptotagmins in multicellular eukaryotes and their
A graph-based clustering method applied to protein sequences.
Mishra, Pooja; Pandey, Paras Nath
2011-01-01
The number of amino acid sequences is increasing very rapidly in the protein databases like Swiss-Prot, Uniprot, PIR and others, but the structure of only some amino acid sequences are found in the Protein Data Bank. Thus, an important problem in genomics is automatically clustering homologous protein sequences when only sequence information is available. Here, we use graph theoretic techniques for clustering amino acid sequences. A similarity graph is defined and clusters in that graph correspond to connected subgraphs. Cluster analysis seeks grouping of amino acid sequences into subsets based on distance or similarity score between pairs of sequences. Our goal is to find disjoint subsets, called clusters, such that two criteria are satisfied: homogeneity: sequences in the same cluster are highly similar to each other; and separation: sequences in different clusters have low similarity to each other. We tested our method on several subsets of SCOP (Structural Classification of proteins) database, a gold standard for protein structure classification. The results show that for a given set of proteins the number of clusters we obtained is close to the superfamilies in that set; there are fewer singeltons; and the method correctly groups most remote homologs.
Tuning of the sequence technique
Laude, Dominique; Baudrie, Véronique; Elghozi, Jean-Luc
2009-01-01
The sequence method was first described in cats, and applied in different species including humans. Up to now, there is no systematic study of the spontaneous baroreflex sensitivity (BRS) estimated by the sequence method to mice.